Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

. 2019 May 08 ; 119 (9) : 5607-5774. [epub] 20190312

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid30859819

Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.

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Gorter E.; Grendel F. On Bimolecular Layers of Lipoids on the Chromocytes of the Blood. J. Exp. Med. 1925, 41, 439–443. 10.1084/jem.41.4.439. PubMed DOI PMC

Robertson J. The Ultrastructure of Cell Membranes and Their Derivatives. Biochem. Soc. Symp. 1959, 16, 3–43. PubMed

Lenard J.; Singer S. J. Protein Conformation in Cell Membrane Preparations as Studied by Optical Rotatory Dispersion and Circular Dichroism. Proc. Natl. Acad. Sci. U. S. A. 1966, 56, 1828–1835. 10.1073/pnas.56.6.1828. PubMed DOI PMC

Singer S. J.; Nicolson G. L. The Fluid Mosaic Model of the Structure of Cell Membranes. Science 1972, 175, 720–731. 10.1126/science.175.4023.720. PubMed DOI

Phillips M. C.; Ladbrooke B. D.; Chapman D. Molecular Interactions in Mixed Lecithin Systems. Biochim. Biophys. Acta, Biomembr. 1970, 196, 35–44. 10.1016/0005-2736(70)90163-X. PubMed DOI

Oldfield E.; Chapman D. Dynamics of Lipids in Membranes: Heterogeneity and the Role of Cholesterol. FEBS Lett. 1972, 23, 285–297. 10.1016/0014-5793(72)80300-4. PubMed DOI

Shimshick E. J.; McConnell H. M. Lateral Phase Separation in Phospholipid Membranes. Biochemistry 1973, 12, 2351–2360. 10.1021/bi00736a026. PubMed DOI

Mouritsen O. G.; Bloom M. Mattress Model of Lipid-Protein Interactions in Membranes. Biophys. J. 1984, 46, 141–153. 10.1016/S0006-3495(84)84007-2. PubMed DOI PMC

Sackmann E.Physical Basis for Trigger Processes and Membrane Structures. In Biological Membranes; Chapman D., Ed.; Academic Press: London, 1984.

Bagatolli L.; Mouritsen O. Is the Fluid Mosaic (and the Accompanying Raft Hypothesis) a Suitable Model to Describe Fundamental Features of Biological Membranes? What May Be Missing?. Front. Plant Sci. 2013, 4, 457.10.3389/fpls.2013.00457. PubMed DOI PMC

Mouritsen O. G.; Bagatolli L. A. Lipid Domains in Model Membranes: A Brief Historical Perspective. Essays Biochem. 2015, 57, 1–19. 10.1042/bse0570001. PubMed DOI

Simons K.; Ikonen E. Functional Rafts in Cell Membranes. Nature 1997, 387, 569–572. 10.1038/42408. PubMed DOI

Simons K.; Van Meer G. Lipid Sorting in Epithelial Cells. Biochemistry 1988, 27, 6197–6202. 10.1021/bi00417a001. PubMed DOI

Hjort Ipsen J.; Karlström G.; Mourtisen O. G.; Wennerström H.; Zuckermann M. J. Phase Equilibria in the Phosphatidylcholine-Cholesterol System. Biochim. Biophys. Acta, Biomembr. 1987, 905, 162–172. 10.1016/0005-2736(87)90020-4. PubMed DOI

Lingwood D.; Simons K. Lipid Rafts As a Membrane-Organizing Principle. Science 2010, 327, 46–50. 10.1126/science.1174621. PubMed DOI

Niemelä P. S.; Miettinen M. S.; Monticelli L.; Hammaren H.; Bjelkmar P.; Murtola T.; Lindahl E.; Vattulainen I. Membrane Proteins Diffuse as Dynamic Complexes with Lipids. J. Am. Chem. Soc. 2010, 132, 7574–7575. 10.1021/ja101481b. PubMed DOI

Sezgin E.; Levental I.; Mayor S.; Eggeling C. The Mystery of Membrane Organization: Composition, Regulation and Roles of Lipid Rafts. Nat. Rev. Mol. Cell Biol. 2017, 18, 361–374. 10.1038/nrm.2017.16. PubMed DOI PMC

Goldstine H. H.; Goldstine A. The Electronic Numerical Integrator and Computer (ENIAC). Math. Tables Aids Comput. 1946, 2, 97–110. 10.2307/2002620. DOI

Metropolis N.Los Alamos Science. Spec. Issue 1987, 125.

Metropolis N.; Ulam S. The Monte Carlo Method. J. Am. Stat. Assoc. 1949, 44, 335–341. 10.1080/01621459.1949.10483310. PubMed DOI

Metropolis N.; Rosenbluth A. W.; Rosenbluth M. N.; Teller A. H.; Teller E. Equation of State Calculations by Fast Computing Machines. J. Chem. Phys. 1953, 21, 1087–1092. 10.1063/1.1699114. DOI

Metropolis N. C.; Reitwiesner G.; von Neumann J. Statistical Treatment of Values of First 2,000 Decimal Digits of e and of π Calculated on the ENIAC. Math. Comput. 1950, 4, 109–109. 10.1090/S0025-5718-1950-0037598-8. DOI

Hull T.; Dobell A. Random Number Generators. SIAM Rev. 1962, 4, 230–254. 10.1137/1004061. DOI

Knuth D. E.; Knuth D. E.. Seminumerical Algorithms, 2nd ed., 25th print.; The art of computer programming; Addison-Wesley: Reading, Mass., 1996.

L’Ecuyer P.Random Number Generation. In Handbook of Computational Statistics: Concepts and Methods; Gentle J. E., Härdle W. K., Mori Y., Eds.; Springer Handbooks of Computational Statistics; Springer-Verlag: Berlin Heidelberg, 2012.

Alder B. J.; Wainwright T. E. Phase Transition for a Hard Sphere System. J. Chem. Phys. 1957, 27, 1208–1209. 10.1063/1.1743957. DOI

Rahman A. Correlations in the Motion of Atoms in Liquid Argon. Phys. Rev. 1964, 136, A405–A411. 10.1103/PhysRev.136.A405. DOI

McCammon J. A.; Gelin B. R.; Karplus M. Dynamics of Folded Proteins. Nature 1977, 267, 585–590. 10.1038/267585a0. PubMed DOI

Duan Y.; Kollman P. A. Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution. Science 1998, 282, 740–744. 10.1126/science.282.5389.740. PubMed DOI

Pastor R. W. Molecular Dynamics and Monte Carlo Simulations of Lipid Bilayers. Curr. Opin. Struct. Biol. 1994, 4, 486–492. 10.1016/S0959-440X(94)90209-7. DOI

Kox A. J.; Michels J. P. J.; Wiegel F. W. Simulation of a Lipid Monolayer Using Molecular Dynamics. Nature 1980, 287, 317–319. 10.1038/287317a0. DOI

van der Ploeg P.; Berendsen H. J. C. Molecular Dynamics Simulation of a Bilayer Membrane. J. Chem. Phys. 1982, 76, 3271–3276. 10.1063/1.443321. DOI

Jönsson B.; Edholm O.; Teleman O. Molecular Dynamics Simulations of a Sodium Octanoate Micelle in Aqueous Solution. J. Chem. Phys. 1986, 85, 2259–2271. 10.1063/1.451122. DOI

Scott H. L. Lipid-Cholesterol Interactions. Monte Carlo Simulations and Theory. Biophys. J. 1991, 59, 445–455. 10.1016/S0006-3495(91)82238-X. PubMed DOI PMC

Chiu S. W.; Jakobsson E.; Scott H. L. Combined Monte Carlo and Molecular Dynamics Simulation of Hydrated Lipid-Cholesterol Lipid Bilayers at Low Cholesterol Concentration. Biophys. J. 2001, 80, 1104–1114. 10.1016/S0006-3495(01)76088-2. PubMed DOI PMC

Chiu S. W.; Jakobsson E.; Subramaniam S.; Scott H. L. Combined Monte Carlo and Molecular Dynamics Simulation of Fully Hydrated Dioleyl and Palmitoyl-Oleyl Phosphatidylcholine Lipid Bilayers. Biophys. J. 1999, 77, 2462–2469. 10.1016/S0006-3495(99)77082-7. PubMed DOI PMC

Venable R. M.; Zhang Y.; Hardy B. J.; Pastor R. W. Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: An Investigation of Membrane Fluidity. Science 1993, 262, 223–226. 10.1126/science.8211140. PubMed DOI

Heller H.; Schaefer M.; Schulten K. Molecular Dynamics Simulation of a Bilayer of 200 Lipids in the Gel and in the Liquid Crystal Phase. J. Phys. Chem. 1993, 97, 8343–8360. 10.1021/j100133a034. DOI

Marrink S. J.; Berkowitz M.; Berendsen H. J. C. Molecular Dynamics Simulation of a Membrane/Water Interface: The Ordering of Water and Its Relation to the Hydration Force. Langmuir 1993, 9, 3122–3131. 10.1021/la00035a062. DOI

Berendsen H. J. C.; Marrink S.-J. Molecular Dynamics of Water Transport through Membranes: Water from Solvent to Solute. Pure Appl. Chem. 1993, 65, 2513–2520. 10.1351/pac199365122513. DOI

Egberts E.; Marrink S.-J.; Berendsen H. J. C. Molecular Dynamics Simulation of a Phospholipid Membrane. Eur. Biophys. J. 1994, 22, 423–436. 10.1007/BF00180163. PubMed DOI

Berger O.; Edholm O.; Jähnig F. Molecular Dynamics Simulations of a Fluid Bilayer of Dipalmitoylphosphatidylcholine at Full Hydration, Constant Pressure, and Constant Temperature. Biophys. J. 1997, 72, 2002–2013. 10.1016/S0006-3495(97)78845-3. PubMed DOI PMC

Essex J. W.; Hann M. M.; Richards W. G. Molecular Dynamics Simulation of a Hydrated Phospholipid Bilayer. Philos. Trans. R. Soc. London B. Biol. Sci. 1994, 344, 239–260. 10.1098/rstb.1994.0064. PubMed DOI

Vattulainen I.; Róg T. Lipid Membranes: Theory and Simulations Bridged to Experiments. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2251–2253. 10.1016/j.bbamem.2016.06.007. PubMed DOI

Lyubartsev A. P.; Rabinovich A. L. Force Field Development for Lipid Membrane Simulations. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2483–2497. 10.1016/j.bbamem.2015.12.033. PubMed DOI

Javanainen M.; Martinez-Seara H. Efficient Preparation and Analysis of Membrane and Membrane Protein Systems. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2468–2482. 10.1016/j.bbamem.2016.02.036. PubMed DOI

Neale C.; Pomès R. Sampling Errors in Free Energy Simulations of Small Molecules in Lipid Bilayers. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2539–2548. 10.1016/j.bbamem.2016.03.006. PubMed DOI

Wong-ekkabut J.; Karttunen M. The Good, the Bad and the User in Soft Matter Simulations. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2529–2538. 10.1016/j.bbamem.2016.02.004. PubMed DOI

Ollila O. H. S.; Pabst G. Atomistic Resolution Structure and Dynamics of Lipid Bilayers in Simulations and Experiments. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2512–2528. 10.1016/j.bbamem.2016.01.019. PubMed DOI

Botan A.; Favela-Rosales F.; Fuchs P. F. J.; Javanainen M.; Kanduč M.; Kulig W.; Lamberg A.; Loison C.; Lyubartsev A.; Miettinen M. S.; et al. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions. J. Phys. Chem. B 2015, 119, 15075–15088. 10.1021/acs.jpcb.5b04878. PubMed DOI PMC

Catte A.; Girych M.; Javanainen M.; Loison C.; Melcr J.; Miettinen M. S.; Monticelli L.; Määttä J.; Oganesyan V. S.; Ollila O. H. S.; et al. Molecular Electrometer and Binding of Cations to Phospholipid Bilayers. Phys. Chem. Chem. Phys. 2016, 18, 32560–32569. 10.1039/C6CP04883H. PubMed DOI

Piana S.; Klepeis J. L.; Shaw D. E. Assessing the Accuracy of Physical Models Used in Protein-Folding Simulations: Quantitative Evidence from Long Molecular Dynamics Simulations. Curr. Opin. Struct. Biol. 2014, 24, 98–105. 10.1016/j.sbi.2013.12.006. PubMed DOI

Javanainen M.; Martinez-Seara H.; Vattulainen I. Nanoscale Membrane Domain Formation Driven by Cholesterol. Sci. Rep. 2017, 7, 1143.10.1038/s41598-017-01247-9. PubMed DOI PMC

Manna M.; Niemelä M.; Tynkkynen J.; Javanainen M.; Kulig W.; Müller D. J.; Rog T.; Vattulainen I. Mechanism of Allosteric Regulation of β2-Adrenergic Receptor by Cholesterol. eLife 2016, 5, e18432.10.7554/eLife.18432. PubMed DOI PMC

Javanainen M.; Martinez-Seara H.; Metzler R.; Vattulainen I. Diffusion of Integral Membrane Proteins in Protein-Rich Membranes. J. Phys. Chem. Lett. 2017, 8, 4308–4313. 10.1021/acs.jpclett.7b01758. PubMed DOI

Koldsø H.; Sansom M. S. P. Organization and Dynamics of Receptor Proteins in a Plasma Membrane. J. Am. Chem. Soc. 2015, 137, 14694–14704. 10.1021/jacs.5b08048. PubMed DOI PMC

Guixà-González R.; Javanainen M.; Gómez-Soler M.; Cordobilla B.; Domingo J. C.; Sanz F.; Pastor M.; Ciruela F.; Martinez-Seara H.; Selent J. Membrane Omega-3 Fatty Acids Modulate the Oligomerisation Kinetics of Adenosine A2A and Dopamine D2 Receptors. Sci. Rep. 2016, 6, 19839.10.1038/srep19839. PubMed DOI PMC

Harayama T.; Riezman H. Understanding the Diversity of Membrane Lipid Composition. Nat. Rev. Mol. Cell Biol. 2018, 19, 281–296. 10.1038/nrm.2017.138. PubMed DOI

Shahidi F.; Zhong Y. Lipid Oxidation and Improving the Oxidative Stability. Chem. Soc. Rev. 2010, 39, 4067–4079. 10.1039/b922183m. PubMed DOI

Yin H.; Xu L.; Porter N. A. Free Radical Lipid Peroxidation: Mechanisms and Analysis. Chem. Rev. 2011, 111, 5944–5972. 10.1021/cr200084z. PubMed DOI

Shevchenko A.; Simons K. Lipidomics: Coming to Grips with Lipid Diversity. Nat. Rev. Mol. Cell Biol. 2010, 11, 593–598. 10.1038/nrm2934. PubMed DOI

Dhawan V.; Magarkar A.; Joshi G.; Makhija D.; Jain A.; Shah J.; Reddy B. V. V.; Krishnapriya M.; Róg T.; Bunker A.; et al. Stearylated Cycloarginine Nanosystems for Intracellular Delivery – Simulations, Formulation and Proof of Concept. RSC Adv. 2016, 6, 113538–113550. 10.1039/C6RA16432C. DOI

Magarkar A.; Róg T.; Bunker A. A Computational Study Suggests That Replacing PEG with PMOZ. May Increase Exposure of Hydrophobic Targeting Moiety. Eur. J. Pharm. Sci. 2017, 103, 128–135. 10.1016/j.ejps.2017.03.008. PubMed DOI

Lehtinen J.; Magarkar A.; Stepniewski M.; Hakola S.; Bergman M.; Róg T.; Yliperttula M.; Urtti A.; Bunker A. Analysis of Cause of Failure of New Targeting Peptide in PEGylated Liposome: Molecular Modeling as Rational Design Tool for Nanomedicine. Eur. J. Pharm. Sci. 2012, 46, 121–130. 10.1016/j.ejps.2012.02.009. PubMed DOI

Pathak P.; Dhawan V.; Magarkar A.; Danne R.; Govindarajan S.; Ghosh S.; Steiniger F.; Chaudhari P.; Gopal V.; Bunker A.; et al. Design of Cholesterol Arabinogalactan Anchored Liposomes for Asialoglycoprotein Receptor Mediated Targeting to Hepatocellular Carcinoma: In Silico Modeling, in Vitro and in Vivo Evaluation. Int. J. Pharm. 2016, 509, 149–158. 10.1016/j.ijpharm.2016.05.041. PubMed DOI

Magarkar A.; Róg T.; Bunker A. Molecular Dynamics Simulation of PEGylated Membranes with Cholesterol: Building Toward the DOXIL Formulation. J. Phys. Chem. C 2014, 118, 15541–15549. 10.1021/jp504962m. DOI

Magarkar A.; Karakas E.; Stepniewski M.; Róg T.; Bunker A. Molecular Dynamics Simulation of PEGylated Bilayer Interacting with Salt Ions: A Model of the Liposome Surface in the Bloodstream. J. Phys. Chem. B 2012, 116, 4212–4219. 10.1021/jp300184z. PubMed DOI

Stepniewski M.; Pasenkiewicz-Gierula M.; Róg T.; Danne R.; Orlowski A.; Karttunen M.; Urtti A.; Yliperttula M.; Vuorimaa E.; Bunker A. Study of PEGylated Lipid Layers as a Model for PEGylated Liposome Surfaces: Molecular Dynamics Simulation and Langmuir Monolayer Studies. Langmuir 2011, 27, 7788–7798. 10.1021/la200003n. PubMed DOI

Ríos-Marco P.; Marco C.; Gálvez X.; Jiménez-López J. M.; Carrasco M. P. Alkylphospholipids: An Update on Molecular Mechanisms and Clinical Relevance. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 1657–1667. 10.1016/j.bbamem.2017.02.016. PubMed DOI

Mobarak E.; Javanainen M.; Kulig W.; Honigmann A.; Sezgin E.; Aho N.; Eggeling C.; Rog T.; Vattulainen I. How to Minimize Dye-Induced Perturbations While Studying Biomembrane Structure and Dynamics: PEG Linkers as a Rational Alternative. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 2436–2445. 10.1016/j.bbamem.2018.07.003. PubMed DOI

Rissanen S.; Grzybek M.; Orłowski A.; Róg T.; Cramariuc O.; Levental I.; Eggeling C.; Sezgin E.; Vattulainen I. Phase Partitioning of GM1 and Its Bodipy-Labeled Analog Determine Their Different Binding to Cholera Toxin. Front. Physiol. 2017, 8, 252.10.3389/fphys.2017.00252. PubMed DOI PMC

Björkbom A.; Róg T.; Kaszuba K.; Kurita M.; Yamaguchi S.; Lönnfors M.; Nyholm T. K. M.; Vattulainen I.; Katsumura S.; Slotte J. P. Effect of Sphingomyelin Headgroup Size on Molecular Properties and Interactions with Cholesterol. Biophys. J. 2010, 99, 3300–3308. 10.1016/j.bpj.2010.09.049. PubMed DOI PMC

Kepczynski M.; Róg T. Functionalized Lipids and Surfactants for Specific Applications. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2362–2379. 10.1016/j.bbamem.2016.02.038. PubMed DOI

Bunker A.; Magarkar A.; Viitala T. Rational Design of Liposomal Drug Delivery Systems, a Review: Combined Experimental and Computational Studies of Lipid Membranes, Liposomes and Their PEGylation. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2334–2352. 10.1016/j.bbamem.2016.02.025. PubMed DOI

Faller R. Molecular Modeling of Lipid Probes and Their Influence on the Membrane. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2353–2361. 10.1016/j.bbamem.2016.02.014. PubMed DOI

Shiffka S. J.; Kane M. A.; Swaan P. W. Planar Bile Acids in Health and Disease. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 2269–2276. 10.1016/j.bbamem.2017.08.019. PubMed DOI PMC

Braverman N. E.; Moser A. B. Functions of Plasmalogen Lipids in Health and Disease. Biochim. Biophys. Acta, Mol. Basis Dis. 2012, 1822, 1442–1452. 10.1016/j.bbadis.2012.05.008. PubMed DOI

Toker A. The Biology and Biochemistry of Diacylglycerol Signalling. EMBO Rep. 2005, 6, 310–314. 10.1038/sj.embor.7400378. PubMed DOI PMC

Carrasco S.; Mérida I. Diacylglycerol, When Simplicity Becomes Complex. Trends Biochem. Sci. 2007, 32, 27–36. 10.1016/j.tibs.2006.11.004. PubMed DOI

Zegarlińska J.; Piaścik M.; Sikorski A. F.; Czogalla A. Phosphatidic Acid - a Simple Phospholipid with Multiple Faces. Acta Biochim. Polym. 2018, 65, 163–171. 10.18388/abp.2018_2592. PubMed DOI

Kwolek U.; Kulig W.; Wydro P.; Nowakowska M.; Róg T.; Kepczynski M. Effect of Phosphatidic Acid on Biomembrane: Experimental and Molecular Dynamics Simulations Study. J. Phys. Chem. B 2015, 119, 10042–10051. 10.1021/acs.jpcb.5b03604. PubMed DOI

Athenstaedt K.; Daum G. Phosphatidic Acid, a Key Intermediate in Lipid Metabolism. Eur. J. Biochem. 1999, 266, 1–16. 10.1046/j.1432-1327.1999.00822.x. PubMed DOI

Wang X.; Devaiah S. P.; Zhang W.; Welti R. Signaling Functions of Phosphatidic Acid. Prog. Lipid Res. 2006, 45, 250–278. 10.1016/j.plipres.2006.01.005. PubMed DOI

Testerink C.; Munnik T. Phosphatidic Acid: A Multifunctional Stress Signaling Lipid in Plants. Trends Plant Sci. 2005, 10, 368–375. 10.1016/j.tplants.2005.06.002. PubMed DOI

Phospholipases in Plant Signaling. In Signaling and Communication in Plants; Wang X., Ed.; Springer Berlin Heidelberg: Berlin, Heidelberg, 2014; Vol. 20, 10.1007/978-3-642-42011-5. DOI

Mejia E. M.; Hatch G. M. Mitochondrial Phospholipids: Role in Mitochondrial Function. J. Bioenerg. Biomembr. 2016, 48, 99–112. 10.1007/s10863-015-9601-4. PubMed DOI

Kooijman E. E.; Chupin V.; de Kruijff B.; Burger K. N. J. Modulation of Membrane Curvature by Phosphatidic Acid and Lysophosphatidic Acid: Biophysical Properties of Phosphatidic Acid and Lysophosphatidic Acid. Traffic 2003, 4, 162–174. 10.1034/j.1600-0854.2003.00086.x. PubMed DOI

Kooijman E. E.; Tieleman D. P.; Testerink C.; Munnik T.; Rijkers D. T. S.; Burger K. N. J.; de Kruijff B. An Electrostatic/Hydrogen Bond Switch as the Basis for the Specific Interaction of Phosphatidic Acid with Proteins. J. Biol. Chem. 2007, 282, 11356–11364. 10.1074/jbc.M609737200. PubMed DOI

Kooijman E. E.; Burger K. N. J. Biophysics and Function of Phosphatidic Acid: A Molecular Perspective. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2009, 1791, 881–888. 10.1016/j.bbalip.2009.04.001. PubMed DOI

Magarkar A.; Róg T.; Bunker A. Molecular Dynamics Simulation of Inverse-Phosphocholine Lipids. J. Phys. Chem. C 2014, 118, 19444–19449. 10.1021/jp505633y. DOI

Sohlenkamp C.; Geiger O. Bacterial Membrane Lipids: Diversity in Structures and Pathways. FEMS Microbiol. Rev. 2016, 40, 133–159. 10.1093/femsre/fuv008. PubMed DOI

Steimle A.; Autenrieth I. B.; Frick J.-S. Structure and Function: Lipid A Modifications in Commensals and Pathogens. Int. J. Med. Microbiol. 2016, 306, 290–301. 10.1016/j.ijmm.2016.03.001. PubMed DOI

Leventis P. A.; Grinstein S. The Distribution and Function of Phosphatidylserine in Cellular Membranes. Annu. Rev. Biophys. 2010, 39, 407–427. 10.1146/annurev.biophys.093008.131234. PubMed DOI

Bevers E. M.; Williamson P. L. Getting to the Outer Leaflet: Physiology of Phosphatidylserine Exposure at the Plasma Membrane. Physiol. Rev. 2016, 96, 605–645. 10.1152/physrev.00020.2015. PubMed DOI

Rysavy N. M.; Shimoda L. M. N.; Dixon A. M.; Speck M.; Stokes A. J.; Turner H.; Umemoto E. Y. Beyond Apoptosis: The Mechanism and Function of Phosphatidylserine Asymmetry in the Membrane of Activating Mast Cells. Bioarchitecture 2014, 4, 127–137. 10.1080/19490992.2014.995516. PubMed DOI PMC

Llorente A.; Skotland T.; Sylvänne T.; Kauhanen D.; Róg T.; Orłowski A.; Vattulainen I.; Ekroos K.; Sandvig K. Molecular Lipidomics of Exosomes Released by PC-3 Prostate Cancer Cells. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2013, 1831, 1302–1309. 10.1016/j.bbalip.2013.04.011. PubMed DOI

Nakamura Y. Plant Phospholipid Diversity: Emerging Functions in Metabolism and Protein–Lipid Interactions. Trends Plant Sci. 2017, 22, 1027–1040. 10.1016/j.tplants.2017.09.002. PubMed DOI

Schink K. O.; Tan K.-W.; Stenmark H. Phosphoinositides in Control of Membrane Dynamics. Annu. Rev. Cell Dev. Biol. 2016, 32, 143–171. 10.1146/annurev-cellbio-111315-125349. PubMed DOI

Marat A. L.; Haucke V. Phosphatidylinositol 3-phosphates—at the Interface between Cell Signalling and Membrane Traffic. EMBO J. 2016, 35, 561–579. 10.15252/embj.201593564. PubMed DOI PMC

Choy C. H.; Han B.-K.; Botelho R. J. Phosphoinositide Diversity, Distribution, and Effector Function: Stepping Out of the Box. BioEssays 2017, 39, 1700121.10.1002/bies.201700121. PubMed DOI

Hölzl G.; Dörmann P. Structure and Function of Glycoglycerolipids in Plants and Bacteria. Prog. Lipid Res. 2007, 46, 225–243. 10.1016/j.plipres.2007.05.001. PubMed DOI

Domonkos I.; Laczkó-Dobos H.; Gombos Z. Lipid-Assisted Protein–Protein Interactions That Support Photosynthetic and Other Cellular Activities. Prog. Lipid Res. 2008, 47, 422–435. 10.1016/j.plipres.2008.05.003. PubMed DOI

Quehenberger O.; Armando A. M.; Dennis E. A. High Sensitivity Quantitative Lipidomics Analysis of Fatty Acids in Biological Samples by Gas Chromatography–Mass Spectrometry. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2011, 1811, 648–656. 10.1016/j.bbalip.2011.07.006. PubMed DOI PMC

Kim H.-Y.; Huang B. X.; Spector A. A. Phosphatidylserine in the Brain: Metabolism and Function. Prog. Lipid Res. 2014, 56, 1–18. 10.1016/j.plipres.2014.06.002. PubMed DOI PMC

Brennan P. J.; Griffin P. F. S.; Lösel D. M.; Tyrrell D. The Lipids of Fungi. Prog. Chem. Fats Other Lipids 1975, 14, 49–89. 10.1016/0079-6832(75)90002-6. PubMed DOI

Kosa G.; Zimmermann B.; Kohler A.; Ekeberg D.; Afseth N. K.; Mounier J.; Shapaval V. High-Throughput Screening of Mucoromycota Fungi for Production of Low- and High-Value Lipids. Biotechnol. Biofuels 2018, 11, 66.10.1186/s13068-018-1070-7. PubMed DOI PMC

Mysyakina I. S.; Sergeeva Y. E.; Bokareva D. A. Lipid Composition of the Spores of Zygomycetous and Ascomycetous Fungi during Cessation of the Exogenous Dormancy State. Microbiology 2018, 87, 51–59. 10.1134/S0026261718010125. DOI

Sinanoglou V. J.; Zoumpoulakis P.; Heropoulos G.; Proestos C.; Ćirić A.; Petrovic J.; Glamoclija J.; Sokovic M. Lipid and Fatty Acid Profile of the Edible Fungus Laetiporus Sulphurous. Antifungal and Antibacterial Properties. J. Food Sci. Technol. 2014, 52, 3264–3272. 10.1007/s13197-014-1377-8. PubMed DOI PMC

Zelles L. Fatty Acid Patterns of Phospholipids and Lipopolysaccharides in the Characterisation of Microbial Communities in Soil: A Review. Biol. Fertil. Soils 1999, 29, 111–129. 10.1007/s003740050533. DOI

Sawangkeaw R.; Ngamprasertsith S. A Review of Lipid-Based Biomasses as Feedstocks for Biofuels Production. Renewable Sustainable Energy Rev. 2013, 25, 97–108. 10.1016/j.rser.2013.04.007. DOI

Kulig W.; Pasenkiewicz-Gierula M.; Róg T. Cis and Trans Unsaturated Phosphatidylcholine Bilayers: A Molecular Dynamics Simulation Study. Chem. Phys. Lipids 2016, 195, 12–20. 10.1016/j.chemphyslip.2015.07.002. PubMed DOI

Róg T.; Murzyn K.; Gurbiel R.; Takaoka Y.; Kusumi A.; Pasenkiewicz-Gierula M. Effects of Phospholipid Unsaturation on the Bilayer Nonpolar Region: A Molecular Simulation Study. J. Lipid Res. 2004, 45, 326–336. 10.1194/jlr.M300187-JLR200. PubMed DOI

Vähäheikkilä M.; Peltomaa T.; Róg T.; Vazdar M.; Pöyry S.; Vattulainen I. How Cardiolipin Peroxidation Alters the Properties of the Inner Mitochondrial Membrane?. Chem. Phys. Lipids 2018, 214, 15–23. 10.1016/j.chemphyslip.2018.04.005. PubMed DOI

Cwiklik L.; Jungwirth P. Massive Oxidation of Phospholipid Membranes Leads to Pore Creation and Bilayer Disintegration. Chem. Phys. Lett. 2010, 486, 99–103. 10.1016/j.cplett.2010.01.010. DOI

Beranova L.; Cwiklik L.; Jurkiewicz P.; Hof M.; Jungwirth P. Oxidation Changes Physical Properties of Phospholipid Bilayers: Fluorescence Spectroscopy and Molecular Simulations. Langmuir 2010, 26, 6140–6144. 10.1021/la100657a. PubMed DOI

Boonnoy P.; Jarerattanachat V.; Karttunen M.; Wong-ekkabut J. Bilayer Deformation, Pores, and Micellation Induced by Oxidized Lipids. J. Phys. Chem. Lett. 2015, 6, 4884–4888. 10.1021/acs.jpclett.5b02405. PubMed DOI

Jurkiewicz P.; Olżyńska A.; Cwiklik L.; Conte E.; Jungwirth P.; Megli F. M.; Hof M. Biophysics of Lipid Bilayers Containing Oxidatively Modified Phospholipids: Insights from Fluorescence and EPR Experiments and from MD Simulations. Biochim. Biophys. Acta, Biomembr. 2012, 1818, 2388–2402. 10.1016/j.bbamem.2012.05.020. PubMed DOI

Van der Paal J.; Neyts E. C.; Verlackt C. C. W.; Bogaerts A. Effect of Lipid Peroxidation on Membrane Permeability of Cancer and Normal Cells Subjected to Oxidative Stress. Chem. Sci. 2016, 7, 489–498. 10.1039/C5SC02311D. PubMed DOI PMC

Deigner H.-P.; Hermetter A. Oxidized Phospholipids: Emerging Lipid Mediators in Pathophysiology. Curr. Opin. Lipidol. 2008, 19, 289–294. 10.1097/MOL.0b013e3282fe1d0e. PubMed DOI

Fruhwirth G. O.; Loidl A.; Hermetter A. Oxidized Phospholipids: From Molecular Properties to Disease. Biochim. Biophys. Acta, Mol. Basis Dis. 2007, 1772, 718–736. 10.1016/j.bbadis.2007.04.009. PubMed DOI

Pham-Huy L. A.; He H.; Pham-Huy C. Free Radicals, Antioxidants in Disease and Health. Int. J. Biomed. Sci. IJBS 2008, 4, 89–96. PubMed PMC

Kates M.; Syz J.-Y.; Gosser D.; Haines T. H. pH-Dissociation Characteristics of Cardiolipin and Its 2′-Deoxy Analogue. Lipids 1993, 28, 877–882. 10.1007/BF02537494. PubMed DOI

Haines T. H.; Dencher N. A. Cardiolipin: A Proton Trap for Oxidative Phosphorylation. FEBS Lett. 2002, 528, 35–39. 10.1016/S0014-5793(02)03292-1. PubMed DOI

Nichols-Smith S.; Kuhl T. Electrostatic Interactions between Model Mitochondrial Membranes. Colloids Surf., B 2005, 41, 121–127. 10.1016/j.colsurfb.2004.11.003. PubMed DOI

Kooijman E. E.; Swim L. A.; Graber Z. T.; Tyurina Y. Y.; Bayır H.; Kagan V. E. Magic Angle Spinning 31P NMR Spectroscopy Reveals Two Essentially Identical Ionization States for the Cardiolipin Phosphates in Phospholipid Liposomes. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 61–68. 10.1016/j.bbamem.2016.10.013. PubMed DOI PMC

Sathappa M.; Alder N. N. The Ionization Properties of Cardiolipin and Its Variants in Model Bilayers. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 1362–1372. 10.1016/j.bbamem.2016.03.007. PubMed DOI PMC

Olofsson G.; Sparr E. Ionization Constants pKa of Cardiolipin. PLoS One 2013, 8, e73040.10.1371/journal.pone.0073040. PubMed DOI PMC

Maguire J. J.; Tyurina Y. Y.; Mohammadyani D.; Kapralov A. A.; Anthonymuthu T. S.; Qu F.; Amoscato A. A.; Sparvero L. J.; Tyurin V. A.; Planas-Iglesias J.; et al. Known Unknowns of Cardiolipin Signaling: The Best Is yet to Come. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2017, 1862, 8–24. 10.1016/j.bbalip.2016.08.001. PubMed DOI PMC

Cheng H.; Mancuso D. J.; Jiang X.; Guan S.; Yang J.; Yang K.; Sun G.; Gross R. W.; Han X. Shotgun Lipidomics Reveals the Temporally Dependent, Highly Diversified Cardiolipin Profile in the Mammalian Brain: Temporally Coordinated Postnatal Diversification of Cardiolipin Molecular Species with Neuronal Remodeling †. Biochemistry 2008, 47, 5869–5880. 10.1021/bi7023282. PubMed DOI PMC

Han X.; Yang K.; Yang J.; Cheng H.; Gross R. W. Shotgun Lipidomics of Cardiolipin Molecular Species in Lipid Extracts of Biological Samples. J. Lipid Res. 2006, 47, 864–879. 10.1194/jlr.D500044-JLR200. PubMed DOI PMC

Karlsson K.-A. Sphingolipid Long Chain Bases. Lipids 1970, 5, 878–891. 10.1007/BF02531119. PubMed DOI

Ramstedt B.; Slotte J. P. Membrane Properties of Sphingomyelins. FEBS Lett. 2002, 531, 33–37. 10.1016/S0014-5793(02)03406-3. PubMed DOI

Slotte J. P. Biological Functions of Sphingomyelins. Prog. Lipid Res. 2013, 52, 424–437. 10.1016/j.plipres.2013.05.001. PubMed DOI

Manna M.; Róg T.; Vattulainen I. The Challenges of Understanding Glycolipid Functions: An Open Outlook Based on Molecular Simulations. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2014, 1841, 1130–1145. 10.1016/j.bbalip.2013.12.016. PubMed DOI

Slotte J. P. Molecular Properties of Various Structurally Defined Sphingomyelins – Correlation of Structure with Function. Prog. Lipid Res. 2013, 52, 206–219. 10.1016/j.plipres.2012.12.001. PubMed DOI

Gulshan K.; Smith J. D. Sphingomyelin Regulation of Plasma Membrane Asymmetry, Efflux and Reverse Cholesterol Transport. Clin. Lipidol. 2014, 9, 383–393. 10.2217/clp.14.28. DOI

Müller C. P.; Reichel M.; Mühle C.; Rhein C.; Gulbins E.; Kornhuber J. Brain Membrane Lipids in Major Depression and Anxiety Disorders. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2015, 1851, 1052–1065. 10.1016/j.bbalip.2014.12.014. PubMed DOI

Karunakaran I.; van Echten-Deckert G. Sphingosine 1-Phosphate – A Double Edged Sword in the Brain. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 1573–1582. 10.1016/j.bbamem.2017.03.008. PubMed DOI

Li L. K.; So L.; Spector A. Membrane Cholesterol and Phospholipid in Consecutive Concentric Sections of Human Lenses. J. Lipid Res. 1985, 26, 600–609. PubMed

Subczynski W. K.; Raguz M.; Widomska J.; Mainali L.; Konovalov A. Functions of Cholesterol and the Cholesterol Bilayer Domain Specific to the Fiber-Cell Plasma Membrane of the Eye Lens. J. Membr. Biol. 2012, 245, 51–68. 10.1007/s00232-011-9412-4. PubMed DOI PMC

Jain M.; Ngoy S.; Sheth S. A.; Swanson R. A.; Rhee E. P.; Liao R.; Clish C. B.; Mootha V. K.; Nilsson R. A Systematic Survey of Lipids across Mouse Tissues. Am. J. Physiol.-Endocrinol. Metab. 2014, 306, E854–E868. 10.1152/ajpendo.00371.2013. PubMed DOI PMC

Iwai I.; Han H.; Hollander L. d.; Svensson S.; Öfverstedt L.-G.; Anwar J.; Brewer J.; Bloksgaard M.; Laloeuf A.; Nosek D.; et al. The Human Skin Barrier Is Organized as Stacked Bilayers of Fully Extended Ceramides with Cholesterol Molecules Associated with the Ceramide Sphingoid Moiety. J. Invest. Dermatol. 2012, 132, 2215–2225. 10.1038/jid.2012.43. PubMed DOI

Boncheva M. The Physical Chemistry of the Stratum Corneum Lipids. Int. J. Cosmet. Sci. 2014, 36, 505–515. 10.1111/ics.12162. PubMed DOI

van Meer G.; Voelker D. R.; Feigenson G. W. Membrane Lipids: Where They Are and How They Behave. Nat. Rev. Mol. Cell Biol. 2008, 9, 112–124. 10.1038/nrm2330. PubMed DOI PMC

Giang H.; Schick M. On the Puzzling Distribution of Cholesterol in the Plasma Membrane. Chem. Phys. Lipids 2016, 199, 35–38. 10.1016/j.chemphyslip.2015.12.002. PubMed DOI

Ohvo-Rekilä H.; Ramstedt B.; Leppimäki P.; Peter Slotte J. Cholesterol Interactions with Phospholipids in Membranes. Prog. Lipid Res. 2002, 41, 66–97. 10.1016/S0163-7827(01)00020-0. PubMed DOI

Róg T.; Vattulainen I. Cholesterol, Sphingolipids, and Glycolipids: What Do We Know about Their Role in Raft-like Membranes?. Chem. Phys. Lipids 2014, 184, 82–104. 10.1016/j.chemphyslip.2014.10.004. PubMed DOI

de Meyer F.; Smit B. Effect of Cholesterol on the Structure of a Phospholipid Bilayer. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 3654–3658. 10.1073/pnas.0809959106. PubMed DOI PMC

Róg T.; Pasenkiewicz-Gierula M.; Vattulainen I.; Karttunen M. Ordering Effects of Cholesterol and Its Analogues. Biochim. Biophys. Acta, Biomembr. 2009, 1788, 97–121. 10.1016/j.bbamem.2008.08.022. PubMed DOI

Magarkar A.; Dhawan V.; Kallinteri P.; Viitala T.; Elmowafy M.; Róg T.; Bunker A. Cholesterol Level Affects Surface Charge of Lipid Membranes in Saline Solution. Sci. Rep. 2015, 4, 5005.10.1038/srep05005. PubMed DOI PMC

Kaushik S.; Massey A. C.; Cuervo A. M. Lysosome Membrane Lipid Microdomains: Novel Regulators of Chaperone-Mediated Autophagy. EMBO J. 2006, 25, 3921–3933. 10.1038/sj.emboj.7601283. PubMed DOI PMC

Rayermann S. P.; Rayermann G. E.; Cornell C. E.; Merz A. J.; Keller S. L. Hallmarks of Reversible Separation of Living, Unperturbed Cell Membranes into Two Liquid Phases. Biophys. J. 2017, 113, 2425–2432. 10.1016/j.bpj.2017.09.029. PubMed DOI PMC

Lingwood D.; Kaiser H.-J.; Levental I.; Simons K. Lipid Rafts as Functional Heterogeneity in Cell Membranes. Biochem. Soc. Trans. 2009, 37, 955–960. 10.1042/BST0370955. PubMed DOI

Simons K.; Gerl M. J. Revitalizing Membrane Rafts: New Tools and Insights. Nat. Rev. Mol. Cell Biol. 2010, 11, 688–699. 10.1038/nrm2977. PubMed DOI

Owen M. C.; Kulig W.; Rog T.; Vattulainen I.; Strodel B. Cholesterol Protects the Oxidized Lipid Bilayer from Water Injury: An All-Atom Molecular Dynamics Study. J. Membr. Biol. 2018, 251, 521–534. 10.1007/s00232-018-0028-9. PubMed DOI

Schuck S. Polarized Sorting in Epithelial Cells: Raft Clustering and the Biogenesis of the Apical Membrane. J. Cell Sci. 2004, 117, 5955–5964. 10.1242/jcs.01596. PubMed DOI

Diaz-Rohrer B. B.; Levental K. R.; Simons K.; Levental I. Membrane Raft Association Is a Determinant of Plasma Membrane Localization. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 8500–8505. 10.1073/pnas.1404582111. PubMed DOI PMC

Simons K.; Toomre D. Lipid Rafts and Signal Transduction. Nat. Rev. Mol. Cell Biol. 2000, 1, 31–39. 10.1038/35036052. PubMed DOI

Allen J. A.; Halverson-Tamboli R. A.; Rasenick M. M. Lipid Raft Microdomains and Neurotransmitter Signalling. Nat. Rev. Neurosci. 2007, 8, 128–140. 10.1038/nrn2059. PubMed DOI

Agarwal S. R.; Gratwohl J.; Cozad M.; Yang P.-C.; Clancy C. E.; Harvey R. D. Compartmentalized CAMP Signaling Associated With Lipid Raft and Non-Raft Membrane Domains in Adult Ventricular Myocytes. Front. Pharmacol. 2018, 9, 332.10.3389/fphar.2018.00332. PubMed DOI PMC

Varshney P.; Yadav V.; Saini N. Lipid Rafts in Immune Signalling: Current Progress and Future Perspective. Immunology 2016, 149, 13–24. 10.1111/imm.12617. PubMed DOI PMC

Kulig W.; Cwiklik L.; Jurkiewicz P.; Rog T.; Vattulainen I. Cholesterol Oxidation Products and Their Biological Importance. Chem. Phys. Lipids 2016, 199, 144–160. 10.1016/j.chemphyslip.2016.03.001. PubMed DOI

Kulig W.; Jurkiewicz P.; Olżyńska A.; Tynkkynen J.; Javanainen M.; Manna M.; Rog T.; Hof M.; Vattulainen I.; Jungwirth P. Experimental Determination and Computational Interpretation of Biophysical Properties of Lipid Bilayers Enriched by Cholesteryl Hemisuccinate. Biochim. Biophys. Acta, Biomembr. 2015, 1848, 422–432. 10.1016/j.bbamem.2014.10.032. PubMed DOI

Kulig W.; Mikkolainen H.; Olżyńska A.; Jurkiewicz P.; Cwiklik L.; Hof M.; Vattulainen I.; Jungwirth P.; Rog T. Bobbing of Oxysterols: Molecular Mechanism for Translocation of Tail-Oxidized Sterols through Biological Membranes. J. Phys. Chem. Lett. 2018, 9, 1118–1123. 10.1021/acs.jpclett.8b00211. PubMed DOI

Kurzchalia T. V.; Ward S. Why Do Worms Need Cholesterol?. Nat. Cell Biol. 2003, 5, 684–688. 10.1038/ncb0803-684. PubMed DOI

Clayton R. B. The Utilization of Sterols by Insects. J. Lipid Res. 1964, 5, 3–19. PubMed

Hannich J. T.; Umebayashi K.; Riezman H. Distribution and Functions of Sterols and Sphingolipids. Cold Spring Harbor Perspect. Biol. 2011, 3, a004762–a004762. 10.1101/cshperspect.a004762. PubMed DOI PMC

Janson E. M.; Grebenok R. J.; Behmer S. T.; Abbot P. Same Host-Plant, Different Sterols: Variation in Sterol Metabolism in an Insect Herbivore Community. J. Chem. Ecol. 2009, 35, 1309–1319. 10.1007/s10886-009-9713-6. PubMed DOI

Gachumi G.; El-Aneed A. Mass Spectrometric Approaches for the Analysis of Phytosterols in Biological Samples. J. Agric. Food Chem. 2017, 65, 10141–10156. 10.1021/acs.jafc.7b03785. PubMed DOI

Ostlund R. E. Phytosterols in Human Nutrition. Annu. Rev. Nutr. 2002, 22, 533–549. 10.1146/annurev.nutr.22.020702.075220. PubMed DOI

Valitova J. N.; Sulkarnayeva A. G.; Minibayeva F. V. Plant Sterols: Diversity, Biosynthesis, and Physiological Functions. Biochemistry 2016, 81, 819–834. 10.1134/S0006297916080046. PubMed DOI

Genser B.; Silbernagel G.; De Backer G.; Bruckert E.; Carmena R.; Chapman M. J.; Deanfield J.; Descamps O. S.; Rietzschel E. R.; Dias K. C.; et al. Plant Sterols and Cardiovascular Disease: A Systematic Review and Meta-Analysis. Eur. Heart J. 2012, 33, 444–451. 10.1093/eurheartj/ehr441. PubMed DOI PMC

Silbernagel G.; Genser B.; Nestel P.; März W. Plant Sterols and Atherosclerosis:. Curr. Opin. Lipidol. 2013, 24, 12–17. 10.1097/MOL.0b013e32835b6271. PubMed DOI

Ajagbe B. O.; Othman R. A.; Myrie S. B. Plant Sterols, Stanols, and Sitosterolemia. J. AOAC Int. 2015, 98, 716–723. 10.5740/jaoacint.SGEAjagbe. PubMed DOI PMC

He W.-S.; Zhu H.; Chen Z.-Y. Plant Sterols: Chemical and Enzymatic Structural Modifications and Effects on Their Cholesterol-Lowering Activity. J. Agric. Food Chem. 2018, 66, 3047–3062. 10.1021/acs.jafc.8b00059. PubMed DOI

Corrêa R. C. G.; Peralta R. M.; Bracht A.; Ferreira I. C. F. R. The Emerging Use of Mycosterols in Food Industry along with the Current Trend of Extended Use of Bioactive Phytosterols. Trends Food Sci. Technol. 2017, 67, 19–35. 10.1016/j.tifs.2017.06.012. DOI

Weete J. D.; Abril M.; Blackwell M. Phylogenetic Distribution of Fungal Sterols. PLoS One 2010, 5, e10899.10.1371/journal.pone.0010899. PubMed DOI PMC

Dhingra S.; Cramer R. A. Regulation of Sterol Biosynthesis in the Human Fungal Pathogen Aspergillus Fumigatus: Opportunities for Therapeutic Development. Front. Microbiol. 2017, 8, 92.10.3389/fmicb.2017.00092. PubMed DOI PMC

Kornspan J. D.; Rottem S. The Phospholipid Profile of Mycoplasmas. J. Lipids 2012, 2012, 1–8. 10.1155/2012/640762. PubMed DOI PMC

Wei J. H.; Yin X.; Welander P. V. Sterol Synthesis in Diverse Bacteria. Front. Microbiol. 2016, 7, 990.10.3389/fmicb.2016.00990. PubMed DOI PMC

Belin B. J.; Busset N.; Giraud E.; Molinaro A.; Silipo A.; Newman D. K. Hopanoid Lipids: From Membranes to Plant–Bacteria Interactions. Nat. Rev. Microbiol. 2018, 16, 304–315. 10.1038/nrmicro.2017.173. PubMed DOI PMC

Sáenz J. P.; Sezgin E.; Schwille P.; Simons K. Functional Convergence of Hopanoids and Sterols in Membrane Ordering. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 14236–14240. 10.1073/pnas.1212141109. PubMed DOI PMC

Sáenz J. P.; Grosser D.; Bradley A. S.; Lagny T. J.; Lavrynenko O.; Broda M.; Simons K. Hopanoids as Functional Analogues of Cholesterol in Bacterial Membranes. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 11971–11976. 10.1073/pnas.1515607112. PubMed DOI PMC

Neuvonen M.; Manna M.; Mokkila S.; Javanainen M.; Rog T.; Liu Z.; Bittman R.; Vattulainen I.; Ikonen E. Enzymatic Oxidation of Cholesterol: Properties and Functional Effects of Cholestenone in Cell Membranes. PLoS One 2014, 9, e103743.10.1371/journal.pone.0103743. PubMed DOI PMC

Pourmousa M.; Róg T.; Mikkeli R.; Vattulainen l.; Solanko L. M.; Wüstner D.; List N. H.; Kongsted J.; Karttunen M. Dehydroergosterol as an Analogue for Cholesterol: Why It Mimics Cholesterol So Well—or Does It?. J. Phys. Chem. B 2014, 118, 7345–7357. 10.1021/jp406883k. PubMed DOI

Hölttä-Vuori M.; Uronen R.-L.; Repakova J.; Salonen E.; Vattulainen I.; Panula P.; Li Z.; Bittman R.; Ikonen E. BODIPY-Cholesterol: A New Tool to Visualize Sterol Trafficking in Living Cells and Organisms. Traffic 2008, 9, 1839–1849. 10.1111/j.1600-0854.2008.00801.x. PubMed DOI

Hulce J. J.; Cognetta A. B.; Niphakis M. J.; Tully S. E.; Cravatt B. F. Proteome-Wide Mapping of Cholesterol-Interacting Proteins in Mammalian Cells. Nat. Methods 2013, 10, 259–264. 10.1038/nmeth.2368. PubMed DOI PMC

Jiang X.; Covey D. F. Total Synthesis of Ent-Cholesterol via a Steroid C,D-Ring Side-Chain Synthon. J. Org. Chem. 2002, 67, 4893–4900. 10.1021/jo025535k. PubMed DOI

Róg T.; Pasenkiewicz-Gierula M. Effects of Epicholesterol on the Phosphatidylcholine Bilayer: A Molecular Simulation Study. Biophys. J. 2003, 84, 1818–1826. 10.1016/S0006-3495(03)74989-3. PubMed DOI PMC

Róg T.; Pöyry S.; Vattulainen I. Building Synthetic Sterols Computationally – Unlocking the Secrets of Evolution?. Front. Bioeng. Biotechnol. 2015, 3, 121.10.3389/fbioe.2015.00121. PubMed DOI PMC

Pöyry S.; Róg T.; Karttunen M.; Vattulainen I. Significance of Cholesterol Methyl Groups. J. Phys. Chem. B 2008, 112, 2922–2929. 10.1021/jp7100495. PubMed DOI

Róg T.; Pasenkiewicz-Gierula M.; Vattulainen I.; Karttunen M. What Happens If Cholesterol Is Made Smoother. Biophys. J. 2007, 92, 3346–3357. 10.1529/biophysj.106.095497. PubMed DOI PMC

Mydock-McGrane L.; Rath N. P.; Covey D. F. Synthesis of a Smoothened Cholesterol: 18,19-Di-nor-Cholesterol. J. Org. Chem. 2014, 79, 5636–5643. 10.1021/jo500813n. PubMed DOI PMC

Meyer T.; Baek D. J.; Bittman R.; Haralampiev I.; Müller P.; Herrmann A.; Huster D.; Scheidt H. A. Membrane Properties of Cholesterol Analogs with an Unbranched Aliphatic Side Chain. Chem. Phys. Lipids 2014, 184, 1–6. 10.1016/j.chemphyslip.2014.08.002. PubMed DOI

Benvegnu T.; Brard M.; Plusquellec D. Archaeabacteria Bipolar Lipid Analogues: Structure, Synthesis and Lyotropic Properties. Curr. Opin. Colloid Interface Sci. 2004, 8, 469–479. 10.1016/j.cocis.2004.01.005. DOI

Koga Y. Thermal Adaptation of the Archaeal and Bacterial Lipid Membranes. Archaea 2012, 2012, 1–6. 10.1155/2012/789652. PubMed DOI PMC

Sprott G. D.Archaeal Membrane Lipids and Applications. eLS; John Wiley & Sons, Ltd, Ed.; John Wiley & Sons, Ltd: Chichester, UK, 2011; Vol. 15, 10.1002/9780470015902.a0000385.pub3. DOI

Yang Y.; Lee M.; Fairn G. D. Phospholipid Subcellular Localization and Dynamics. J. Biol. Chem. 2018, 293, 6230–6240. 10.1074/jbc.R117.000582. PubMed DOI PMC

Menon A. K.; Levine T. P. The Cellular Lipid Landscape. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2016, 1861, 755–756. 10.1016/j.bbalip.2016.05.004. PubMed DOI

Daleke D. L. Regulation of Transbilayer Plasma Membrane Phospholipid Asymmetry. J. Lipid Res. 2003, 44, 233–242. 10.1194/jlr.R200019-JLR200. PubMed DOI

Kobayashi T.; Menon A. K. Transbilayer Lipid Asymmetry. Curr. Biol. 2018, 28, R386–R391. 10.1016/j.cub.2018.01.007. PubMed DOI

Panatala R.; Hennrich H.; Holthuis J. C. M. Inner Workings and Biological Impact of Phospholipid Flippases. J. Cell Sci. 2015, 128, 2021–2032. 10.1242/jcs.102715. PubMed DOI

Andersen J. P.; Vestergaard A. L.; Mikkelsen S. A.; Mogensen L. S.; et al. P4-ATPases as Phospholipid Flippases—Structure, Function, and Enigmas. Front. Physiol. 2016, 7, 275.10.3389/fphys.2016.00275. PubMed DOI PMC

Hankins H. M.; Baldridge R. D.; Xu P.; Graham T. R. Role of Flippases, Scramblases and Transfer Proteins in Phosphatidylserine Subcellular Distribution. Traffic 2015, 16, 35–47. 10.1111/tra.12233. PubMed DOI PMC

Mondal M.; Mesmin B.; Mukherjee S.; Maxfield F. R. Sterols Are Mainly in the Cytoplasmic Leaflet of the Plasma Membrane and the Endocytic Recycling Compartment in CHO Cells. Mol. Biol. Cell 2009, 20, 581–588. 10.1091/mbc.e08-07-0785. PubMed DOI PMC

Liu S.-L.; Sheng R.; Jung J. H.; Wang L.; Stec E.; O’Connor M. J.; Song S.; Bikkavilli R. K.; Winn R. A.; Lee D.; et al. Orthogonal Lipid Sensors Identify Transbilayer Asymmetry of Plasma Membrane Cholesterol. Nat. Chem. Biol. 2017, 13, 268–274. 10.1038/nchembio.2268. PubMed DOI PMC

Solanko L. M.; Sullivan D. P.; Sere Y. Y.; Szomek M.; Lunding A.; Solanko K. A.; Pizovic A.; Stanchev L. D.; Pomorski T. G.; Menon A. K.; et al. Ergosterol Is Mainly Located in the Cytoplasmic Leaflet of the Yeast Plasma Membrane. Traffic 2018, 19, 198–214. 10.1111/tra.12545. PubMed DOI

Brooks-Wilson A.; Marcil M.; Clee S. M.; Zhang L.-H.; Roomp K.; van Dam M.; Yu L.; Brewer C.; Collins J. A.; Molhuizen H. O. F.; et al. Mutations in ABC1 in Tangier Disease and Familial High-Density Lipoprotein Deficiency. Nat. Genet. 1999, 22, 336–345. 10.1038/11905. PubMed DOI

Phillips M. C. Is ABCA1 a Lipid Transfer Protein?. J. Lipid Res. 2018, 59, 749–763. 10.1194/jlr.R082313. PubMed DOI PMC

Courtney K. C.; Pezeshkian W.; Raghupathy R.; Zhang C.; Darbyson A.; Ipsen J. H.; Ford D. A.; Khandelia H.; Presley J. F.; Zha X. C24 Sphingolipids Govern the Transbilayer Asymmetry of Cholesterol and Lateral Organization of Model and Live-Cell Plasma Membranes. Cell Rep. 2018, 24, 1037–1049. 10.1016/j.celrep.2018.06.104. PubMed DOI

Maekawa M.; Fairn G. D. Complementary Probes Reveal That Phosphatidylserine Is Required for the Proper Transbilayer Distribution of Cholesterol. J. Cell Sci. 2015, 128, 1422–1433. 10.1242/jcs.164715. PubMed DOI

Yesylevskyy S. O.; Demchenko A. P. How Cholesterol Is Distributed between Monolayers in Asymmetric Lipid Membranes. Eur. Biophys. J. 2012, 41, 1043–1054. 10.1007/s00249-012-0863-z. PubMed DOI

Falkovich S. G.; Martinez-Seara H.; Nesterenko A. M.; Vattulainen I.; Gurtovenko A. A. What Can We Learn about Cholesterol’s Transmembrane Distribution Based on Cholesterol-Induced Changes in Membrane Dipole Potential?. J. Phys. Chem. Lett. 2016, 7, 4585–4590. 10.1021/acs.jpclett.6b02123. PubMed DOI

Michaelson D. M.; Barkai G.; Barenholz Y. Asymmetry of Lipid Organization in Cholinergic Synaptic Vesicle Membranes. Biochem. J. 1983, 211, 155–162. 10.1042/bj2110155. PubMed DOI PMC

Higgins J. A.; Dawson R. M. C. Asymmetry of the Phospholipid Bilayer of Rat Liver Endoplasmic Reticulum. Biochim. Biophys. Acta, Biomembr. 1977, 470, 342–356. 10.1016/0005-2736(77)90126-2. PubMed DOI

Ma Z.; Liu Z.; Huang X. Membrane Phospholipid Asymmetry Counters the Adverse Effects of Sterol Overloading in the Golgi Membrane of Drosophila. Genetics 2012, 190, 1299–1308. 10.1534/genetics.111.137687. PubMed DOI PMC

Bick R. J.; Van Winkle B. W.; Taffet G. E. Cardiac Sarcoplasmic Reticulum Membrane Lipid Asymmetries. Ann. N. Y. Acad. Sci. 1998, 853, 365–367. 10.1111/j.1749-6632.1998.tb08301.x. PubMed DOI

Róg T.; Orłowski A.; Llorente A.; Skotland T.; Sylvänne T.; Kauhanen D.; Ekroos K.; Sandvig K.; Vattulainen I. Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 281–288. 10.1016/j.bbamem.2015.12.003. PubMed DOI

Manna M.; Javanainen M.; Monne H. M.-S.; Gabius H.-J.; Rog T.; Vattulainen I. Long-Chain GM1 Gangliosides Alter Transmembrane Domain Registration through Interdigitation. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 870–878. 10.1016/j.bbamem.2017.01.033. PubMed DOI

Li L. K.; So L.; Spector A. Age-Dependent Changes in the Distribution and Concentration of Human Lens Cholesterol and Phospholipids. Biochim. Biophys. Acta, Lipids Lipid Metab. 1987, 917, 112–120. 10.1016/0005-2760(87)90291-8. PubMed DOI

Tulodziecka K.; Diaz-Rohrer B. B.; Farley M. M.; Chan R. B.; Di Paolo G.; Levental K. R.; Waxham M. N.; Levental I. Remodeling of the Postsynaptic Plasma Membrane during Neural Development. Mol. Biol. Cell 2016, 27, 3480–3489. 10.1091/mbc.e16-06-0420. PubMed DOI PMC

Pietiläinen K. H.; Róg T.; Seppänen-Laakso T.; Virtue S.; Gopalacharyulu P.; Tang J.; Rodriguez-Cuenca S.; Maciejewski A.; Naukkarinen J.; Ruskeepää A.-L.; et al. Association of Lipidome Remodeling in the Adipocyte Membrane with Acquired Obesity in Humans. PLoS Biol. 2011, 9, e1000623.10.1371/journal.pbio.1000623. PubMed DOI PMC

Butt A. H.; Rasool N.; Khan Y. D. A Treatise to Computational Approaches Towards Prediction of Membrane Protein and Its Subtypes. J. Membr. Biol. 2017, 250, 55–76. 10.1007/s00232-016-9937-7. PubMed DOI

Takamori S.; Holt M.; Stenius K.; Lemke E. A.; Grønborg M.; Riedel D.; Urlaub H.; Schenck S.; Brügger B.; Ringler P.; et al. Molecular Anatomy of a Trafficking Organelle. Cell 2006, 127, 831–846. 10.1016/j.cell.2006.10.030. PubMed DOI

Fagerberg L.; Jonasson K.; von Heijne G.; Uhlén M.; Berglund L. Prediction of the Human Membrane Proteome. Proteomics 2010, 10, 1141–1149. 10.1002/pmic.200900258. PubMed DOI

Scherer W. F.; Syverton J. T.; Gey G. O. Studies on the Propagation in Vitro of Poliomyelitis Viruses. IV. Viral Multiplication in a Stable Strain of Human Malignant Epithelial Cells (Strain HeLa) Derived from an Epidermoid Carcinoma of the Cervix. J. Exp. Med. 1953, 97, 695–710. 10.1084/jem.97.5.695. PubMed DOI PMC

Nagaraj N.; Wisniewski J. R.; Geiger T.; Cox J.; Kircher M.; Kelso J.; Paabo S.; Mann M. Deep Proteome and Transcriptome Mapping of a Human Cancer Cell Line. Mol. Syst. Biol. 2011, 7, 548–548. 10.1038/msb.2011.81. PubMed DOI PMC

Liu J.; Rost B. Comparing Function and Structure between Entire Proteomes. Protein Sci. 2001, 10, 1970–1979. 10.1110/ps.10101. PubMed DOI PMC

Vit O.; Petrak J. Integral Membrane Proteins in Proteomics. How to Break Open the Black Box?. J. Proteomics 2017, 153, 8–20. 10.1016/j.jprot.2016.08.006. PubMed DOI

Garrow A. G.; Agnew A.; Westhead D. R. TMB-Hunt: An Amino Acid Composition Based Method to Screen Proteomes for Beta-Barrel Transmembrane Proteins. BMC Bioinf. 2005, 6, 56.10.1186/1471-2105-6-56. PubMed DOI PMC

Chaturvedi D.; Mahalakshmi R. Transmembrane β-Barrels: Evolution, Folding and Energetics. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 2467–2482. 10.1016/j.bbamem.2017.09.020. PubMed DOI PMC

Almén M.; Nordström K. J.; Fredriksson R.; Schiöth H. B. Mapping the Human Membrane Proteome: A Majority of the Human Membrane Proteins Can Be Classified According to Function and Evolutionary Origin. BMC Biol. 2009, 7, 50.10.1186/1741-7007-7-50. PubMed DOI PMC

Yin H.; Flynn A. D. Drugging Membrane Protein Interactions. Annu. Rev. Biomed. Eng. 2016, 18, 51–76. 10.1146/annurev-bioeng-092115-025322. PubMed DOI PMC

Yıldırım M. A.; Goh K.-I.; Cusick M. E.; Barabási A.-L.; Vidal M. Drug—Target Network. Nat. Biotechnol. 2007, 25, 1119–1126. 10.1038/nbt1338. PubMed DOI

Dobson L.; Reményi I.; Tusnády G. E. The Human Transmembrane Proteome. Biol. Direct 2015, 10, 31.10.1186/s13062-015-0061-x. PubMed DOI PMC

Lomize A. L.; Lomize M. A.; Krolicki S. R.; Pogozheva I. D. Membranome: A Database for Proteome-Wide Analysis of Single-Pass Membrane Proteins. Nucleic Acids Res. 2017, 45, D250–D255. 10.1093/nar/gkw712. PubMed DOI PMC

Pogozheva I. D.; Lomize A. L. Evolution and Adaptation of Single-Pass Transmembrane Proteins. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 364–377. 10.1016/j.bbamem.2017.11.002. PubMed DOI

Bocharov E. V.; Mineev K. S.; Pavlov K. V.; Akimov S. A.; Kuznetsov A. S.; Efremov R. G.; Arseniev A. S. Helix-Helix Interactions in Membrane Domains of Bitopic Proteins: Specificity and Role of Lipid Environment. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 561–576. 10.1016/j.bbamem.2016.10.024. PubMed DOI

Polyansky A. A.; Chugunov A. O.; Volynsky P. E.; Krylov N. A.; Nolde D. E.; Efremov R. G. PREDDIMER: A Web Server for Prediction of Transmembrane Helical Dimers. Bioinformatics 2014, 30, 889–890. 10.1093/bioinformatics/btt645. PubMed DOI

Lomize A. L.; Pogozheva I. D. TMDOCK: An Energy-Based Method for Modeling α-Helical Dimers in Membranes. J. Mol. Biol. 2017, 429, 390–398. 10.1016/j.jmb.2016.09.005. PubMed DOI

Lomize A. L.; Hage J. M.; Pogozheva I. D. Membranome 2.0: Database for Proteome-Wide Profiling of Bitopic Proteins and Their Dimers. Bioinformatics 2018, 34, 1061–1062. 10.1093/bioinformatics/btx720. PubMed DOI

Mueller B. K.; Subramaniam S.; Senes A. A Frequent, GxxxG-Mediated, Transmembrane Association Motif Is Optimized for the Formation of Interhelical Cα-H Hydrogen Bonds. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, E888–E895. 10.1073/pnas.1319944111. PubMed DOI PMC

Cymer F.; Veerappan A.; Schneider D. Transmembrane Helix–Helix Interactions Are Modulated by the Sequence Context and by Lipid Bilayer Properties. Biochim. Biophys. Acta, Biomembr. 2012, 1818, 963–973. 10.1016/j.bbamem.2011.07.035. PubMed DOI

Shimizu K.; Cao W.; Saad G.; Shoji M.; Terada T. Comparative Analysis of Membrane Protein Structure Databases. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 1077–1091. 10.1016/j.bbamem.2018.01.005. PubMed DOI

Cross T. A.; Murray D. T.; Watts A. Helical Membrane Protein Conformations and Their Environment. Eur. Biophys. J. 2013, 42, 731–755. 10.1007/s00249-013-0925-x. PubMed DOI PMC

Moraes I.; Evans G.; Sanchez-Weatherby J.; Newstead S.; Stewart P. D. S. Membrane Protein Structure Determination — The next Generation. Biochim. Biophys. Acta, Biomembr. 2014, 1838, 78–87. 10.1016/j.bbamem.2013.07.010. PubMed DOI PMC

Kendrew J. C.; Bodo G.; Dintzis H. M.; Parrish R. G.; Wyckoff H.; Phillips D. C. A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis. Nature 1958, 181, 662–666. 10.1038/181662a0. PubMed DOI

Deisenhofer J.; Epp O.; Miki K.; Huber R.; Michel H. Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3Å Resolution. Nature 1985, 318, 618–624. 10.1038/318618a0. PubMed DOI

Stetsenko A.; Guskov A. An Overview of the Top Ten Detergents Used for Membrane Protein Crystallization. Crystals 2017, 7, 197.10.3390/cryst7070197. DOI

Caffrey M. A Comprehensive Review of the Lipid Cubic Phase or in Meso Method for Crystallizing Membrane and Soluble Proteins and Complexes. Acta Crystallogr., Sect. F: Struct. Biol. Commun. 2015, 71, 3–18. 10.1107/S2053230X14026843. PubMed DOI PMC

Song Y.; Kenworthy A. K.; Sanders C. R. Cholesterol as a Co-Solvent and a Ligand for Membrane Proteins: Cholesterol-Protein Interactions. Protein Sci. 2014, 23, 1–22. 10.1002/pro.2385. PubMed DOI PMC

Kulig W.; Tynkkynen J.; Javanainen M.; Manna M.; Rog T.; Vattulainen I.; Jungwirth P. How Well Does Cholesteryl Hemisuccinate Mimic Cholesterol in Saturated Phospholipid Bilayers?. J. Mol. Model. 2014, 20, 2121.10.1007/s00894-014-2121-z. PubMed DOI

Loll P. J. Membrane Proteins, Detergents and Crystals: What Is the State of the Art?. Acta Crystallogr., Sect. F: Struct. Biol. Commun. 2014, 70, 1576–1583. 10.1107/S2053230X14025035. PubMed DOI PMC

Gutmann T.; Kim K. H.; Grzybek M.; Walz T.; Coskun Ü. Visualization of Ligand-Induced Transmembrane Signaling in the Full-Length Human Insulin Receptor. J. Cell Biol. 2018, 217, 1643–1649. 10.1083/jcb.201711047. PubMed DOI PMC

Manna M.; Kulig W.; Javanainen M.; Tynkkynen J.; Hensen U.; Müller D. J.; Rog T.; Vattulainen I. How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: β2-Adrenergic Receptor in the Spotlight. J. Chem. Theory Comput. 2015, 11, 3432–3445. 10.1021/acs.jctc.5b00070. PubMed DOI

Hanson M. A.; Cherezov V.; Griffith M. T.; Roth C. B.; Jaakola V.-P.; Chien E. Y. T.; Velasquez J.; Kuhn P.; Stevens R. C. A Specific Cholesterol Binding Site Is Established by the 2.8 Å Structure of the Human β2-Adrenergic Receptor. Structure 2008, 16, 897–905. 10.1016/j.str.2008.05.001. PubMed DOI PMC

Radoicic J.; Lu G. J.; Opella S. J. NMR Structures of Membrane Proteins in Phospholipid Bilayers. Q. Rev. Biophys. 2014, 47, 249–283. 10.1017/S0033583514000080. PubMed DOI PMC

Park S. H.; Das B. B.; Casagrande F.; Tian Y.; Nothnagel H. J.; Chu M.; Kiefer H.; Maier K.; De Angelis A. A.; Marassi F. M.; et al. Structure of the Chemokine Receptor CXCR1 in Phospholipid Bilayers. Nature 2012, 491, 779–783. 10.1038/nature11580. PubMed DOI PMC

Bordignon E.; Bleicken S. New Limits of Sensitivity of Site-Directed Spin Labeling Electron Paramagnetic Resonance for Membrane Proteins. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 841–853. 10.1016/j.bbamem.2017.12.009. PubMed DOI

Bai X.; McMullan G.; Scheres S. H. How Cryo-EM Is Revolutionizing Structural Biology. Trends Biochem. Sci. 2015, 40, 49–57. 10.1016/j.tibs.2014.10.005. PubMed DOI

Murata K.; Wolf M. Cryo-Electron Microscopy for Structural Analysis of Dynamic Biological Macromolecules. Biochim. Biophys. Acta, Gen. Subj. 2018, 1862, 324–334. 10.1016/j.bbagen.2017.07.020. PubMed DOI

Mio K.; Sato C. Lipid Environment of Membrane Proteins in Cryo-EM Based Structural Analysis. Biophys. Rev. 2018, 10, 307–316. 10.1007/s12551-017-0371-6. PubMed DOI PMC

Vinothkumar K. R. Membrane Protein Structures without Crystals, by Single Particle Electron Cryomicroscopy. Curr. Opin. Struct. Biol. 2015, 33, 103–114. 10.1016/j.sbi.2015.07.009. PubMed DOI PMC

Lee S. C.; Khalid S.; Pollock N. L.; Knowles T. J.; Edler K.; Rothnie A. J.; Thomas O. R. T.; Dafforn T. R. Encapsulated Membrane Proteins: A Simplified System for Molecular Simulation. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2549–2557. 10.1016/j.bbamem.2016.02.039. PubMed DOI

Lee S. C.; Knowles T. J.; Postis V. L. G.; Jamshad M.; Parslow R. A.; Lin Y.; Goldman A.; Sridhar P.; Overduin M.; Muench S. P.; et al. A Method for Detergent-Free Isolation of Membrane Proteins in Their Local Lipid Environment. Nat. Protoc. 2016, 11, 1149–1162. 10.1038/nprot.2016.070. PubMed DOI

Nasr M. L.; Baptista D.; Strauss M.; Sun Z.-Y. J.; Grigoriu S.; Huser S.; Plückthun A.; Hagn F.; Walz T.; Hogle J. M.; et al. Covalently Circularized Nanodiscs for Studying Membrane Proteins and Viral Entry. Nat. Methods 2017, 14, 49–52. 10.1038/nmeth.4079. PubMed DOI PMC

Autzen H. E.; Myasnikov A. G.; Campbell M. G.; Asarnow D.; Julius D.; Cheng Y. Structure of the Human TRPM4 Ion Channel in a Lipid Nanodisc. Science 2018, 359, 228–232. 10.1126/science.aar4510. PubMed DOI PMC

White S.Membrane Proteins of Known 3D Structure. http://blanco.biomol.uci.edu/mpstruc/ (accessed Aug 5, 2018).

Almeida J. G.; Preto A. J.; Koukos P. I.; Bonvin A. M. J. J.; Moreira I. S. Membrane Proteins Structures: A Review on Computational Modeling Tools. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 2021–2039. 10.1016/j.bbamem.2017.07.008. PubMed DOI

Grigorieff N.; Ceska T. A.; Downing K. H.; Baldwin J. M.; Henderson R. Electron-Crystallographic Refinement of the Structure of Bacteriorhodopsin. J. Mol. Biol. 1996, 259, 393–421. 10.1006/jmbi.1996.0328. PubMed DOI

Laganowsky A.; Reading E.; Allison T. M.; Ulmschneider M. B.; Degiacomi M. T.; Baldwin A. J.; Robinson C. V. Membrane Proteins Bind Lipids Selectively to Modulate Their Structure and Function. Nature 2014, 510, 172–175. 10.1038/nature13419. PubMed DOI PMC

Poveda J. A.; Marcela Giudici A.; Lourdes Renart M.; Morales A.; González-Ros J. M. Towards Understanding the Molecular Basis of Ion Channel Modulation by Lipids: Mechanistic Models and Current Paradigms. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 1507–1516. 10.1016/j.bbamem.2017.04.003. PubMed DOI

Ciardo M. G.; Ferrer-Montiel A. Lipids as Central Modulators of Sensory TRP Channels. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 1615–1628. 10.1016/j.bbamem.2017.04.012. PubMed DOI

Yeagle P. L. Non-Covalent Binding of Membrane Lipids to Membrane Proteins. Biochim. Biophys. Acta, Biomembr. 2014, 1838, 1548–1559. 10.1016/j.bbamem.2013.11.009. PubMed DOI

Paradies G.; Paradies V.; De Benedictis V.; Ruggiero F. M.; Petrosillo G. Functional Role of Cardiolipin in Mitochondrial Bioenergetics. Biochim. Biophys. Acta, Bioenerg. 2014, 1837, 408–417. 10.1016/j.bbabio.2013.10.006. PubMed DOI

Planas-Iglesias J.; Dwarakanath H.; Mohammadyani D.; Yanamala N.; Kagan V. E.; Klein-Seetharaman J. Cardiolipin Interactions with Proteins. Biophys. J. 2015, 109, 1282–1294. 10.1016/j.bpj.2015.07.034. PubMed DOI PMC

Fiedorczuk K.; Letts J. A.; Degliesposti G.; Kaszuba K.; Skehel M.; Sazanov L. A. Atomic Structure of the Entire Mammalian Mitochondrial Complex I. Nature 2016, 538, 406–410. 10.1038/nature19794. PubMed DOI PMC

Wu M.; Gu J.; Guo R.; Huang Y.; Yang M. Structure of Mammalian Respiratory Supercomplex I1III2IV1. Cell 2016, 167, 1598–1609.e10. 10.1016/j.cell.2016.11.012. PubMed DOI

Su X.; Ma J.; Wei X.; Cao P.; Zhu D.; Chang W.; Liu Z.; Zhang X.; Li M. Structure and Assembly Mechanism of Plant C2S2M2 Type PSII-LHCII Supercomplex. Science 2017, 357, 815–820. 10.1126/science.aan0327. PubMed DOI

Poulikakos P.; Vassilacopoulou D.; Fragoulis E. G. L-DOPA Decarboxylase Association with Membranes in Mouse Brain. Neurochem. Res. 2001, 26, 479–485. 10.1023/A:1010952610387. PubMed DOI

Moravcevic K.; Oxley C. L.; Lemmon M. A. Conditional Peripheral Membrane Proteins: Facing up to Limited Specificity. Structure 2012, 20, 15–27. 10.1016/j.str.2011.11.012. PubMed DOI PMC

Colón-González F.; Kazanietz M. G. C1 Domains Exposed: From Diacylglycerol Binding to Protein–Protein Interactions. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2006, 1761, 827–837. 10.1016/j.bbalip.2006.05.001. PubMed DOI

Stahelin R. V.; Scott J. L.; Frick C. T. Cellular and Molecular Interactions of Phosphoinositides and Peripheral Proteins. Chem. Phys. Lipids 2014, 182, 3–18. 10.1016/j.chemphyslip.2014.02.002. PubMed DOI PMC

Bilkova E.; Pleskot R.; Rissanen S.; Sun S.; Czogalla A.; Cwiklik L.; Róg T.; Vattulainen I.; Cremer P. S.; Jungwirth P.; et al. Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition. J. Am. Chem. Soc. 2017, 139, 4019–4024. 10.1021/jacs.6b11760. PubMed DOI PMC

Johannes L.; Wunder C.; Shafaq-Zadah M. Glycolipids and Lectins in Endocytic Uptake Processes. J. Mol. Biol. 2016, 428, 4792–4818. 10.1016/j.jmb.2016.10.027. PubMed DOI

Wernick N. L. B.; Chinnapen D. J.-F.; Cho J. A.; Lencer W. I. Cholera Toxin: An Intracellular Journey into the Cytosol by Way of the Endoplasmic Reticulum. Toxins 2010, 2, 310–325. 10.3390/toxins2030310. PubMed DOI PMC

Hammache D.; Yahi N.; Maresca M.; Piéroni G.; Fantini J. Human Erythrocyte Glycosphingolipids as Alternative Cofactors for Human Immunodeficiency Virus Type 1 (HIV-1) Entry: Evidence for CD4-Induced Interactions between HIV-1 Gp120 and Reconstituted Membrane Microdomains of Glycosphingolipids (Gb3 and GM3). J. Virol. 1999, 73, 5244–5248. PubMed PMC

Stace C.; Manifava M.; Delon C.; Coadwell J.; Cockcroft S.; Ktistakis N. T. PA Binding of Phosphatidylinositol 4-Phosphate 5-Kinase. Adv. Enzyme Regul. 2008, 48, 55–72. 10.1016/j.advenzreg.2007.11.008. PubMed DOI

Capelluto D. G. S.; Zhao X.; Lucas A.; Lemkul J. A.; Xiao S.; Fu X.; Sun F.; Bevan D. R.; Finkielstein C. V. Biophysical and Molecular-Dynamics Studies of Phosphatidic Acid Binding by the Dvl-2 DEP Domain. Biophys. J. 2014, 106, 1101–1111. 10.1016/j.bpj.2014.01.032. PubMed DOI PMC

Eaton J. M.; Takkellapati S.; Lawrence R. T.; McQueeney K. E.; Boroda S.; Mullins G. R.; Sherwood S. G.; Finck B. N.; Villén J.; Harris T. E. Lipin 2 Binds Phosphatidic Acid by the Electrostatic Hydrogen Bond Switch Mechanism Independent of Phosphorylation. J. Biol. Chem. 2014, 289, 18055–18066. 10.1074/jbc.M114.547604. PubMed DOI PMC

Putta P.; Rankenberg J.; Korver R. A.; van Wijk R.; Munnik T.; Testerink C.; Kooijman E. E. Phosphatidic Acid Binding Proteins Display Differential Binding as a Function of Membrane Curvature Stress and Chemical Properties. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2709–2716. 10.1016/j.bbamem.2016.07.014. PubMed DOI

Schlattner U.; Tokarska-Schlattner M.; Ramirez S.; Brückner A.; Kay L.; Polge C.; Epand R. F.; Lee R. M.; Lacombe M.-L.; Epand R. M. Mitochondrial Kinases and Their Molecular Interaction with Cardiolipin. Biochim. Biophys. Acta, Biomembr. 2009, 1788, 2032–2047. 10.1016/j.bbamem.2009.04.018. PubMed DOI

Sinibaldi F.; Howes B. D.; Piro M. C.; Polticelli F.; Bombelli C.; Ferri T.; Coletta M.; Smulevich G.; Santucci R. Extended Cardiolipin Anchorage to Cytochrome c: A Model for Protein–Mitochondrial Membrane Binding. JBIC, J. Biol. Inorg. Chem. 2010, 15, 689–700. 10.1007/s00775-010-0636-z. PubMed DOI

Chu C. T.; Ji J.; Dagda R. K.; Jiang J. F.; Tyurina Y. Y.; Kapralov A. A.; Tyurin V. A.; Yanamala N.; Shrivastava I. H.; Mohammadyani D.; et al. Cardiolipin Externalization to the Outer Mitochondrial Membrane Acts as an Elimination Signal for Mitophagy in Neuronal Cells. Nat. Cell Biol. 2013, 15, 1197–1205. 10.1038/ncb2837. PubMed DOI PMC

Han X.; Shi Y.; Liu G.; Guo Y.; Yang Y. Activation of ROP6 GTPase by Phosphatidylglycerol in Arabidopsis. Front. Plant Sci. 2018, 9, 347.10.3389/fpls.2018.00347. PubMed DOI PMC

Al-Mulla F.; Bitar M. S.; Taqi Z.; Yeung K. C. RKIP: Much More than Raf Kinase Inhibitory Protein. J. Cell. Physiol. 2013, 228, 1688–1702. 10.1002/jcp.24335. PubMed DOI

Vallée B. S.; Tauc P.; Brochon J.-C.; Maget-Dana R.; Lelièvre D.; Metz-Boutigue M.-H.; Bureaud N.; Schoentgen F. Behaviour of Bovine Phosphatidylethanolamine-Binding Protein with Model Membranes.: Evidence of Affinity for Negatively Charged Membranes. Eur. J. Biochem. 2001, 268, 5831–5841. 10.1046/j.0014-2956.2001.02528.x. PubMed DOI

Nguyen N.; Shteyn V.; Melia T. J. Sensing Membrane Curvature in Macroautophagy. J. Mol. Biol. 2017, 429, 457–472. 10.1016/j.jmb.2017.01.006. PubMed DOI PMC

Merritt E. A.; Sarfaty S.; Hol W. G. J.; Jobling M. G.; Holmes R. K.; Chang T.; Hirst T. R. Structural Studies of Receptor Binding by Cholera Toxin Mutants. Protein Sci. 1997, 6, 1516–1528. 10.1002/pro.5560060716. PubMed DOI PMC

Neu U.; Woellner K.; Gauglitz G.; Stehle T. Structural Basis of GM1 Ganglioside Recognition by Simian Virus 40. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 5219–5224. 10.1073/pnas.0710301105. PubMed DOI PMC

Ströh L. J.; Gee G. V.; Blaum B. S.; Dugan A. S.; Feltkamp M. C. W.; Atwood W. J.; Stehle T. Trichodysplasia Spinulosa-Associated Polyomavirus Uses a Displaced Binding Site on VP1 to Engage Sialylated Glycolipids. PLoS Pathog. 2015, 11, e1005112.10.1371/journal.ppat.1005112. PubMed DOI PMC

Ströh L. J.; Maginnis M. S.; Blaum B. S.; Nelson C. D. S.; Neu U.; Gee G. V.; O’Hara B. A.; Motamedi N.; DiMaio D.; Atwood W. J.; et al. The Greater Affinity of JC Polyomavirus Capsid for α2,6-Linked Lactoseries Tetrasaccharide c than for Other Sialylated Glycans Is a Major Determinant of Infectivity. J. Virol. 2015, 89, 6364–6375. 10.1128/JVI.00489-15. PubMed DOI PMC

Ng N. M.; Littler D. R.; Paton A. W.; Le Nours J.; Rossjohn J.; Paton J. C.; Beddoe T. EcxAB Is a Founding Member of a New Family of Metalloprotease AB5 Toxins with a Hybrid Cholera-like B Subunit. Structure 2013, 21, 2003–2013. 10.1016/j.str.2013.08.024. PubMed DOI

Blaum B. S.; Frank M.; Walker R. C.; Neu U.; Stehle T. Complement Factor H and Simian Virus 40 Bind the GM1 Ganglioside in Distinct Conformations. Glycobiology 2016, 26, 532–539. 10.1093/glycob/cwv170. PubMed DOI

Bian C.-F.; Zhang Y.; Sun H.; Li D.-F.; Wang D.-C. Structural Basis for Distinct Binding Properties of the Human Galectins to Thomsen-Friedenreich Antigen. PLoS One 2011, 6, e25007.10.1371/journal.pone.0025007. PubMed DOI PMC

Feng L.; Sun H.; Zhang Y.; Li D.-F.; Wang D.-C. Structural Insights into the Recognition Mechanism between an Antitumor Galectin AAL and the Thomsen-Friedenreich Antigen. FASEB J. 2010, 24, 3861–3868. 10.1096/fj.10-159111. PubMed DOI PMC

Han Y.-B.; Chen L.-Q.; Li Z.; Tan Y.-M.; Feng Y.; Yang G.-Y. Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases. J. Biol. Chem. 2017, 292, 4789–4800. 10.1074/jbc.M116.763821. PubMed DOI PMC

Chinthalapudi K.; Rangarajan E. S.; Brown D. T.; Izard T. Differential Lipid Binding of Vinculin Isoforms Promotes Quasi-Equivalent Dimerization. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 9539–9544. 10.1073/pnas.1600702113. PubMed DOI PMC

Garcia-Alai M. M.; Heidemann J.; Skruzny M.; Gieras A.; Mertens H. D. T.; Svergun D. I.; Kaksonen M.; Uetrecht C.; Meijers R. Epsin and Sla2 Form Assemblies through Phospholipid Interfaces. Nat. Commun. 2018, 9, 328.10.1038/s41467-017-02443-x. PubMed DOI PMC

Coudevylle N.; Montaville P.; Leonov A.; Zweckstetter M.; Becker S. Structural Determinants for Ca2+ and Phosphatidylinositol 4,5-Bisphosphate Binding by the C2A Domain of Rabphilin-3A. J. Biol. Chem. 2008, 283, 35918–35928. 10.1074/jbc.M804094200. PubMed DOI

Posner M. G.; Upadhyay A.; Ishima R.; Kalli A. C.; Harris G.; Kremerskothen J.; Sansom M. S. P.; Crennell S. J.; Bagby S. Distinctive Phosphoinositide- and Ca2+-Binding Properties of Normal and Cognitive Performance–Linked Variant Forms of KIBRA C2 Domain. J. Biol. Chem. 2018, 293, 9335–9344. 10.1074/jbc.RA118.002279. PubMed DOI PMC

Saad J. S.; Miller J.; Tai J.; Kim A.; Ghanam R. H.; Summers M. F. Structural Basis for Targeting HIV-1 Gag Proteins to the Plasma Membrane for Virus Assembly. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 11364–11369. 10.1073/pnas.0602818103. PubMed DOI PMC

Kono N.; Ohto U.; Hiramatsu T.; Urabe M.; Uchida Y.; Satow Y.; Arai H. Impaired α-TTP-PIPs Interaction Underlies Familial Vitamin E Deficiency. Science 2013, 340, 1106–1110. 10.1126/science.1233508. PubMed DOI

Chinthalapudi K.; Mandati V.; Zheng J.; Sharff A. J.; Bricogne G.; Griffin P. R.; Kissil J.; Izard T. Lipid Binding Promotes the Open Conformation and Tumor-Suppressive Activity of Neurofibromin 2. Nat. Commun. 2018, 9, 1338.10.1038/s41467-018-03648-4. PubMed DOI PMC

Miller M. S.; Schmidt-Kittler O.; Bolduc D. M.; Brower E. T.; Chaves-Moreira D.; Allaire M.; Kinzler K. W.; Jennings I. G.; Thompson P. E.; Cole P. A.; et al. Structural Basis of nSH2 Regulation and Lipid Binding in PI3Kα. Oncotarget 2014, 5, 5198–5208. 10.18632/oncotarget.2263. PubMed DOI PMC

Wu B.; Chien E. Y. T.; Mol C. D.; Fenalti G.; Liu W.; Katritch V.; Abagyan R.; Brooun A.; Wells P.; Bi F. C.; et al. Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists. Science 2010, 330, 1066–1071. 10.1126/science.1194396. PubMed DOI PMC

Ferré S. The GPCR Heterotetramer: Challenging Classical Pharmacology. Trends Pharmacol. Sci. 2015, 36, 145–152. 10.1016/j.tips.2015.01.002. PubMed DOI PMC

Cordomí A.; Navarro G.; Aymerich M. S.; Franco R. Structures for G-Protein-Coupled Receptor Tetramers in Complex with G Proteins. Trends Biochem. Sci. 2015, 40, 548–551. 10.1016/j.tibs.2015.07.007. PubMed DOI

Gaitonde S. A.; González-Maeso J. Contribution of Heteromerization to G Protein-Coupled Receptor Function. Curr. Opin. Pharmacol. 2017, 32, 23–31. 10.1016/j.coph.2016.10.006. PubMed DOI PMC

El Moustaine D.; Granier S.; Doumazane E.; Scholler P.; Rahmeh R.; Bron P.; Mouillac B.; Baneres J.-L.; Rondard P.; Pin J.-P. Distinct Roles of Metabotropic Glutamate Receptor Dimerization in Agonist Activation and G-Protein Coupling. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 16342–16347. 10.1073/pnas.1205838109. PubMed DOI PMC

Whorton M. R.; Bokoch M. P.; Rasmussen S. G. F.; Huang B.; Zare R. N.; Kobilka B.; Sunahara R. K. A Monomeric G Protein-Coupled Receptor Isolated in a High-Density Lipoprotein Particle Efficiently Activates Its G Protein. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 7682–7687. 10.1073/pnas.0611448104. PubMed DOI PMC

Han Y.; Moreira I. S.; Urizar E.; Weinstein H.; Javitch J. A. Allosteric Communication between Protomers of Dopamine Class A GPCR Dimers Modulates Activation. Nat. Chem. Biol. 2009, 5, 688–695. 10.1038/nchembio.199. PubMed DOI PMC

Hern J. A.; Baig A. H.; Mashanov G. I.; Birdsall B.; Corrie J. E. T.; Lazareno S.; Molloy J. E.; Birdsall N. J. M. Formation and Dissociation of M1 Muscarinic Receptor Dimers Seen by Total Internal Reflection Fluorescence Imaging of Single Molecules. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 2693–2698. 10.1073/pnas.0907915107. PubMed DOI PMC

Dorsch S.; Klotz K.-N.; Engelhardt S.; Lohse M. J.; Bünemann M. Analysis of Receptor Oligomerization by FRAP Microscopy. Nat. Methods 2009, 6, 225–230. 10.1038/nmeth.1304. PubMed DOI

Parmar V. K.; Grinde E.; Mazurkiewicz J. E.; Herrick-Davis K. Beta2-Adrenergic Receptor Homodimers: Role of Transmembrane Domain 1 and Helix 8 in Dimerization and Cell Surface Expression. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 1445–1455. 10.1016/j.bbamem.2016.12.007. PubMed DOI PMC

Huang J.; Chen S.; Zhang J. J.; Huang X.-Y. Crystal Structure of Oligomeric β1-Adrenergic G Protein–Coupled Receptors in Ligand-Free Basal State. Nat. Struct. Mol. Biol. 2013, 20, 419–425. 10.1038/nsmb.2504. PubMed DOI PMC

Bonaventura J.; Navarro G.; Casadó-Anguera V.; Azdad K.; Rea W.; Moreno E.; Brugarolas M.; Mallol J.; Canela E. I.; Lluís C.; et al. Allosteric Interactions between Agonists and Antagonists within the Adenosine A2A Receptor-Dopamine D2 Receptor Heterotetramer. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, E3609–E3618. 10.1073/pnas.1507704112. PubMed DOI PMC

Gahbauer S.; Böckmann R. A. Membrane-Mediated Oligomerization of G Protein Coupled Receptors and Its Implications for GPCR Function. Front. Physiol. 2016, 7, 494.10.3389/fphys.2016.00494. PubMed DOI PMC

Chothe P. P.; Czuba L. C.; Moore R. H.; Swaan P. W. Human Bile Acid Transporter ASBT (SLC10A2) Forms Functional Non-Covalent Homodimers and Higher Order Oligomers. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 645–653. 10.1016/j.bbamem.2017.11.016. PubMed DOI PMC

Valley C. C.; Lewis A. K.; Sachs J. N. Piecing It Together: Unraveling the Elusive Structure-Function Relationship in Single-Pass Membrane Receptors. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 1398–1416. 10.1016/j.bbamem.2017.01.016. PubMed DOI PMC

Chung I. Optical Measurement of Receptor Tyrosine Kinase Oligomerization on Live Cells. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 1436–1444. 10.1016/j.bbamem.2017.03.026. PubMed DOI

Althoff T.; Mills D. J.; Popot J.-L.; Kühlbrandt W. Arrangement of Electron Transport Chain Components in Bovine Mitochondrial Supercomplex I1III2IV1: Cryo-EM of Respiratory Chain Supercomplex. EMBO J. 2011, 30, 4652–4664. 10.1038/emboj.2011.324. PubMed DOI PMC

Kühlbrandt W. Structure and Function of Mitochondrial Membrane Protein Complexes. BMC Biol. 2015, 13, 89.10.1186/s12915-015-0201-x. PubMed DOI PMC

Schorr S.; van der Laan M. Integrative Functions of the Mitochondrial Contact Site and Cristae Organizing System. Semin. Cell Dev. Biol. 2018, 76, 191–200. 10.1016/j.semcdb.2017.09.021. PubMed DOI

Ikon N.; Ryan R. O. Cardiolipin and Mitochondrial Cristae Organization. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 1156–1163. 10.1016/j.bbamem.2017.03.013. PubMed DOI PMC

Pfeffer S.; Dudek J.; Zimmermann R.; Förster F. Organization of the Native Ribosome–Translocon Complex at the Mammalian Endoplasmic Reticulum Membrane. Biochim. Biophys. Acta, Gen. Subj. 2016, 1860, 2122–2129. 10.1016/j.bbagen.2016.06.024. PubMed DOI

Pfeffer S.; Brandt F.; Hrabe T.; Lang S.; Eibauer M.; Zimmermann R.; Förster F. Structure and 3D Arrangement of Endoplasmic Reticulum Membrane-Associated Ribosomes. Structure 2012, 20, 1508–1518. 10.1016/j.str.2012.06.010. PubMed DOI

Rees D. M.; Leslie A. G. W.; Walker J. E. The Structure of the Membrane Extrinsic Region of Bovine ATP Synthase. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 21597–21601. 10.1073/pnas.0910365106. PubMed DOI PMC

Symersky J.; Pagadala V.; Osowski D.; Krah A.; Meier T.; Faraldo-Gómez J. D.; Mueller D. M. Structure of the c10 Ring of the Yeast Mitochondrial ATP Synthase in the Open Conformation. Nat. Struct. Mol. Biol. 2012, 19, 485–491. 10.1038/nsmb.2284. PubMed DOI PMC

Davies K. M.; Strauss M.; Daum B.; Kief J. H.; Osiewacz H. D.; Rycovska A.; Zickermann V.; Kuhlbrandt W. Macromolecular Organization of ATP Synthase and Complex I in Whole Mitochondria. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 14121–14126. 10.1073/pnas.1103621108. PubMed DOI PMC

Lapuente-Brun E.; Moreno-Loshuertos R.; Acin-Perez R.; Latorre-Pellicer A.; Colas C.; Balsa E.; Perales-Clemente E.; Quiros P. M.; Calvo E.; Rodriguez-Hernandez M. A.; et al. Supercomplex Assembly Determines Electron Flux in the Mitochondrial Electron Transport Chain. Science 2013, 340, 1567–1570. 10.1126/science.1230381. PubMed DOI

Bock L. V.; Blau C.; Schröder G. F.; Davydov I. I.; Fischer N.; Stark H.; Rodnina M. V.; Vaiana A. C.; Grubmüller H. Energy Barriers and Driving Forces in TRNA Translocation through the Ribosome. Nat. Struct. Mol. Biol. 2013, 20, 1390–1396. 10.1038/nsmb.2690. PubMed DOI

Frauenfeld J.; Gumbart J.; van derSluis E. O.; Funes S.; Gartmann M.; Beatrix B.; Mielke T.; Berninghausen O.; Becker T.; Schulten K.; et al. Cryo-EM Structure of the Ribosome–SecYE Complex in the Membrane Environment. Nat. Struct. Mol. Biol. 2011, 18, 614–621. 10.1038/nsmb.2026. PubMed DOI PMC

Sothiselvam S.; Liu B.; Han W.; Ramu H.; Klepacki D.; Atkinson G. C.; Brauer A.; Remm M.; Tenson T.; Schulten K.; et al. Macrolide Antibiotics Allosterically Predispose the Ribosome for Translation Arrest. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 9804–9809. 10.1073/pnas.1403586111. PubMed DOI PMC

Perilla J. R.; Goh B. C.; Cassidy C. K.; Liu B.; Bernardi R. C.; Rudack T.; Yu H.; Wu Z.; Schulten K. Molecular Dynamics Simulations of Large Macromolecular Complexes. Curr. Opin. Struct. Biol. 2015, 31, 64–74. 10.1016/j.sbi.2015.03.007. PubMed DOI PMC

Venditti R.; Wilson C.; De Matteis M. A. Exiting the ER: What We Know and What We Don’t. Trends Cell Biol. 2014, 24, 9–18. 10.1016/j.tcb.2013.08.005. PubMed DOI

von Appen A.; Kosinski J.; Sparks L.; Ori A.; DiGuilio A. L.; Vollmer B.; Mackmull M.-T.; Banterle N.; Parca L.; Kastritis P.; et al. In Situ Structural Analysis of the Human Nuclear Pore Complex. Nature 2015, 526, 140–143. 10.1038/nature15381. PubMed DOI PMC

Schwartz T. U. The Structure Inventory of the Nuclear Pore Complex. J. Mol. Biol. 2016, 428, 1986–2000. 10.1016/j.jmb.2016.03.015. PubMed DOI PMC

Borgese N. Getting Membrane Proteins on and off the Shuttle Bus between the Endoplasmic Reticulum and the Golgi Complex. J. Cell Sci. 2016, 129, 1537–1545. 10.1242/jcs.183335. PubMed DOI

Jovanovic-Talisman T.; Zilman A. Protein Transport by the Nuclear Pore Complex: Simple Biophysics of a Complex Biomachine. Biophys. J. 2017, 113, 6–14. 10.1016/j.bpj.2017.05.024. PubMed DOI PMC

Sakiyama Y.; Panatala R.; Lim R. Y. H. Structural Dynamics of the Nuclear Pore Complex. Semin. Cell Dev. Biol. 2017, 68, 27–33. 10.1016/j.semcdb.2017.05.021. PubMed DOI

Jensen O. N. Interpreting the Protein Language Using Proteomics. Nat. Rev. Mol. Cell Biol. 2006, 7, 391–403. 10.1038/nrm1939. PubMed DOI

Khoury G. A.; Baliban R. C.; Floudas C. A. Proteome-Wide Post-Translational Modification Statistics: Frequency Analysis and Curation of the Swiss-Prot Database. Sci. Rep. 2011, 1, 90.10.1038/srep00090. PubMed DOI PMC

Humphrey S. J.; James D. E.; Mann M. Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation. Trends Endocrinol. Metab. 2015, 26, 676–687. 10.1016/j.tem.2015.09.013. PubMed DOI

Huang J.; Wang F.; Ye M.; Zou H. Enrichment and Separation Techniques for Large-Scale Proteomics Analysis of the Protein Post-Translational Modifications. J. Chromatogr. A 2014, 1372, 1–17. 10.1016/j.chroma.2014.10.107. PubMed DOI

Prabakaran S.; Lippens G.; Steen H.; Gunawardena J. Post-Translational Modification: Nature’s Escape from Genetic Imprisonment and the Basis for Dynamic Information Encoding: Information Encoding by Post-Translational Modification. Wiley Interdiscip. Rev. Syst. Biol. Med. 2012, 4, 565–583. 10.1002/wsbm.1185. PubMed DOI PMC

Gianazza E.; Parravicini C.; Primi R.; Miller I.; Eberini I. In Silico Prediction and Characterization of Protein Post-Translational Modifications. J. Proteomics 2016, 134, 65–75. 10.1016/j.jprot.2015.09.026. PubMed DOI

Yang Y.-S.; Wang C.-C.; Chen B.-H.; Hou Y.-H.; Hung K.-S.; Mao Y.-C. Tyrosine Sulfation as a Protein Post-Translational Modification. Molecules 2015, 20, 2138–2164. 10.3390/molecules20022138. PubMed DOI PMC

Nørskov-Lauritsen L.; Bräuner-Osborne H. Role of Post-Translational Modifications on Structure, Function and Pharmacology of Class C G Protein-Coupled Receptors. Eur. J. Pharmacol. 2015, 763, 233–240. 10.1016/j.ejphar.2015.05.015. PubMed DOI

Hirano A.; Fu Y.-H.; Ptáček L. J. The Intricate Dance of Post-Translational Modifications in the Rhythm of Life. Nat. Struct. Mol. Biol. 2016, 23, 1053–1060. 10.1038/nsmb.3326. PubMed DOI

Fujita M.; Kinoshita T. GPI-Anchor Remodeling: Potential Functions of GPI-Anchors in Intracellular Trafficking and Membrane Dynamics. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2012, 1821, 1050–1058. 10.1016/j.bbalip.2012.01.004. PubMed DOI

Apweiler R. On the Frequency of Protein Glycosylation, as Deduced from Analysis of the SWISS-PROT Database. Biochim. Biophys. Acta, Gen. Subj. 1999, 1473, 4–8. 10.1016/S0304-4165(99)00165-8. PubMed DOI

Ferreira I. G.; Pucci M.; Venturi G.; Malagolini N.; Chiricolo M.; Dall’Olio F. Glycosylation as a Main Regulator of Growth and Death Factor Receptors Signaling. Int. J. Mol. Sci. 2018, 19, 580.10.3390/ijms19020580. PubMed DOI PMC

Takahashi M.; Hasegawa Y.; Gao C.; Kuroki Y.; Taniguchi N. N-Glycans of Growth Factor Receptors: Their Role in Receptor Function and Disease Implications. Clin. Sci. 2016, 130, 1781–1792. 10.1042/CS20160273. PubMed DOI

Christiansen M. N.; Chik J.; Lee L.; Anugraham M.; Abrahams J. L.; Packer N. H. Cell Surface Protein Glycosylation in Cancer. Proteomics 2014, 14, 525–546. 10.1002/pmic.201300387. PubMed DOI

Pakkiriswami S.; Couto A.; Nagarajan U.; Georgiou M. Glycosylated Notch and Cancer. Front. Oncol. 2016, 6, 37.10.3389/fonc.2016.00037. PubMed DOI PMC

Lazniewska J.; Weiss N. Glycosylation of Voltage-Gated Calcium Channels in Health and Disease. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 662–668. 10.1016/j.bbamem.2017.01.018. PubMed DOI

Yang X.; Qian K. Protein O-GlcNAcylation: Emerging Mechanisms and Functions. Nat. Rev. Mol. Cell Biol. 2017, 18, 452–465. 10.1038/nrm.2017.22. PubMed DOI PMC

Worth M.; Li H.; Jiang J. Deciphering the Functions of Protein O-GlcNAcylation with Chemistry. ACS Chem. Biol. 2017, 12, 326–335. 10.1021/acschembio.6b01065. PubMed DOI PMC

Peterson S. B.; Hart G. W. New Insights: A Role for O-GlcNAcylation in Diabetic Complications. Crit. Rev. Biochem. Mol. Biol. 2016, 51, 150–161. 10.3109/10409238.2015.1135102. PubMed DOI

Copeland R. J.; Han G.; Hart G. W. O-GlcNAcomics-Revealing Roles of O-GlcNAcylation in Disease Mechanisms and Development of Potential Diagnostics. Proteomics: Clin. Appl. 2013, 7, 597–606. 10.1002/prca.201300001. PubMed DOI PMC

Wani W. Y.; Chatham J. C.; Darley-Usmar V.; McMahon L. L.; Zhang J. O-GlcNAcylation and Neurodegeneration. Brain Res. Bull. 2017, 133, 80–87. 10.1016/j.brainresbull.2016.08.002. PubMed DOI PMC

Ruba A.; Yang W. O-GlcNAc-ylation in the Nuclear Pore Complex. Cell. Mol. Bioeng. 2016, 9, 227–233. 10.1007/s12195-016-0440-0. PubMed DOI PMC

Mailleux F.; Gélinas R.; Beauloye C.; Horman S.; Bertrand L. O-GlcNAcylation, Enemy or Ally during Cardiac Hypertrophy Development?. Biochim. Biophys. Acta, Mol. Basis Dis. 2016, 1862, 2232–2243. 10.1016/j.bbadis.2016.08.012. PubMed DOI

Gournas C.; Saliba E.; Krammer E.-M.; Barthelemy C.; Prévost M.; André B. Transition of Yeast Can1 Transporter to the Inward-Facing State Unveils an α-Arrestin Target Sequence Promoting Its Ubiquitylation and Endocytosis. Mol. Biol. Cell 2017, 28, 2819–2832. 10.1091/mbc.e17-02-0104. PubMed DOI PMC

You H.; Ge Y.; Zhang J.; Cao Y.; Xing J.; Su D.; Huang Y.; Li M.; Qu S.; Sun F.; et al. Derlin-1 Promotes Ubiquitylation and Degradation of the Epithelial Na+ Channel, ENaC. J. Cell Sci. 2017, 130, 1027–1036. 10.1242/jcs.198242. PubMed DOI

Lorenz S.; Cantor A. J.; Rape M.; Kuriyan J. Macromolecular Juggling by Ubiquitylation Enzymes. BMC Biol. 2013, 11, 65.10.1186/1741-7007-11-65. PubMed DOI PMC

McDowell G. S.; Philpott A. Non-Canonical Ubiquitylation: Mechanisms and Consequences. Int. J. Biochem. Cell Biol. 2013, 45, 1833–1842. 10.1016/j.biocel.2013.05.026. PubMed DOI

Resh M. D. Fatty Acylation of Proteins: The Long and the Short of It. Prog. Lipid Res. 2016, 63, 120–131. 10.1016/j.plipres.2016.05.002. PubMed DOI PMC

Peng T.; Thinon E.; Hang H. C. Proteomic Analysis of Fatty-Acylated Proteins. Curr. Opin. Chem. Biol. 2016, 30, 77–86. 10.1016/j.cbpa.2015.11.008. PubMed DOI PMC

Peitzsch R. M.; McLaughlin S. Binding of Acylated Peptides and Fatty Acids to Phospholipid Vesicles: Pertinence to Myristoylated Proteins. Biochemistry 1993, 32, 10436–10443. 10.1021/bi00090a020. PubMed DOI

Kumari B.; Kumar R.; Kumar M. PalmPred: An SVM Based Palmitoylation Prediction Method Using Sequence Profile Information. PLoS One 2014, 9, e89246.10.1371/journal.pone.0089246. PubMed DOI PMC

Blanc M.; David F.; Abrami L.; Migliozzi D.; Armand F.; Bürgi J.; van der Goot F. G. SwissPalm: Protein Palmitoylation Database. F1000Research 2015, 4, 261.10.12688/f1000research.6464.1. PubMed DOI PMC

Porter J. A.; Young K. E.; Beachy P. A. Cholesterol Modification of Hedgehog Signaling Proteins in Animal Development. Science 1996, 274, 255–259. 10.1126/science.274.5285.255. PubMed DOI

Mann R. K.; Beachy P. A. Novel Lipid Modifications of Secreted Protein Signals. Annu. Rev. Biochem. 2004, 73, 891–923. 10.1146/annurev.biochem.73.011303.073933. PubMed DOI

Wang M.; Casey P. J. Protein Prenylation: Unique Fats Make Their Mark on Biology. Nat. Rev. Mol. Cell Biol. 2016, 17, 110–122. 10.1038/nrm.2015.11. PubMed DOI

Palsuledesai C. C.; Distefano M. D. Protein Prenylation: Enzymes, Therapeutics, and Biotechnology Applications. ACS Chem. Biol. 2015, 10, 51–62. 10.1021/cb500791f. PubMed DOI PMC

Benetka W.; Koranda M.; Eisenhaber F. Protein Prenylation: An (Almost) Comprehensive Overview on Discovery History, Enzymology, and Significance in Physiology and Disease. Monatsh. Chem. 2006, 137, 1241.10.1007/s00706-006-0534-9. DOI

Berndt N.; Hamilton A. D.; Sebti S. M. Targeting Protein Prenylation for Cancer Therapy. Nat. Rev. Cancer 2011, 11, 775–791. 10.1038/nrc3151. PubMed DOI PMC

Xu N.; Shen N.; Wang X.; Jiang S.; Xue B.; Li C. Protein Prenylation and Human Diseases: A Balance of Protein Farnesylation and Geranylgeranylation. Sci. China: Life Sci. 2015, 58, 328–335. 10.1007/s11427-015-4836-1. PubMed DOI

Fujita M.; Kinoshita T. Structural Remodeling of GPI Anchors during Biosynthesis and after Attachment to Proteins. FEBS Lett. 2010, 584, 1670–1677. 10.1016/j.febslet.2009.10.079. PubMed DOI

Zurzolo C.; Simons K. Glycosylphosphatidylinositol-Anchored Proteins: Membrane Organization and Transport. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 632–639. 10.1016/j.bbamem.2015.12.018. PubMed DOI

Pawar K.; Singh B. Understanding Clinical Significance of GPI Anchored Proteins in Mammalian System: Special Emphasis on Genetic Disorders of GPI Anchor Biosynthesis Pathway. Int. J. Med. Res. Health Sci. 2017, 6, 53–58.

Ichimura Y.; Kirisako T.; Takao T.; Satomi Y.; Shimonishi Y.; Ishihara N.; Mizushima N.; Tanida I.; Kominami E.; Ohsumi M.; et al. A Ubiquitin-like System Mediates Protein Lipidation. Nature 2000, 408, 488–492. 10.1038/35044114. PubMed DOI

Kabeya Y. LC3, GABARAP and GATE16 Localize to Autophagosomal Membrane Depending on Form-II Formation. J. Cell Sci. 2004, 117, 2805–2812. 10.1242/jcs.01131. PubMed DOI

Nath S.; Dancourt J.; Shteyn V.; Puente G.; Fong W. M.; Nag S.; Bewersdorf J.; Yamamoto A.; Antonny B.; Melia T. J. Lipidation of the LC3/GABARAP Family of Autophagy Proteins Relies on a Membrane-Curvature-Sensing Domain in Atg3. Nat. Cell Biol. 2014, 16, 415–424. 10.1038/ncb2940. PubMed DOI PMC

Sharma V. K.; Graham N. J. D. Oxidation of Amino Acids, Peptides and Proteins by Ozone: A Review. Ozone: Sci. Eng. 2010, 32, 81–90. 10.1080/01919510903510507. DOI

Lushchak V. I. Free Radical Oxidation of Proteins and Its Relationship with Functional State of Organisms. Biochemistry 2007, 72, 809–827. 10.1134/S0006297907080020. PubMed DOI

Stadtman E. R.; Levine R. L. Free Radical-Mediated Oxidation of Free Amino Acids and Amino Acid Residues in Proteins. Amino Acids 2003, 25, 207–218. 10.1007/s00726-003-0011-2. PubMed DOI

Shacter E. Quantification and Significance of Protein Oxidation in Biological Samples. Drug Metab. Rev. 2000, 32, 307–326. 10.1081/DMR-100102336. PubMed DOI

Kelly F. J.; Mudway I. S. Protein Oxidation at the Air-Lung Interface. Amino Acids 2003, 25, 375–396. 10.1007/s00726-003-0024-x. PubMed DOI PMC

Barelli S.; Canellini G.; Thadikkaran L.; Crettaz D.; Quadroni M.; Rossier J. S.; Tissot J.-D.; Lion N. Oxidation of Proteins: Basic Principles and Perspectives for Blood Proteomics. Proteomics: Clin. Appl. 2008, 2, 142–157. 10.1002/prca.200780009. PubMed DOI

Dunlop R. A.; Brunk U. T.; Rodgers K. J. Oxidized Proteins: Mechanisms of Removal and Consequences of Accumulation. IUBMB Life 2009, 61, 522–527. 10.1002/iub.189. PubMed DOI

Bader N.; Grune T. Protein Oxidation and Proteolysis. Biol. Chem. 2006, 387, 1351.10.1515/BC.2006.169. PubMed DOI

Costa V.; Quintanilha A.; Moradas-Ferreira P. Protein Oxidation, Repair Mechanisms and Proteolysis in Saccharomyces Cerevisiae. IUBMB Life 2007, 59, 293–298. 10.1080/15216540701225958. PubMed DOI

Brennan M.-L.; Hazen S. L. Amino Acid and Protein Oxidation in Cardiovascular Disease. Amino Acids 2003, 25, 365–374. 10.1007/s00726-003-0023-y. PubMed DOI

Cheignon C.; Tomas M.; Bonnefont-Rousselot D.; Faller P.; Hureau C.; Collin F. Oxidative Stress and the Amyloid Beta Peptide in Alzheimer’s Disease. Redox Biol. 2018, 14, 450–464. 10.1016/j.redox.2017.10.014. PubMed DOI PMC

van der Vlies D.; Woudenberg J.; Post J. A. Protein Oxidation in Aging: Endoplasmic Reticulum as a Target. Amino Acids 2003, 25, 397–407. 10.1007/s00726-003-0025-9. PubMed DOI

Trnková L.; Dršata J.; Boušová I. Oxidation as an Important Factor of Protein Damage: Implications for Maillard Reaction. J. Biosci. 2015, 40, 419–439. 10.1007/s12038-015-9523-7. PubMed DOI

Zhang W.; Xiao S.; Ahn D. U. Protein Oxidation: Basic Principles and Implications for Meat Quality. Crit. Rev. Food Sci. Nutr. 2013, 53, 1191–1201. 10.1080/10408398.2011.577540. PubMed DOI

Ginsberg M. H. Integrin Activation. BMB Rep 2014, 47, 655–659. 10.5483/BMBRep.2014.47.12.241. PubMed DOI PMC

Morse E. M.; Brahme N. N.; Calderwood D. A. Integrin Cytoplasmic Tail Interactions. Biochemistry 2014, 53, 810–820. 10.1021/bi401596q. PubMed DOI PMC

Manninen A.; Varjosalo M. A Proteomics View on Integrin-Mediated Adhesions. Proteomics 2017, 17, 1600022.10.1002/pmic.201600022. PubMed DOI

Theocharis A. D.; Skandalis S. S.; Gialeli C.; Karamanos N. K. Extracellular Matrix Structure. Adv. Drug Delivery Rev. 2016, 97, 4–27. 10.1016/j.addr.2015.11.001. PubMed DOI

Changede R.; Sheetz M. Integrin and Cadherin Clusters: A Robust Way to Organize Adhesions for Cell Mechanics. BioEssays 2017, 39, e201600123.10.1002/bies.201600123. PubMed DOI

Tarbell J. M.; Cancel L. M. The Glycocalyx and Its Significance in Human Medicine. J. Intern. Med. 2016, 280, 97–113. 10.1111/joim.12465. PubMed DOI

Curry F. E.; Adamson R. H. Endothelial Glycocalyx: Permeability Barrier and Mechanosensor. Ann. Biomed. Eng. 2012, 40, 828–839. 10.1007/s10439-011-0429-8. PubMed DOI PMC

Alphonsus C. S.; Rodseth R. N. The Endothelial Glycocalyx: A Review of the Vascular Barrier. Anaesthesia 2014, 69, 777–784. 10.1111/anae.12661. PubMed DOI

Tarbell J. M.; Pahakis M. Y. Mechanotransduction and the Glycocalyx. J. Intern. Med. 2006, 259, 339–350. 10.1111/j.1365-2796.2006.01620.x. PubMed DOI

Nieuwdorp M.; Meuwese M. C.; Vink H.; Hoekstra J. B.; Kastelein J. J.; Stroes E. S. The Endothelial Glycocalyx: A Potential Barrier between Health and Vascular Disease. Curr. Opin. Lipidol. 2005, 16, 507–511. 10.1097/01.mol.0000181325.08926.9c. PubMed DOI

Salmon A. H.; Satchell S. C. Endothelial Glycocalyx Dysfunction in Disease: Albuminuria and Increased Microvascular Permeability. J. Pathol. 2012, 226, 562–574. 10.1002/path.3964. PubMed DOI

Reitsma S.; Slaaf D. W.; Vink H.; van Zandvoort M. A. M. J.; oude Egbrink M. G. A. The Endothelial Glycocalyx: Composition, Functions, and Visualization. Pfluegers Arch. 2007, 454, 345–359. 10.1007/s00424-007-0212-8. PubMed DOI PMC

Weinbaum S.; Tarbell J. M.; Damiano E. R. The Structure and Function of the Endothelial Glycocalyx Layer. Annu. Rev. Biomed. Eng. 2007, 9, 121–167. 10.1146/annurev.bioeng.9.060906.151959. PubMed DOI

Leonova E. I.; Galzitskaya O. V. Structure and Functions of Syndecans in Vertebrates. Biochemistry 2013, 78, 1071–1085. 10.1134/S0006297913100015. PubMed DOI

Shin J.; Lee W.; Lee D.; Koo B. K.; Han I.; Lim Y.; Woods A.; Couchman J. R.; Oh E. S. Solution Structure of the Dimeric Cytoplasmic Domain of Syndecan-4. Biochemistry 2001, 40, 8471–8478. 10.1021/bi002750r. PubMed DOI

Svensson G.; Awad W.; Håkansson M.; Mani K.; Logan D. T. Crystal Structure of N-Glycosylated Human Glypican-1 Core Protein: Structure of Two Loops Evolutionarily Conserved in Vertebrate Glypican-1. J. Biol. Chem. 2012, 287, 14040–14051. 10.1074/jbc.M111.322487. PubMed DOI PMC

Awad W.; Svensson Birkedal G.; Thunnissen M. M. G. M.; Mani K.; Logan D. T. Improvements in the Order, Isotropy and Electron Density of Glypican-1 Crystals by Controlled Dehydration. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2013, 69, 2524–2533. 10.1107/S0907444913025250. PubMed DOI PMC

Awad W.; Adamczyk B.; Örnros J.; Karlsson N. G.; Mani K.; Logan D. T. Structural Aspects of N-Glycosylations and the C-Terminal Region in Human Glypican-1. J. Biol. Chem. 2015, 290, 22991–23008. 10.1074/jbc.M115.660878. PubMed DOI PMC

Teriete P.; Banerji S.; Noble M.; Blundell C. D.; Wright A. J.; Pickford A. R.; Lowe E.; Mahoney D. J.; Tammi M. I.; Kahmann J. D.; et al. Structure of the Regulatory Hyaluronan Binding Domain in the Inflammatory Leukocyte Homing Receptor CD44. Mol. Cell 2004, 13, 483–496. 10.1016/S1097-2765(04)00080-2. PubMed DOI

Banerji S.; Wright A. J.; Noble M.; Mahoney D. J.; Campbell I. D.; Day A. J.; Jackson D. G. Structures of the Cd44–Hyaluronan Complex Provide Insight into a Fundamental Carbohydrate-Protein Interaction. Nat. Struct. Mol. Biol. 2007, 14, 234–239. 10.1038/nsmb1201. PubMed DOI

Campbell H. K.; Maiers J. L.; DeMali K. A. Interplay between Tight Junctions & Adherens Junctions. Exp. Cell Res. 2017, 358, 39–44. 10.1016/j.yexcr.2017.03.061. PubMed DOI PMC

Dejana E. Endothelial Cell–Cell Junctions: Happy Together. Nat. Rev. Mol. Cell Biol. 2004, 5, 261–270. 10.1038/nrm1357. PubMed DOI

Giepmans B. N. G.; van IJzendoorn S. C. D. Epithelial Cell–Cell Junctions and Plasma Membrane Domains. Biochim. Biophys. Acta, Biomembr. 2009, 1788, 820–831. 10.1016/j.bbamem.2008.07.015. PubMed DOI

Balda M. S.; Matter K. Tight Junctions as Regulators of Tissue Remodelling. Curr. Opin. Cell Biol. 2016, 42, 94–101. 10.1016/j.ceb.2016.05.006. PubMed DOI

Shin K.; Fogg V. C.; Margolis B. Tight Junctions and Cell Polarity. Annu. Rev. Cell Dev. Biol. 2006, 22, 207–235. 10.1146/annurev.cellbio.22.010305.104219. PubMed DOI

Zihni C.; Mills C.; Matter K.; Balda M. S. Tight Junctions: From Simple Barriers to Multifunctional Molecular Gates. Nat. Rev. Mol. Cell Biol. 2016, 17, 564–580. 10.1038/nrm.2016.80. PubMed DOI

Bauer H.-C.; Krizbai I. A.; Bauer H.; Traweger A. You Shall Not Pass”—Tight Junctions of the Blood Brain Barrier. Front. Neurosci. 2014, 8, 392.10.3389/fnins.2014.00392. PubMed DOI PMC

Tietz S.; Engelhardt B. Brain Barriers: Crosstalk between Complex Tight Junctions and Adherens Junctions. J. Cell Biol. 2015, 209, 493–506. 10.1083/jcb.201412147. PubMed DOI PMC

Sluysmans S.; Vasileva E.; Spadaro D.; Shah J.; Rouaud F.; Citi S. The Role of Apical Cell-Cell Junctions and Associated Cytoskeleton in Mechanotransduction: Junctions, Cytoskeleton and Mechanotransduction. Biol. Cell 2017, 109, 139–161. 10.1111/boc.201600075. PubMed DOI

Mège R. M.; Ishiyama N. Integration of Cadherin Adhesion and Cytoskeleton at Adherens Junctions. Cold Spring Harbor Perspect. Biol. 2017, 9, a028738.10.1101/cshperspect.a028738. PubMed DOI PMC

Harrison O. J.; Jin X.; Hong S.; Bahna F.; Ahlsen G.; Brasch J.; Wu Y.; Vendome J.; Felsovalyi K.; Hampton C. M.; et al. The Extracellular Architecture of Adherens Junctions Revealed by Crystal Structures of Type I Cadherins. Structure 2011, 19, 244–256. 10.1016/j.str.2010.11.016. PubMed DOI PMC

Ishiyama N.; Lee S.-H.; Liu S.; Li G.-Y.; Smith M. J.; Reichardt L. F.; Ikura M. Dynamic and Static Interactions between p120 Catenin and E-Cadherin Regulate the Stability of Cell-Cell Adhesion. Cell 2010, 141, 117–128. 10.1016/j.cell.2010.01.017. PubMed DOI

Huber A. H.; Weis W. I. The Structure of the Beta-Catenin/E-Cadherin Complex and the Molecular Basis of Diverse Ligand Recognition by Beta-Catenin. Cell 2001, 105, 391–402. 10.1016/S0092-8674(01)00330-0. PubMed DOI

Pokutta S.; Weis W. I. Structure of the Dimerization and Beta-Catenin-Binding Region of Alpha-Catenin. Mol. Cell 2000, 5, 533–543. 10.1016/S1097-2765(00)80447-5. PubMed DOI

Rangarajan E. S.; Izard T. Dimer Asymmetry Defines α-Catenin Interactions. Nat. Struct. Mol. Biol. 2013, 20, 188–193. 10.1038/nsmb.2479. PubMed DOI PMC

Ishiyama N.; Tanaka N.; Abe K.; Yang Y. J.; Abbas Y. M.; Umitsu M.; Nagar B.; Bueler S. A.; Rubinstein J. L.; Takeichi M.; et al. An Autoinhibited Structure of α-Catenin and Its Implications for Vinculin Recruitment to Adherens Junctions. J. Biol. Chem. 2013, 288, 15913–15925. 10.1074/jbc.M113.453928. PubMed DOI PMC

Cong Y.; Topf M.; Sali A.; Matsudaira P.; Dougherty M.; Chiu W.; Schmid M. F. Crystallographic Conformers of Actin in a Biologically Active Bundle of Filaments. J. Mol. Biol. 2008, 375, 331–336. 10.1016/j.jmb.2007.10.027. PubMed DOI PMC

Meşe G.; Richard G.; White T. W. Gap Junctions: Basic Structure and Function. J. Invest. Dermatol. 2007, 127, 2516–2524. 10.1038/sj.jid.5700770. PubMed DOI

Maeda S.; Nakagawa S.; Suga M.; Yamashita E.; Oshima A.; Fujiyoshi Y.; Tsukihara T. Structure of the Connexin 26 Gap Junction Channel at 3.5 Å Resolution. Nature 2009, 458, 597–602. 10.1038/nature07869. PubMed DOI

Garrod D.; Chidgey M. Desmosome Structure, Composition and Function. Biochim. Biophys. Acta, Biomembr. 2008, 1778, 572–587. 10.1016/j.bbamem.2007.07.014. PubMed DOI

Delva E.; Tucker D. K.; Kowalczyk A. P. The Desmosome. Cold Spring Harbor Perspect. Biol. 2009, 1, a002543–a002543. 10.1101/cshperspect.a002543. PubMed DOI PMC

Al-Jassar C.; Bikker H.; Overduin M.; Chidgey M. Mechanistic Basis of Desmosome-Targeted Diseases. J. Mol. Biol. 2013, 425, 4006–4022. 10.1016/j.jmb.2013.07.035. PubMed DOI PMC

Mahoney M. G.; Sadowski S.; Brennan D.; Pikander P.; Saukko P.; Wahl J.; Aho H.; Heikinheimo K.; Bruckner-Tuderman L.; Fertala A.; et al. Compound Heterozygous Desmoplakin Mutations Result in a Phenotype with a Combination of Myocardial, Skin, Hair, and Enamel Abnormalities. J. Invest. Dermatol. 2010, 130, 968–978. 10.1038/jid.2009.357. PubMed DOI PMC

Broussard J. A.; Getsios S.; Green K. J. Desmosome Regulation and Signaling in Disease. Cell Tissue Res. 2015, 360, 501–512. 10.1007/s00441-015-2136-5. PubMed DOI PMC

Nitoiu D.; Etheridge S. L.; Kelsell D. P. Insights into Desmosome Biology from Inherited Human Skin Disease and Cardiocutaneous Syndromes. Cell Commun. Adhes. 2014, 21, 129–140. 10.3109/15419061.2014.908854. PubMed DOI

Panchin Y. V. Evolution of Gap Junction Proteins - the Pannexin Alternative. J. Exp. Biol. 2005, 208, 1415–1419. 10.1242/jeb.01547. PubMed DOI

Beyer E. C.; Berthoud V. M. Gap Junction Gene and Protein Families: Connexins, Innexins, and Pannexins. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 5–8. 10.1016/j.bbamem.2017.05.016. PubMed DOI PMC

Oshima A. Structure and Closure of Connexin Gap Junction Channels. FEBS Lett. 2014, 588, 1230–1237. 10.1016/j.febslet.2014.01.042. PubMed DOI

Valiunas V.; Cohen I. S.; Brink P. R. Defining the Factors That Affect Solute Permeation of Gap Junction Channels. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 96–101. 10.1016/j.bbamem.2017.07.002. PubMed DOI PMC

Falk M. M.; Bell C. L.; Kells Andrews R. M.; Murray S. A. Molecular Mechanisms Regulating Formation, Trafficking and Processing of Annular Gap Junctions. BMC Cell Biol. 2016, 17, S22.10.1186/s12860-016-0087-7. PubMed DOI PMC

Hall D. H. Gap Junctions in C. Elegans : Their Roles in Behavior and Development: Gap Junctions in C. Elegans. Dev. Neurobiol. 2017, 77, 587–596. 10.1002/dneu.22408. PubMed DOI PMC

Shimizu K.; Stopfer M. Gap Junctions. Curr. Biol. 2013, 23, R1026–R1031. 10.1016/j.cub.2013.10.067. PubMed DOI

Cronier L.; Crespin S.; Strale P.-O.; Defamie N.; Mesnil M. Gap Junctions and Cancer: New Functions for an Old Story. Antioxid. Redox Signaling 2009, 11, 323–338. 10.1089/ars.2008.2153. PubMed DOI

Meda P. Gap Junction Proteins Are Key Drivers of Endocrine Function. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 124–140. 10.1016/j.bbamem.2017.03.005. PubMed DOI

Srinivas M.; Verselis V. K.; White T. W. Human Diseases Associated with Connexin Mutations. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 192–201. 10.1016/j.bbamem.2017.04.024. PubMed DOI PMC

Rovegno M.; Sáez J. C. Role of Astrocyte Connexin Hemichannels in Cortical Spreading Depression. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 216–223. 10.1016/j.bbamem.2017.08.014. PubMed DOI

Mesnil M.; Aasen T.; Boucher J.; Chépied A.; Cronier L.; Defamie N.; Kameritsch P.; Laird D. W.; Lampe P. D.; Lathia J. D.; et al. An Update on Minding the Gap in Cancer. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 237–243. 10.1016/j.bbamem.2017.06.015. PubMed DOI

Boucher J.; Monvoisin A.; Vix J.; Mesnil M.; Thuringer D.; Debiais F.; Cronier L. Connexins, Important Players in the Dissemination of Prostate Cancer Cells. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 202–215. 10.1016/j.bbamem.2017.06.020. PubMed DOI

Kim Y.; Davidson J. O.; Green C. R.; Nicholson L. F. B.; O’Carroll S. J.; Zhang J. Connexins and Pannexins in Cerebral Ischemia. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 224–236. 10.1016/j.bbamem.2017.03.018. PubMed DOI

Burch-Smith T. M.; Zambryski P. C. Plasmodesmata Paradigm Shift: Regulation from Without Versus Within. Annu. Rev. Plant Biol. 2012, 63, 239–260. 10.1146/annurev-arplant-042811-105453. PubMed DOI

Bloemendal S.; Kück U. Cell-to-Cell Communication in Plants, Animals, and Fungi: A Comparative Review. Naturwissenschaften 2013, 100, 3–19. 10.1007/s00114-012-0988-z. PubMed DOI

Wolf S.; Hématy K.; Höfte H. Growth Control and Cell Wall Signaling in Plants. Annu. Rev. Plant Biol. 2012, 63, 381–407. 10.1146/annurev-arplant-042811-105449. PubMed DOI

Hamann T. The Plant Cell Wall Integrity Maintenance Mechanism – A Case Study of a Cell Wall Plasma Membrane Signaling Network. Phytochemistry 2015, 112, 100–109. 10.1016/j.phytochem.2014.09.019. PubMed DOI

Kim S.-J.; Brandizzi F. The Plant Secretory Pathway for the Trafficking of Cell Wall Polysaccharides and Glycoproteins. Glycobiology 2016, 26, 940–949. 10.1093/glycob/cww044. PubMed DOI

Liu Z.; Persson S.; Sanchez-Rodriguez C. At the Border: The Plasma Membrane-Cell Wall Continuum. J. Exp. Bot. 2015, 66, 1553–1563. 10.1093/jxb/erv019. PubMed DOI

Lehman T. A.; Smertenko A.; Sanguinet K. A. Auxin, Microtubules, and Vesicle Trafficking: Conspirators behind the Cell Wall. J. Exp. Bot. 2017, 68, 3321–3329. 10.1093/jxb/erx205. PubMed DOI

Siegel S. D.; Liu J.; Ton-That H. Biogenesis of the Gram-Positive Bacterial Cell Envelope. Curr. Opin. Microbiol. 2016, 34, 31–37. 10.1016/j.mib.2016.07.015. PubMed DOI PMC

Dhar S.; Kumari H.; Balasubramanian D.; Mathee K. Cell-Wall Recycling and Synthesis in Escherichia Coli and Pseudomonas Aeruginosa – Their Role in the Development of Resistance. J. Med. Microbiol. 2018, 67, 1–21. 10.1099/jmm.0.000636. PubMed DOI

Riedlová K.; Nekardová M.; Kačer P.; Syslová K.; Vazdar M.; Jungwirth P.; Kudová E.; Cwiklik L. Distributions of Therapeutically Promising Neurosteroids in Cellular Membranes. Chem. Phys. Lipids 2017, 203, 78–86. 10.1016/j.chemphyslip.2016.12.004. PubMed DOI

Mistou M.-Y.; Sutcliffe I. C.; van Sorge N. M. Bacterial Glycobiology: Rhamnose-Containing Cell Wall Polysaccharides in Gram-Positive Bacteria. FEMS Microbiol. Rev. 2016, 40, 464–479. 10.1093/femsre/fuw006. PubMed DOI PMC

Hopke A.; Brown A. J. P.; Hall R. A.; Wheeler R. T. Dynamic Fungal Cell Wall Architecture in Stress Adaptation and Immune Evasion. Trends Microbiol. 2018, 26, 284–295. 10.1016/j.tim.2018.01.007. PubMed DOI PMC

Free S. J.Fungal Cell Wall Organization and Biosynthesis. In Advances in Genetics; Friedmann T., Dunlap J. C., Goodwin S. F., Eds.; Elsevier: 2013; Vol. 81, pp 33–82. 10.1016/B978-0-12-407677-8.00002-6. PubMed DOI

Kock C.; Dufrêne Y. F.; Heinisch J. J. Up against the Wall: Is Yeast Cell Wall Integrity Ensured by Mechanosensing in Plasma Membrane Microdomains?. Appl. Environ. Microbiol. 2015, 81, 806–811. 10.1128/AEM.03273-14. PubMed DOI PMC

Yoshimi A.; Miyazawa K.; Abe K. Cell Wall Structure and Biogenesis in Aspergillus Species. Biosci., Biotechnol., Biochem. 2016, 80, 1700–1711. 10.1080/09168451.2016.1177446. PubMed DOI

Gow N. A. R.; Latge J.-P.; Munro C. A.. The Fungal Cell Wall: Structure, Biosynthesis, and Function. In The Fungal Kingdom; Heitman J., Howlett B. J., Crous P. W., Stukenbrock E. H., James T. Y., Gow N. A. R., Eds.; American Society of Microbiology Press: Washington, DC, 2017; pp 267–292.

Orlean P. Architecture and Biosynthesis of the Saccharomyces Cerevisiae Cell Wall. Genetics 2012, 192, 775–818. 10.1534/genetics.112.144485. PubMed DOI PMC

Bugg T. D. H.; Braddick D.; Dowson C. G.; Roper D. I. Bacterial Cell Wall Assembly: Still an Attractive Antibacterial Target. Trends Biotechnol. 2011, 29, 167–173. 10.1016/j.tibtech.2010.12.006. PubMed DOI

Oppedijk S. F.; Martin N. I.; Breukink E. Hit ’em Where It Hurts: The Growing and Structurally Diverse Family of Peptides That Target Lipid-II. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 947–957. 10.1016/j.bbamem.2015.10.024. PubMed DOI

Kim S. J.; Chang J.; Singh M. Peptidoglycan Architecture of Gram-Positive Bacteria by Solid-State NMR. Biochim. Biophys. Acta, Biomembr. 2015, 1848, 350–362. 10.1016/j.bbamem.2014.05.031. PubMed DOI PMC

Swoboda J. G.; Campbell J.; Meredith T. C.; Walker S. Wall Teichoic Acid Function, Biosynthesis, and Inhibition. ChemBioChem 2010, 11, 35–45. 10.1002/cbic.200900557. PubMed DOI PMC

Boudreau M. A.; Fisher J. F.; Mobashery S. Messenger Functions of the Bacterial Cell Wall-Derived Muropeptides. Biochemistry 2012, 51, 2974–2990. 10.1021/bi300174x. PubMed DOI PMC

Münch D.; Sahl H.-G. Structural Variations of the Cell Wall Precursor Lipid II in Gram-Positive Bacteria — Impact on Binding and Efficacy of Antimicrobial Peptides. Biochim. Biophys. Acta, Biomembr. 2015, 1848, 3062–3071. 10.1016/j.bbamem.2015.04.014. PubMed DOI

Vollmer W.Peptidoglycan. In Molecular Medical Microbiology; Tang Y.-W., Sails A., Eds.; Elsevier: 2015; pp 105–124, 10.1016/B978-0-12-397169-2.00006-8. DOI

Yadav A. K.; Espaillat A. Bacterial Strategies to Preserve Cell Wall Integrity Against Environmental Threats. Front. Microbiol. 2018, 9, 206410.3389/fmicb.2018.02064. PubMed DOI PMC

Radkov A. D.; Hsu Y.-P.; Booher G.; VanNieuwenhze M. S. Imaging Bacterial Cell Wall Biosynthesis. Annu. Rev. Biochem. 2018, 87, 991–1014. 10.1146/annurev-biochem-062917-012921. PubMed DOI PMC

Ruiz N. Filling Holes in Peptidoglycan Biogenesis of Escherichia Coli. Curr. Opin. Microbiol. 2016, 34, 1–6. 10.1016/j.mib.2016.07.010. PubMed DOI PMC

Nicolson G. L. The Fluid—Mosaic Model of Membrane Structure: Still Relevant to Understanding the Structure, Function and Dynamics of Biological Membranes after More than 40 Years. Biochim. Biophys. Acta, Biomembr. 2014, 1838, 1451–1466. 10.1016/j.bbamem.2013.10.019. PubMed DOI

Pike L. J. Rafts Defined: A Report on the Keystone Symposium on Lipid Rafts and Cell Function. J. Lipid Res. 2006, 47, 1597–1598. 10.1194/jlr.E600002-JLR200. PubMed DOI

Sevcsik E.; Schütz G. J. With or without Rafts? Alternative Views on Cell Membranes. BioEssays 2016, 38, 129–139. 10.1002/bies.201500150. PubMed DOI PMC

Eggeling C.; Ringemann C.; Medda R.; Schwarzmann G.; Sandhoff K.; Polyakova S.; Belov V. N.; Hein B.; von Middendorff C.; Schönle A.; et al. Direct Observation of the Nanoscale Dynamics of Membrane Lipids in a Living Cell. Nature 2009, 457, 1159–1162. 10.1038/nature07596. PubMed DOI

Regmi R.; Winkler P. M.; Flauraud V.; Borgman K. J. E.; Manzo C.; Brugger J.; Rigneault H.; Wenger J.; García-Parajo M. F. Planar Optical Nanoantennas Resolve Cholesterol-Dependent Nanoscale Heterogeneities in the Plasma Membrane of Living Cells. Nano Lett. 2017, 17, 6295–6302. 10.1021/acs.nanolett.7b02973. PubMed DOI

Bernardino de la Serna J.; Schütz G. J.; Eggeling C.; Cebecauer M. There Is No Simple Model of the Plasma Membrane Organization. Front. Cell Dev. Biol. 2016, 4, 106.10.3389/fcell.2016.00106. PubMed DOI PMC

Marsh D. Liquid-Ordered Phases Induced by Cholesterol: A Compendium of Binary Phase Diagrams. Biochim. Biophys. Acta, Biomembr. 2010, 1798, 688–699. 10.1016/j.bbamem.2009.12.027. PubMed DOI

Marsh D. Cholesterol-Induced Fluid Membrane Domains: A Compendium of Lipid-Raft Ternary Phase Diagrams. Biochim. Biophys. Acta, Biomembr. 2009, 1788, 2114–2123. 10.1016/j.bbamem.2009.08.004. PubMed DOI

Veatch S. L.; Keller S. L. Seeing Spots: Complex Phase Behavior in Simple Membranes. Biochim. Biophys. Acta, Mol. Cell Res. 2005, 1746, 172–185. 10.1016/j.bbamcr.2005.06.010. PubMed DOI

Feigenson G. W. Phase Diagrams and Lipid Domains in Multicomponent Lipid Bilayer Mixtures. Biochim. Biophys. Acta, Biomembr. 2009, 1788, 47–52. 10.1016/j.bbamem.2008.08.014. PubMed DOI PMC

Feigenson G. W.; Buboltz J. T. Ternary Phase Diagram of Dipalmitoyl-PC/Dilauroyl-PC/Cholesterol: Nanoscopic Domain Formation Driven by Cholesterol. Biophys. J. 2001, 80, 2775–2788. 10.1016/S0006-3495(01)76245-5. PubMed DOI PMC

Korlach J.; Schwille P.; Webb W. W.; Feigenson G. W. Characterization of Lipid Bilayer Phases by Confocal Microscopy and Fluorescence Correlation Spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 8461–8466. 10.1073/pnas.96.15.8461. PubMed DOI PMC

Veatch S. L.; Keller S. L. Separation of Liquid Phases in Giant Vesicles of Ternary Mixtures of Phospholipids and Cholesterol. Biophys. J. 2003, 85, 3074–3083. 10.1016/S0006-3495(03)74726-2. PubMed DOI PMC

Veatch S. L.; Keller S. L. Organization in Lipid Membranes Containing Cholesterol. Phys. Rev. Lett. 2002, 89, 268101.10.1103/PhysRevLett.89.268101. PubMed DOI

Dietrich C.; Bagatolli L. A.; Volovyk Z. N.; Thompson N. L.; Levi M.; Jacobson K.; Gratton E. Lipid Rafts Reconstituted in Model Membranes. Biophys. J. 2001, 80, 1417–1428. 10.1016/S0006-3495(01)76114-0. PubMed DOI PMC

Veatch S. L.; Keller S. L. Miscibility Phase Diagrams of Giant Vesicles Containing Sphingomyelin. Phys. Rev. Lett. 2005, 94, 148101.10.1103/PhysRevLett.94.148101. PubMed DOI

Vist M. R.; Davis J. H. Phase Equilibria of Cholesterol/Dipalmitoylphosphatidylcholine Mixtures: Deuterium Nuclear Magnetic Resonance and Differential Scanning Calorimetry. Biochemistry 1990, 29, 451–464. 10.1021/bi00454a021. PubMed DOI

Rheinstädter M. C.; Mouritsen O. G. Small-Scale Structure in Fluid Cholesterol–Lipid Bilayers. Curr. Opin. Colloid Interface Sci. 2013, 18, 440–447. 10.1016/j.cocis.2013.07.001. DOI

Schmid F. Physical Mechanisms of Micro- and Nanodomain Formation in Multicomponent Lipid Membranes. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 509–528. 10.1016/j.bbamem.2016.10.021. PubMed DOI

Winkler P. M.; Regmi R.; Flauraud V.; Brugger J.; Rigneault H.; Wenger J.; García-Parajo M. F. Transient Nanoscopic Phase Separation in Biological Lipid Membranes Resolved by Planar Plasmonic Antennas. ACS Nano 2017, 11, 7241–7250. 10.1021/acsnano.7b03177. PubMed DOI

Wu H.-M.; Lin Y.-H.; Yen T.-C.; Hsieh C.-L. Nanoscopic Substructures of Raft-Mimetic Liquid-Ordered Membrane Domains Revealed by High-Speed Single-Particle Tracking. Sci. Rep. 2016, 6, 20542.10.1038/srep20542. PubMed DOI PMC

Baumgart T.; Hammond A. T.; Sengupta P.; Hess S. T.; Holowka D. A.; Baird B. A.; Webb W. W. Large-Scale Fluid/Fluid Phase Separation of Proteins and Lipids in Giant Plasma Membrane Vesicles. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 3165–3170. 10.1073/pnas.0611357104. PubMed DOI PMC

Honerkamp-Smith A. R.; Veatch S. L.; Keller S. L. An Introduction to Critical Points for Biophysicists; Observations of Compositional Heterogeneity in Lipid Membranes. Biochim. Biophys. Acta, Biomembr. 2009, 1788, 53–63. 10.1016/j.bbamem.2008.09.010. PubMed DOI PMC

Veatch S. L.; Cicuta P.; Sengupta P.; Honerkamp-Smith A.; Holowka D.; Baird B. Critical Fluctuations in Plasma Membrane Vesicles. ACS Chem. Biol. 2008, 3, 287–293. 10.1021/cb800012x. PubMed DOI

Veatch S. L.; Soubias O.; Keller S. L.; Gawrisch K. Critical Fluctuations in Domain-Forming Lipid Mixtures. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 17650–17655. 10.1073/pnas.0703513104. PubMed DOI PMC

May S. Trans-Monolayer Coupling of Fluid Domains in Lipid Bilayers. Soft Matter 2009, 5, 3148–3156. 10.1039/b901647c. DOI

Mitra E. D.; Whitehead S. C.; Holowka D.; Baird B.; Sethna J. P. Computation of a Theoretical Membrane Phase Diagram and the Role of Phase in Lipid-Raft-Mediated Protein Organization. J. Phys. Chem. B 2018, 122, 3500–3513. 10.1021/acs.jpcb.7b10695. PubMed DOI PMC

Leekumjorn S.; Sum A. K. Molecular Studies of the Gel to Liquid-Crystalline Phase Transition for Fully Hydrated DPPC and DPPE Bilayers. Biochim. Biophys. Acta, Biomembr. 2007, 1768, 354–365. 10.1016/j.bbamem.2006.11.003. PubMed DOI

Tjörnhammar R.; Edholm O. Reparameterized United Atom Model for Molecular Dynamics Simulations of Gel and Fluid Phosphatidylcholine Bilayers. J. Chem. Theory Comput. 2014, 10, 5706–5715. 10.1021/ct500589z. PubMed DOI

de Vries A. H.; Yefimov S.; Mark A. E.; Marrink S. J. Molecular Structure of the Lecithin Ripple Phase. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 5392–5396. 10.1073/pnas.0408249102. PubMed DOI PMC

Marrink S. J.; Risselada J.; Mark A. E. Simulation of Gel Phase Formation and Melting in Lipid Bilayers Using a Coarse Grained Model. Chem. Phys. Lipids 2005, 135, 223–244. 10.1016/j.chemphyslip.2005.03.001. PubMed DOI

Rodgers J. M.; Sørensen J.; de Meyer F. J.-M.; Schiøtt B.; Smit B. Understanding the Phase Behavior of Coarse-Grained Model Lipid Bilayers through Computational Calorimetry. J. Phys. Chem. B 2012, 116, 1551–1569. 10.1021/jp207837v. PubMed DOI

Arnarez C.; Webb A.; Rouvière E.; Lyman E. Hysteresis and the Cholesterol Dependent Phase Transition in Binary Lipid Mixtures with the Martini Model. J. Phys. Chem. B 2016, 120, 13086–13093. 10.1021/acs.jpcb.6b09728. PubMed DOI PMC

Waheed Q.; Tjörnhammar R.; Edholm O. Phase Transitions in Coarse-Grained Lipid Bilayers Containing Cholesterol by Molecular Dynamics Simulations. Biophys. J. 2012, 103, 2125–2133. 10.1016/j.bpj.2012.10.014. PubMed DOI PMC

Ogata K.; Nakamura S. Improvement of Parameters of the AMBER Potential Force Field for Phospholipids for Description of Thermal Phase Transitions. J. Phys. Chem. B 2015, 119, 9726–9739. 10.1021/acs.jpcb.5b01656. PubMed DOI

Pluhackova K.; Kirsch S. A.; Han J.; Sun L.; Jiang Z.; Unruh T.; Böckmann R. A. A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers. J. Phys. Chem. B 2016, 120, 3888–3903. 10.1021/acs.jpcb.6b01870. PubMed DOI

Faller R.; Marrink S.-J. Simulation of Domain Formation in DLPC–DSPC Mixed Bilayers. Langmuir 2004, 20, 7686–7693. 10.1021/la0492759. PubMed DOI

Pyrkova D. V.; Tarasova N. K.; Pyrkov T. V.; Krylov N. A.; Efremov R. G. Atomic-Scale Lateral Heterogeneity and Dynamics of Two-Component Lipid Bilayers Composed of Saturated and Unsaturated Phosphatidylcholines. Soft Matter 2011, 7, 2569–2579. 10.1039/c0sm00701c. DOI

Wong B. Y.; Faller R. Phase Behavior and Dynamic Heterogeneities in Lipids: A Coarse-Grained Simulation Study of DPPC–DPPE Mixtures. Biochim. Biophys. Acta, Biomembr. 2007, 1768, 620–627. 10.1016/j.bbamem.2006.12.009. PubMed DOI

Rosetti C.; Pastorino C. Polyunsaturated and Saturated Phospholipids in Mixed Bilayers: A Study from the Molecular Scale to the Lateral Lipid Organization. J. Phys. Chem. B 2011, 115, 1002–1013. 10.1021/jp1082888. PubMed DOI

Baoukina S.; Mendez-Villuendas E.; Bennett W. F. D.; Tieleman D. P. Computer Simulations of the Phase Separation in Model Membranes. Faraday Discuss. 2013, 161, 63–75. 10.1039/C2FD20117H. PubMed DOI

Ohvo-Rekilä H. Cholesterol Interactions with Phospholipids in Membranes. Prog. Lipid Res. 2002, 41, 66–97. 10.1016/S0163-7827(01)00020-0. PubMed DOI

Boughter C. T.; Monje-Galvan V.; Im W.; Klauda J. B. Influence of Cholesterol on Phospholipid Bilayer Structure and Dynamics. J. Phys. Chem. B 2016, 120, 11761–11772. 10.1021/acs.jpcb.6b08574. PubMed DOI

Wang E.; Klauda J. B. Examination of Mixtures Containing Sphingomyelin and Cholesterol by Molecular Dynamics Simulations. J. Phys. Chem. B 2017, 121, 4833–4844. 10.1021/acs.jpcb.7b01832. PubMed DOI

Martinez-Seara H.; Róg T.; Karttunen M.; Vattulainen I.; Reigada R. Cholesterol Induces Specific Spatial and Orientational Order in Cholesterol/Phospholipid Membranes. PLoS One 2010, 5, e11162.10.1371/journal.pone.0011162. PubMed DOI PMC

Garg S.; Castro-Roman F.; Porcar L.; Butler P.; Bautista P. J.; Krzyzanowski N.; Perez-Salas U. Cholesterol Solubility Limit in Lipid Membranes Probed by Small Angle Neutron Scattering and MD Simulations. Soft Matter 2014, 10, 9313–9317. 10.1039/C4SM01219D. PubMed DOI

Díaz-Tejada C.; Ariz-Extreme I.; Awasthi N.; Hub J. S. Quantifying Lateral Inhomogeneity of Cholesterol-Containing Membranes. J. Phys. Chem. Lett. 2015, 6, 4799–4803. 10.1021/acs.jpclett.5b02414. PubMed DOI

Zhang Y.; Lervik A.; Seddon J.; Bresme F. A Coarse-Grained Molecular Dynamics Investigation of the Phase Behavior of DPPC/Cholesterol Mixtures. Chem. Phys. Lipids 2015, 185, 88–98. 10.1016/j.chemphyslip.2014.07.011. PubMed DOI

Wang Y.; Gkeka P.; Fuchs J. E.; Liedl K. R.; Cournia Z. DPPC-Cholesterol Phase Diagram Using Coarse-Grained Molecular Dynamics Simulations. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2846–2857. 10.1016/j.bbamem.2016.08.005. PubMed DOI

Melo M. N.; Ingólfsson H. I.; Marrink S. J. Parameters for Martini Sterols and Hopanoids Based on a Virtual-Site Description. J. Chem. Phys. 2015, 143, 243152.10.1063/1.4937783. PubMed DOI

Lee I.-H.; Saha S.; Polley A.; Huang H.; Mayor S.; Rao M.; Groves J. T. Live Cell Plasma Membranes Do Not Exhibit a Miscibility Phase Transition over a Wide Range of Temperatures. J. Phys. Chem. B 2015, 119, 4450–4459. 10.1021/jp512839q. PubMed DOI

de Almeida R. F. M.; Fedorov A.; Prieto M. Sphingomyelin/Phosphatidylcholine/Cholesterol Phase Diagram: Boundaries and Composition of Lipid Rafts. Biophys. J. 2003, 85, 2406–2416. 10.1016/S0006-3495(03)74664-5. PubMed DOI PMC

Niemelä P. S.; Ollila S.; Hyvönen M. T.; Karttunen M.; Vattulainen I. Assessing the Nature of Lipid Raft Membranes. PLoS Comput. Biol. 2007, 3, e34.10.1371/journal.pcbi.0030034. PubMed DOI PMC

Bera I.; Klauda J. B. Molecular Simulations of Mixed Lipid Bilayers with Sphingomyelin, Glycerophospholipids, and Cholesterol. J. Phys. Chem. B 2017, 121, 5197–5208. 10.1021/acs.jpcb.7b00359. PubMed DOI

Aittoniemi J.; Niemelä P. S.; Hyvönen M. T.; Karttunen M.; Vattulainen I. Insight into the Putative Specific Interactions between Cholesterol, Sphingomyelin, and Palmitoyl-Oleoyl Phosphatidylcholine. Biophys. J. 2007, 92, 1125–1137. 10.1529/biophysj.106.088427. PubMed DOI PMC

Yang J.; Martí J.; Calero C. Pair Interactions among Ternary DPPC/POPC/Cholesterol Mixtures in Liquid-Ordered and Liquid-Disordered Phases. Soft Matter 2016, 12, 4557–4561. 10.1039/C6SM00345A. PubMed DOI

Wang C.; Krause M. R.; Regen S. L. Push and Pull Forces in Lipid Raft Formation: The Push Can Be as Important as the Pull. J. Am. Chem. Soc. 2015, 137, 664–666. 10.1021/ja5115437. PubMed DOI

de Joannis J.; Coppock P. S.; Yin F.; Mori M.; Zamorano A.; Kindt J. T. Atomistic Simulation of Cholesterol Effects on Miscibility of Saturated and Unsaturated Phospholipids: Implications for Liquid-Ordered/Liquid-Disordered Phase Coexistence. J. Am. Chem. Soc. 2011, 133, 3625–3634. 10.1021/ja110425s. PubMed DOI

Sodt A. J.; Sandar M. L.; Gawrisch K.; Pastor R. W.; Lyman E. The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers. J. Am. Chem. Soc. 2014, 136, 725–732. 10.1021/ja4105667. PubMed DOI PMC

Sodt A. J.; Pastor R. W.; Lyman E. Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin. Biophys. J. 2015, 109, 948–955. 10.1016/j.bpj.2015.07.036. PubMed DOI PMC

Pandit S. A.; Vasudevan S.; Chiu S. W.; Jay Mashl R.; Jakobsson E.; Scott H. L. Sphingomyelin-Cholesterol Domains in Phospholipid Membranes: Atomistic Simulation. Biophys. J. 2004, 87, 1092–1100. 10.1529/biophysj.104.041939. PubMed DOI PMC

Pandit S. A.; Jakobsson E.; Scott H. L. Simulation of the Early Stages of Nano-Domain Formation in Mixed Bilayers of Sphingomyelin, Cholesterol, and Dioleylphosphatidylcholine. Biophys. J. 2004, 87, 3312–3322. 10.1529/biophysj.104.046078. PubMed DOI PMC

Apajalahti T.; Niemelä P.; Govindan P. N.; Miettinen M. S.; Salonen E.; Marrink S.-J.; Vattulainen I. Concerted Diffusion of Lipids in Raft-like Membranes. Faraday Discuss. 2010, 144, 411–430. 10.1039/B901487J. PubMed DOI

Bennett W. F. D.; Tieleman D. P. Computer Simulations of Lipid Membrane Domains. Biochim. Biophys. Acta, Biomembr. 2013, 1828, 1765–1776. 10.1016/j.bbamem.2013.03.004. PubMed DOI

Baoukina S.; Tieleman D. P.. Computer Simulations of Phase Separation in Lipid Bilayers and Monolayers. In Methods in Membrane Lipids; Owen D. M., Ed.; Springer New York: New York, NY, 2015; Vol. 1232, pp 307–322, 10.1007/978-1-4939-1752-5_21. PubMed DOI

Risselada H. J.; Marrink S. J. The Molecular Face of Lipid Rafts in Model Membranes. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 17367–17372. 10.1073/pnas.0807527105. PubMed DOI PMC

Uppamoochikkal P.; Tristram-Nagle S.; Nagle J. F. Orientation of Tie-Lines in the Phase Diagram of DOPC/DPPC/Cholesterol Model Biomembranes. Langmuir 2010, 26, 17363–17368. 10.1021/la103024f. PubMed DOI PMC

Pantelopulos G. A.; Nagai T.; Bandara A.; Panahi A.; Straub J. E. Critical Size Dependence of Domain Formation Observed in Coarse-Grained Simulations of Bilayers Composed of Ternary Lipid Mixtures. J. Chem. Phys. 2017, 147, 095101.10.1063/1.4999709. PubMed DOI PMC

Davis R. S.; Sunil Kumar P. B.; Sperotto M. M.; Laradji M. Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field. J. Phys. Chem. B 2013, 117, 4072–4080. 10.1021/jp4000686. PubMed DOI

Rosetti C.; Pastorino C. Comparison of Ternary Bilayer Mixtures with Asymmetric or Symmetric Unsaturated Phosphatidylcholine Lipids by Coarse Grained Molecular Dynamics Simulations. J. Phys. Chem. B 2012, 116, 3525–3537. 10.1021/jp212406u. PubMed DOI

Domański J.; Marrink S. J.; Schäfer L. V. Transmembrane Helices Can Induce Domain Formation in Crowded Model Membranes. Biochim. Biophys. Acta, Biomembr. 2012, 1818, 984–994. 10.1016/j.bbamem.2011.08.021. PubMed DOI

Lin X.; Lorent J. H.; Skinkle A. D.; Levental K. R.; Waxham M. N.; Gorfe A. A.; Levental I. Domain Stability in Biomimetic Membranes Driven by Lipid Polyunsaturation. J. Phys. Chem. B 2016, 120, 11930–11941. 10.1021/acs.jpcb.6b06815. PubMed DOI PMC

Hakobyan D.; Heuer A. Key Molecular Requirements for Raft Formation in Lipid/Cholesterol Membranes. PLoS One 2014, 9, e87369.10.1371/journal.pone.0087369. PubMed DOI PMC

Carpenter T. S.; López C. A.; Neale C.; Montour C.; Ingólfsson H. I.; Di Natale F.; Lightstone F. C.; Gnanakaran S. Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field. J. Chem. Theory Comput. 2018, 14, 6050–6062. 10.1021/acs.jctc.8b00496. PubMed DOI

Fowler P. W.; Williamson J. J.; Sansom M. S. P.; Olmsted P. D. Roles of Interleaflet Coupling and Hydrophobic Mismatch in Lipid Membrane Phase-Separation Kinetics. J. Am. Chem. Soc. 2016, 138, 11633–11642. 10.1021/jacs.6b04880. PubMed DOI PMC

Goh S. L.; Amazon J. J.; Feigenson G. W. Toward a Better Raft Model: Modulated Phases in the Four-Component Bilayer, DSPC/DOPC/POPC/CHOL. Biophys. J. 2013, 104, 853–862. 10.1016/j.bpj.2013.01.003. PubMed DOI PMC

Ackerman D. G.; Feigenson G. W. Multiscale Modeling of Four-Component Lipid Mixtures: Domain Composition, Size, Alignment, and Properties of the Phase Interface. J. Phys. Chem. B 2015, 119, 4240–4250. 10.1021/jp511083z. PubMed DOI PMC

Schäfer L. V.; Marrink S. J. Partitioning of Lipids at Domain Boundaries in Model Membranes. Biophys. J. 2010, 99, L91–L93. 10.1016/j.bpj.2010.08.072. PubMed DOI PMC

Ackerman D. G.; Feigenson G. W. Effects of Transmembrane α-Helix Length and Concentration on Phase Behavior in Four-Component Lipid Mixtures: A Molecular Dynamics Study. J. Phys. Chem. B 2016, 120, 4064–4077. 10.1021/acs.jpcb.6b00611. PubMed DOI

Perlmutter J. D.; Sachs J. N. Interleaflet Interaction and Asymmetry in Phase Separated Lipid Bilayers: Molecular Dynamics Simulations. J. Am. Chem. Soc. 2011, 133, 6563–6577. 10.1021/ja106626r. PubMed DOI

Usery R. D.; Enoki T. A.; Wickramasinghe S. P.; Weiner M. D.; Tsai W.-C.; Kim M. B.; Wang S.; Torng T. L.; Ackerman D. G.; Heberle F. A.; et al. Line Tension Controls Liquid-Disordered + Liquid-Ordered Domain Size Transition in Lipid Bilayers. Biophys. J. 2017, 112, 1431–1443. 10.1016/j.bpj.2017.02.033. PubMed DOI PMC

Palmieri B.; Grant M.; Safran S. A. Prediction of the Dependence of the Line Tension on the Composition of Linactants and the Temperature in Phase Separated Membranes. Langmuir 2014, 30, 11734–11745. 10.1021/la502347a. PubMed DOI

Heberle F. A.; Doktorova M.; Goh S. L.; Standaert R. F.; Katsaras J.; Feigenson G. W. Hybrid and Nonhybrid Lipids Exert Common Effects on Membrane Raft Size and Morphology. J. Am. Chem. Soc. 2013, 135, 14932–14935. 10.1021/ja407624c. PubMed DOI

Rosetti C. M.; Montich G. G.; Pastorino C. Molecular Insight into the Line Tension of Bilayer Membranes Containing Hybrid Polyunsaturated Lipids. J. Phys. Chem. B 2017, 121, 1587–1600. 10.1021/acs.jpcb.6b10836. PubMed DOI

Dupuy A. D.; Engelman D. M. Protein Area Occupancy at the Center of the Red Blood Cell Membrane. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 2848–2852. 10.1073/pnas.0712379105. PubMed DOI PMC

Kusumi A.; Nakada C.; Ritchie K.; Murase K.; Suzuki K.; Murakoshi H.; Kasai R. S.; Kondo J.; Fujiwara T. Paradigm Shift of the Plasma Membrane Concept from the Two-Dimensional Continuum Fluid to the Partitioned Fluid: High-Speed Single-Molecule Tracking of Membrane Molecules. Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 351–378. 10.1146/annurev.biophys.34.040204.144637. PubMed DOI

Fischer T.; Jelger Risselada H.; Vink R. L. C. Membrane Lateral Structure: The Influence of Immobilized Particles on Domain Size. Phys. Chem. Chem. Phys. 2012, 14, 14500.10.1039/c2cp41417a. PubMed DOI

Schick M. Strongly Correlated Rafts in Both Leaves of an Asymmetric Bilayer. J. Phys. Chem. B 2018, 122, 3251–3258. 10.1021/acs.jpcb.7b08890. PubMed DOI

Tian J.; Nickels J.; Katsaras J.; Cheng X. Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies. J. Phys. Chem. B 2016, 120, 8438–8448. 10.1021/acs.jpcb.6b02148. PubMed DOI

Iwabuchi K.; Nakayama H.; Iwahara C.; Takamori K. Significance of Glycosphingolipid Fatty Acid Chain Length on Membrane Microdomain-Mediated Signal Transduction. FEBS Lett. 2010, 584, 1642–1652. 10.1016/j.febslet.2009.10.043. PubMed DOI

Weiner M. D.; Feigenson G. W. Presence and Role of Midplane Cholesterol in Lipid Bilayers Containing Registered or Antiregistered Phase Domains. J. Phys. Chem. B 2018, 122, 8193–8200. 10.1021/acs.jpcb.8b03949. PubMed DOI

Thallmair S.; Ingólfsson H. I.; Marrink S. J. Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models. J. Phys. Chem. Lett. 2018, 9, 5527–5533. 10.1021/acs.jpclett.8b01877. PubMed DOI PMC

Hakobyan D.; Heuer A. Phase Separation in a Lipid/Cholesterol System: Comparison of Coarse-Grained and United-Atom Simulations. J. Phys. Chem. B 2013, 117, 3841–3851. 10.1021/jp312245y. PubMed DOI

Barnoud J.; Rossi G.; Marrink S. J.; Monticelli L. Hydrophobic Compounds Reshape Membrane Domains. PLoS Comput. Biol. 2014, 10, e1003873.10.1371/journal.pcbi.1003873. PubMed DOI PMC

Reigada R.; Sagues F. Chloroform Alters Interleaflet Coupling in Lipid Bilayers: An Entropic Mechanism. J. R. Soc., Interface 2015, 12, 20150197–20150197. 10.1098/rsif.2015.0197. PubMed DOI PMC

Moiset G.; López C. A.; Bartelds R.; Syga L.; Rijpkema E.; Cukkemane A.; Baldus M.; Poolman B.; Marrink S. J. Disaccharides Impact the Lateral Organization of Lipid Membranes. J. Am. Chem. Soc. 2014, 136, 16167–16175. 10.1021/ja505476c. PubMed DOI

Rossi G.; Barnoud J.; Monticelli L. Polystyrene Nanoparticles Perturb Lipid Membranes. J. Phys. Chem. Lett. 2014, 5, 241–246. 10.1021/jz402234c. PubMed DOI

Bochicchio D.; Panizon E.; Monticelli L.; Rossi G. Interaction of Hydrophobic Polymers with Model Lipid Bilayers. Sci. Rep. 2017, 7, 6357.10.1038/s41598-017-06668-0. PubMed DOI PMC

Muddana H. S.; Chiang H. H.; Butler P. J. Tuning Membrane Phase Separation Using Nonlipid Amphiphiles. Biophys. J. 2012, 102, 489–497. 10.1016/j.bpj.2011.12.033. PubMed DOI PMC

Ingólfsson H. I.; Melo M. N.; van Eerden F. J.; Arnarez C.; Lopez C. A.; Wassenaar T. A.; Periole X.; de Vries A. H.; Tieleman D. P.; Marrink S. J. Lipid Organization of the Plasma Membrane. J. Am. Chem. Soc. 2014, 136, 14554–14559. 10.1021/ja507832e. PubMed DOI

Gu R.-X.; Ingólfsson H. I.; de Vries A. H.; Marrink S. J.; Tieleman D. P. Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations. J. Phys. Chem. B 2017, 121, 3262–3275. 10.1021/acs.jpcb.6b07142. PubMed DOI PMC

Koldsø H.; Shorthouse D.; Hélie J.; Sansom M. S. P. Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers. PLoS Comput. Biol. 2014, 10, e1003911.10.1371/journal.pcbi.1003911. PubMed DOI PMC

Ingólfsson H. I.; Carpenter T. S.; Bhatia H.; Bremer P.-T.; Marrink S. J.; Lightstone F. C. Computational Lipidomics of the Neuronal Plasma Membrane. Biophys. J. 2017, 113, 2271–2280. 10.1016/j.bpj.2017.10.017. PubMed DOI PMC

Baoukina S.; Ingólfsson H. I.; Marrink S. J.; Tieleman D. P. Curvature-Induced Sorting of Lipids in Plasma Membrane Tethers. Adv. Theory Simul. 2018, 1, 1800034.10.1002/adts.201800034. DOI

Flinner N.; Schleiff E. Dynamics of the Glycophorin A Dimer in Membranes of Native-Like Composition Uncovered by Coarse-Grained Molecular Dynamics Simulations. PLoS One 2015, 10, e0133999.10.1371/journal.pone.0133999. PubMed DOI PMC

Hedger G.; Sansom M. S. P. Lipid Interaction Sites on Channels, Transporters and Receptors: Recent Insights from Molecular Dynamics Simulations. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2390–2400. 10.1016/j.bbamem.2016.02.037. PubMed DOI PMC

Koldsø H.; Sansom M. S. P. Local Lipid Reorganization by a Transmembrane Protein Domain. J. Phys. Chem. Lett. 2012, 3, 3498–3502. 10.1021/jz301570w. PubMed DOI PMC

Vögele M.; Köfinger J.; Hummer G. Hydrodynamics of Diffusion in Lipid Membrane Simulations. Phys. Rev. Lett. 2018, 120, 268104.10.1103/PhysRevLett.120.268104. PubMed DOI

Parton D. L.; Tek A.; Baaden M.; Sansom M. S. P. Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations. PLoS Comput. Biol. 2013, 9, e1003034.10.1371/journal.pcbi.1003034. PubMed DOI PMC

Duncan A. L.; Reddy T.; Koldsø H.; Hélie J.; Fowler P. W.; Chavent M.; Sansom M. S. P. Protein Crowding and Lipid Complexity Influence the Nanoscale Dynamic Organization of Ion Channels in Cell Membranes. Sci. Rep. 2017, 7, 16647.10.1038/s41598-017-16865-6. PubMed DOI PMC

Sharma S.; Kim B. N.; Stansfeld P. J.; Sansom M. S. P.; Lindau M. A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry. PLoS One 2015, 10, e0144814.10.1371/journal.pone.0144814. PubMed DOI PMC

van den Bogaart G.; Meyenberg K.; Risselada H. J.; Amin H.; Willig K. I.; Hubrich B. E.; Dier M.; Hell S. W.; Grubmüller H.; Diederichsen U.; et al. Membrane Protein Sequestering by Ionic Protein–Lipid Interactions. Nature 2011, 479, 552–555. 10.1038/nature10545. PubMed DOI PMC

Corradi V.; Mendez-Villuendas E.; Ingólfsson H. I.; Gu R.-X.; Siuda I.; Melo M. N.; Moussatova A.; DeGagné L. J.; Sejdiu B. I.; Singh G.; et al. Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins. ACS Cent. Sci. 2018, 4, 709–717. 10.1021/acscentsci.8b00143. PubMed DOI PMC

Einstein A. In Investigations on the Theory of the Brownian Movement; Fürth R., Ed.; Cowper, A. D., Translator; Dover Publications, 1956.

Vattulainen I.; Mouritsen O. G.. Diffusion in Membranes. In Diffusion in Condensed Matter; Heitjans P., Kärger J., Eds.; Springer: Berlin, Heidelberg, 2005; pp 471–509, 10.1007/3-540-30970-5_12. DOI

Wieser S.; Weghuber J.; Sams M.; Stockinger H.; Schütz G. J. Cell-to-Cell Variability in the Diffusion Constants of the Plasma Membrane Proteins CD59 and CD147. Soft Matter 2009, 5, 3287–3294. 10.1039/b902266j. DOI

Milo R.; Phillips R.. Cell Biology by the Numbers; Garland Science, Taylor & Francis Group: New York, NY, 2016.

Bag N.; Yap D. H. X.; Wohland T. Temperature Dependence of Diffusion in Model and Live Cell Membranes Characterized by Imaging Fluorescence Correlation Spectroscopy. Biochim. Biophys. Acta, Biomembr. 2014, 1838, 802–813. 10.1016/j.bbamem.2013.10.009. PubMed DOI

Metzler R.; Jeon J.-H.; Cherstvy A. G. Non-Brownian Diffusion in Lipid Membranes: Experiments and Simulations. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2451–2467. 10.1016/j.bbamem.2016.01.022. PubMed DOI

Falck E.; Róg T.; Karttunen M.; Vattulainen I. Lateral Diffusion in Lipid Membranes through Collective Flows. J. Am. Chem. Soc. 2008, 130, 44–45. 10.1021/ja7103558. PubMed DOI

Ayton G. S.; Voth G. A. Mesoscopic Lateral Diffusion in Lipid Bilayers. Biophys. J. 2004, 87, 3299–3311. 10.1529/biophysj.104.047811. PubMed DOI PMC

Busch S.; Smuda C.; Pardo L. C.; Unruh T. Molecular Mechanism of Long-Range Diffusion in Phospholipid Membranes Studied by Quasielastic Neutron Scattering. J. Am. Chem. Soc. 2010, 132, 3232–3233. 10.1021/ja907581s. PubMed DOI

Lautner L.; Pluhackova K.; Barth N. K. H.; Seydel T.; Lohstroh W.; Böckmann R. A.; Unruh T. Dynamic Processes in Biological Membrane Mimics Revealed by Quasielastic Neutron Scattering. Chem. Phys. Lipids 2017, 206, 28–42. 10.1016/j.chemphyslip.2017.05.009. PubMed DOI

Armstrong C. L.; Trapp M.; Peters J.; Seydel T.; Rheinstädter M. C. Short Range Ballistic Motion in Fluid Lipid Bilayers Studied by Quasi-Elastic Neutron Scattering. Soft Matter 2011, 7, 8358–8362. 10.1039/c1sm05691c. DOI

Chavent M.; Reddy T.; Goose J.; Dahl A. C. E.; Stone J. E.; Jobard B.; Sansom M. S. P. Methodologies for the Analysis of Instantaneous Lipid Diffusion in MD Simulations of Large Membrane Systems. Faraday Discuss. 2014, 169, 455–475. 10.1039/C3FD00145H. PubMed DOI PMC

Starr F. W.; Hartmann B.; Douglas J. F. Dynamical Clustering and a Mechanism for Raft-like Structures in a Model Lipid Membrane. Soft Matter 2014, 10, 3036–3047. 10.1039/c3sm53187b. PubMed DOI PMC

Jacobson K.; Mouritsen O. G.; Anderson R. G. W. Lipid Rafts: At a Crossroad between Cell Biology and Physics. Nat. Cell Biol. 2007, 9, 7–14. 10.1038/ncb0107-7. PubMed DOI

Aponte-Santamaria C.; Briones R.; Schenk A. D.; Walz T.; de Groot B. L. Molecular Driving Forces Defining Lipid Positions around Aquaporin-0. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 9887–9892. 10.1073/pnas.1121054109. PubMed DOI PMC

Cohen M. H.; Turnbull D. Molecular Transport in Liquids and Glasses. J. Chem. Phys. 1959, 31, 1164–1169. 10.1063/1.1730566. DOI

Almeida P. F. F.; Vaz W. L. C.; Thompson T. E. Lateral Diffusion in the Liquid Phases of Dimyristoylphosphatidylcholine/Cholesterol Lipid Bilayers: A Free Volume Analysis. Biochemistry 1992, 31, 6739–6747. 10.1021/bi00144a013. PubMed DOI

Galla H. J.; Hartmann W.; Theilen U.; Sackmann E. On Two-Dimensional Passive Random Walk in Lipid Bilayers and Fluid Pathways in Biomembranes. J. Membr. Biol. 1979, 48, 215–236. 10.1007/BF01872892. PubMed DOI

MacCarthy J. E.; Kozak J. J. Lateral Diffusion in Fluid Systems. J. Chem. Phys. 1982, 77, 2214–2216. 10.1063/1.444032. DOI

O’Leary T. J. Lateral Diffusion of Lipids in Complex Biological Membranes. Proc. Natl. Acad. Sci. U. S. A. 1987, 84, 429–433. 10.1073/pnas.84.2.429. PubMed DOI PMC

Vaz W. L. C.; Clegg R. M.; Hallmann D. Translational Diffusion of Lipids in Liquid Crystalline Phase Phosphatidylcholine Multibilayers. A Comparison of Experiment with Theory. Biochemistry 1985, 24, 781–786. 10.1021/bi00324a037. PubMed DOI

Macedo P. B.; Litovitz T. A. On the Relative Roles of Free Volume and Activation Energy in the Viscosity of Liquids. J. Chem. Phys. 1965, 42, 245–256. 10.1063/1.1695683. DOI

Javanainen M.; Monticelli L.; de la Serna J. B.; Vattulainen I. Free Volume Theory Applied to Lateral Diffusion in Langmuir Monolayers: Atomistic Simulations for a Protein-Free Model of Lung Surfactant. Langmuir 2010, 26, 15436–15444. 10.1021/la102454m. PubMed DOI

Arrhenius S. Über Die Reaktionsgeschwindigkeit Bei Der Inversion von Rohrzucker Durch Säuren. Z. Phys. Chem. 1889, 4U, 226–248. 10.1515/zpch-1889-0416. DOI

Filippov A.; Orädd G.; Lindblom G. The Effect of Cholesterol on the Lateral Diffusion of Phospholipids in Oriented Bilayers. Biophys. J. 2003, 84, 3079–3086. 10.1016/S0006-3495(03)70033-2. PubMed DOI PMC

Falck E.; Patra M.; Karttunen M.; Hyvönen M. T.; Vattulainen I. Lessons of Slicing Membranes: Interplay of Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers. Biophys. J. 2004, 87, 1076–1091. 10.1529/biophysj.104.041368. PubMed DOI PMC

Saffman P. G.; Delbrück M. Brownian Motion in Biological Membranes. Proc. Natl. Acad. Sci. U. S. A. 1975, 72, 3111–3113. 10.1073/pnas.72.8.3111. PubMed DOI PMC

Ramadurai S.; Holt A.; Krasnikov V.; van den Bogaart G.; Killian J. A.; Poolman B. Lateral Diffusion of Membrane Proteins. J. Am. Chem. Soc. 2009, 131, 12650–12656. 10.1021/ja902853g. PubMed DOI

Weiß K.; Neef A.; Van Q.; Kramer S.; Gregor I.; Enderlein J. Quantifying the Diffusion of Membrane Proteins and Peptides in Black Lipid Membranes with 2-Focus Fluorescence Correlation Spectroscopy. Biophys. J. 2013, 105, 455–462. 10.1016/j.bpj.2013.06.004. PubMed DOI PMC

Oswald F.; Varadarajan A.; Lill H.; Peterman E. J. G.; Bollen Y. J. M. MreB-Dependent Organization of the E. Coli Cytoplasmic Membrane Controls Membrane Protein Diffusion. Biophys. J. 2016, 110, 1139–1149. 10.1016/j.bpj.2016.01.010. PubMed DOI PMC

Goose J. E.; Sansom M. S. P. Reduced Lateral Mobility of Lipids and Proteins in Crowded Membranes. PLoS Comput. Biol. 2013, 9, e1003033.10.1371/journal.pcbi.1003033. PubMed DOI PMC

Guigas G.; Weiss M. Size-Dependent Diffusion of Membrane Inclusions. Biophys. J. 2006, 91, 2393–2398. 10.1529/biophysj.106.087031. PubMed DOI PMC

Guigas G.; Weiss M. Influence of Hydrophobic Mismatching on Membrane Protein Diffusion. Biophys. J. 2008, 95, L25–L27. 10.1529/biophysj.108.136069. PubMed DOI PMC

Jeon J.-H.; Monne H. M.-S.; Javanainen M.; Metzler R. Anomalous Diffusion of Phospholipids and Cholesterols in a Lipid Bilayer and Its Origins. Phys. Rev. Lett. 2012, 109, 188103.10.1103/PhysRevLett.109.188103. PubMed DOI

Guigas G.; Weiss M. Effects of Protein Crowding on Membrane Systems. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2441–2450. 10.1016/j.bbamem.2015.12.021. PubMed DOI

Weiss M.Crowding, Diffusion, and Biochemical Reactions. In New Models of the Cell Nucleus: Crowding, Entropic Forces, Phase Separation, and Fractals; Hancock R., Jeon K. W., Eds.; International Review of Cell and Molecular Biology; Academic Press, 2014; Vol. 307, Chapter 11, pp 383–417, 10.1016/B978-0-12-800046-5.00011-4. PubMed DOI

Jeon J.-H.; Javanainen M.; Martinez-Seara H.; Metzler R.; Vattulainen I. Protein Crowding in Lipid Bilayers Gives Rise to Non-Gaussian Anomalous Lateral Diffusion of Phospholipids and Proteins. Phys. Rev. X 2016, 6, 021006.10.1103/PhysRevX.6.021006. DOI

Peters R.; Cherry R. J. Lateral and Rotational Diffusion of Bacteriorhodopsin in Lipid Bilayers: Experimental Test of the Saffman-Delbrück Equations. Proc. Natl. Acad. Sci. U. S. A. 1982, 79, 4317–4321. 10.1073/pnas.79.14.4317. PubMed DOI PMC

Casuso I.; Khao J.; Chami M.; Paul-Gilloteaux P.; Husain M.; Duneau J.-P.; Stahlberg H.; Sturgis J. N.; Scheuring S. Characterization of the Motion of Membrane Proteins Using High-Speed Atomic Force Microscopy. Nat. Nanotechnol. 2012, 7, 525–529. 10.1038/nnano.2012.109. PubMed DOI

Munguira I.; Casuso I.; Takahashi H.; Rico F.; Miyagi A.; Chami M.; Scheuring S. Glasslike Membrane Protein Diffusion in a Crowded Membrane. ACS Nano 2016, 10, 2584–2590. 10.1021/acsnano.5b07595. PubMed DOI

Koldsø H.; Reddy T.; Fowler P. W.; Duncan A. L.; Sansom M. S. P. Membrane Compartmentalization Reducing the Mobility of Lipids and Proteins within a Model Plasma Membrane. J. Phys. Chem. B 2016, 120, 8873–8881. 10.1021/acs.jpcb.6b05846. PubMed DOI PMC

Yamamoto E.; Akimoto T.; Kalli A. C.; Yasuoka K.; Sansom M. S. P. Dynamic Interactions between a Membrane Binding Protein and Lipids Induce Fluctuating Diffusivity. Sci. Adv. 2017, 3, e1601871.10.1126/sciadv.1601871. PubMed DOI PMC

Yamamoto E.; Kalli A. C.; Akimoto T.; Yasuoka K.; Sansom M. S. P. Anomalous Dynamics of a Lipid Recognition Protein on a Membrane Surface. Sci. Rep. 2016, 5, 18245.10.1038/srep18245. PubMed DOI PMC

Kalay Z.; Fujiwara T. K.; Otaka A.; Kusumi A. Lateral Diffusion in a Discrete Fluid Membrane with Immobile Particles. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 2014, 89, 022724.10.1103/PhysRevE.89.022724. PubMed DOI

Saxton M. J. Lateral Diffusion in an Archipelago. Single-Particle Diffusion. Biophys. J. 1993, 64, 1766–1780. 10.1016/S0006-3495(93)81548-0. PubMed DOI PMC

Saxton M. J. The Spectrin Network as a Barrier to Lateral Diffusion in Erythrocytes. A Percolation Analysis. Biophys. J. 1989, 55, 21–28. 10.1016/S0006-3495(89)82776-6. PubMed DOI PMC

Saxton M. J. Lateral Diffusion in an Archipelago. Distance Dependence of the Diffusion Coefficient. Biophys. J. 1989, 56, 615–622. 10.1016/S0006-3495(89)82708-0. PubMed DOI PMC

Javanainen M.; Martinez-Seara H.; Vattulainen I. Excessive Aggregation of Membrane Proteins in the Martini Model. PLoS One 2017, 12, e0187936.10.1371/journal.pone.0187936. PubMed DOI PMC

Camley B. A.; Lerner M. G.; Pastor R. W.; Brown F. L. H. Strong Influence of Periodic Boundary Conditions on Lateral Diffusion in Lipid Bilayer Membranes. J. Chem. Phys. 2015, 143, 243113.10.1063/1.4932980. PubMed DOI PMC

Venable R. M.; Ingólfsson H. I.; Lerner M. G.; Perrin B. S.; Camley B. A.; Marrink S. J.; Brown F. L. H.; Pastor R. W. Lipid and Peptide Diffusion in Bilayers: The Saffman–Delbrück Model and Periodic Boundary Conditions. J. Phys. Chem. B 2017, 121, 3443–3457. 10.1021/acs.jpcb.6b09111. PubMed DOI PMC

Vögele M.; Hummer G. Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes. J. Phys. Chem. B 2016, 120, 8722–8732. 10.1021/acs.jpcb.6b05102. PubMed DOI

Gurtovenko A. A.; Javanainen M.; Lolicato F.; Vattulainen I.. The Devil Is in the Details: What Do We Really Track in Single-Particle Tracking iSCAT Experiments? 2018, Manuscript in preparation. PubMed

Lehninger A. L.; Nelson D. L.; Cox M. M.. Lehninger Principles of Biochemistry, 6th ed.; W.H. Freeman: New York, 2013.

Casciola M.; Tarek M. A Molecular Insight into the Electro-Transfer of Small Molecules through Electropores Driven by Electric Fields. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2278–2289. 10.1016/j.bbamem.2016.03.022. PubMed DOI

Kirsch S. A.; Böckmann R. A. Membrane Pore Formation in Atomistic and Coarse-Grained Simulations. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2266–2277. 10.1016/j.bbamem.2015.12.031. PubMed DOI

Awoonor-Williams E.; Rowley C. N. Molecular Simulation of Nonfacilitated Membrane Permeation. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 1672–1687. 10.1016/j.bbamem.2015.12.014. PubMed DOI

Shinoda W. Permeability across Lipid Membranes. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2254–2265. 10.1016/j.bbamem.2016.03.032. PubMed DOI

Qiao B.; Olvera de la Cruz M. Driving Force for Water Permeation Across Lipid Membranes. J. Phys. Chem. Lett. 2013, 4, 3233–3237. 10.1021/jz401730s. DOI

Conte E.; Megli F. M.; Khandelia H.; Jeschke G.; Bordignon E. Lipid Peroxidation and Water Penetration in Lipid Bilayers: A W-Band EPR Study. Biochim. Biophys. Acta, Biomembr. 2013, 1828, 510–517. 10.1016/j.bbamem.2012.09.026. PubMed DOI

Wong-Ekkabut J.; Xu Z.; Triampo W.; Tang I. M.; Tieleman D. P.; Monticelli L. Effect of Lipid Peroxidation on the Properties of Lipid Bilayers: A Molecular Dynamics Study. Biophys. J. 2007, 93, 4225–4236. 10.1529/biophysj.107.112565. PubMed DOI PMC

Khandelia H.; Mouritsen O. G. Lipid Gymnastics: Evidence of Complete Acyl Chain Reversal in Oxidized Phospholipids from Molecular Simulations. Biophys. J. 2009, 96, 2734–2743. 10.1016/j.bpj.2009.01.007. PubMed DOI PMC

Lis M.; Wizert A.; Przybylo M.; Langner M.; Swiatek J.; Jungwirth P.; Cwiklik L. The Effect of Lipid Oxidation on the Water Permeability of Phospholipids Bilayers. Phys. Chem. Chem. Phys. 2011, 13, 17555.10.1039/c1cp21009b. PubMed DOI

Lee H.; Malmstadt N. Effect of Low Levels of Lipid Oxidation on the Curvature, Dynamics, and Permeability of Lipid Bilayers and Their Interactions with Cationic Nanoparticles. J. Phys. D: Appl. Phys. 2018, 51, 164002.10.1088/1361-6463/aab4b8. DOI

Su J.; Zhao Y.; Fang C.; Shi Y. Asymmetric Osmotic Water Permeation through a Vesicle Membrane. J. Chem. Phys. 2017, 146, 204902.10.1063/1.4983749. PubMed DOI PMC

Saito H.; Shinoda W. Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers: A Molecular Dynamics Study. J. Phys. Chem. B 2011, 115, 15241–15250. 10.1021/jp201611p. PubMed DOI

Mathai J. C.; Tristram-Nagle S.; Nagle J. F.; Zeidel M. L. Structural Determinants of Water Permeability through the Lipid Membrane. J. Gen. Physiol. 2008, 131, 69–76. 10.1085/jgp.200709848. PubMed DOI PMC

Issack B. B.; Peslherbe G. H. Effects of Cholesterol on the Thermodynamics and Kinetics of Passive Transport of Water through Lipid Membranes. J. Phys. Chem. B 2015, 119, 9391–9400. 10.1021/jp510497r. PubMed DOI

Hartkamp R.; Moore T. C.; Iacovella C. R.; Thompson M. A.; Bulsara P. A.; Moore D. J.; McCabe C. Composition Dependence of Water Permeation Across Multicomponent Gel-Phase Bilayers. J. Phys. Chem. B 2018, 122, 3113–3123. 10.1021/acs.jpcb.8b00747. PubMed DOI PMC

Krieg P.; Fürstenberger G. The Role of Lipoxygenases in Epidermis. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2014, 1841, 390–400. 10.1016/j.bbalip.2013.08.005. PubMed DOI

Del Regno A.; Notman R. Permeation Pathways through Lateral Domains in Model Membranes of Skin Lipids. Phys. Chem. Chem. Phys. 2018, 20, 2162–2174. 10.1039/C7CP03258G. PubMed DOI

Das C.; Noro M. G.; Olmsted P. D. Simulation Studies of Stratum Corneum Lipid Mixtures. Biophys. J. 2009, 97, 1941–1951. 10.1016/j.bpj.2009.06.054. PubMed DOI PMC

Gupta R.; Dwadasi B. S.; Rai B. Molecular Dynamics Simulation of Skin Lipids: Effect of Ceramide Chain Lengths on Bilayer Properties. J. Phys. Chem. B 2016, 120, 12536–12546. 10.1021/acs.jpcb.6b08059. PubMed DOI

Gupta R.; Sridhar D. B.; Rai B. Molecular Dynamics Simulation Study of Permeation of Molecules through Skin Lipid Bilayer. J. Phys. Chem. B 2016, 120, 8987–8996. 10.1021/acs.jpcb.6b05451. PubMed DOI

Li L.; Vorobyov I.; Allen T. W. Potential of Mean Force and pKa Profile Calculation for a Lipid Membrane-Exposed Arginine Side Chain. J. Phys. Chem. B 2008, 112, 9574–9587. 10.1021/jp7114912. PubMed DOI

MacCallum J. L.; Bennett W. F. D.; Tieleman D. P. Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations. Biophys. J. 2008, 94, 3393–3404. 10.1529/biophysj.107.112805. PubMed DOI PMC

Li L.; Vorobyov I.; Allen T. W. The Different Interactions of Lysine and Arginine Side Chains with Lipid Membranes. J. Phys. Chem. B 2013, 117, 11906–11920. 10.1021/jp405418y. PubMed DOI PMC

Panahi A.; Brooks C. L. Membrane Environment Modulates the pKa Values of Transmembrane Helices. J. Phys. Chem. B 2015, 119, 4601–4607. 10.1021/acs.jpcb.5b00289. PubMed DOI PMC

Johansson A. C. V.; Lindahl E. Titratable Amino Acid Solvation in Lipid Membranes as a Function of Protonation State. J. Phys. Chem. B 2009, 113, 245–253. 10.1021/jp8048873. PubMed DOI

Bonhenry D.; Tarek M.; Dehez F. Effects of Phospholipid Composition on the Transfer of a Small Cationic Peptide Across a Model Biological Membrane. J. Chem. Theory Comput. 2013, 9, 5675–5684. 10.1021/ct400576e. PubMed DOI

Gleason N. J.; Vostrikov V. V.; Greathouse D. V.; Koeppe R. E. Buried Lysine, but Not Arginine, Titrates and Alters Transmembrane Helix Tilt. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 1692–1695. 10.1073/pnas.1215400110. PubMed DOI PMC

Bonhenry D.; Dehez F.; Tarek M. Effects of Hydration on the Protonation State of a Lysine Analog Crossing a Phospholipid Bilayer – Insights from Molecular Dynamics and Free-Energy Calculations. Phys. Chem. Chem. Phys. 2018, 20, 9101–9107. 10.1039/C8CP00312B. PubMed DOI

Witek J.; Keller B. G.; Blatter M.; Meissner A.; Wagner T.; Riniker S. Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. J. Chem. Inf. Model. 2016, 56, 1547–1562. 10.1021/acs.jcim.6b00251. PubMed DOI

Witek J.; Mühlbauer M.; Keller B. G.; Blatter M.; Meissner A.; Wagner T.; Riniker S. Interconversion Rates between Conformational States as Rationale for the Membrane Permeability of Cyclosporines. ChemPhysChem 2017, 18, 3309–3314. 10.1002/cphc.201700995. PubMed DOI

Wang C. K.; Swedberg J. E.; Harvey P. J.; Kaas Q.; Craik D. J. Conformational Flexibility Is a Determinant of Permeability for Cyclosporin. J. Phys. Chem. B 2018, 122, 2261–2276. 10.1021/acs.jpcb.7b12419. PubMed DOI

Leontiadou H.; Mark A. E.; Marrink S. J. Antimicrobial Peptides in Action. J. Am. Chem. Soc. 2006, 128, 12156–12161. 10.1021/ja062927q. PubMed DOI

Li J.; Liu S.; Lakshminarayanan R.; Bai Y.; Pervushin K.; Verma C.; Beuerman R. W. Molecular Simulations Suggest How a Branched Antimicrobial Peptide Perturbs a Bacterial Membrane and Enhances Permeability. Biochim. Biophys. Acta, Biomembr. 2013, 1828, 1112–1121. 10.1016/j.bbamem.2012.12.015. PubMed DOI

Sengupta D.; Leontiadou H.; Mark A. E.; Marrink S.-J. Toroidal Pores Formed by Antimicrobial Peptides Show Significant Disorder. Biochim. Biophys. Acta, Biomembr. 2008, 1778, 2308–2317. 10.1016/j.bbamem.2008.06.007. PubMed DOI

Wang Y.; Chen C. H.; Hu D.; Ulmschneider M. B.; Ulmschneider J. P. Spontaneous Formation of Structurally Diverse Membrane Channel Architectures from a Single Antimicrobial Peptide. Nat. Commun. 2016, 7, 13535.10.1038/ncomms13535. PubMed DOI PMC

Mukherjee S.; Kar R. K.; Nanga R. P. R.; Mroue K. H.; Ramamoorthy A.; Bhunia A. Accelerated Molecular Dynamics Simulation Analysis of MSI-594 in a Lipid Bilayer. Phys. Chem. Chem. Phys. 2017, 19, 19289–19299. 10.1039/C7CP01941F. PubMed DOI PMC

Jedlovszky P.; Mezei M. Calculation of the Free Energy Profile of H2O, O2, CO, CO2, NO, and CHCl3 in a Lipid Bilayer with a Cavity Insertion Variant of the Widom Method. J. Am. Chem. Soc. 2000, 122, 5125–5131. 10.1021/ja000156z. DOI

Pártay L. B.; Jedlovszky P.; Hoang P. N. M.; Picaud S.; Mezei M. Free-Energy Profile of Small Solute Molecules at the Free Surfaces of Water and Ice, as Determined by Cavity Insertion Widom Calculations. J. Phys. Chem. C 2007, 111, 9407–9416. 10.1021/jp0719816. DOI

Yuan H.; Jameson C. J.; Murad S. Exploring Gas Permeability of Lipid Membranes Using Coarse-Grained Molecular Dynamics. Mol. Simul. 2009, 35, 953–961. 10.1080/08927020902763839. DOI

Mayne C. G.; Arcario M. J.; Mahinthichaichan P.; Baylon J. L.; Vermaas J. V.; Navidpour L.; Wen P.-C.; Thangapandian S.; Tajkhorshid E. The Cellular Membrane as a Mediator for Small Molecule Interaction with Membrane Proteins. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2290–2304. 10.1016/j.bbamem.2016.04.016. PubMed DOI PMC

Dotson R. J.; Smith C. R.; Bueche K.; Angles G.; Pias S. C. Influence of Cholesterol on the Oxygen Permeability of Membranes: Insight from Atomistic Simulations. Biophys. J. 2017, 112, 2336–2347. 10.1016/j.bpj.2017.04.046. PubMed DOI PMC

Boron W. F.; Endeward V.; Gros G.; Musa-Aziz R.; Pohl P. Intrinsic CO2 Permeability of Cell Membranes and Potential Biological Relevance of CO2 Channels. ChemPhysChem 2011, 12, 1017–1019. 10.1002/cphc.201100034. PubMed DOI

Herrera M.; Garvin J. L. Aquaporins as Gas Channels. Pfluegers Arch. 2011, 462, 623–630. 10.1007/s00424-011-1002-x. PubMed DOI

Endeward V.; Arias-Hidalgo M.; Al-Samir S.; Gros G. CO2 Permeability of Biological Membranes and Role of CO2 Channels. Membranes 2017, 7, 61.10.3390/membranes7040061. PubMed DOI PMC

Yuan H.; Jameson C. J.; Murad S. Diffusion of Gases across Lipid Membranes with OmpA Channel: A Molecular Dynamics Study. Mol. Phys. 2010, 108, 1569–1581. 10.1080/00268976.2010.484396. DOI

Geyer R. R.; Musa-Aziz R.; Enkavi G.; Mahinthichaichan P.; Tajkhorshid E.; Boron W. F. Movement of NH3 through the Human Urea Transporter B: A New Gas Channel. Am. J. Physiol.-Ren. Physiol. 2013, 304, F1447–F1457. 10.1152/ajprenal.00609.2012. PubMed DOI PMC

Wang Y.; Tajkhorshid E. Nitric Oxide Conduction by the Brain Aquaporin AQP4. Proteins: Struct., Funct., Genet. 2009, 78, 661–670. 10.1002/prot.22595. PubMed DOI PMC

Wang Y.; Cohen J.; Boron W. F.; Schulten K.; Tajkhorshid E. Exploring Gas Permeability of Cellular Membranes and Membrane Channels with Molecular Dynamics. J. Struct. Biol. 2007, 157, 534–544. 10.1016/j.jsb.2006.11.008. PubMed DOI

Hub J. S.; Winkler F. K.; Merrick M.; de Groot B. L. Potentials of Mean Force and Permeabilities for Carbon Dioxide, Ammonia, and Water Flux across a Rhesus Protein Channel and Lipid Membranes. J. Am. Chem. Soc. 2010, 132, 13251–13263. 10.1021/ja102133x. PubMed DOI

Javanainen M.; Vattulainen I.; Monticelli L. On Atomistic Models for Molecular Oxygen. J. Phys. Chem. B 2017, 121, 518–528. 10.1021/acs.jpcb.6b11183. PubMed DOI

Plesnar E.; Szczelina R.; Subczynski W. K.; Pasenkiewicz-Gierula M. Is the Cholesterol Bilayer Domain a Barrier to Oxygen Transport into the Eye Lens?. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 434–441. 10.1016/j.bbamem.2017.10.020. PubMed DOI PMC

Subczynski W. K.; Hyde J. S.; Kusumi A. Oxygen Permeability of Phosphatidylcholine—Cholesterol Membranes. Proc. Natl. Acad. Sci. U. S. A. 1989, 86, 4474–4478. 10.1073/pnas.86.12.4474. PubMed DOI PMC

Wang H.; Ren X.; Meng F. Molecular Dynamics Simulation of Six β-Blocker Drugs Passing across POPC Bilayer. Mol. Simul. 2016, 42, 56–63. 10.1080/08927022.2015.1008470. DOI

Ghaemi Z.; Alberga D.; Carloni P.; Laio A.; Lattanzi G. Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations. J. Chem. Theory Comput. 2016, 12, 4093–4099. 10.1021/acs.jctc.5b01126. PubMed DOI

Li J.; Beuerman R. W.; Verma C. S. Molecular Insights into the Membrane Affinities of Model Hydrophobes. ACS Omega 2018, 3, 2498–2507. 10.1021/acsomega.7b01759. PubMed DOI PMC

Lopes D.; Jakobtorweihen S.; Nunes C.; Sarmento B.; Reis S. Shedding Light on the Puzzle of Drug-Membrane Interactions: Experimental Techniques and Molecular Dynamics Simulations. Prog. Lipid Res. 2017, 65, 24–44. 10.1016/j.plipres.2016.12.001. PubMed DOI

Yacoub T. J.; Reddy A. S.; Szleifer I. Structural Effects and Translocation of Doxorubicin in a DPPC/Chol Bilayer: The Role of Cholesterol. Biophys. J. 2011, 101, 378–385. 10.1016/j.bpj.2011.06.015. PubMed DOI PMC

Khajeh A.; Modarress H. Effect of Cholesterol on Behavior of 5-Fluorouracil (5-FU) in a DMPC Lipid Bilayer, a Molecular Dynamics Study. Biophys. Chem. 2014, 187–188, 43–50. 10.1016/j.bpc.2014.01.004. PubMed DOI

Khajeh A.; Modarress H. The Influence of Cholesterol on Interactions and Dynamics of Ibuprofen in a Lipid Bilayer. Biochim. Biophys. Acta, Biomembr. 2014, 1838, 2431–2438. 10.1016/j.bbamem.2014.05.029. PubMed DOI

Zhang L.; Bennett W. F. D.; Zheng T.; Ouyang P.-K.; Ouyang X.; Qiu X.; Luo A.; Karttunen M.; Chen P. Effect of Cholesterol on Cellular Uptake of Cancer Drugs Pirarubicin and Ellipticine. J. Phys. Chem. B 2016, 120, 3148–3156. 10.1021/acs.jpcb.5b12337. PubMed DOI

Lee C. T.; Comer J.; Herndon C.; Leung N.; Pavlova A.; Swift R. V.; Tung C.; Rowley C. N.; Amaro R. E.; Chipot C.; et al. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J. Chem. Inf. Model. 2016, 56, 721–733. 10.1021/acs.jcim.6b00022. PubMed DOI PMC

Ghaemi Z.; Minozzi M.; Carloni P.; Laio A. A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations. J. Phys. Chem. B 2012, 116, 8714–8721. 10.1021/jp301083h. PubMed DOI

Comer J.; Schulten K.; Chipot C. Calculation of Lipid-Bilayer Permeabilities Using an Average Force. J. Chem. Theory Comput. 2014, 10, 554–564. 10.1021/ct400925s. PubMed DOI

Nitschke N.; Atkovska K.; Hub J. S. Accelerating Potential of Mean Force Calculations for Lipid Membrane Permeation: System Size, Reaction Coordinate, Solute-Solute Distance, and Cutoffs. J. Chem. Phys. 2016, 145, 125101.10.1063/1.4963192. PubMed DOI

Votapka L. W.; Lee C. T.; Amaro R. E. Two Relations to Estimate Membrane Permeability Using Milestoning. J. Phys. Chem. B 2016, 120, 8606–8616. 10.1021/acs.jpcb.6b02814. PubMed DOI PMC

Dickson C. J.; Hornak V.; Pearlstein R. A.; Duca J. S. Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling. J. Am. Chem. Soc. 2017, 139, 442–452. 10.1021/jacs.6b11215. PubMed DOI

Kopelevich D. I. One-Dimensional Potential of Mean Force Underestimates Activation Barrier for Transport across Flexible Lipid Membranes. J. Chem. Phys. 2013, 139, 134906.10.1063/1.4823500. PubMed DOI

Neale C.; Madill C.; Rauscher S.; Pomès R. Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal. J. Chem. Theory Comput. 2013, 9, 3686–3703. 10.1021/ct301005b. PubMed DOI

Filipe H. A. L.; Javanainen M.; Salvador A.; Galvão A. M.; Vattulainen I.; Loura L. M. S.; Moreno M. J. Quantitative Assessment of Methods Used To Obtain Rate Constants from Molecular Dynamics Simulations—Translocation of Cholesterol across Lipid Bilayers. J. Chem. Theory Comput. 2018, 14, 3840–3848. 10.1021/acs.jctc.8b00150. PubMed DOI

LeVine M. V.; Cuendet M. A.; Khelashvili G.; Weinstein H. Allosteric Mechanisms of Molecular Machines at the Membrane: Transport by Sodium-Coupled Symporters. Chem. Rev. 2016, 116, 6552–6587. 10.1021/acs.chemrev.5b00627. PubMed DOI

Denning E. J.; Beckstein O. Influence of Lipids on Protein-Mediated Transmembrane Transport. Chem. Phys. Lipids 2013, 169, 57–71. 10.1016/j.chemphyslip.2013.02.007. PubMed DOI

Koshy C.; Ziegler C. Structural Insights into Functional Lipid–Protein Interactions in Secondary Transporters. Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 476–487. 10.1016/j.bbagen.2014.05.010. PubMed DOI

Chavent M.; Duncan A. L.; Sansom M. S. Molecular Dynamics Simulations of Membrane Proteins and Their Interactions: From Nanoscale to Mesoscale. Curr. Opin. Struct. Biol. 2016, 40, 8–16. 10.1016/j.sbi.2016.06.007. PubMed DOI PMC

Grouleff J.; Irudayam S. J.; Skeby K. K.; Schiøtt B. The Influence of Cholesterol on Membrane Protein Structure, Function, and Dynamics Studied by Molecular Dynamics Simulations. Biochim. Biophys. Acta, Biomembr. 2015, 1848, 1783–1795. 10.1016/j.bbamem.2015.03.029. PubMed DOI

Wang Y.; Shaikh S. A.; Tajkhorshid E. Exploring Transmembrane Diffusion Pathways With Molecular Dynamics. Physiology 2010, 25, 142–154. 10.1152/physiol.00046.2009. PubMed DOI PMC

Ozu M.; Alvarez H. A.; McCarthy A. N.; Grigera J. R.; Chara O. Molecular Dynamics of Water in the Neighborhood of Aquaporins. Eur. Biophys. J. 2013, 42, 223–239. 10.1007/s00249-012-0880-y. PubMed DOI

Hub J. S.; Grubmüller H.; de Groot B. L.. Dynamics and Energetics of Permeation Through Aquaporins. What Do We Learn from Molecular Dynamics Simulations? In Aquaporins; Beitz E., Hofmann F., Eds.; Springer Berlin Heidelberg: Berlin, Heidelberg, 2009; Vol. 190, pp 57–76, 10.1007/978-3-540-79885-9_3. PubMed DOI

de Groot B. L.; Grubmüller H. The Dynamics and Energetics of Water Permeation and Proton Exclusion in Aquaporins. Curr. Opin. Struct. Biol. 2005, 15, 176–183. 10.1016/j.sbi.2005.02.003. PubMed DOI

Sachdeva R.; Singh B. Insights into Structural Mechanisms of Gating Induced Regulation of Aquaporins. Prog. Biophys. Mol. Biol. 2014, 114, 69–79. 10.1016/j.pbiomolbio.2014.01.002. PubMed DOI

Mangiatordi G.; Alberga D.; Trisciuzzi D.; Lattanzi G.; Nicolotti O. Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future. Int. J. Mol. Sci. 2016, 17, 1119.10.3390/ijms17071119. PubMed DOI PMC

Kosinska Eriksson U.; Fischer G.; Friemann R.; Enkavi G.; Tajkhorshid E.; Neutze R. Subangstrom Resolution X-Ray Structure Details Aquaporin-Water Interactions. Science 2013, 340, 1346–1349. 10.1126/science.1234306. PubMed DOI PMC

Tajkhorshid E. Control of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning. Science 2002, 296, 525–530. 10.1126/science.1067778. PubMed DOI

Jensen M. Ø.; Tajkhorshid E.; Schulten K. The Mechanism of Glycerol Conduction in Aquaglyceroporins. Structure 2001, 9, 1083–1093. 10.1016/S0969-2126(01)00668-2. PubMed DOI

Savage D. F.; O’Connell J. D.; Miercke L. J. W.; Finer-Moore J.; Stroud R. M. Structural Context Shapes the Aquaporin Selectivity Filter. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 17164–17169. 10.1073/pnas.1009864107. PubMed DOI PMC

Oliva R.; Calamita G.; Thornton J. M.; Pellegrini-Calace M. Electrostatics of Aquaporin and Aquaglyceroporin Channels Correlates with Their Transport Selectivity. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 4135–4140. 10.1073/pnas.0910632107. PubMed DOI PMC

Padhi S.; Priyakumar U. D. Microsecond Simulation of Human Aquaporin 2 Reveals Structural Determinants of Water Permeability and Selectivity. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 10–16. 10.1016/j.bbamem.2016.10.011. PubMed DOI

de Groot B. L.; Grubmüller H. Water Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF. Science 2001, 294, 2353–2357. 10.1126/science.1062459. PubMed DOI

Martínez-Ballesta M. d. C.; Carvajal M. Mutual Interactions between Aquaporins and Membrane Components. Front. Plant Sci. 2016, 7, 1322.10.3389/fpls.2016.01322. PubMed DOI PMC

Stansfeld P. J.; Jefferys E. E.; Sansom M. S. P. Multiscale Simulations Reveal Conserved Patterns of Lipid Interactions with Aquaporins. Structure 2013, 21, 810–819. 10.1016/j.str.2013.03.005. PubMed DOI PMC

Briones R.; Aponte-Santamaría C.; de Groot B. L. Localization and Ordering of Lipids Around Aquaporin-0: Protein and Lipid Mobility Effects. Front. Physiol. 2017, 8, 124.10.3389/fphys.2017.00124. PubMed DOI PMC

Haswell E. S.; Phillips R.; Rees D. C. Mechanosensitive Channels: What Can They Do and How Do They Do It?. Structure 2011, 19, 1356–1369. 10.1016/j.str.2011.09.005. PubMed DOI PMC

Jeon J.; Voth G. A. Gating of the Mechanosensitive Channel Protein MscL: The Interplay of Membrane and Protein. Biophys. J. 2008, 94, 3497–3511. 10.1529/biophysj.107.109850. PubMed DOI PMC

Meyer G. R.; Gullingsrud J.; Schulten K.; Martinac B. Molecular Dynamics Study of MscL Interactions with a Curved Lipid Bilayer. Biophys. J. 2006, 91, 1630–1637. 10.1529/biophysj.106.080721. PubMed DOI PMC

Gullingsrud J.; Kosztin D.; Schulten K. Structural Determinants of MscL Gating Studied by Molecular Dynamics Simulations. Biophys. J. 2001, 80, 2074–2081. 10.1016/S0006-3495(01)76181-4. PubMed DOI PMC

Khalili-Araghi F.; Gumbart J.; Wen P.-C.; Sotomayor M.; Tajkhorshid E.; Schulten K. Molecular Dynamics Simulations of Membrane Channels and Transporters. Curr. Opin. Struct. Biol. 2009, 19, 128–137. 10.1016/j.sbi.2009.02.011. PubMed DOI PMC

Gullingsrud J.; Schulten K. Lipid Bilayer Pressure Profiles and Mechanosensitive Channel Gating. Biophys. J. 2004, 86, 3496–3509. 10.1529/biophysj.103.034322. PubMed DOI PMC

Samuli Ollila O. H.; Louhivuori M.; Marrink S. J.; Vattulainen I. Protein Shape Change Has a Major Effect on the Gating Energy of a Mechanosensitive Channel. Biophys. J. 2011, 100, 1651–1659. 10.1016/j.bpj.2011.02.027. PubMed DOI PMC

Louhivuori M.; Risselada H. J.; van der Giessen E.; Marrink S. J. Release of Content through Mechano-Sensitive Gates in Pressurized Liposomes. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 19856–19860. 10.1073/pnas.1001316107. PubMed DOI PMC

Mukherjee N.; Jose M. D.; Birkner J. P.; Walko M.; Ingólfsson H. I.; Dimitrova A.; Arnarez C.; Marrink S. J.; Koçer A. The Activation Mode of the Mechanosensitive Ion Channel, MscL, by Lysophosphatidylcholine Differs from Tension-Induced Gating. FASEB J. 2014, 28, 4292–4302. 10.1096/fj.14-251579. PubMed DOI PMC

Elmore D. E.; Dougherty D. A. Investigating Lipid Composition Effects on the Mechanosensitive Channel of Large Conductance (MscL) Using Molecular Dynamics Simulations. Biophys. J. 2003, 85, 1512–1524. 10.1016/S0006-3495(03)74584-6. PubMed DOI PMC

Vanegas J. M.; Arroyo M. Force Transduction and Lipid Binding in MscL: A Continuum-Molecular Approach. PLoS One 2014, 9, e113947.10.1371/journal.pone.0113947. PubMed DOI PMC

Sawada Y.; Murase M.; Sokabe M. The Gating Mechanism of the Bacterial Mechanosensitive Channel MscL Revealed by Molecular Dynamics Simulations: From Tension Sensing to Channel Opening. Channels 2012, 6, 317–331. 10.4161/chan.21895. PubMed DOI PMC

Bavi N.; Cortes D. M.; Cox C. D.; Rohde P. R.; Liu W.; Deitmer J. W.; Bavi O.; Strop P.; Hill A. P.; Rees D.; et al. The Role of MscL Amphipathic N Terminus Indicates a Blueprint for Bilayer-Mediated Gating of Mechanosensitive Channels. Nat. Commun. 2016, 7, 11984.10.1038/ncomms11984. PubMed DOI PMC

Vasquez V.; Sotomayor M.; Cordero-Morales J.; Schulten K.; Perozo E. A Structural Mechanism for MscS Gating in Lipid Bilayers. Science 2008, 321, 1210–1214. 10.1126/science.1159674. PubMed DOI PMC

Sotomayor M.; Vásquez V.; Perozo E.; Schulten K. Ion Conduction through MscS as Determined by Electrophysiology and Simulation. Biophys. J. 2007, 92, 886–902. 10.1529/biophysj.106.095232. PubMed DOI PMC

Sotomayor M.; Schulten K. Molecular Dynamics Study of Gating in the Mechanosensitive Channel of Small Conductance MscS. Biophys. J. 2004, 87, 3050–3065. 10.1529/biophysj.104.046045. PubMed DOI PMC

Sotomayor M.; van der Straaten T. A.; Ravaioli U.; Schulten K. Electrostatic Properties of the Mechanosensitive Channel of Small Conductance MscS. Biophys. J. 2006, 90, 3496–3510. 10.1529/biophysj.105.080069. PubMed DOI PMC

Malcolm H. R.; Heo Y.-Y.; Elmore D. E.; Maurer J. A. Defining the Role of the Tension Sensor in the Mechanosensitive Channel of Small Conductance. Biophys. J. 2011, 101, 345–352. 10.1016/j.bpj.2011.05.058. PubMed DOI PMC

Tombola F.; Pathak M. M.; Isacoff E. Y. How Does Voltage Open an Ion Channel?. Annu. Rev. Cell Dev. Biol. 2006, 22, 23–52. 10.1146/annurev.cellbio.21.020404.145837. PubMed DOI

Yu F. H.; Catterall W. A. The VGL-Chanome: A Protein Superfamily Specialized for Electrical Signaling and Ionic Homeostasis. Sci. Signaling 2004, 2004, re15–re15. 10.1126/stke.2532004re15. PubMed DOI

Chen L.; Zhang Q.; Qiu Y.; Li Z.; Chen Z.; Jiang H.; Li Y.; Yang H. Migration of PIP2 Lipids on Voltage-Gated Potassium Channel Surface Influences Channel Deactivation. Sci. Rep. 2015, 5, 15079.10.1038/srep15079. PubMed DOI PMC

Yazdi S.; Stein M.; Elinder F.; Andersson M.; Lindahl E. The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel. PLoS Comput. Biol. 2016, 12, e1004704.10.1371/journal.pcbi.1004704. PubMed DOI PMC

Ottosson N. E.; Silverå Ejneby M.; Wu X.; Yazdi S.; Konradsson P.; Lindahl E.; Elinder F. A Drug Pocket at the Lipid Bilayer–Potassium Channel Interface. Sci. Adv. 2017, 3, e1701099.10.1126/sciadv.1701099. PubMed DOI PMC

MacKinnon R. Potassium Channels. FEBS Lett. 2003, 555, 62–65. 10.1016/S0014-5793(03)01104-9. PubMed DOI

MacKinnon R.; Cohen S. L.; Kuo A.; Lee A.; Chait B. T. Structural Conservation in Prokaryotic and Eukaryotic Potassium Channels. Science 1998, 280, 106–109. 10.1126/science.280.5360.106. PubMed DOI

Doyle D. A.; Cabral J. M.; Pfuetzner R. A.; Kuo A.; Gulbis J. M.; Cohen S. L.; Chait B. T.; MacKinnon R. The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity. Science 1998, 280, 69–77. 10.1126/science.280.5360.69. PubMed DOI

Bucher D.; Rothlisberger U. Molecular Simulations of Ion Channels: A Quantum Chemist’s Perspective. J. Gen. Physiol. 2010, 135, 549–554. 10.1085/jgp.201010404. PubMed DOI PMC

Musgaard M.; Paramo T.; Domicevica L.; Andersen O. J.; Biggin P. C. Insights into Channel Dysfunction from Modelling and Molecular Dynamics Simulations. Neuropharmacology 2018, 132, 20–30. 10.1016/j.neuropharm.2017.06.030. PubMed DOI

de Groot B. L.; Koepfer D.; Song C.; Gruene T.; Sheldrick G. M.; Zachariae U. The Molecular Dynamics of Ion Channel Permeation, Selectivity and Gating. Biophys. J. 2016, 110, 9a.10.1016/j.bpj.2015.11.101. DOI

Delemotte L.; Klein M.; TAREK M. Molecular Dynamics Simulations of Voltage-Gated Cation Channels: Insights on Voltage-Sensor Domain Function and Modulation. Front. Pharmacol. 2012, 3, 97.10.3389/fphar.2012.00097. PubMed DOI PMC

Hénin J.; Salari R.; Murlidaran S.; Brannigan G. A Predicted Binding Site for Cholesterol on the GABAA Receptor. Biophys. J. 2014, 106, 1938–1949. 10.1016/j.bpj.2014.03.024. PubMed DOI PMC

Jardetzky O. Simple Allosteric Model for Membrane Pumps. Nature 1966, 211, 969–970. 10.1038/211969a0. PubMed DOI

Drew D.; Boudker O. Shared Molecular Mechanisms of Membrane Transporters. Annu. Rev. Biochem. 2016, 85, 543–572. 10.1146/annurev-biochem-060815-014520. PubMed DOI

Ryan R. M.; Vandenberg R. J. Elevating the Alternating-Access Model. Nat. Struct. Mol. Biol. 2016, 23, 187–189. 10.1038/nsmb.3179. PubMed DOI

Li J.; Shaikh S. A.; Enkavi G.; Wen P.-C.; Huang Z.; Tajkhorshid E. Transient Formation of Water-Conducting States in Membrane Transporters. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 7696–7701. 10.1073/pnas.1218986110. PubMed DOI PMC

Eicher T.; Seeger M. A.; Anselmi C.; Zhou W.; Brandstätter L.; Verrey F.; Diederichs K.; Faraldo-Gómez J. D.; Pos K. M. Coupling of Remote Alternating-Access Transport Mechanisms for Protons and Substrates in the Multidrug Efflux Pump AcrB. eLife 2014, 3, e03145.10.7554/eLife.03145. PubMed DOI PMC

Sasseville L. J.; Cuervo J. E.; Lapointe J.-Y.; Noskov S. Y. The Structural Pathway for Water Permeation through Sodium-Glucose Cotransporters. Biophys. J. 2011, 101, 1887–1895. 10.1016/j.bpj.2011.09.019. PubMed DOI PMC

Choe S.; Rosenberg J. M.; Abramson J.; Wright E. M.; Grabe M. Water Permeation through the Sodium-Dependent Galactose Cotransporter VSGLT. Biophys. J. 2010, 99, L56–L58. 10.1016/j.bpj.2010.08.055. PubMed DOI PMC

McGreevy R.; Singharoy A.; Li Q.; Zhang J.; Xu D.; Perozo E.; Schulten K. XMDFF: Molecular Dynamics Flexible Fitting of Low-Resolution X-Ray Structures. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2014, 70, 2344–2355. 10.1107/S1399004714013856. PubMed DOI PMC

Trabuco L. G.; Villa E.; Mitra K.; Frank J.; Schulten K. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics. Structure 2008, 16, 673–683. 10.1016/j.str.2008.03.005. PubMed DOI PMC

Vermaas J. V.; Trebesch N.; Mayne C. G.; Thangapandian S.; Shekhar M.; Mahinthichaichan P.; Baylon J. L.; Jiang T.; Wang Y.; Muller M. P.; et al.Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. Methods in Enzymology; Elsevier, 2016; Vol. 578, pp 373–428, 10.1016/bs.mie.2016.05.042. PubMed DOI PMC

Coudray N.; Seyler S. L.; Lasala R.; Zhang Z.; Clark K. M.; Dumont M. E.; Rohou A.; Beckstein O.; Stokes D. L. Structure of the SLC4 Transporter Bor1p in an Inward-Facing Conformation: Structure of the SLC4 Transporter Bor1p. Protein Sci. 2017, 26, 130–145. 10.1002/pro.3061. PubMed DOI PMC

Coudray N.; Valvo S.; Hu M.; Lasala R.; Kim C.; Vink M.; Zhou M.; Provasi D.; Filizola M.; Tao J.; et al. Inward-Facing Conformation of the Zinc Transporter YiiP Revealed by Cryoelectron Microscopy. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 2140–2145. 10.1073/pnas.1215455110. PubMed DOI PMC

Bozzi A. T.; Bane L. B.; Weihofen W. A.; Singharoy A.; Guillen E. R.; Ploegh H. L.; Schulten K.; Gaudet R. Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter. Structure 2016, 24, 2102–2114. 10.1016/j.str.2016.09.017. PubMed DOI PMC

López C. A.; Travers T.; Pos K. M.; Zgurskaya H. I.; Gnanakaran S. Dynamics of Intact MexAB-OprM Efflux Pump: Focusing on the MexA-OprM Interface. Sci. Rep. 2017, 7, 16521.10.1038/s41598-017-16497-w. PubMed DOI PMC

Diskowski M.; Mehdipour A. R.; Wunnicke D.; Mills D. J.; Mikusevic V.; Bärland N.; Hoffmann J.; Morgner N.; Steinhoff H.-J.; Hummer G.; et al. Helical Jackknives Control the Gates of the Double-Pore K+ Uptake System KtrAB. eLife 2017, 6, e24303.10.7554/eLife.24303. PubMed DOI PMC

Zhao C.; Noskov S. Y. The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters. PLoS Comput. Biol. 2013, 9, e1003296.10.1371/journal.pcbi.1003296. PubMed DOI PMC

Thomas J. R.; Gedeon P. C.; Grant B. J.; Madura J. D. LeuT Conformational Sampling Utilizing Accelerated Molecular Dynamics and Principal Component Analysis. Biophys. J. 2012, 103, L1–L3. 10.1016/j.bpj.2012.05.002. PubMed DOI PMC

Moradi M.; Enkavi G.; Tajkhorshid E. Atomic-Level Characterization of Transport Cycle Thermodynamics in the Glycerol-3-Phosphate:Phosphate Antiporter. Nat. Commun. 2015, 6, 8393.10.1038/ncomms9393. PubMed DOI PMC

Mori T.; Miyashita N.; Im W.; Feig M.; Sugita Y. Molecular Dynamics Simulations of Biological Membranes and Membrane Proteins Using Enhanced Conformational Sampling Algorithms. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 1635–1651. 10.1016/j.bbamem.2015.12.032. PubMed DOI PMC

Harpole T. J.; Delemotte L. Conformational Landscapes of Membrane Proteins Delineated by Enhanced Sampling Molecular Dynamics Simulations. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 909–926. 10.1016/j.bbamem.2017.10.033. PubMed DOI

Latorraca N. R.; Fastman N. M.; Venkatakrishnan A. J.; Frommer W. B.; Dror R. O.; Feng L. Mechanism of Substrate Translocation in an Alternating Access Transporter. Cell 2017, 169, 96–107.e12. 10.1016/j.cell.2017.03.010. PubMed DOI PMC

Stansfeld P. J.; Sansom M. S. P. Molecular Simulation Approaches to Membrane Proteins. Structure 2011, 19, 1562–1572. 10.1016/j.str.2011.10.002. PubMed DOI

Shaikh S. A.; Li J.; Enkavi G.; Wen P.-C.; Huang Z.; Tajkhorshid E. Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations. Biochemistry 2013, 52, 569–587. 10.1021/bi301086x. PubMed DOI PMC

Autzen H. E.; Siuda I.; Sonntag Y.; Nissen P.; Møller J. V.; Thøgersen L. Regulation of the Ca2+-ATPase by Cholesterol: A Specific or Non-Specific Effect?. Mol. Membr. Biol. 2015, 32, 75–87. 10.3109/09687688.2015.1073382. PubMed DOI

Manepalli S.; Surratt C. K.; Madura J. D.; Nolan T. L. Monoamine Transporter Structure, Function, Dynamics, and Drug Discovery: A Computational Perspective. AAPS J. 2012, 14, 820–831. 10.1208/s12248-012-9391-0. PubMed DOI PMC

Loland C. J. The Use of LeuT as a Model in Elucidating Binding Sites for Substrates and Inhibitors in Neurotransmitter Transporters. Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 500–510. 10.1016/j.bbagen.2014.04.011. PubMed DOI

Shi Y. Common Folds and Transport Mechanisms of Secondary Active Transporters. Annu. Rev. Biophys. 2013, 42, 51–72. 10.1146/annurev-biophys-083012-130429. PubMed DOI

Sohail A.; Jayaraman K.; Venkatesan S.; Gotfryd K.; Daerr M.; Gether U.; Loland C. J.; Wanner K. T.; Freissmuth M.; Sitte H. H.; et al. The Environment Shapes the Inner Vestibule of LeuT. PLoS Comput. Biol. 2016, 12, e1005197.10.1371/journal.pcbi.1005197. PubMed DOI PMC

Mondal S.; Khelashvili G.; Shi L.; Weinstein H. The Cost of Living in the Membrane: A Case Study of Hydrophobic Mismatch for the Multi-Segment Protein LeuT. Chem. Phys. Lipids 2013, 169, 27–38. 10.1016/j.chemphyslip.2013.01.006. PubMed DOI PMC

Mondal S.; Khelashvili G.; Weinstein H. Not Just an Oil Slick: How the Energetics of Protein-Membrane Interactions Impacts the Function and Organization of Transmembrane Proteins. Biophys. J. 2014, 106, 2305–2316. 10.1016/j.bpj.2014.04.032. PubMed DOI PMC

Gur M.; Zomot E.; Cheng M. H.; Bahar I. Energy Landscape of LeuT from Molecular Simulations. J. Chem. Phys. 2015, 143, 243134.10.1063/1.4936133. PubMed DOI PMC

Cheng M. H.; Bahar I. Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-Terminal Segment in Regulating Transport Cycle. PLoS Comput. Biol. 2014, 10, e1003879.10.1371/journal.pcbi.1003879. PubMed DOI PMC

Shi L.; Quick M.; Zhao Y.; Weinstein H.; Javitch J. A. The Mechanism of a Neurotransmitter:Sodium Symporter—Inward Release of Na+ and Substrate Is Triggered by Substrate in a Second Binding Site. Mol. Cell 2008, 30, 667–677. 10.1016/j.molcel.2008.05.008. PubMed DOI PMC

Zeppelin T.; Ladefoged L. K.; Sinning S.; Periole X.; Schiøtt B. A Direct Interaction of Cholesterol with the Dopamine Transporter Prevents Its Out-to-Inward Transition. PLoS Comput. Biol. 2018, 14, e1005907.10.1371/journal.pcbi.1005907. PubMed DOI PMC

Penmatsa A.; Wang K. H.; Gouaux E. X-Ray Structure of Dopamine Transporter Elucidates Antidepressant Mechanism. Nature 2013, 503, 85–90. 10.1038/nature12533. PubMed DOI PMC

Wang K. H.; Penmatsa A.; Gouaux E. Neurotransmitter and Psychostimulant Recognition by the Dopamine Transporter. Nature 2015, 521, 322–327. 10.1038/nature14431. PubMed DOI PMC

Coleman J. A.; Green E. M.; Gouaux E. X-Ray Structures and Mechanism of the Human Serotonin Transporter. Nature 2016, 532, 334–339. 10.1038/nature17629. PubMed DOI PMC

Ferraro M.; Masetti M.; Recanatini M.; Cavalli A.; Bottegoni G. Mapping Cholesterol Interaction Sites on Serotonin Transporter through Coarse-Grained Molecular Dynamics. PLoS One 2016, 11, e0166196.10.1371/journal.pone.0166196. PubMed DOI PMC

Laursen L.; Severinsen K.; Kristensen K. B.; Periole X.; Overby M.; Müller H. K.; Schiøtt B.; Sinning S. Cholesterol Binding to a Conserved Site Modulates the Conformation, Pharmacology, and Transport Kinetics of the Human Serotonin Transporter. J. Biol. Chem. 2018, 293, 3510–3523. 10.1074/jbc.M117.809046. PubMed DOI PMC

Khelashvili G.; Doktorova M.; Sahai M. A.; Johner N.; Shi L.; Weinstein H. Computational Modeling of the N-Terminus of the Human Dopamine Transporter and Its Interaction with PIP2-Containing Membranes: Modeling of DAT N-Terminus/PIP2 Interactions. Proteins: Struct., Funct., Genet. 2015, 83, 952–969. 10.1002/prot.24792. PubMed DOI PMC

Khelashvili G.; Stanley N.; Sahai M. A.; Medina J.; LeVine M. V.; Shi L.; De Fabritiis G.; Weinstein H. Spontaneous Inward Opening of the Dopamine Transporter Is Triggered by PIP2-Regulated Dynamics of the N-Terminus. ACS Chem. Neurosci. 2015, 6, 1825–1837. 10.1021/acschemneuro.5b00179. PubMed DOI PMC

Cheng M. H.; Garcia-Olivares J.; Wasserman S.; DiPietro J.; Bahar I. Allosteric Modulation of Human Dopamine Transporter Activity under Conditions Promoting Its Dimerization. J. Biol. Chem. 2017, 292, 12471–12482. 10.1074/jbc.M116.763565. PubMed DOI PMC

Periole X.; Zeppelin T.; Schiøtt B. Dimer Interface of the Human Serotonin Transporter and Effect of the Membrane Composition. Sci. Rep. 2018, 8, 5080.10.1038/s41598-018-22912-7. PubMed DOI PMC

Anderluh A.; Hofmaier T.; Klotzsch E.; Kudlacek O.; Stockner T.; Sitte H. H.; Schütz G. J. Direct PIP2 Binding Mediates Stable Oligomer Formation of the Serotonin Transporter. Nat. Commun. 2017, 8, 14089.10.1038/ncomms14089. PubMed DOI PMC

Gupta K.; Donlan J. A. C.; Hopper J. T. S.; Uzdavinys P.; Landreh M.; Struwe W. B.; Drew D.; Baldwin A. J.; Stansfeld P. J.; Robinson C. V. The Role of Interfacial Lipids in Stabilizing Membrane Protein Oligomers. Nature 2017, 541, 421–424. 10.1038/nature20820. PubMed DOI PMC

Gur M.; Cheng M. H.; Zomot E.; Bahar I. Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters. J. Phys. Chem. B 2017, 121, 3657–3666. 10.1021/acs.jpcb.6b09876. PubMed DOI PMC

Cheng X.; Kim J.-K.; Kim Y.; Bowie J. U.; Im W. Molecular Dynamics Simulation Strategies for Protein–Micelle Complexes. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 1566–1572. 10.1016/j.bbamem.2015.12.012. PubMed DOI PMC

Khelashvili G.; LeVine M. V.; Shi L.; Quick M.; Javitch J. A.; Weinstein H. The Membrane Protein LeuT in Micellar Systems: Aggregation Dynamics and Detergent Binding to the S2 Site. J. Am. Chem. Soc. 2013, 135, 14266–14275. 10.1021/ja405984v. PubMed DOI PMC

LeVine M. V.; Khelashvili G.; Shi L.; Quick M.; Javitch J. A.; Weinstein H. Role of Annular Lipids in the Functional Properties of Leucine Transporter LeuT Proteomicelles. Biochemistry 2016, 55, 850–859. 10.1021/acs.biochem.5b01268. PubMed DOI PMC

Adhikary S.; Deredge D. J.; Nagarajan A.; Forrest L. R.; Wintrode P. L.; Singh S. K. Conformational Dynamics of a Neurotransmitter:Sodium Symporter in a Lipid Bilayer. Proc. Natl. Acad. Sci. U. S. A. 2017, 114, E1786–E1795. 10.1073/pnas.1613293114. PubMed DOI PMC

Lezon T. R.; Bahar I. Constraints Imposed by the Membrane Selectively Guide the Alternating Access Dynamics of the Glutamate Transporter GltPh. Biophys. J. 2012, 102, 1331–1340. 10.1016/j.bpj.2012.02.028. PubMed DOI PMC

Akyuz N.; Georgieva E. R.; Zhou Z.; Stolzenberg S.; Cuendet M. A.; Khelashvili G.; Altman R. B.; Terry D. S.; Freed J. H.; Weinstein H.; et al. Transport Domain Unlocking Sets the Uptake Rate of an Aspartate Transporter. Nature 2015, 518, 68–73. 10.1038/nature14158. PubMed DOI PMC

Montigny C.; Lyons J.; Champeil P.; Nissen P.; Lenoir G. On the Molecular Mechanism of Flippase- and Scramblase-Mediated Phospholipid Transport. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2016, 1861, 767–783. 10.1016/j.bbalip.2015.12.020. PubMed DOI

Pomorski T.; Menon A. K. Lipid Flippases and Their Biological Functions. Cell. Mol. Life Sci. 2006, 63, 2908–2921. 10.1007/s00018-006-6167-7. PubMed DOI PMC

Neumann J.; Rose-Sperling D.; Hellmich U. A. Diverse Relations between ABC Transporters and Lipids: An Overview. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 605–618. 10.1016/j.bbamem.2016.09.023. PubMed DOI

Furuta T.; Yamaguchi T.; Kato H.; Sakurai M. Analysis of the Structural and Functional Roles of Coupling Helices in the ATP-Binding Cassette Transporter MsbA through Enzyme Assays and Molecular Dynamics Simulations. Biochemistry 2014, 53, 4261–4272. 10.1021/bi500255j. PubMed DOI

Moradi M.; Tajkhorshid E. Mechanistic Picture for Conformational Transition of a Membrane Transporter at Atomic Resolution. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 18916–18921. 10.1073/pnas.1313202110. PubMed DOI PMC

Haubertin D. Y.; Madaoui H.; Sanson A.; Guérois R.; Orlowski S. Molecular Dynamics Simulations of E. Coli MsbA Transmembrane Domain: Formation of a Semipore Structure. Biophys. J. 2006, 91, 2517–2531. 10.1529/biophysj.106.084020. PubMed DOI PMC

Ward A. B.; Guvench O.; Hills R. D. Coarse Grain Lipid-Protein Molecular Interactions and Diffusion with MsbA Flippase. Proteins: Struct., Funct., Genet. 2012, 80, 2178–2190. 10.1002/prot.24108. PubMed DOI

Bechara C.; Nöll A.; Morgner N.; Degiacomi M. T.; Tampé R.; Robinson C. V. A Subset of Annular Lipids Is Linked to the Flippase Activity of an ABC Transporter. Nat. Chem. 2015, 7, 255–262. 10.1038/nchem.2172. PubMed DOI

Sharom F. Complex Interplay between the P-Glycoprotein Multidrug Efflux Pump and the Membrane: Its Role in Modulating Protein Function. Front. Oncol. 2014, 4, 41.10.3389/fonc.2014.00041. PubMed DOI PMC

Domicevica L.; Koldsø H.; Biggin P. C. Multiscale Molecular Dynamics Simulations of Lipid Interactions with P-Glycoprotein in a Complex Membrane. J. Mol. Graphics Modell. 2018, 80, 147–156. 10.1016/j.jmgm.2017.12.022. PubMed DOI

Barreto-Ojeda E.; Corradi V.; Gu R.-X.; Tieleman D. P. Coarse-Grained Molecular Dynamics Simulations Reveal Lipid Access Pathways in P-Glycoprotein. J. Gen. Physiol. 2018, 150, 417–429. 10.1085/jgp.201711907. PubMed DOI PMC

Morra G.; Razavi A. M.; Pandey K.; Weinstein H.; Menon A. K.; Khelashvili G. Mechanisms of Lipid Scrambling by the G Protein-Coupled Receptor Opsin. Structure 2018, 26, 356–367.e3. 10.1016/j.str.2017.11.020. PubMed DOI PMC

Nieminen T. A Study of Rhodopsin as a Potential Phospholipid Scramblase. Master’s thesis; Tampere University of Technology: Tampere, Finland, 2012.

Manna M.; Nieminen T.; Vattulainen I.. Rhodopsin as a Potential Phospholipid Scramblase. 2019, Manuscript in preparation.

Verchère A.; Ou W.-L.; Ploier B.; Morizumi T.; Goren M. A.; Bütikofer P.; Ernst O. P.; Khelashvili G.; Menon A. K. Light-Independent Phospholipid Scramblase Activity of Bacteriorhodopsin from Halobacterium Salinarum. Sci. Rep. 2017, 7, 9522.10.1038/s41598-017-09835-5. PubMed DOI PMC

Sapay N.; Bennett W. F. D.; Tieleman D. P. Molecular Simulations of Lipid Flip-Flop in the Presence of Model Transmembrane Helices. Biochemistry 2010, 49, 7665–7673. 10.1021/bi100878q. PubMed DOI

Wong L. H.; Čopič A.; Levine T. P. Advances on the Transfer of Lipids by Lipid Transfer Proteins. Trends Biochem. Sci. 2017, 42, 516–530. 10.1016/j.tibs.2017.05.001. PubMed DOI PMC

Grabon A.; Orłowski A.; Tripathi A.; Vuorio J.; Javanainen M.; Róg T.; Lönnfors M.; McDermott M. I.; Siebert G.; Somerharju P.; et al. Dynamics and Energetics of the Mammalian Phosphatidylinositol Transfer Protein Phospholipid Exchange Cycle. J. Biol. Chem. 2017, 292, 14438–14455. 10.1074/jbc.M117.791467. PubMed DOI PMC

Enkavi G.; Mikkolainen H.; Güngör B.; Ikonen E.; Vattulainen I. Concerted Regulation of NPC2 Binding to Endosomal/Lysosomal Membranes by Bis(Monoacylglycero)Phosphate and Sphingomyelin. PLoS Comput. Biol. 2017, 13, e1005831.10.1371/journal.pcbi.1005831. PubMed DOI PMC

Subramanian K.; Balch W. E. NPC1/NPC2 Function as a Tag Team Duo to Mobilize Cholesterol. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 15223–15224. 10.1073/pnas.0808256105. PubMed DOI PMC

Estiu G.; Khatri N.; Wiest O. Computational Studies of the Cholesterol Transport between NPC2 and the N-Terminal Domain of NPC1 (NPC1(NTD)). Biochemistry 2013, 52, 6879–6891. 10.1021/bi4005478. PubMed DOI

Gong X.; Qian H.; Zhou X.; Wu J.; Wan T.; Cao P.; Huang W.; Zhao X.; Wang X.; Wang P.; et al. Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection. Cell 2016, 165, 1467–1478. 10.1016/j.cell.2016.05.022. PubMed DOI PMC

Li X.; Lu F.; Trinh M. N.; Schmiege P.; Seemann J.; Wang J.; Blobel G. 3.3 Å Structure of Niemann–Pick C1 Protein Reveals Insights into the Function of the C-Terminal Luminal Domain in Cholesterol Transport. Proc. Natl. Acad. Sci. U. S. A. 2017, 114, 9116–9121. 10.1073/pnas.1711716114. PubMed DOI PMC

Li X.; Saha P.; Li J.; Blobel G.; Pfeffer S. R. Clues to the Mechanism of Cholesterol Transfer from the Structure of NPC1Middle Lumenal Domain Bound to NPC2. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 10079–10084. 10.1073/pnas.1611956113. PubMed DOI PMC

Cooper G. M.; Hausman R. E. The Cell: A Molecular Approach. Yale J. Biol. Med. 2014, 87, 603–604.

Zhang X.; Rebane A. A.; Ma L.; Li F.; Jiao J.; Qu H.; Pincet F.; Rothman J. E.; Zhang Y. Stability, Folding Dynamics, and Long-Range Conformational Transition of the Synaptic t-SNARE Complex. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, E8031–E8040. 10.1073/pnas.1605748113. PubMed DOI PMC

Chernomordik L. V.; Zimmerberg J.; Kozlov M. M. Membranes of the World Unite!. J. Cell Biol. 2006, 175, 201–207. 10.1083/jcb.200607083. PubMed DOI PMC

Risselada H. J.; Grubmüller H. How SNARE Molecules Mediate Membrane Fusion: Recent Insights from Molecular Simulations. Curr. Opin. Struct. Biol. 2012, 22, 187–196. 10.1016/j.sbi.2012.01.007. PubMed DOI

Gardner J. M.; Abrams C. F. Lipid Flip-Flop vs. Lateral Diffusion in the Relaxation of Hemifusion Diaphragms. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 1452–1459. 10.1016/j.bbamem.2018.04.007. PubMed DOI

Cooke I. R.; Kremer K.; Deserno M. Tunable Generic Model for Fluid Bilayer Membranes. Phys. Rev. E 2005, 72, 011506.10.1103/PhysRevE.72.011506. PubMed DOI

Risselada H. J.; Smirnova Y.; Grubmüller H. Free Energy Landscape of Rim-Pore Expansion in Membrane Fusion. Biophys. J. 2014, 107, 2287–2295. 10.1016/j.bpj.2014.08.022. PubMed DOI PMC

Yoo J.; Jackson M. B.; Cui Q. A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores. Biophys. J. 2013, 104, 841–852. 10.1016/j.bpj.2012.12.043. PubMed DOI PMC

Bao H.; Goldschen-Ohm M.; Jeggle P.; Chanda B.; Edwardson J. M.; Chapman E. R. Exocytotic Fusion Pores Are Composed of Both Lipids and Proteins. Nat. Struct. Mol. Biol. 2016, 23, 67–73. 10.1038/nsmb.3141. PubMed DOI PMC

Sharma S.; Lindau M. The Mystery of the Fusion Pore. Nat. Struct. Mol. Biol. 2016, 23, 5–6. 10.1038/nsmb.3157. PubMed DOI PMC

Fortoul N.; Singh P.; Hui C.-Y.; Bykhovskaia M.; Jagota A. Coarse-Grained Model of SNARE-Mediated Docking. Biophys. J. 2015, 108, 2258–2269. 10.1016/j.bpj.2015.03.053. PubMed DOI PMC

Zheng W. All-Atom and Coarse-Grained Simulations of the Forced Unfolding Pathways of the SNARE Complex: Forced Unfolding Simulations of SNARE. Proteins: Struct., Funct., Genet. 2014, 82, 1376–1386. 10.1002/prot.24505. PubMed DOI

Go N. Theoretical Studies of Protein Folding. Annu. Rev. Biophys. Bioeng. 1983, 12, 183–210. 10.1146/annurev.bb.12.060183.001151. PubMed DOI

Tekpinar M.; Zheng W. Unzipping of Neuronal Snare Protein with Steered Molecular Dynamics Occurs in Three Steps. J. Mol. Model. 2014, 20, 2381.10.1007/s00894-014-2381-7. PubMed DOI

Han J.; Pluhackova K.; Bruns D.; Böckmann R. A. Synaptobrevin Transmembrane Domain Determines the Structure and Dynamics of the SNARE Motif and the Linker Region. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 855–865. 10.1016/j.bbamem.2016.01.030. PubMed DOI

Ngatchou A. N.; Kisler K.; Fang Q.; Walter A. M.; Zhao Y.; Bruns D.; Sørensen J. B.; Lindau M. Role of the Synaptobrevin C Terminus in Fusion Pore Formation. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 18463–18468. 10.1073/pnas.1006727107. PubMed DOI PMC

D’Agostino M.; Risselada H. J.; Mayer A. Steric Hindrance of SNARE Transmembrane Domain Organization Impairs the Hemifusion-to-fusion Transition. EMBO Rep. 2016, 17, 1590–1608. 10.15252/embr.201642209. PubMed DOI PMC

Lindau M.; Hall B. A.; Chetwynd A.; Beckstein O.; Sansom M. S. P. Coarse-Grain Simulations Reveal Movement of the Synaptobrevin C-Terminus in Response to Piconewton Forces. Biophys. J. 2012, 103, 959–969. 10.1016/j.bpj.2012.08.007. PubMed DOI PMC

Blanchard A. E.; Arcario M. J.; Schulten K.; Tajkhorshid E. A Highly Tilted Membrane Configuration for the Prefusion State of Synaptobrevin. Biophys. J. 2014, 107, 2112–2121. 10.1016/j.bpj.2014.09.013. PubMed DOI PMC

Ohkubo Y. Z.; Pogorelov T. V.; Arcario M. J.; Christensen G. A.; Tajkhorshid E. Accelerating Membrane Insertion of Peripheral Proteins with a Novel Membrane Mimetic Model. Biophys. J. 2012, 102, 2130–2139. 10.1016/j.bpj.2012.03.015. PubMed DOI PMC

Dai Y.; Seeger M.; Weng J.; Song S.; Wang W.; Tan Y.-W. Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6. Sci. Rep. 2016, 6, 30282.10.1038/srep30282. PubMed DOI PMC

Han J.; Pluhackova K.; Wassenaar T. A.; Böckmann R. A. Synaptobrevin Transmembrane Domain Dimerization Studied by Multiscale Molecular Dynamics Simulations. Biophys. J. 2015, 109, 760–771. 10.1016/j.bpj.2015.06.049. PubMed DOI PMC

Fang Q.; Zhao Y.; Herbst A. D.; Kim B. N.; Lindau M. Positively Charged Amino Acids at the SNAP-25 C Terminus Determine Fusion Rates, Fusion Pore Properties, and Energetics of Tight SNARE Complex Zippering. J. Neurosci. 2015, 35, 3230–3239. 10.1523/JNEUROSCI.2905-14.2015. PubMed DOI PMC

Bar-On D.; Nachliel E.; Gutman M.; Ashery U. Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding. PLoS Comput. Biol. 2011, 7, e1001097.10.1371/journal.pcbi.1001097. PubMed DOI PMC

D’Agostino M.; Risselada H. J.; Lürick A.; Ungermann C.; Mayer A. A Tethering Complex Drives the Terminal Stage of SNARE-Dependent Membrane Fusion. Nature 2017, 10.1038/nature24469. PubMed DOI

Bykhovskaia M.; Jagota A.; Gonzalez A.; Vasin A.; Littleton J. T. Interaction of the Complexin Accessory Helix with the C-Terminus of the SNARE Complex: Molecular-Dynamics Model of the Fusion Clamp. Biophys. J. 2013, 105, 679–690. 10.1016/j.bpj.2013.06.018. PubMed DOI PMC

Vasin A.; Volfson D.; Littleton J. T.; Bykhovskaia M. Interaction of the Complexin Accessory Helix with Synaptobrevin Regulates Spontaneous Fusion. Biophys. J. 2016, 111, 1954–1964. 10.1016/j.bpj.2016.09.017. PubMed DOI PMC

Zheng W. Probing the Structural Dynamics of the SNARE Recycling Machine Based on Coarse-Grained Modeling: Coarse-Grained Modeling of SNARE Recycling Machine. Proteins: Struct., Funct., Genet. 2016, 84, 1055–1066. 10.1002/prot.25052. PubMed DOI

Osterberg J. R.; Chon N. L.; Boo A.; Maynard F. A.; Lin H.; Knight J. D. Membrane Docking of the Synaptotagmin 7 C2A Domain: Electron Paramagnetic Resonance Measurements Show Contributions from Two Membrane Binding Loops. Biochemistry 2015, 54, 5684–5695. 10.1021/acs.biochem.5b00421. PubMed DOI PMC

Wu Z.; Schulten K. Synaptotagmin’s Role in Neurotransmitter Release Likely Involves Ca2+-Induced Conformational Transition. Biophys. J. 2014, 107, 1156–1166. 10.1016/j.bpj.2014.07.041. PubMed DOI PMC

Fealey M. E.; Binder B. P.; Uversky V. N.; Hinderliter A.; Thomas D. D. Structural Impact of Phosphorylation and Dielectric Constant Variation on Synaptotagmin’s IDR. Biophys. J. 2018, 114, 550–561. 10.1016/j.bpj.2017.12.013. PubMed DOI PMC

Chon N. L.; Osterberg J. R.; Henderson J.; Khan H. M.; Reuter N.; Knight J. D.; Lin H. Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions. Biochemistry 2015, 54, 5696–5711. 10.1021/acs.biochem.5b00422. PubMed DOI

Wu B.; Guo W. The Exocyst at a Glance. J. Cell Sci. 2015, 128, 2957–2964. 10.1242/jcs.156398. PubMed DOI PMC

Zhao Y.; Liu J.; Yang C.; Capraro B. R.; Baumgart T.; Bradley R. P.; Ramakrishnan N.; Xu X.; Radhakrishnan R.; Svitkina T.; et al. Exo70 Generates Membrane Curvature for Morphogenesis and Cell Migration. Dev. Cell 2013, 26, 266–278. 10.1016/j.devcel.2013.07.007. PubMed DOI PMC

Pleskot R.; Cwiklik L.; Jungwirth P.; Žárský V.; Potocký M. Membrane Targeting of the Yeast Exocyst Complex. Biochim. Biophys. Acta, Biomembr. 2015, 1848, 1481–1489. 10.1016/j.bbamem.2015.03.026. PubMed DOI

Mei K.; Li Y.; Wang S.; Shao G.; Wang J.; Ding Y.; Luo G.; Yue P.; Liu J.-J.; Wang X.; et al. Cryo-EM Structure of the Exocyst Complex. Nat. Struct. Mol. Biol. 2018, 25, 139–146. 10.1038/s41594-017-0016-2. PubMed DOI PMC

Milosevic I. Revisiting the Role of Clathrin-Mediated Endoytosis in Synaptic Vesicle Recycling. Front. Cell. Neurosci. 2018, 12, 27.10.3389/fncel.2018.00027. PubMed DOI PMC

Meinecke M.; Boucrot E.; Camdere G.; Hon W.-C.; Mittal R.; McMahon H. T. Cooperative Recruitment of Dynamin and BIN/Amphiphysin/Rvs (BAR) Domain-Containing Proteins Leads to GTP-Dependent Membrane Scission. J. Biol. Chem. 2013, 288, 6651–6661. 10.1074/jbc.M112.444869. PubMed DOI PMC

Blood P. D.; Voth G. A. Direct Observation of Bin/Amphiphysin/Rvs (BAR) Domain-Induced Membrane Curvature by Means of Molecular Dynamics Simulations. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 15068–15072. 10.1073/pnas.0603917103. PubMed DOI PMC

Cui H.; Ayton G. S.; Voth G. A. Membrane Binding by the Endophilin N-BAR Domain. Biophys. J. 2009, 97, 2746–2753. 10.1016/j.bpj.2009.08.043. PubMed DOI PMC

Blood P. D.; Swenson R. D.; Voth G. A. Factors Influencing Local Membrane Curvature Induction by N-BAR Domains as Revealed by Molecular Dynamics Simulations. Biophys. J. 2008, 95, 1866–1876. 10.1529/biophysj.107.121160. PubMed DOI PMC

Takemura K.; Hanawa-Suetsugu K.; Suetsugu S.; Kitao A. Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature. Sci. Rep. 2017, 7, 6808.10.1038/s41598-017-06334-5. PubMed DOI PMC

Arkhipov A.; Yin Y.; Schulten K. Four-Scale Description of Membrane Sculpting by BAR Domains. Biophys. J. 2008, 95, 2806–2821. 10.1529/biophysj.108.132563. PubMed DOI PMC

Yin Y.; Arkhipov A.; Schulten K. Simulations of Membrane Tubulation by Lattices of Amphiphysin N-BAR Domains. Structure 2009, 17, 882–892. 10.1016/j.str.2009.03.016. PubMed DOI PMC

Yu H.; Schulten K. Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations. PLoS Comput. Biol. 2013, 9, e1002892.10.1371/journal.pcbi.1002892. PubMed DOI PMC

Lyman E.; Cui H.; Voth G. A. Water under the BAR. Biophys. J. 2010, 99, 1783–1790. 10.1016/j.bpj.2010.06.074. PubMed DOI PMC

Simunovic M.; Evergren E.; Golushko I.; Prévost C.; Renard H.-F.; Johannes L.; McMahon H. T.; Lorman V.; Voth G. A.; Bassereau P. How Curvature-Generating Proteins Build Scaffolds on Membrane Nanotubes. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 11226–11231. 10.1073/pnas.1606943113. PubMed DOI PMC

Ayton G. S.; Lyman E.; Krishna V.; Swenson R. D.; Mim C.; Unger V. M.; Voth G. A. New Insights into BAR Domain-Induced Membrane Remodeling. Biophys. J. 2009, 97, 1616–1625. 10.1016/j.bpj.2009.06.036. PubMed DOI PMC

Ayton G. S.; Voth G. A. Multiscale Simulation of Protein Mediated Membrane Remodeling. Semin. Cell Dev. Biol. 2010, 21, 357–362. 10.1016/j.semcdb.2009.11.011. PubMed DOI PMC

Picas L.; Viaud J.; Schauer K.; Vanni S.; Hnia K.; Fraisier V.; Roux A.; Bassereau P.; Gaits-Iacovoni F.; Payrastre B.; et al. BIN1/M-Amphiphysin2 Induces Clustering of Phosphoinositides to Recruit Its Downstream Partner Dynamin. Nat. Commun. 2014, 5, 5647.10.1038/ncomms6647. PubMed DOI

Kalli A. C.; Morgan G.; Sansom M. S. P. Interactions of the Auxilin-1 PTEN-like Domain with Model Membranes Result in Nanoclustering of Phosphatidyl Inositol Phosphates. Biophys. J. 2013, 105, 137–145. 10.1016/j.bpj.2013.05.012. PubMed DOI PMC

Faelber K.; Posor Y.; Gao S.; Held M.; Roske Y.; Schulze D.; Haucke V.; Noé F.; Daumke O. Crystal Structure of Nucleotide-Free Dynamin. Nature 2011, 477, 556–560. 10.1038/nature10369. PubMed DOI

Reubold T. F.; Faelber K.; Plattner N.; Posor Y.; Ketel K.; Curth U.; Schlegel J.; Anand R.; Manstein D. J.; Noé F.; et al. Crystal Structure of the Dynamin Tetramer. Nature 2015, 525, 404–408. 10.1038/nature14880. PubMed DOI

Abdel-Hamid M.; McCluskey A. Silico Docking, Molecular Dynamics and Binding Energy Insights into the Bolinaquinone-Clathrin Terminal Domain Binding Site. Molecules 2014, 19, 6609–6622. 10.3390/molecules19056609. PubMed DOI PMC

Pinot M.; Vanni S.; Pagnotta S.; Lacas-Gervais S.; Payet L.-A.; Ferreira T.; Gautier R.; Goud B.; Antonny B.; Barelli H. Polyunsaturated Phospholipids Facilitate Membrane Deformation and Fission by Endocytic Proteins. Science 2014, 345, 693–697. 10.1126/science.1255288. PubMed DOI

Lai C.-L.; Jao C. C.; Lyman E.; Gallop J. L.; Peter B. J.; McMahon H. T.; Langen R.; Voth G. A. Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain. J. Mol. Biol. 2012, 423, 800–817. 10.1016/j.jmb.2012.08.010. PubMed DOI PMC

Tourdot R. W.; Bradley R. P.; Ramakrishnan N.; Radhakrishnan R. Multiscale Computational Models in Physical Systems Biology of Intracellular Trafficking. IET Syst. Biol. 2014, 8, 198–213. 10.1049/iet-syb.2013.0057. PubMed DOI PMC

Fahy E.; Sud M.; Cotter D.; Subramaniam S. LIPID MAPS Online Tools for Lipid Research. Nucleic Acids Res. 2007, 35, W606–W612. 10.1093/nar/gkm324. PubMed DOI PMC

Sud M.; Fahy E.; Cotter D.; Brown A.; Dennis E. A.; Glass C. K.; Merrill A. H.; Murphy R. C.; Raetz C. R. H.; Russell D. W.; et al. LMSD: LIPID MAPS Structure Database. Nucleic Acids Res. 2007, 35, D527–D532. 10.1093/nar/gkl838. PubMed DOI PMC

Kaszuba K.; Grzybek M.; Orłowski A.; Danne R.; Róg T.; Simons K.; Coskun Ü.; Vattulainen I. N-Glycosylation as Determinant of Epidermal Growth Factor Receptor Conformation in Membranes. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 4334–4339. 10.1073/pnas.1503262112. PubMed DOI PMC

Watts A.; Volotovski I. D.; Marsh D. Rhodopsin-Lipid Associations in Bovine Rod Outer Segment Membranes. Identification of Immobilized Lipid by Spin-Labels. Biochemistry 1979, 18, 5006–5013. 10.1021/bi00589a031. PubMed DOI

Fretten P.; Morris S. J.; Watts A.; Marsh D. Lipid-Lipid and Lipid-Protein Interactions in Chromaffin Granule Membranes. Biochim. Biophys. Acta, Biomembr. 1980, 598, 247–259. 10.1016/0005-2736(80)90003-6. PubMed DOI

Marsh D.; Watts A.; Pates R. D.; Uhl R.; Knowles P. F.; Esmann M. ESR Spin-Label Studies of Lipid-Protein Interactions in Membranes. Biophys. J. 1982, 37, 265–274. 10.1016/S0006-3495(82)84675-4. PubMed DOI PMC

Sooksawate T.; Simmonds M. A. Effects of Membrane Cholesterol on the Sensitivity of the GABAA Receptor to GABA in Acutely Dissociated Rat Hippocampal Neurones. Neuropharmacology 2001, 40, 178–184. 10.1016/S0028-3908(00)00159-3. PubMed DOI

Saxena R.; Chattopadhyay A. Membrane Cholesterol Stabilizes the Human Serotonin1A Receptor. Biochim. Biophys. Acta, Biomembr. 2012, 1818, 2936–2942. 10.1016/j.bbamem.2012.07.032. PubMed DOI

Zocher M.; Zhang C.; Rasmussen S. G. F.; Kobilka B. K.; Muller D. J. Cholesterol Increases Kinetic, Energetic, and Mechanical Stability of the Human β2-Adrenergic Receptor. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, E3463–E3472. 10.1073/pnas.1210373109. PubMed DOI PMC

Phillips R.; Ursell T.; Wiggins P.; Sens P. Emerging Roles for Lipids in Shaping Membrane-Protein Function. Nature 2009, 459, 379–385. 10.1038/nature08147. PubMed DOI PMC

Bretscher M. S. Asymmetrical Lipid Bilayer Structure for Biological Membranes. Nature. New Biol. 1972, 236, 11–12. 10.1038/newbio236011a0. PubMed DOI

Carquin M.; D’Auria L.; Pollet H.; Bongarzone E. R.; Tyteca D. Recent Progress on Lipid Lateral Heterogeneity in Plasma Membranes: From Rafts to Submicrometric Domains. Prog. Lipid Res. 2016, 62, 1–24. 10.1016/j.plipres.2015.12.004. PubMed DOI PMC

Pedersen B. P.; Nissen P. Membrane Proteins — Do We Catch up with the Breathless Pace of Soluble Protein Structural Biology?. Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 447–448. 10.1016/j.bbagen.2015.01.001. PubMed DOI

MacDonald R. I. Temperature and Ionic Effects on the Interaction of Erythroid Spectrin with Phosphatidylserine Membranes. Biochemistry 1993, 32, 6957–6964. 10.1021/bi00078a021. PubMed DOI

O’Toole P. J.; Wolfe C.; Ladha S.; Cherry R. J. Rapid Diffusion of Spectrin Bound to a Lipid Surface. Biochim. Biophys. Acta, Biomembr. 1999, 1419, 64–70. 10.1016/S0005-2736(99)00048-6. PubMed DOI

de Jong K.; Rettig M. P.; Low P. S.; Kuypers F. A. Protein Kinase C Activation Induces Phosphatidylserine Exposure on Red Blood Cells. Biochemistry 2002, 41, 12562–12567. 10.1021/bi025882o. PubMed DOI

Meers P.; Mealy T. Calcium-Dependent Annexin V Binding to Phospholipids: Stoichiometry, Specificity, and the Role of Negative Charge. Biochemistry 1993, 32, 11711–11721. 10.1021/bi00094a030. PubMed DOI

Shiratsuchi A.; Umeda M.; Ohba Y.; Nakanishi Y. Recognition of Phosphatidylserine on the Surface of Apoptotic Spermatogenic Cells and Subsequent Phagocytosis by Sertoli Cells of the Rat. J. Biol. Chem. 1997, 272, 2354–2358. 10.1074/jbc.272.4.2354. PubMed DOI

Bratton D. L.; Fadok V. A.; Richter D. A.; Kailey J. M.; Guthrie L. A.; Henson P. M. Appearance of Phosphatidylserine on Apoptotic Cells Requires Calcium-Mediated Nonspecific Flip-Flop and Is Enhanced by Loss of the Aminophospholipid Translocase. J. Biol. Chem. 1997, 272, 26159–26165. 10.1074/jbc.272.42.26159. PubMed DOI

Castegna A.; Lauderback C. M.; Mohmmad-Abdul H.; Butterfield D. A. Modulation of Phospholipid Asymmetry in Synaptosomal Membranes by the Lipid Peroxidation Products, 4-Hydroxynonenal and Acrolein: Implications for Alzheimer’s Disease. Brain Res. 2004, 1004, 193–197. 10.1016/j.brainres.2004.01.036. PubMed DOI

Liu J.; Epand R. F.; Durrant D.; Grossman D.; Chi N.; Epand R. M.; Lee R. M. Role of Phospholipid Scramblase 3 in the Regulation of Tumor Necrosis Factor-α-Induced Apoptosis. Biochemistry 2008, 47, 4518–4529. 10.1021/bi701962c. PubMed DOI

Ndebele K.; Gona P.; Jin T.-G.; Benhaga N.; Chalah A.; Degli-Esposti M.; Khosravi-Far R. Tumor Necrosis Factor (TNF)-Related Apoptosis-Inducing Ligand (TRAIL) Induced Mitochondrial Pathway to Apoptosis and Caspase Activation Is Potentiated by Phospholipid Scramblase-3. Apoptosis 2008, 13, 845–856. 10.1007/s10495-008-0219-4. PubMed DOI PMC

Hamon Y.; Broccardo C.; Chambenoit O.; Luciani M.-F.; Toti F.; Chaslin S.; Freyssinet J.-M.; Devaux P. F.; McNeish J.; Marguet D.; et al. ABC1 Promotes Engulfment of Apoptotic Cells and Transbilayer Redistribution of Phosphatidylserine. Nat. Cell Biol. 2000, 2, 399–406. 10.1038/35017029. PubMed DOI

McConnell H. M.; Kornberg R. D. Inside-Outside Transitions of Phospholipids in Vesicle Membranes. Biochemistry 1971, 10, 1111–1120. 10.1021/bi00783a003. PubMed DOI

Nakano M.; Fukuda M.; Kudo T.; Matsuzaki N.; Azuma T.; Sekine K.; Endo H.; Handa T. Flip-Flop of Phospholipids in Vesicles: Kinetic Analysis with Time-Resolved Small-Angle Neutron Scattering. J. Phys. Chem. B 2009, 113, 6745–6748. 10.1021/jp900913w. PubMed DOI

Lange Y.; Dolde J.; Steck T. L. The Rate of Transmembrane Movement of Cholesterol in the Human Erythrocyte. J. Biol. Chem. 1981, 256, 5321–5323. PubMed

Lange Y.; Cohen C. M.; Poznansky M. J. Transmembrane Movement of Cholesterol in Human Erythrocytes. Proc. Natl. Acad. Sci. U. S. A. 1977, 74, 1538–1542. 10.1073/pnas.74.4.1538. PubMed DOI PMC

Steck T. L.; Ye J.; Lange Y. Probing Red Cell Membrane Cholesterol Movement with Cyclodextrin. Biophys. J. 2002, 83, 2118–2125. 10.1016/S0006-3495(02)73972-6. PubMed DOI PMC

Bruckner R. J.; Mansy S. S.; Ricardo A.; Mahadevan L.; Szostak J. W. Flip-Flop-Induced Relaxation of Bending Energy: Implications for Membrane Remodeling. Biophys. J. 2009, 97, 3113–3122. 10.1016/j.bpj.2009.09.025. PubMed DOI PMC

Garg S.; Porcar L.; Woodka A. C.; Butler P. D.; Perez-Salas U. Noninvasive Neutron Scattering Measurements Reveal Slower Cholesterol Transport in Model Lipid Membranes. Biophys. J. 2011, 101, 370–377. 10.1016/j.bpj.2011.06.014. PubMed DOI PMC

Imparato A.; Shillcock J. C.; Lipowsky R. Lateral and Transverse Diffusion in Two-Component Bilayer Membranes. Eur. Phys. J. E: Soft Matter Biol. Phys. 2003, 11, 21–28. 10.1140/epje/i2002-10125-x. PubMed DOI

Son M.; London E. The Dependence of Lipid Asymmetry upon Phosphatidylcholine Acyl Chain Structure. J. Lipid Res. 2013, 54, 223–231. 10.1194/jlr.M032722. PubMed DOI PMC

John K.; Schreiber S.; Kubelt J.; Herrmann A.; Müller P. Transbilayer Movement of Phospholipids at the Main Phase Transition of Lipid Membranes: Implications for Rapid Flip-Flop in Biological Membranes. Biophys. J. 2002, 83, 3315–3323. 10.1016/S0006-3495(02)75332-0. PubMed DOI PMC

de Vries A. H.; Mark A. E.; Marrink S. J. Molecular Dynamics Simulation of the Spontaneous Formation of a Small DPPC Vesicle in Water in Atomistic Detail. J. Am. Chem. Soc. 2004, 126, 4488–4489. 10.1021/ja0398417. PubMed DOI

Gurtovenko A. A.; Onike O. I.; Anwar J. Chemically Induced Phospholipid Translocation Across Biological Membranes. Langmuir 2008, 24, 9656–9660. 10.1021/la801431f. PubMed DOI

Dickey A. N.; Faller R. How Alcohol Chain-Length and Concentration Modulate Hydrogen Bond Formation in a Lipid Bilayer. Biophys. J. 2007, 92, 2366–2376. 10.1529/biophysj.106.097022. PubMed DOI PMC

Kandasamy S. K.; Larson R. G. Cation and Anion Transport through Hydrophilic Pores in Lipid Bilayers. J. Chem. Phys. 2006, 125, 074901.10.1063/1.2217737. PubMed DOI

Gurtovenko A. A.; Vattulainen I. Molecular Mechanism for Lipid Flip-Flops. J. Phys. Chem. B 2007, 111, 13554–13559. 10.1021/jp077094k. PubMed DOI

Róg T.; Stimson L. M.; Pasenkiewicz-Gierula M.; Vattulainen I.; Karttunen M. Replacing the Cholesterol Hydroxyl Group with the Ketone Group Facilitates Sterol Flip-Flop and Promotes Membrane Fluidity. J. Phys. Chem. B 2008, 112, 1946–1952. 10.1021/jp075078h. PubMed DOI

Arai N.; Akimoto T.; Yamamoto E.; Yasui M.; Yasuoka K. Poisson Property of the Occurrence of Flip-Flops in a Model Membrane. J. Chem. Phys. 2014, 140, 064901.10.1063/1.4863330. PubMed DOI

Kučerka N.; Perlmutter J. D.; Pan J.; Tristram-Nagle S.; Katsaras J.; Sachs J. N. The Effect of Cholesterol on Short- and Long-Chain Monounsaturated Lipid Bilayers as Determined by Molecular Dynamics Simulations and X-Ray Scattering. Biophys. J. 2008, 95, 2792–2805. 10.1529/biophysj.107.122465. PubMed DOI PMC

Choubey A.; Kalia R. K.; Malmstadt N.; Nakano A.; Vashishta P. Cholesterol Translocation in a Phospholipid Membrane. Biophys. J. 2013, 104, 2429–2436. 10.1016/j.bpj.2013.04.036. PubMed DOI PMC

Baker M. K.; Abrams C. F. Dynamics of Lipids, Cholesterol, and Transmembrane α-Helices from Microsecond Molecular Dynamics Simulations. J. Phys. Chem. B 2014, 118, 13590–13600. 10.1021/jp507027t. PubMed DOI PMC

Bennett W. F. D.; MacCallum J. L.; Hinner M. J.; Marrink S. J.; Tieleman D. P. Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments. J. Am. Chem. Soc. 2009, 131, 12714–12720. 10.1021/ja903529f. PubMed DOI

Sapay N.; Bennett W. F. D.; Tieleman D. P. Thermodynamics of Flip-Flop and Desorption for a Systematic Series of Phosphatidylcholine Lipids. Soft Matter 2009, 5, 3295.10.1039/b902376c. DOI

Anglin T. C.; Conboy J. C. Kinetics and Thermodynamics of Flip-Flop in Binary Phospholipid Membranes Measured by Sum-Frequency Vibrational Spectroscopy. Biochemistry 2009, 48, 10220–10234. 10.1021/bi901096j. PubMed DOI

Jo S.; Rui H.; Lim J. B.; Klauda J. B.; Im W. Cholesterol Flip-Flop: Insights from Free Energy Simulation Studies. J. Phys. Chem. B 2010, 114, 13342–13348. 10.1021/jp108166k. PubMed DOI

Parisio G.; Sperotto M. M.; Ferrarini A. Flip-Flop of Steroids in Phospholipid Bilayers: Effects of the Chemical Structure on Transbilayer Diffusion. J. Am. Chem. Soc. 2012, 134, 12198–12208. 10.1021/ja304007t. PubMed DOI

Marrink S. J.; Tieleman D. P. Perspective on the Martini Model. Chem. Soc. Rev. 2013, 42, 6801.10.1039/c3cs60093a. PubMed DOI

Marrink S. J.; Risselada H. J.; Yefimov S.; Tieleman D. P.; de Vries A. H. The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. J. Phys. Chem. B 2007, 111, 7812–7824. 10.1021/jp071097f. PubMed DOI

Ogushi F.; Ishitsuka R.; Kobayashi T.; Sugita Y. Rapid Flip-Flop Motions of Diacylglycerol and Ceramide in Phospholipid Bilayers. Chem. Phys. Lett. 2012, 522, 96–102. 10.1016/j.cplett.2011.11.057. DOI

Yesylevskyy S. O.; Demchenko A. P.. Cholesterol Behavior in Asymmetric Lipid Bilayers: Insights from Molecular Dynamics Simulations. In Methods in Membrane Lipids; Owen D. M., Ed.; Springer New York: New York, NY, 2015; Vol. 1232, pp 291–306, 10.1007/978-1-4939-1752-5_20. PubMed DOI

Yesylevskyy S. O.; Demchenko A. P.; Kraszewski S.; Ramseyer C. Cholesterol Induces Uneven Curvature of Asymmetric Lipid Bilayers. Sci. World J. 2013, 2013, 1–10. 10.1155/2013/965230. PubMed DOI PMC

Kästner J. Umbrella Sampling: Umbrella Sampling. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2011, 1, 932–942. 10.1002/wcms.66. DOI

Maximova T.; Moffatt R.; Ma B.; Nussinov R.; Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput. Biol. 2016, 12, e1004619.10.1371/journal.pcbi.1004619. PubMed DOI PMC

Bennett W. F. D.; Tieleman D. P. Water Defect and Pore Formation in Atomistic and Coarse-Grained Lipid Membranes: Pushing the Limits of Coarse Graining. J. Chem. Theory Comput. 2011, 7, 2981–2988. 10.1021/ct200291v. PubMed DOI

Bennett W. F. D.; Sapay N.; Tieleman D. P. Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers. Biophys. J. 2014, 106, 210–219. 10.1016/j.bpj.2013.11.4486. PubMed DOI PMC

Nicol F.; Nir S.; Szoka F. C. Effect of Cholesterol and Charge on Pore Formation in Bilayer Vesicles by a pH-Sensitive Peptide. Biophys. J. 1996, 71, 3288–3301. 10.1016/S0006-3495(96)79521-8. PubMed DOI PMC

Volinsky R.; Cwiklik L.; Jurkiewicz P.; Hof M.; Jungwirth P.; Kinnunen P. K. J. Oxidized Phosphatidylcholines Facilitate Phospholipid Flip-Flop in Liposomes. Biophys. J. 2011, 101, 1376–1384. 10.1016/j.bpj.2011.07.051. PubMed DOI PMC

Volinsky R.; Kinnunen P. K. J. Oxidized Phosphatidylcholines in Membrane-Level Cellular Signaling: From Biophysics to Physiology and Molecular Pathology. FEBS J. 2013, 280, 2806–2816. 10.1111/febs.12247. PubMed DOI

Razzokov J.; Yusupov M.; Vanuytsel S.; Neyts E. C.; Bogaerts A. Phosphatidylserine Flip-Flop Induced by Oxidation of the Plasma Membrane: A Better Insight by Atomic Scale Modeling. Plasma Processes Polym. 2017, 14, 1700013.10.1002/ppap.201700013. DOI

Lin J.; Dargazany R.; Alexander-Katz A. Lipid Flip-Flop and Pore Nucleation on Zwitterionic Bilayers Are Asymmetric under Ionic Imbalance. Small 2017, 13, 1603708.10.1002/smll.201603708. PubMed DOI

Bennett W. F. D.; Tieleman D. P. Molecular Simulation of Rapid Translocation of Cholesterol, Diacylglycerol, and Ceramide in Model Raft and Nonraft Membranes. J. Lipid Res. 2012, 53, 421–429. 10.1194/jlr.M022491. PubMed DOI PMC

Lange Y.; Ye J.; Rigney M.; Steck T. L. Regulation of Endoplasmic Reticulum Cholesterol by Plasma Membrane Cholesterol. J. Lipid Res. 1999, 40, 2264–2270. PubMed

Lange Y.; Ye J.; Strebel F. Movement of 25-Hydroxycholesterol from the Plasma Membrane to the Rough Endoplasmic Reticulum in Cultured Hepatoma Cells. J. Lipid Res. 1995, 36, 1092–1097. PubMed

Moro G. J.; Ferrarini A.; Polimeno A.; Nordio P. L.. Models of Conformational Dynamics. In Reactive and Flexible Molecules in Liquids; Dorfmüller T., Ed.; Springer Netherlands: Dordrecht, 1989; pp 107–139, 10.1007/978-94-009-1043-0_7. DOI

Langer J. S. Statistical Theory of the Decay of Metastable States. Ann. Phys. 1969, 54, 258–275. 10.1016/0003-4916(69)90153-5. DOI

Kramers H. A. Brownian Motion in a Field of Force and the Diffusion Model of Chemical Reactions. Physica 1940, 7, 284–304. 10.1016/S0031-8914(40)90098-2. DOI

Parisio G.; Ferrarini A. Solute Partitioning into Lipid Bilayers: An Implicit Model for Nonuniform and Ordered Environment. J. Chem. Theory Comput. 2010, 6, 2267–2280. 10.1021/ct100210u. PubMed DOI

Wei C.; Pohorille A. Flip-Flop of Oleic Acid in a Phospholipid Membrane: Rate and Mechanism. J. Phys. Chem. B 2014, 118, 12919–12926. 10.1021/jp508163e. PubMed DOI

Filipe H. A. L.; Moreno M. J.; Róg T.; Vattulainen I.; Loura L. M. S. How To Tackle the Issues in Free Energy Simulations of Long Amphiphiles Interacting with Lipid Membranes: Convergence and Local Membrane Deformations. J. Phys. Chem. B 2014, 118, 3572–3581. 10.1021/jp501622d. PubMed DOI

Neale C.; Bennett W. F. D.; Tieleman D. P.; Pomès R. Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers. J. Chem. Theory Comput. 2011, 7, 4175–4188. 10.1021/ct200316w. PubMed DOI

Spiwok V.; Sucur Z.; Hosek P. Enhanced Sampling Techniques in Biomolecular Simulations. Biotechnol. Adv. 2015, 33, 1130–1140. 10.1016/j.biotechadv.2014.11.011. PubMed DOI

Bacci M.; Vitalis A.; Caflisch A. A Molecular Simulation Protocol to Avoid Sampling Redundancy and Discover New States. Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 889–902. 10.1016/j.bbagen.2014.08.013. PubMed DOI

Bernardi R. C.; Melo M. C. R.; Schulten K. Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems. Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 872–877. 10.1016/j.bbagen.2014.10.019. PubMed DOI PMC

Wymann M. P.; Schneiter R. Lipid Signalling in Disease. Nat. Rev. Mol. Cell Biol. 2008, 9, 162–176. 10.1038/nrm2335. PubMed DOI

Overington J. P.; Al-Lazikani B.; Hopkins A. L. How Many Drug Targets Are There?. Nat. Rev. Drug Discovery 2006, 5, 993–996. 10.1038/nrd2199. PubMed DOI

Hunte C.; Richers S. Lipids and Membrane Protein Structures. Curr. Opin. Struct. Biol. 2008, 18, 406–411. 10.1016/j.sbi.2008.03.008. PubMed DOI

Rose P. W.; Prlić A.; Altunkaya A.; Bi C.; Bradley A. R.; Christie C. H.; Costanzo L. D.; Duarte J. M.; Dutta S.; Feng Z.; et al. The RCSB Protein Data Bank: Integrative View of Protein, Gene and 3D Structural Information. Nucleic Acids Res. 2017, 45, D271–D281. 10.1093/nar/gkw1000. PubMed DOI PMC

Pierce K. L.; Premont R. T.; Lefkowitz R. J. Seven-Transmembrane Receptors: Signalling. Nat. Rev. Mol. Cell Biol. 2002, 3, 639–650. 10.1038/nrm908. PubMed DOI

Latorraca N. R.; Venkatakrishnan A. J.; Dror R. O. GPCR Dynamics: Structures in Motion. Chem. Rev. 2017, 117, 139–155. 10.1021/acs.chemrev.6b00177. PubMed DOI

Oates J.; Watts A. Uncovering the Intimate Relationship between Lipids, Cholesterol and GPCR Activation. Curr. Opin. Struct. Biol. 2011, 21, 802–807. 10.1016/j.sbi.2011.09.007. PubMed DOI

Staubach S.; Hanisch F.-G. Lipid Rafts: Signaling and Sorting Platforms of Cells and Their Roles in Cancer. Expert Rev. Proteomics 2011, 8, 263–277. 10.1586/epr.11.2. PubMed DOI

Chini B. G-Protein Coupled Receptors in Lipid Rafts and Caveolae: How, When and Why Do They Go There?. J. Mol. Endocrinol. 2004, 32, 325–338. 10.1677/jme.0.0320325. PubMed DOI

Albert A. D.; Young J. E.; Yeagle P. L. Rhodopsin-Cholesterol Interactions in Bovine Rod Outer Segment Disk Membranes. Biochim. Biophys. Acta, Biomembr. 1996, 1285, 47–55. 10.1016/S0005-2736(96)00145-9. PubMed DOI

Li J.; Edwards P. C.; Burghammer M.; Villa C.; Schertler G. F. X. Structure of Bovine Rhodopsin in a Trigonal Crystal Form. J. Mol. Biol. 2004, 343, 1409–1438. 10.1016/j.jmb.2004.08.090. PubMed DOI

Horsefield R.; Norden K.; Fellert M.; Backmark A.; Tornroth-Horsefield S.; Terwisscha van Scheltinga A. C.; Kvassman J.; Kjellbom P.; Johanson U.; Neutze R. High-Resolution x-Ray Structure of Human Aquaporin 5. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 13327–13332. 10.1073/pnas.0801466105. PubMed DOI PMC

Cherezov V.; Rosenbaum D. M.; Hanson M. A.; Rasmussen S. G. F.; Thian F. S.; Kobilka T. S.; Choi H.-J.; Kuhn P.; Weis W. I.; Kobilka B. K.; et al. High-Resolution Crystal Structure of an Engineered Human β2-Adrenergic G Protein-Coupled Receptor. Science 2007, 318, 1258–1265. 10.1126/science.1150577. PubMed DOI PMC

Pucadyil T. J.; Chattopadhyay A. Cholesterol Modulates Ligand Binding and G-Protein Coupling to Serotonin1A Receptors from Bovine Hippocampus. Biochim. Biophys. Acta, Biomembr. 2004, 1663, 188–200. 10.1016/j.bbamem.2004.03.010. PubMed DOI

Harikumar K. G.; Puri V.; Singh R. D.; Hanada K.; Pagano R. E.; Miller L. J. Differential Effects of Modification of Membrane Cholesterol and Sphingolipids on the Conformation, Function, and Trafficking of the G Protein-Coupled Cholecystokinin Receptor. J. Biol. Chem. 2005, 280, 2176–2185. 10.1074/jbc.M410385200. PubMed DOI

Gimpl G.; Fahrenholz F. Cholesterol as Stabilizer of the Oxytocin Receptor. Biochim. Biophys. Acta, Biomembr. 2002, 1564, 384–392. 10.1016/S0005-2736(02)00475-3. PubMed DOI

Chakraborty H.; Chattopadhyay A. Excitements and Challenges in GPCR Oligomerization: Molecular Insight from FRET. ACS Chem. Neurosci. 2015, 6, 199–206. 10.1021/cn500231d. PubMed DOI

Oates J.; Faust B.; Attrill H.; Harding P.; Orwick M.; Watts A. The Role of Cholesterol on the Activity and Stability of Neurotensin Receptor 1. Biochim. Biophys. Acta, Biomembr. 2012, 1818, 2228–2233. 10.1016/j.bbamem.2012.04.010. PubMed DOI

Mitchell D. C.; Straume M.; Litman B. J. Role of Sn-1-Saturated,Sn-2-Polyunsaturated Phospholipids in Control of Membrane Receptor Conformational Equilibrium: Effects of Cholesterol and Acyl Chain Unsaturation on the Metarhodopsin I.Tautm. Metarhodopsin II Equilibrium. Biochemistry 1992, 31, 662–670. 10.1021/bi00118a005. PubMed DOI

Mitchell D. C.; Niu S.-L.; Litman B. J. Enhancement of G Protein-Coupled Signaling by DHA Phospholipids. Lipids 2003, 38, 437–443. 10.1007/s11745-003-1081-1. PubMed DOI

Bennett M. P.; Mitchell D. C. Regulation of Membrane Proteins by Dietary Lipids: Effects of Cholesterol and Docosahexaenoic Acid Acyl Chain-Containing Phospholipids on Rhodopsin Stability and Function. Biophys. J. 2008, 95, 1206–1216. 10.1529/biophysj.107.122788. PubMed DOI PMC

Gibson N. J.; Brown M. F. Lipid Headgroup and Acyl Chain Composition Modulate the MI-MII Equilibrium of Rhodopsin in Recombinant Membranes. Biochemistry 1993, 32, 2438–2454. 10.1021/bi00060a040. PubMed DOI

Brown M. F. Modulation of Rhodopsin Function by Properties of the Membrane Bilayer. Chem. Phys. Lipids 1994, 73, 159–180. 10.1016/0009-3084(94)90180-5. PubMed DOI

Horn J. N.; Kao T.-C.; Grossfield A.. Coarse-Grained Molecular Dynamics Provides Insight into the Interactions of Lipids and Cholesterol with Rhodopsin. In G Protein-Coupled Receptors - Modeling and Simulation; Filizola M., Ed.; Springer Netherlands: Dordrecht, 2014; Vol. 796, pp 75–94, 10.1007/978-94-007-7423-0_5. PubMed DOI PMC

Grossfield A.; Feller S. E.; Pitman M. C. A Role for Direct Interactions in the Modulation of Rhodopsin by ω-3 Polyunsaturated Lipids. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 4888–4893. 10.1073/pnas.0508352103. PubMed DOI PMC

Pitman M. C.; Grossfield A.; Suits F.; Feller S. E. Role of Cholesterol and Polyunsaturated Chains in Lipid–Protein Interactions: Molecular Dynamics Simulation of Rhodopsin in a Realistic Membrane Environment. J. Am. Chem. Soc. 2005, 127, 4576–4577. 10.1021/ja042715y. PubMed DOI

Grossfield A.; Feller S. E.; Pitman M. C. Contribution of Omega-3 Fatty Acids to the Thermodynamics of Membrane Protein Solvation. J. Phys. Chem. B 2006, 110, 8907–8909. 10.1021/jp060405r. PubMed DOI

Khelashvili G.; Grossfield A.; Feller S. E.; Pitman M. C.; Weinstein H. Structural and Dynamic Effects of Cholesterol at Preferred Sites of Interaction with Rhodopsin Identified from Microsecond Length Molecular Dynamics Simulations. Proteins: Struct., Funct., Genet. 2009, 76, 403–417. 10.1002/prot.22355. PubMed DOI PMC

Feller S. E.; Gawrisch K.; Woolf T. B. Rhodopsin Exhibits a Preference for Solvation by Polyunsaturated Docosohexaenoic Acid. J. Am. Chem. Soc. 2003, 125, 4434–4435. 10.1021/ja0345874. PubMed DOI

Patra S. M.; Chakraborty S.; Shahane G.; Prasanna X.; Sengupta D.; Maiti P. K.; Chattopadhyay A. Differential Dynamics of the Serotonin1A Receptor in Membrane Bilayers of Varying Cholesterol Content Revealed by All Atom Molecular Dynamics Simulation. Mol. Membr. Biol. 2015, 32, 127–137. 10.3109/09687688.2015.1096971. PubMed DOI

Paila Y. D.; Tiwari S.; Sengupta D.; Chattopadhyay A. Molecular Modeling of the Human Serotonin1A Receptor: Role of Membrane Cholesterol in Ligand Binding of the Receptor. Mol. BioSyst. 2011, 7, 224–234. 10.1039/C0MB00148A. PubMed DOI

Shan J.; Khelashvili G.; Mondal S.; Mehler E. L.; Weinstein H. Ligand-Dependent Conformations and Dynamics of the Serotonin 5-HT2A Receptor Determine Its Activation and Membrane-Driven Oligomerization Properties. PLoS Comput. Biol. 2012, 8, e1002473.10.1371/journal.pcbi.1002473. PubMed DOI PMC

Jafurulla M.; Tiwari S.; Chattopadhyay A. Identification of Cholesterol Recognition Amino Acid Consensus (CRAC) Motif in G-Protein Coupled Receptors. Biochem. Biophys. Res. Commun. 2011, 404, 569–573. 10.1016/j.bbrc.2010.12.031. PubMed DOI

Sengupta D.; Chattopadhyay A. Identification of Cholesterol Binding Sites in the Serotonin1A Receptor. J. Phys. Chem. B 2012, 116, 12991–12996. 10.1021/jp309888u. PubMed DOI

Hurst D. P.; Grossfield A.; Lynch D. L.; Feller S.; Romo T. D.; Gawrisch K.; Pitman M. C.; Reggio P. H. A Lipid Pathway for Ligand Binding Is Necessary for a Cannabinoid G Protein-Coupled Receptor. J. Biol. Chem. 2010, 285, 17954–17964. 10.1074/jbc.M109.041590. PubMed DOI PMC

Lyman E.; Higgs C.; Kim B.; Lupyan D.; Shelley J. C.; Farid R.; Voth G. A. A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A2A Adenosine Receptor. Structure 2009, 17, 1660–1668. 10.1016/j.str.2009.10.010. PubMed DOI PMC

Ng H. W.; Laughton C. A.; Doughty S. W. Molecular Dynamics Simulations of the Adenosine A2a Receptor in POPC and POPE Lipid Bilayers: Effects of Membrane on Protein Behavior. J. Chem. Inf. Model. 2014, 54, 573–581. 10.1021/ci400463z. PubMed DOI

Lee J. Y.; Lyman E. Predictions for Cholesterol Interaction Sites on the A2A Adenosine Receptor. J. Am. Chem. Soc. 2012, 134, 16512–16515. 10.1021/ja307532d. PubMed DOI PMC

Prasanna X.; Chattopadhyay A.; Sengupta D.. Role of Lipid-Mediated Effects in β2-Adrenergic Receptor Dimerization. In Biochemical Roles of Eukaryotic Cell Surface Macromolecules; Chakrabarti A., Surolia A., Eds.; Springer International Publishing: Cham, 2015; Vol. 842, pp 247–261, 10.1007/978-3-319-11280-0_16. PubMed DOI

Neale C.; Herce H. D.; Pomès R.; García A. E. Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor?. Biophys. J. 2015, 109, 1652–1662. 10.1016/j.bpj.2015.08.028. PubMed DOI PMC

Cang X.; Du Y.; Mao Y.; Wang Y.; Yang H.; Jiang H. Mapping the Functional Binding Sites of Cholesterol in β2-Adrenergic Receptor by Long-Time Molecular Dynamics Simulations. J. Phys. Chem. B 2013, 117, 1085–1094. 10.1021/jp3118192. PubMed DOI

Cang X.; Yang L.; Yang J.; Luo C.; Zheng M.; Yu K.; Yang H.; Jiang H. Cholesterol-β1AR Interaction versus Cholesterol-β2AR Interaction. Proteins: Struct., Funct., Genet. 2014, 82, 760–770. 10.1002/prot.24456. PubMed DOI

Liu W.; Chun E.; Thompson A. A.; Chubukov P.; Xu F.; Katritch V.; Han G. W.; Roth C. B.; Heitman L. H.; IJzerman A. P.; et al. Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions. Science 2012, 337, 232–236. 10.1126/science.1219218. PubMed DOI PMC

Ploier B.; Caro L. N.; Morizumi T.; Pandey K.; Pearring J. N.; Goren M. A.; Finnemann S. C.; Graumann J.; Arshavsky V. Y.; Dittman J. S.; et al. Dimerization Deficiency of Enigmatic Retinitis Pigmentosa-Linked Rhodopsin Mutants. Nat. Commun. 2016, 7, 12832.10.1038/ncomms12832. PubMed DOI PMC

Goren M. A.; Morizumi T.; Menon I.; Joseph J. S.; Dittman J. S.; Cherezov V.; Stevens R. C.; Ernst O. P.; Menon A. K. Constitutive Phospholipid Scramblase Activity of a G Protein-Coupled Receptor. Nat. Commun. 2014, 5, 5115.10.1038/ncomms6115. PubMed DOI PMC

Genheden S.; Essex J. W.; Lee A. G. G. Protein Coupled Receptor Interactions with Cholesterol Deep in the Membrane. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 268–281. 10.1016/j.bbamem.2016.12.001. PubMed DOI

Yuan S.; Wu R.; Latek D.; Trzaskowski B.; Filipek S. Lipid Receptor S1P1 Activation Scheme Concluded from Microsecond All-Atom Molecular Dynamics Simulations. PLoS Comput. Biol. 2013, 9, e1003261.10.1371/journal.pcbi.1003261. PubMed DOI PMC

Baier C. J.; Fantini J.; Barrantes F. J. Disclosure of Cholesterol Recognition Motifs in Transmembrane Domains of the Human Nicotinic Acetylcholine Receptor. Sci. Rep. 2011, 1, 69.10.1038/srep00069. PubMed DOI PMC

Cheng M. H.; Xu Y.; Tang P. Anionic Lipid and Cholesterol Interactions with α4β2 nAChR: Insights from MD Simulations. J. Phys. Chem. B 2009, 113, 6964–6970. 10.1021/jp900714b. PubMed DOI PMC

Bocquet N.; Nury H.; Baaden M.; Le Poupon C.; Changeux J.-P.; Delarue M.; Corringer P.-J. X-Ray Structure of a Pentameric Ligand-Gated Ion Channel in an Apparently Open Conformation. Nature 2009, 457, 111–114. 10.1038/nature07462. PubMed DOI

Singh A. K.; McMillan J.; Bukiya A. N.; Burton B.; Parrill A. L.; Dopico A. M. Multiple Cholesterol Recognition/Interaction Amino Acid Consensus (CRAC) Motifs in Cytosolic C Tail of Slo1 Subunit Determine Cholesterol Sensitivity of Ca2+- and Voltage-Gated K+ (BK) Channels. J. Biol. Chem. 2012, 287, 20509–20521. 10.1074/jbc.M112.356261. PubMed DOI PMC

Rosenhouse-Dantsker A.; Noskov S.; Durdagi S.; Logothetis D. E.; Levitan I. Identification of Novel Cholesterol-Binding Regions in Kir2 Channels. J. Biol. Chem. 2013, 288, 31154–31164. 10.1074/jbc.M113.496117. PubMed DOI PMC

Hedger G.; Shorthouse D.; Koldsø H.; Sansom M. S. P. Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor. J. Phys. Chem. B 2016, 120, 8154–8163. 10.1021/acs.jpcb.6b01387. PubMed DOI PMC

Schmidt M. R.; Stansfeld P. J.; Tucker S. J.; Sansom M. S. P. Simulation-Based Prediction of Phosphatidylinositol 4,5-Bisphosphate Binding to an Ion Channel. Biochemistry 2013, 52, 279–281. 10.1021/bi301350s. PubMed DOI PMC

O’Connor J. W.; Klauda J. B. Lipid Membranes with a Majority of Cholesterol: Applications to the Ocular Lens and Aquaporin 0. J. Phys. Chem. B 2011, 115, 6455–6464. 10.1021/jp108650u. PubMed DOI

Pliotas C.; Naismith J. H. Spectator No More, the Role of the Membrane in Regulating Ion Channel Function. Curr. Opin. Struct. Biol. 2017, 45, 59–66. 10.1016/j.sbi.2016.10.017. PubMed DOI

Pliotas C.; Dahl A. C. E.; Rasmussen T.; Mahendran K. R.; Smith T. K.; Marius P.; Gault J.; Banda T.; Rasmussen A.; Miller S.; et al. The Role of Lipids in Mechanosensation. Nat. Struct. Mol. Biol. 2015, 22, 991–998. 10.1038/nsmb.3120. PubMed DOI PMC

Arkhipov A.; Shan Y.; Das R.; Endres N. F.; Eastwood M. P.; Wemmer D. E.; Kuriyan J.; Shaw D. E. Architecture and Membrane Interactions of the EGF Receptor. Cell 2013, 152, 557–569. 10.1016/j.cell.2012.12.030. PubMed DOI PMC

Hedger G.; Sansom M. S. P.; Koldsø H. The Juxtamembrane Regions of Human Receptor Tyrosine Kinases Exhibit Conserved Interaction Sites with Anionic Lipids. Sci. Rep. 2015, 5, 9198.10.1038/srep09198. PubMed DOI PMC

Prakash A.; Janosi L.; Doxastakis M. Self-Association of Models of Transmembrane Domains of ErbB Receptors in a Lipid Bilayer. Biophys. J. 2010, 99, 3657–3665. 10.1016/j.bpj.2010.10.023. PubMed DOI PMC

Abd Halim K. B.; Koldsø H.; Sansom M. S. P. Interactions of the EGFR Juxtamembrane Domain with PIP2-Containing Lipid Bilayers: Insights from Multiscale Molecular Dynamics Simulations. Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 1017–1025. 10.1016/j.bbagen.2014.09.006. PubMed DOI PMC

Chavent M.; Seiradake E.; Jones E. Y.; Sansom M. S. P. Structures of the EphA2 Receptor at the Membrane: Role of Lipid Interactions. Structure 2016, 24, 337–347. 10.1016/j.str.2015.11.008. PubMed DOI PMC

Poblete H.; Oyarzún I.; Olivero P.; Comer J.; Zuñiga M.; Sepulveda R. V.; Báez-Nieto D.; González Leon C.; González-Nilo F.; Latorre R. Molecular Determinants of Phosphatidylinositol 4,5-Bisphosphate (PI(4,5)P2) Binding to Transient Receptor Potential V1 (TRPV1) Channels. J. Biol. Chem. 2015, 290, 2086–2098. 10.1074/jbc.M114.613620. PubMed DOI PMC

Antollini S. S.; Barrantes F. J. Fatty Acid Regulation of Voltage- and Ligand-Gated Ion Channel Function. Front. Physiol. 2016, 7, 573.10.3389/fphys.2016.00573. PubMed DOI PMC

Baenziger J. E.; Hénault C. M.; Therien J. P. D.; Sun J. Nicotinic Acetylcholine Receptor–Lipid Interactions: Mechanistic Insight and Biological Function. Biochim. Biophys. Acta, Biomembr. 2015, 1848, 1806–1817. 10.1016/j.bbamem.2015.03.010. PubMed DOI

Barrantes F. J.; Bermudez V.; Borroni M. V.; Antollini S. S.; Pediconi M. F.; Baier J. C.; Bonini I.; Gallegos C.; Roccamo A. M.; Valles A. S.; et al. Boundary Lipids In The Nicotinic Acetylcholine Receptor Microenvironment. J. Mol. Neurosci. 2010, 40, 87–90. 10.1007/s12031-009-9262-z. PubMed DOI

Taylor K. C.; Sanders C. R. Regulation of KCNQ/Kv7 Family Voltage-Gated K+ Channels by Lipids. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 586–597. 10.1016/j.bbamem.2016.10.023. PubMed DOI PMC

Kalli A. C.; Sansom M. S. P.; Reithmeier R. A. F. Molecular Dynamics Simulations of the Bacterial UraA H+-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin. PLoS Comput. Biol. 2015, 11, e1004123.10.1371/journal.pcbi.1004123. PubMed DOI PMC

Bolivar J. H.; Muñoz-García J. C.; Castro-Dopico T.; Dijkman P. M.; Stansfeld P. J.; Watts A. Interaction of Lipids with the Neurotensin Receptor 1. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 1278–1287. 10.1016/j.bbamem.2016.02.032. PubMed DOI

Kalli A. C.; Rog T.; Vattulainen I.; Campbell I. D.; Sansom M. S. P. The Integrin Receptor in Biologically Relevant Bilayers: Insights from Molecular Dynamics Simulations. J. Membr. Biol. 2017, 250, 337–351. 10.1007/s00232-016-9908-z. PubMed DOI PMC

Orłowski A.; Kukkurainen S.; Pöyry A.; Rissanen S.; Vattulainen I.; Hytönen V. P.; Róg T. PIP2 and Talin Join Forces to Activate Integrin. J. Phys. Chem. B 2015, 119, 12381–12389. 10.1021/acs.jpcb.5b06457. PubMed DOI

Human Genome Sequencing Consortium I. Finishing the Euchromatic Sequence of the Human Genome. Nature 2004, 431, 931–945. 10.1038/nature03001. PubMed DOI

Nørregaard Jensen O. Modification-Specific Proteomics: Characterization of Post-Translational Modifications by Mass Spectrometry. Curr. Opin. Chem. Biol. 2004, 8, 33–41. 10.1016/j.cbpa.2003.12.009. PubMed DOI

The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2010, 38, D142–D148. 10.1093/nar/gkp846. PubMed DOI PMC

Liu J.; Qian C.; Cao X. Post-Translational Modification Control of Innate Immunity. Immunity 2016, 45, 15–30. 10.1016/j.immuni.2016.06.020. PubMed DOI

Bah A.; Forman-Kay J. D. Modulation of Intrinsically Disordered Protein Function by Post-Translational Modifications. J. Biol. Chem. 2016, 291, 6696–6705. 10.1074/jbc.R115.695056. PubMed DOI PMC

Kikuchi A.; Kishida S.; Yamamoto H. Regulation of Wnt Signaling by Protein-Protein Interaction and Post-Translational Modifications. Exp. Mol. Med. 2006, 38, 1–10. 10.1038/emm.2006.1. PubMed DOI

Zhao S.; Xu W.; Jiang W.; Yu W.; Lin Y.; Zhang T.; Yao J.; Zhou L.; Zeng Y.; Li H.; et al. Regulation of Cellular Metabolism by Protein Lysine Acetylation. Science 2010, 327, 1000–1004. 10.1126/science.1179689. PubMed DOI PMC

Deribe Y. L.; Pawson T.; Dikic I. Post-Translational Modifications in Signal Integration. Nat. Struct. Mol. Biol. 2010, 17, 666–672. 10.1038/nsmb.1842. PubMed DOI

Fonseca-Maldonado R.; Vieira D. S.; Alponti J. S.; Bonneil E.; Thibault P.; Ward R. J. Engineering the Pattern of Protein Glycosylation Modulates the Thermostability of a GH11 Xylanase. J. Biol. Chem. 2013, 288, 25522–25534. 10.1074/jbc.M113.485953. PubMed DOI PMC

Lu D.; Yang C.; Liu Z. How Hydrophobicity and the Glycosylation Site of Glycans Affect Protein Folding and Stability: A Molecular Dynamics Simulation. J. Phys. Chem. B 2012, 116, 390–400. 10.1021/jp203926r. PubMed DOI

Subedi G. P.; Falconer D. J.; Barb A. W. Carbohydrate–Polypeptide Contacts in the Antibody Receptor CD16A Identified through Solution NMR Spectroscopy. Biochemistry 2017, 56, 3174–3177. 10.1021/acs.biochem.7b00392. PubMed DOI PMC

Ziomkiewicz I.; Loman A.; Klement R.; Fritsch C.; Klymchenko A. S.; Bunt G.; Jovin T. M.; Arndt-Jovin D. J. Dynamic Conformational Transitions of the EGF Receptor in Living Mammalian Cells Determined by FRET and Fluorescence Lifetime Imaging Microscopy: EGFR Conformations Determined in Live Cells by FLIM. Cytometry, Part A 2013, 83, 794–805. 10.1002/cyto.a.22311. PubMed DOI

Kozer N.; Henderson C.; Jackson J. T.; Nice E. C.; Burgess A. W.; Clayton A. H. A. Evidence for Extended YFP-EGFR Dimers in the Absence of Ligand on the Surface of Living Cells. Phys. Biol. 2011, 8, 066002.10.1088/1478-3975/8/6/066002. PubMed DOI

Polley A.; Orłowski A.; Danne R.; Gurtovenko A. A.; Bernardino de la Serna J.; Eggeling C.; Davis S. J.; Róg T.; Vattulainen I. Glycosylation and Lipids Working in Concert Direct CD2 Ectodomain Orientation and Presentation. J. Phys. Chem. Lett. 2017, 8, 1060–1066. 10.1021/acs.jpclett.6b02824. PubMed DOI PMC

Danne R.; Poojari C.; Martinez-Seara H.; Rissanen S.; Lolicato F.; Róg T.; Vattulainen I. DoGlycans – Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS. J. Chem. Inf. Model. 2017, 57, 2401–2406. 10.1021/acs.jcim.7b00237. PubMed DOI PMC

Lakkaraju A. K.; Abrami L.; Lemmin T.; Blaskovic S.; Kunz B.; Kihara A.; Dal Peraro M.; van der Goot F. G. Palmitoylated Calnexin Is a Key Component of the Ribosome-Translocon Complex: Palmitoylated Calnexin Is a Key Component of the RTC. EMBO J. 2012, 31, 1823–1835. 10.1038/emboj.2012.15. PubMed DOI PMC

Thukral L.; Sengupta D.; Ramkumar A.; Murthy D.; Agrawal N.; Gokhale R. S. The Molecular Mechanism Underlying Recruitment and Insertion of Lipid-Anchored LC3 Protein into Membranes. Biophys. J. 2015, 109, 2067–2078. 10.1016/j.bpj.2015.09.022. PubMed DOI PMC

Janosi L.; Gorfe A. A. Segregation of Negatively Charged Phospholipids by the Polycationic and Farnesylated Membrane Anchor of Kras. Biophys. J. 2010, 99, 3666–3674. 10.1016/j.bpj.2010.10.031. PubMed DOI PMC

Prakash P.; Zhou Y.; Liang H.; Hancock J. F.; Gorfe A. A. Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis. Biophys. J. 2016, 110, 1125–1138. 10.1016/j.bpj.2016.01.019. PubMed DOI PMC

Edler E.; Schulze E.; Stein M. Membrane Localization and Dynamics of Geranylgeranylated Rab5 Hypervariable Region. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 1335–1349. 10.1016/j.bbamem.2017.04.021. PubMed DOI

Vogel A.; Katzka C. P.; Waldmann H.; Arnold K.; Brown M. F.; Huster D. Lipid Modifications of a Ras Peptide Exhibit Altered Packing and Mobility versus Host Membrane as Detected by 2H Solid-State NMR. J. Am. Chem. Soc. 2005, 127, 12263–12272. 10.1021/ja051856c. PubMed DOI

Zhang T.; Luo Q.; Yang L.; Jiang H.; Yang H. Characterizing the Interactions of Two Lipid Modifications with Lipid Rafts: Farnesyl Anchors vs. Palmitoyl Anchors. Eur. Biophys. J. 2018, 47, 19–30. 10.1007/s00249-017-1217-7. PubMed DOI

Sprong H.; van der Sluijs P.; van Meer G. How Proteins Move Lipids and Lipids Move Proteins. Nat. Rev. Mol. Cell Biol. 2001, 2, 504–513. 10.1038/35080071. PubMed DOI

Mellman I.; Nelson W. J. Coordinated Protein Sorting, Targeting and Distribution in Polarized Cells. Nat. Rev. Mol. Cell Biol. 2008, 9, 833–845. 10.1038/nrm2525. PubMed DOI PMC

Cullen P. J. Endosomal Sorting and Signalling: An Emerging Role for Sorting Nexins. Nat. Rev. Mol. Cell Biol. 2008, 9, 574–582. 10.1038/nrm2427. PubMed DOI

Jahn R.; Scheller R. H. SNAREs — Engines for Membrane Fusion. Nat. Rev. Mol. Cell Biol. 2006, 7, 631–643. 10.1038/nrm2002. PubMed DOI

Santiago-Tirado F. H.; Bretscher A. Membrane-Trafficking Sorting Hubs: Cooperation between PI4P and Small GTPases at the Trans-Golgi Network. Trends Cell Biol. 2011, 21, 515–525. 10.1016/j.tcb.2011.05.005. PubMed DOI PMC

Viaud J.; Mansour R.; Antkowiak A.; Mujalli A.; Valet C.; Chicanne G.; Xuereb J.-M.; Terrisse A.-D.; Séverin S.; Gratacap M.-P.; et al. Phosphoinositides: Important Lipids in the Coordination of Cell Dynamics. Biochimie 2016, 125, 250–258. 10.1016/j.biochi.2015.09.005. PubMed DOI

Mayinger P. Phosphoinositides and Vesicular Membrane Traffic. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2012, 1821, 1104–1113. 10.1016/j.bbalip.2012.01.002. PubMed DOI PMC

Chap H. Forty Five Years with Membrane Phospholipids, Phospholipases and Lipid Mediators: A Historical Perspective. Biochimie 2016, 125, 234–249. 10.1016/j.biochi.2016.04.002. PubMed DOI

Marsh D.; Horváth L. I. Structure, Dynamics and Composition of the Lipid-Protein Interface. Perspectives from Spin-Labelling. Biochim. Biophys. Acta, Rev. Biomembr. 1998, 1376, 267–296. 10.1016/S0304-4157(98)00009-4. PubMed DOI

Cartailler J.-P.; Luecke H. X-Ray Crystallographic Analysis of Lipid-Protein Interactions in the Bacteriorhodopsin Purple Membrane. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 285–310. 10.1146/annurev.biophys.32.110601.142516. PubMed DOI

Schmidt T.; Suk J.-E.; Ye F.; Situ A. J.; Mazumder P.; Ginsberg M. H.; Ulmer T. S. Annular Anionic Lipids Stabilize the Integrin αIIbβ3 Transmembrane Complex. J. Biol. Chem. 2015, 290, 8283–8293. 10.1074/jbc.M114.623504. PubMed DOI PMC

Eggensperger S.; Fisette O.; Parcej D.; Schäfer L. V.; Tampé R. An Annular Lipid Belt Is Essential for Allosteric Coupling and Viral Inhibition of the Antigen Translocation Complex TAP (Transporter Associated with Antigen Processing). J. Biol. Chem. 2014, 289, 33098–33108. 10.1074/jbc.M114.592832. PubMed DOI PMC

Polozova A.; Litman B. J. Cholesterol Dependent Recruitment of Di22:6-PC by a G Protein-Coupled Receptor into Lateral Domains. Biophys. J. 2000, 79, 2632–2643. 10.1016/S0006-3495(00)76502-7. PubMed DOI PMC

Schafer L. V.; de Jong D. H.; Holt A.; Rzepiela A. J.; de Vries A. H.; Poolman B.; Killian J. A.; Marrink S. J. Lipid Packing Drives the Segregation of Transmembrane Helices into Disordered Lipid Domains in Model Membranes. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 1343–1348. 10.1073/pnas.1009362108. PubMed DOI PMC

de Jong D. H.; Lopez C. A.; Marrink S. J. Molecular View on Protein Sorting into Liquid-Ordered Membrane Domains Mediated by Gangliosides and Lipid Anchors. Faraday Discuss. 2013, 161, 347–363. 10.1039/C2FD20086D. PubMed DOI

Li H.; Gorfe A. A. Aggregation of Lipid-Anchored Full-Length H-Ras in Lipid Bilayers: Simulations with the MARTINI Force Field. PLoS One 2013, 8, e71018.10.1371/journal.pone.0071018. PubMed DOI PMC

Yoo J.; Cui Q. Membrane-Mediated Protein-Protein Interactions and Connection to Elastic Models: A Coarse-Grained Simulation Analysis of Gramicidin A Association. Biophys. J. 2013, 104, 128–138. 10.1016/j.bpj.2012.11.3813. PubMed DOI PMC

Sun H.; Chen L.; Gao L.; Fang W. Nanodomain Formation of Ganglioside GM1 in Lipid Membrane: Effects of Cholera Toxin-Mediated Cross-Linking. Langmuir 2015, 31, 9105–9114. 10.1021/acs.langmuir.5b01866. PubMed DOI

Pezeshkian W.; Hansen A. G.; Johannes L.; Khandelia H.; Shillcock J. C.; Kumar P. B. S.; Ipsen J. H. Membrane Invagination Induced by Shiga Toxin B-Subunit: From Molecular Structure to Tube Formation. Soft Matter 2016, 12, 5164–5171. 10.1039/C6SM00464D. PubMed DOI

Pezeshkian W.; Gao H.; Arumugam S.; Becken U.; Bassereau P.; Florent J.-C.; Ipsen J. H.; Johannes L.; Shillcock J. C. Mechanism of Shiga Toxin Clustering on Membranes. ACS Nano 2017, 11, 314–324. 10.1021/acsnano.6b05706. PubMed DOI PMC

López C. A.; Sethi A.; Goldstein B.; Wilson B. S.; Gnanakaran S. Membrane-Mediated Regulation of the Intrinsically Disordered CD3ϵ Cytoplasmic Tail of the TCR. Biophys. J. 2015, 108, 2481–2491. 10.1016/j.bpj.2015.03.059. PubMed DOI PMC

Sun F.; Chen L.; Wei P.; Chai M.; Ding X.; Xu L.; Luo S.-Z. Dimerization and Structural Stability of Amyloid Precursor Proteins Affected by the Membrane Microenvironments. J. Chem. Inf. Model. 2017, 57, 1375–1387. 10.1021/acs.jcim.7b00196. PubMed DOI

Lorent J. H.; Diaz-Rohrer B.; Lin X.; Spring K.; Gorfe A. A.; Levental K. R.; Levental I. Structural Determinants and Functional Consequences of Protein Affinity for Membrane Rafts. Nat. Commun. 2017, 8, 1219.10.1038/s41467-017-01328-3. PubMed DOI PMC

Sharpe H. J.; Stevens T. J.; Munro S. A Comprehensive Comparison of Transmembrane Domains Reveals Organelle-Specific Properties. Cell 2010, 142, 158–169. 10.1016/j.cell.2010.05.037. PubMed DOI PMC

Lin X.; Gorfe A. A.; Levental I. Protein Partitioning into Ordered Membrane Domains: Insights from Simulations. Biophys. J. 2018, 114, 1936–1944. 10.1016/j.bpj.2018.03.020. PubMed DOI PMC

Kaiser H.-J.; Orlowski A.; Rog T.; Nyholm T. K. M.; Chai W.; Feizi T.; Lingwood D.; Vattulainen I.; Simons K. Lateral Sorting in Model Membranes by Cholesterol-Mediated Hydrophobic Matching. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 16628–16633. 10.1073/pnas.1103742108. PubMed DOI PMC

Grau B.; Javanainen M.; García-Murria M. J.; Kulig W.; Vattulainen I.; Mingarro I.; Martínez-Gil L. The Role of Hydrophobic Matching on Transmembrane Helix Packing in Cells. Cell Stress 2017, 1, 90–106. 10.15698/cst2017.11.111. PubMed DOI PMC

Heidmann T.; Sobel A.; Popot J.-L.; Changeux J.-P. Reconstitution of a Functional Acetylcholine Receptor. Conservation of the Conformational and Allosteric Transitions and Recovery of the Permeability Response; Role of Lipids. Eur. J. Biochem. 1980, 110, 35–55. 10.1111/j.1432-1033.1980.tb04839.x. PubMed DOI

daCosta C. J. B.; Medaglia S. A.; Lavigne N.; Wang S.; Carswell C. L.; Baenziger J. E. Anionic Lipids Allosterically Modulate Multiple Nicotinic Acetylcholine Receptor Conformational Equilibria. J. Biol. Chem. 2009, 284, 33841–33849. 10.1074/jbc.M109.048280. PubMed DOI PMC

Baenziger J. E.; Domville J. A.; Therien J. P. D.. The Role of Cholesterol in the Activation of Nicotinic Acetylcholine Receptors. Current Topics in Membranes; Elsevier, 2017; Vol. 80, pp 95–137, 10.1016/bs.ctm.2017.05.002. PubMed DOI

Domville J. A.; Baenziger J. E. An Allosteric Link Connecting the Lipid-Protein Interface to the Gating of the Nicotinic Acetylcholine Receptor. Sci. Rep. 2018, 8, 3898.10.1038/s41598-018-22150-x. PubMed DOI PMC

Ghosh M.; Wang L. C.; Ramesh R.; Morgan L. K.; Kenney L. J.; Anand G. S. Lipid-Mediated Regulation of Embedded Receptor Kinases via Parallel Allosteric Relays. Biophys. J. 2017, 112, 643–654. 10.1016/j.bpj.2016.12.027. PubMed DOI PMC

Coskun U.; Grzybek M.; Drechsel D.; Simons K. Regulation of Human EGF Receptor by Lipids. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 9044–9048. 10.1073/pnas.1105666108. PubMed DOI PMC

Prasanna X.; Chattopadhyay A.; Sengupta D. Cholesterol Modulates the Dimer Interface of the β2-Adrenergic Receptor via Cholesterol Occupancy Sites. Biophys. J. 2014, 106, 1290–1300. 10.1016/j.bpj.2014.02.002. PubMed DOI PMC

Zhang Q.; Zhou P.; Chen Z.; Li M.; Jiang H.; Gao Z.; Yang H. Dynamic PIP2 Interactions with Voltage Sensor Elements Contribute to KCNQ2 Channel Gating. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 20093–20098. 10.1073/pnas.1312483110. PubMed DOI PMC

Delemotte L.; Tarek M.; Klein M. L.; Amaral C.; Treptow W. Intermediate States of the Kv1.2 Voltage Sensor from Atomistic Molecular Dynamics Simulations. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 6109–6114. 10.1073/pnas.1102724108. PubMed DOI PMC

Schmidt D.; Jiang Q.-X.; MacKinnon R. Phospholipids and the Origin of Cationic Gating Charges in Voltage Sensors. Nature 2006, 444, 775–779. 10.1038/nature05416. PubMed DOI

Xu Y.; Ramu Y.; Lu Z. Removal of Phospho-Head Groups of Membrane Lipids Immobilizes Voltage Sensors of K+ Channels. Nature 2008, 451, 826–829. 10.1038/nature06618. PubMed DOI PMC

Ramu Y.; Xu Y.; Lu Z. Enzymatic Activation of Voltage-Gated Potassium Channels. Nature 2006, 442, 696–699. 10.1038/nature04880. PubMed DOI

Lingwood D.; Binnington B.; Róg T.; Vattulainen I.; Grzybek M.; Coskun Ü.; Lingwood C. A.; Simons K. Cholesterol Modulates Glycolipid Conformation and Receptor Activity. Nat. Chem. Biol. 2011, 7, 260–262. 10.1038/nchembio.551. PubMed DOI

Prasanna X.; Jafurulla M.; Sengupta D.; Chattopadhyay A. The Ganglioside GM1 Interacts with the Serotonin1A Receptor via the Sphingolipid Binding Domain. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2818–2826. 10.1016/j.bbamem.2016.08.009. PubMed DOI

Arcario M. J.; Mayne C. G.; Tajkhorshid E. Atomistic Models of General Anesthetics for Use in in Silico Biological Studies. J. Phys. Chem. B 2014, 118, 12075–12086. 10.1021/jp502716m. PubMed DOI PMC

Arcario M. J.; Mayne C. G.; Tajkhorshid E. A Membrane-Embedded Pathway Delivers General Anesthetics to Two Interacting Binding Sites in the Gloeobacter Violaceus Ion Channel. J. Biol. Chem. 2017, 292, 9480–9492. 10.1074/jbc.M117.780197. PubMed DOI PMC

Nury H.; Van Renterghem C.; Weng Y.; Tran A.; Baaden M.; Dufresne V.; Changeux J.-P.; Sonner J. M.; Delarue M.; Corringer P.-J. X-Ray Structures of General Anaesthetics Bound to a Pentameric Ligand-Gated Ion Channel. Nature 2011, 469, 428–431. 10.1038/nature09647. PubMed DOI

Hanson S. M.; Newstead S.; Swartz K. J.; Sansom M. S. P. Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation. Biophys. J. 2015, 108, 1425–1434. 10.1016/j.bpj.2015.02.013. PubMed DOI PMC

Melo M. N.; Arnarez C.; Sikkema H.; Kumar N.; Walko M.; Berendsen H. J. C.; Kocer A.; Marrink S. J.; Ingólfsson H. I. High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. J. Am. Chem. Soc. 2017, 139, 2664–2671. 10.1021/jacs.6b11091. PubMed DOI PMC

Jerabek H.; Pabst G.; Rappolt M.; Stockner T. Membrane-Mediated Effect on Ion Channels Induced by the Anesthetic Drug Ketamine. J. Am. Chem. Soc. 2010, 132, 7990–7997. 10.1021/ja910843d. PubMed DOI

Mojumdar E. H.; Lyubartsev A. P. Molecular Dynamics Simulations of Local Anesthetic Articaine in a Lipid Bilayer. Biophys. Chem. 2010, 153, 27–35. 10.1016/j.bpc.2010.10.001. PubMed DOI

Skjevik Å. A.; Haug B. E.; Lygre H.; Teigen K. Intramolecular Hydrogen Bonding in Articaine Can Be Related to Superior Bone Tissue Penetration: A Molecular Dynamics Study. Biophys. Chem. 2011, 154, 18–25. 10.1016/j.bpc.2010.12.002. PubMed DOI

Cascales J. J. L.; Costa S. D. O.; Porasso R. D. Thermodynamic Study of Benzocaine Insertion into Different Lipid Bilayers. J. Chem. Phys. 2011, 135, 135103.10.1063/1.3643496. PubMed DOI

Hansen A. H.; Sørensen K. T.; Mathieu R.; Serer A.; Duelund L.; Khandelia H.; Hansen P. L.; Simonsen A. C. Propofol Modulates the Lipid Phase Transition and Localizes near the Headgroup of Membranes. Chem. Phys. Lipids 2013, 175–176, 84–91. 10.1016/j.chemphyslip.2013.08.002. PubMed DOI

do Canto A. M. T. M.; Carvalho A. J. P.; Ramalho J. P. P.; Loura L. M. S. Molecular Dynamics Simulations of T-20 HIV Fusion Inhibitor Interacting with Model Membranes. Biophys. Chem. 2011, 159, 275–286. 10.1016/j.bpc.2011.08.001. PubMed DOI

Leonis G.; Czyżnikowska Ż.; Megariotis G.; Reis H.; Papadopoulos M. G. Computational Studies of Darunavir into HIV-1 Protease and DMPC Bilayer: Necessary Conditions for Effective Binding and the Role of the Flaps. J. Chem. Inf. Model. 2012, 52, 1542–1558. 10.1021/ci300014z. PubMed DOI

Laurent B.; Murail S.; Shahsavar A.; Sauguet L.; Delarue M.; Baaden M. Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure 2016, 24, 595–605. 10.1016/j.str.2016.02.014. PubMed DOI

Woll K. A.; Peng W.; Liang Q.; Zhi L.; Jacobs J. A.; Maciunas L.; Bhanu N.; Garcia B. A.; Covarrubias M.; Loll P. J.; et al. Photoaffinity Ligand for the Inhalational Anesthetic Sevoflurane Allows Mechanistic Insight into Potassium Channel Modulation. ACS Chem. Biol. 2017, 12, 1353–1362. 10.1021/acschembio.7b00222. PubMed DOI

Sierra-Valdez F. J.; Forero-Quintero L. S.; Zapata-Morin P. A.; Costas M.; Chavez-Reyes A.; Ruiz-Suárez J. C. The Influence of Non Polar and Polar Molecules in Mouse Motile Cells Membranes and Pure Lipid Bilayers. PLoS One 2013, 8, e59364.10.1371/journal.pone.0059364. PubMed DOI PMC

Amjad-Iranagh S.; Yousefpour A.; Haghighi P.; Modarress H. Effects of Protein Binding on a Lipid Bilayer Containing Local Anesthetic Articaine, and the Potential of Mean Force Calculation: A Molecular Dynamics Simulation Approach. J. Mol. Model. 2013, 19, 3831–3842. 10.1007/s00894-013-1917-6. PubMed DOI

Booker R. D.; Sum A. K. Biophysical Changes Induced by Xenon on Phospholipid Bilayers. Biochim. Biophys. Acta, Biomembr. 2013, 1828, 1347–1356. 10.1016/j.bbamem.2013.01.016. PubMed DOI

Martini M. F.; Pickholz M. Molecular Dynamics Study of Uncharged Bupivacaine Enantiomers in Phospholipid Bilayers. Int. J. Quantum Chem. 2012, 112, 3341–3345. 10.1002/qua.24208. DOI

Bernardi R. C.; Pascutti P. G. Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction. J. Chem. Theory Comput. 2012, 8, 2197–2203. 10.1021/ct300213u. PubMed DOI

López Cascales J. J.; Oliveira Costa S. D. Effect of the Interfacial Tension and Ionic Strength on the Thermodynamic Barrier Associated to the Benzocaine Insertion into a Cell Membrane. Biophys. Chem. 2013, 172, 1–7. 10.1016/j.bpc.2012.12.001. PubMed DOI

Darvas M.; Hoang P. N. M.; Picaud S.; Sega M.; Jedlovszky P. Anesthetic Molecules Embedded in a Lipid Membrane: A Computer Simulation Study. Phys. Chem. Chem. Phys. 2012, 14, 12956–12969. 10.1039/c2cp41581j. PubMed DOI

Fábián B.; Sega M.; Voloshin V. P.; Medvedev N. N.; Jedlovszky P. Lateral Pressure Profile and Free Volume Properties in Phospholipid Membranes Containing Anesthetics. J. Phys. Chem. B 2017, 121, 2814–2824. 10.1021/acs.jpcb.7b00990. PubMed DOI

Fábián B.; Darvas M.; Picaud S.; Sega M.; Jedlovszky P. The Effect of Anaesthetics on the Properties of a Lipid Membrane in the Biologically Relevant Phase: A Computer Simulation Study. Phys. Chem. Chem. Phys. 2015, 17, 14750–14760. 10.1039/C5CP00851D. PubMed DOI

Chau P.-L.; Tu K. M.; Liang K. K.; Todorov I. T.; Roser S. J.; Barker R.; Matubayasi N. The Effect of Pressure on Halothane Binding to Hydrated DMPC Bilayers. Mol. Phys. 2012, 110, 1461–1467. 10.1080/00268976.2012.659682. DOI

Tu K. M.; Matubayasi N.; Liang K. K.; Todorov I. T.; Chan S. L.; Chau P.-L. A Possible Molecular Mechanism for the Pressure Reversal of General Anaesthetics: Aggregation of Halothane in POPC Bilayers at High Pressure. Chem. Phys. Lett. 2012, 543, 148–154. 10.1016/j.cplett.2012.06.044. DOI

Woll K. A.; Murlidaran S.; Pinch B. J.; Hénin J.; Wang X.; Salari R.; Covarrubias M.; Dailey W. P.; Brannigan G.; Garcia B. A.; et al. A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of γ-Aminobutyric Acid, Type A (GABAA), Receptor Subunit Binding Selectivity in Synaptosomes. J. Biol. Chem. 2016, 291, 20473–20486. 10.1074/jbc.M116.736975. PubMed DOI PMC

Bruns D.; Riedel D.; Klingauf J.; Jahn R. Quantal Release of Serotonin. Neuron 2000, 28, 205–220. 10.1016/S0896-6273(00)00097-0. PubMed DOI

Cantor R. S. Receptor Desensitization by Neurotransmitters in Membranes: Are Neurotransmitters the Endogenous Anesthetics?. Biochemistry 2003, 42, 11891–11897. 10.1021/bi034534z. PubMed DOI

Milutinovic P. S.; Yang L.; Cantor R. S.; Eger E. I.; Sonner J. M. Anesthetic-Like Modulation of a γ-Aminobutyric Acid Type A, Strychnine-Sensitive Glycine, and N-Methyl-d-Aspartate Receptors by Coreleased Neurotransmitters: Anesth. Anesth. Analg. 2007, 105, 386–392. 10.1213/01.ane.0000267258.17197.7d. PubMed DOI

Seeger H. M.; Gudmundsson M. L.; Heimburg T. How Anesthetics, Neurotransmitters, and Antibiotics Influence the Relaxation Processes in Lipid Membranes. J. Phys. Chem. B 2007, 111, 13858–13866. 10.1021/jp075346b. PubMed DOI

Sonner J. M.; Cantor R. S. Molecular Mechanisms of Drug Action: An Emerging View. Annu. Rev. Biophys. 2013, 42, 143–167. 10.1146/annurev-biophys-083012-130341. PubMed DOI

Cantor R. S. Lateral Pressures in Cell Membranes: A Mechanism for Modulation of Protein Function. J. Phys. Chem. B 1997, 101, 1723–1725. 10.1021/jp963911x. DOI

Peters G. H.; Werge M.; Elf-Lind M. N.; Madsen J. J.; Velardez G. F.; Westh P. Interaction of Neurotransmitters with a Phospholipid Bilayer: A Molecular Dynamics Study. Chem. Phys. Lipids 2014, 184, 7–17. 10.1016/j.chemphyslip.2014.08.003. PubMed DOI

Peters G. H.; Wang C.; Cruys-Bagger N.; Velardez G. F.; Madsen J. J.; Westh P. Binding of Serotonin to Lipid Membranes. J. Am. Chem. Soc. 2013, 135, 2164–2171. 10.1021/ja306681d. PubMed DOI

Diener E.; Biswas-Diener R.. Happiness; Blackwell Publishing Ltd.: Oxford, UK, 2008. 10.1002/9781444305159. DOI

Robertson R. W. The Relationships between Leisure and Happiness. World Leis. J. 2016, 58, 242–244. 10.1080/16078055.2016.1225880. DOI

Orłowski A.; Grzybek M.; Bunker A.; Pasenkiewicz-Gierula M.; Vattulainen I.; Männistö P. T.; Róg T. Strong Preferences of Dopamine and l-Dopa towards Lipid Head Group: Importance of Lipid Composition and Implication for Neurotransmitter Metabolism: Neurotransmitters and Membranes. J. Neurochem. 2012, 122, 681–690. 10.1111/j.1471-4159.2012.07813.x. PubMed DOI

Harrison P. J.; Weinberger D. R. Schizophrenia Genes, Gene Expression and Neuropathology: On the Matter of Their Convergence. Mol. Psychiatry 2005, 10, 40–68. 10.1038/sj.mp.4001558. PubMed DOI

Schmitt A.; Wilczek K.; Blennow K.; Maras A.; Jatzko A.; Petroianu G.; Braus D. F.; Gattaz W. F. Altered Thalamic Membrane Phospholipids in Schizophrenia: A Postmortem Study. Biol. Psychiatry 2004, 56, 41–45. 10.1016/j.biopsych.2004.03.019. PubMed DOI

Wang C.; Ye F.; Velardez G. F.; Peters G. H.; Westh P. Affinity of Four Polar Neurotransmitters for Lipid Bilayer Membranes. J. Phys. Chem. B 2011, 115, 196–203. 10.1021/jp108368w. PubMed DOI

Shen C.; Xue M.; Qiu H.; Guo W. Insertion of Neurotransmitters into a Lipid Bilayer Membrane and Its Implication on Membrane Stability: A Molecular Dynamics Study. ChemPhysChem 2017, 18, 626–633. 10.1002/cphc.201601184. PubMed DOI

Postila P. A.; Vattulainen I.; Róg T. Selective Effect of Cell Membrane on Synaptic Neurotransmission. Sci. Rep. 2016, 6, 19345.10.1038/srep19345. PubMed DOI PMC

Reigada R. Atomistic Study of Lipid Membranes Containing Chloroform: Looking for a Lipid-Mediated Mechanism of Anesthesia. PLoS One 2013, 8, e52631.10.1371/journal.pone.0052631. PubMed DOI PMC

Mokkila S.; Postila P. A.; Rissanen S.; Juhola H.; Vattulainen I.; Róg T. Calcium Assists Dopamine Release by Preventing Aggregation on the Inner Leaflet of Presynaptic Vesicles. ACS Chem. Neurosci. 2017, 8, 1242–1250. 10.1021/acschemneuro.6b00395. PubMed DOI

Puchkov D.; Haucke V. Greasing the Synaptic Vesicle Cycle by Membrane Lipids. Trends Cell Biol. 2013, 23, 493–503. 10.1016/j.tcb.2013.05.002. PubMed DOI

Whited A. M.; Johs A. The Interactions of Peripheral Membrane Proteins with Biological Membranes. Chem. Phys. Lipids 2015, 192, 51–59. 10.1016/j.chemphyslip.2015.07.015. PubMed DOI

Zwaal R. F. A.; Comfurius P.; Bevers E. M. Lipid–Protein Interactions in Blood Coagulation. Biochim. Biophys. Acta, Rev. Biomembr. 1998, 1376, 433–453. 10.1016/S0304-4157(98)00018-5. PubMed DOI

Harrison S. C. Viral Membrane Fusion. Nat. Struct. Mol. Biol. 2008, 15, 690–698. 10.1038/nsmb.1456. PubMed DOI PMC

Murray D.; Arbuzova A.; Hangyás-Mihályné G.; Gambhir A.; Ben-Tal N.; Honig B.; McLaughlin S. Electrostatic Properties of Membranes Containing Acidic Lipids and Adsorbed Basic Peptides: Theory and Experiment. Biophys. J. 1999, 77, 3176–3188. 10.1016/S0006-3495(99)77148-1. PubMed DOI PMC

Johnson J. E.; Cornell R. B. Amphitropic Proteins: Regulation by Reversible Membrane Interactions (Review). Mol. Membr. Biol. 1999, 16, 217–235. 10.1080/096876899294544. PubMed DOI

Kim J.; Mosior M.; Chung L. A.; Wu H.; McLaughlin S. Binding of Peptides with Basic Residues to Membranes Containing Acidic Phospholipids. Biophys. J. 1991, 60, 135–148. 10.1016/S0006-3495(91)82037-9. PubMed DOI PMC

Ben-Tal N.; Honig B.; Peitzsch R. M.; Denisov G.; McLaughlin S. Binding of Small Basic Peptides to Membranes Containing Acidic Lipids: Theoretical Models and Experimental Results. Biophys. J. 1996, 71, 561–575. 10.1016/S0006-3495(96)79280-9. PubMed DOI PMC

Kirchhausen T. Imaging Endocytic Clathrin Structures in Living Cells. Trends Cell Biol. 2009, 19, 596–605. 10.1016/j.tcb.2009.09.002. PubMed DOI PMC

Kalli A. C.; Devaney I.; Sansom M. S. P. Interactions of Phosphatase and Tensin Homologue (PTEN) Proteins with Phosphatidylinositol Phosphates: Insights from Molecular Dynamics Simulations of PTEN and Voltage Sensitive Phosphatase. Biochemistry 2014, 53, 1724–1732. 10.1021/bi5000299. PubMed DOI PMC

Lumb C. N.; Sansom M. S. P. Finding a Needle in a Haystack: The Role of Electrostatics in Target Lipid Recognition by PH Domains. PLoS Comput. Biol. 2012, 8, e1002617.10.1371/journal.pcbi.1002617. PubMed DOI PMC

Lumb C. N.; He J.; Xue Y.; Stansfeld P. J.; Stahelin R. V.; Kutateladze T. G.; Sansom M. S. P. Biophysical and Computational Studies of Membrane Penetration by the GRP1 Pleckstrin Homology Domain. Structure 2011, 19, 1338–1346. 10.1016/j.str.2011.04.010. PubMed DOI PMC

Naughton F. B.; Kalli A. C.; Sansom M. S. P. Association of Peripheral Membrane Proteins with Membranes: Free Energy of Binding of GRP1 PH Domain with Phosphatidylinositol Phosphate-Containing Model Bilayers. J. Phys. Chem. Lett. 2016, 7, 1219–1224. 10.1021/acs.jpclett.6b00153. PubMed DOI PMC

Lai C.-L.; Srivastava A.; Pilling C.; Chase A. R.; Falke J. J.; Voth G. A. Molecular Mechanism of Membrane Binding of the GRP1 PH Domain. J. Mol. Biol. 2013, 425, 3073–3090. 10.1016/j.jmb.2013.05.026. PubMed DOI PMC

Chan K. C.; Lu L.; Sun F.; Fan J. Molecular Details of the PH Domain of ACAP1BAR-PH Protein Binding to PIP-Containing Membrane. J. Phys. Chem. B 2017, 121, 3586–3596. 10.1021/acs.jpcb.6b09563. PubMed DOI

Yamamoto E.; Kalli A. C.; Yasuoka K.; Sansom M. S. P. Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High-Throughput Molecular Dynamics. Structure 2016, 24, 1421–1431. 10.1016/j.str.2016.06.002. PubMed DOI PMC

Rogaski B.; Klauda J. B. Membrane-Binding Mechanism of a Peripheral Membrane Protein through Microsecond Molecular Dynamics Simulations. J. Mol. Biol. 2012, 423, 847–861. 10.1016/j.jmb.2012.08.015. PubMed DOI

Pleskot R.; Pejchar P.; Žárský V.; Staiger C. J.; Potocký M. Structural Insights into the Inhibition of Actin-Capping Protein by Interactions with Phosphatidic Acid and Phosphatidylinositol (4,5)-Bisphosphate. PLoS Comput. Biol. 2012, 8, e1002765.10.1371/journal.pcbi.1002765. PubMed DOI PMC

Hakala M.; Kalimeri M.; Enkavi G.; Vattulainen I.; Lappalainen P. Molecular Mechanism for Inhibition of Twinfilin by Phosphoinositides. J. Biol. Chem. 2018, 293, 4818–4829. 10.1074/jbc.RA117.000484. PubMed DOI PMC

Zhang L.; Mao Y. S.; Janmey P. A.; Yin H. L.. Phosphatidylinositol 4, 5 Bisphosphate and the Actin Cytoskeleton. In Phosphoinositides II: The Diverse Biological Functions; Balla T., Wymann M., York J. D., Eds.; Springer Netherlands: Dordrecht, 2012; Vol. 59, pp 177–215, 10.1007/978-94-007-3015-1_6. PubMed DOI

Lamprakis C.; Stocker A.; Cascella M. Mechanisms of Recognition and Binding of α-TTP to the Plasma Membrane by Multi-Scale Molecular Dynamics Simulations. Front. Mol. Biosci. 2015, 2, 36.10.3389/fmolb.2015.00036. PubMed DOI PMC

Busse R. A.; Scacioc A.; Krick R.; Pérez-Lara Á.; Thumm M.; Kühnel K. Characterization of PROPPIN-Phosphoinositide Binding and Role of Loop 6CD in PROPPIN-Membrane Binding. Biophys. J. 2015, 108, 2223–2234. 10.1016/j.bpj.2015.03.045. PubMed DOI PMC

Ghosh R.; de Campos M. K. F.; Huang J.; Huh S. K.; Orlowski A.; Yang Y.; Tripathi A.; Nile A.; Lee H.-C.; Dynowski M.; et al. Sec14-Nodulin Proteins and the Patterning of Phosphoinositide Landmarks for Developmental Control of Membrane Morphogenesis. Mol. Biol. Cell 2015, 26, 1764–1781. 10.1091/mbc.E14-10-1475. PubMed DOI PMC

Charlier L.; Louet M.; Chaloin L.; Fuchs P.; Martinez J.; Muriaux D.; Favard C.; Floquet N. Coarse-Grained Simulations of the HIV-1 Matrix Protein Anchoring: Revisiting Its Assembly on Membrane Domains. Biophys. J. 2014, 106, 577–585. 10.1016/j.bpj.2013.12.019. PubMed DOI PMC

Basu I.; Mukhopadhyay C. Insights into Binding of Cholera Toxin to GM1 Containing Membrane. Langmuir 2014, 30, 15244–15252. 10.1021/la5036618. PubMed DOI

Rodighiero C.; Aman A. T.; Kenny M. J.; Moss J.; Lencer W. I.; Hirst T. R. Structural Basis for the Differential Toxicity of Cholera Toxin and Escherichia Coli Heat-Labile Enterotoxin: Construction of Hybrid Toxins Identifies the A2-Domain as the Determinant of Differential Toxicity. J. Biol. Chem. 1999, 274, 3962–3969. 10.1074/jbc.274.7.3962. PubMed DOI

Arcario M. J.; Tajkhorshid E. Membrane-Induced Structural Rearrangement and Identification of a Novel Membrane Anchor in Talin F2F3. Biophys. J. 2014, 107, 2059–2069. 10.1016/j.bpj.2014.09.022. PubMed DOI PMC

Calderwood D. A.; Zent R.; Grant R.; Rees D. J. G.; Hynes R. O.; Ginsberg M. H. The Talin Head Domain Binds to Integrin β Subunit Cytoplasmic Tails and Regulates Integrin Activation. J. Biol. Chem. 1999, 274, 28071–28074. 10.1074/jbc.274.40.28071. PubMed DOI

Calderwood D. A.; Yan B.; de Pereda J. M.; Alvarez B. G.; Fujioka Y.; Liddington R. C.; Ginsberg M. H. The Phosphotyrosine Binding-like Domain of Talin Activates Integrins. J. Biol. Chem. 2002, 277, 21749–21758. 10.1074/jbc.M111996200. PubMed DOI

Li J.; Ziemba B. P.; Falke J. J.; Voth G. A. Interactions of Protein Kinase C-α C1A and C1B Domains with Membranes: A Combined Computational and Experimental Study. J. Am. Chem. Soc. 2014, 136, 11757–11766. 10.1021/ja505369r. PubMed DOI PMC

Ziemba B. P.; Li J.; Landgraf K. E.; Knight J. D.; Voth G. A.; Falke J. J. Single-Molecule Studies Reveal a Hidden Key Step in the Activation Mechanism of Membrane-Bound Protein Kinase C-α. Biochemistry 2014, 53, 1697–1713. 10.1021/bi4016082. PubMed DOI PMC

Zhang L.; Rajendram M.; Weibel D. B.; Yethiraj A.; Cui Q. Ionic Hydrogen Bonds and Lipid Packing Defects Determine the Binding Orientation and Insertion Depth of RecA on Multicomponent Lipid Bilayers. J. Phys. Chem. B 2016, 120, 8424–8437. 10.1021/acs.jpcb.6b02164. PubMed DOI

Maxfield F. R.; Tabas I. Role of Cholesterol and Lipid Organization in Disease. Nature 2005, 438, 612–621. 10.1038/nature04399. PubMed DOI

Hallman M.; Glumoff V.; Rämet M. Surfactant in Respiratory Distress Syndrome and Lung Injury. Comp. Biochem. Physiol., Part A: Mol. Integr. Physiol. 2001, 129, 287–294. 10.1016/S1095-6433(01)00324-5. PubMed DOI

Cho W.-J.; Trikha S.; Jeremic A. M. Cholesterol Regulates Assembly of Human Islet Amyloid Polypeptide on Model Membranes. J. Mol. Biol. 2009, 393, 765–775. 10.1016/j.jmb.2009.08.055. PubMed DOI

Allott E. H.; Howard L. E.; Cooperberg M. R.; Kane C. J.; Aronson W. J.; Terris M. K.; Amling C. L.; Freedland S. J. Serum Lipid Profile and Risk of Prostate Cancer Recurrence: Results from the SEARCH Database. Cancer Epidemiol., Biomarkers Prev. 2014, 23, 2349–2356. 10.1158/1055-9965.EPI-14-0458. PubMed DOI PMC

Welte M. A. Expanding Roles for Lipid Droplets. Curr. Biol. 2015, 25, R470–R481. 10.1016/j.cub.2015.04.004. PubMed DOI PMC

Walther T. C.; Farese R. V. Lipid Droplets and Cellular Lipid Metabolism. Annu. Rev. Biochem. 2012, 81, 687–714. 10.1146/annurev-biochem-061009-102430. PubMed DOI PMC

Pol A.; Gross S. P.; Parton R. G. Biogenesis of the Multifunctional Lipid Droplet: Lipids, Proteins, and Sites. J. Cell Biol. 2014, 204, 635–646. 10.1083/jcb.201311051. PubMed DOI PMC

Henneré G.; Prognon P.; Brion F.; Nicolis I. Molecular Dynamics Study of a Phospholipid Monolayer at a Water/Triglyceride Interface: Towards Lipid Emulsion Modelling. Chem. Phys. Lipids 2009, 157, 86–93. 10.1016/j.chemphyslip.2008.10.002. PubMed DOI

Henneré G.; Prognon P.; Brion F.; Rosilio V.; Nicolis I. Molecular Dynamics Simulation of a Mixed Lipid Emulsion Model: Influence of the Triglycerides on Interfacial Phospholipid Organization. J. Mol. Struct.: THEOCHEM 2009, 901, 174–185. 10.1016/j.theochem.2009.01.020. DOI

Koivuniemi A.; Heikelä M.; Kovanen P. T.; Vattulainen I.; Hyvönen M. T. Atomistic Simulations of Phosphatidylcholines and Cholesteryl Esters in High-Density Lipoprotein-Sized Lipid Droplet and Trilayer: Clues to Cholesteryl Ester Transport and Storage. Biophys. J. 2009, 96, 4099–4108. 10.1016/j.bpj.2009.01.058. PubMed DOI PMC

Koivuniemi A.; Vuorela T.; Kovanen P. T.; Vattulainen I.; Hyvönen M. T. Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-Grained Simulations. PLoS Comput. Biol. 2012, 8, e1002299.10.1371/journal.pcbi.1002299. PubMed DOI PMC

Ollila O. H. S.; Lamberg A.; Lehtivaara M.; Koivuniemi A.; Vattulainen I. Interfacial Tension and Surface Pressure of High Density Lipoprotein, Low Density Lipoprotein, and Related Lipid Droplets. Biophys. J. 2012, 103, 1236–1244. 10.1016/j.bpj.2012.08.023. PubMed DOI PMC

Prévost C.; Sharp M. E.; Kory N.; Lin Q.; Voth G. A.; Farese R. V.; Walther T. C. Mechanism and Determinants of Amphipathic Helix-Containing Protein Targeting to Lipid Droplets. Dev. Cell 2018, 44, 73–86.e4. 10.1016/j.devcel.2017.12.011. PubMed DOI PMC

Bacle A.; Gautier R.; Jackson C. L.; Fuchs P. F. J.; Vanni S. Interdigitation between Triglycerides and Lipids Modulates Surface Properties of Lipid Droplets. Biophys. J. 2017, 112, 1417–1430. 10.1016/j.bpj.2017.02.032. PubMed DOI PMC

Kulovesi P.; Telenius J.; Koivuniemi A.; Brezesinski G.; Rantamäki A.; Viitala T.; Puukilainen E.; Ritala M.; Wiedmer S. K.; Vattulainen I.; et al. Molecular Organization of the Tear Fluid Lipid Layer. Biophys. J. 2010, 99, 2559–2567. 10.1016/j.bpj.2010.08.001. PubMed DOI PMC

Telenius J.; Koivuniemi A.; Kulovesi P.; Holopainen J. M.; Vattulainen I. Role of Neutral Lipids in Tear Fluid Lipid Layer: Coarse-Grained Simulation Study. Langmuir 2012, 28, 17092–17100. 10.1021/la304366d. PubMed DOI

Khandelia H.; Duelund L.; Pakkanen K. I.; Ipsen J. H. Triglyceride Blisters in Lipid Bilayers: Implications for Lipid Droplet Biogenesis and the Mobile Lipid Signal in Cancer Cell Membranes. PLoS One 2010, 5, e12811.10.1371/journal.pone.0012811. PubMed DOI PMC

Chaban V. V.; Khandelia H. Lipid Structure in Triolein Lipid Droplets. J. Phys. Chem. B 2014, 118, 10335–10340. 10.1021/jp503223z. PubMed DOI

Chaban V. V.; Khandelia H. Distribution of Neutral Lipids in the Lipid Droplet Core. J. Phys. Chem. B 2014, 118, 11145–11151. 10.1021/jp506693d. PubMed DOI

Pan L.; Segrest J. P. Computational Studies of Plasma Lipoprotein Lipids. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2401–2420. 10.1016/j.bbamem.2016.03.010. PubMed DOI

Koivuniemi A.; Vattulainen I.. Modeling of Lipid Membranes and Lipoproteins. In A Systems Biology Approach to Study Metabolic Syndrome; Orešič M., Vidal-Puig A., Eds.; Springer International Publishing: Cham, 2014; pp 299–318, 10.1007/978-3-319-01008-3_15. DOI

Koivuniemi A.; Vattulainen I. Revealing Structural and Dynamical Properties of High Density Lipoproteins through Molecular Simulations. Soft Matter 2012, 8, 1262–1267. 10.1039/C1SM06742G. DOI

Hevonoja T.; Pentikäinen M. O.; Hyvönen M. T.; Kovanen P. T.; Ala-Korpela M. Structure of Low Density Lipoprotein (LDL) Particles: Basis for Understanding Molecular Changes in Modified LDL. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2000, 1488, 189–210. 10.1016/S1388-1981(00)00123-2. PubMed DOI

Murtola T.; Vuorela T. A.; Hyvönen M. T.; Marrink S.-J.; Karttunen M.; Vattulainen I. Low Density Lipoprotein: Structure, Dynamics, and Interactions of ApoB-100 with Lipids. Soft Matter 2011, 7, 8135–8141. 10.1039/c1sm05367a. DOI

Rosenson R. S.; Brewer H. B.; Ansell B. J.; Barter P.; Chapman M. J.; Heinecke J. W.; Kontush A.; Tall A. R.; Webb N. R. Dysfunctional HDL and Atherosclerotic Cardiovascular Disease. Nat. Rev. Cardiol. 2016, 13, 48–60. 10.1038/nrcardio.2015.124. PubMed DOI PMC

Shih A. Y.; Sligar S. G.; Schulten K. Maturation of High-Density Lipoproteins. J. R. Soc., Interface 2009, 6, 863–871. 10.1098/rsif.2009.0173. PubMed DOI PMC

Gogonea V. Structural Insights into High Density Lipoprotein: Old Models and New Facts. Front. Pharmacol. 2016, 6, 318.10.3389/fphar.2015.00318. PubMed DOI PMC

Melchior J. T.; Walker R. G.; Cooke A. L.; Morris J.; Castleberry M.; Thompson T. B.; Jones M. K.; Song H. D.; Rye K.-A.; Oda M. N.; et al. A Consensus Model of Human Apolipoprotein A-I in Its Monomeric and Lipid-Free State. Nat. Struct. Mol. Biol. 2017, 24, 1093–1099. 10.1038/nsmb.3501. PubMed DOI PMC

Oda M. N. Lipid-Free ApoA-I Structure - Origins of Model Diversity. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2017, 1862, 221–233. 10.1016/j.bbalip.2016.11.010. PubMed DOI

Silva R. A. G. D.; Hilliard G. M.; Fang J.; Macha S.; Davidson W. S. A Three-Dimensional Molecular Model of Lipid-Free Apolipoprotein A-I Determined by Cross-Linking/Mass Spectrometry and Sequence Threading. Biochemistry 2005, 44, 2759–2769. 10.1021/bi047717+. PubMed DOI

Pollard R. D.; Fulp B.; Samuel M. P.; Sorci-Thomas M. G.; Thomas M. J. The Conformation of Lipid-Free Human Apolipoprotein A-I in Solution. Biochemistry 2013, 52, 9470–9481. 10.1021/bi401080k. PubMed DOI PMC

Segrest J. P.; Jones M. K.; Shao B.; Heinecke J. W. An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-Ray Structures and Molecular Dynamics Simulations. Biochemistry 2014, 53, 7625–7640. 10.1021/bi501111j. PubMed DOI PMC

Zhang X.; Lei D.; Zhang L.; Rames M.; Zhang S. A Model of Lipid-Free Apolipoprotein A-I Revealed by Iterative Molecular Dynamics Simulation. PLoS One 2015, 10, e0120233.10.1371/journal.pone.0120233. PubMed DOI PMC

Lagerstedt J. O.; Budamagunta M. S.; Liu G. S.; DeValle N. C.; Voss J. C.; Oda M. N. The “Beta-Clasp” Model of Apolipoprotein A-I — A Lipid-Free Solution Structure Determined by Electron Paramagnetic Resonance Spectroscopy. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2012, 1821, 448–455. 10.1016/j.bbalip.2011.12.010. PubMed DOI PMC

Walker R. G.; Deng X.; Melchior J. T.; Morris J.; Tso P.; Jones M. K.; Segrest J. P.; Thompson T. B.; Davidson W. S. The Structure of Human Apolipoprotein A-IV as Revealed by Stable Isotope-Assisted Cross-Linking, Molecular Dynamics, and Small Angle X-Ray Scattering. J. Biol. Chem. 2014, 289, 5596–5608. 10.1074/jbc.M113.541037. PubMed DOI PMC

Todorova N.; Hung A.; Yarovsky I. Lipid Concentration Effects on the Amyloidogenic ApoC-II60–70 Peptide: A Computational Study. J. Phys. Chem. B 2010, 114, 7974–7982. 10.1021/jp102142x. PubMed DOI

Gordon S. M.; Pourmousa M.; Sampson M.; Sviridov D.; Islam R.; Perrin B. S.; Kemeh G.; Pastor R. W.; Remaley A. T. Identification of a Novel Lipid Binding Motif in Apolipoprotein B by the Analysis of Hydrophobic Cluster Domains. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 135–145. 10.1016/j.bbamem.2016.10.019. PubMed DOI PMC

Gu F.; Jones M. K.; Chen J.; Patterson J. C.; Catte A.; Jerome W. G.; Li L.; Segrest J. P. Structures of Discoidal High Density Lipoproteins: A Combined Computational-Experimental Approach. J. Biol. Chem. 2010, 285, 4652–4665. 10.1074/jbc.M109.069914. PubMed DOI PMC

Li L.; Li S.; Jones M. K.; Segrest J. P. Rotational and Hinge Dynamics of Discoidal High Density Lipoproteins Probed by Interchain Disulfide Bond Formation. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2012, 1821, 481–489. 10.1016/j.bbalip.2011.10.013. PubMed DOI PMC

Caulfield T. R. Inter-Ring Rotation of Apolipoprotein A-I Protein Monomers for the Double-Belt Model Using Biased Molecular Dynamics. J. Mol. Graphics Modell. 2011, 29, 1006–1014. 10.1016/j.jmgm.2011.04.005. PubMed DOI

Gursky O.; Jones M. K.; Mei X.; Segrest J. P.; Atkinson D. Structural Basis for Distinct Functions of the Naturally Occurring Cys Mutants of Human Apolipoprotein A-I. J. Lipid Res. 2013, 54, 3244–3257. 10.1194/jlr.R037911. PubMed DOI PMC

Lagerstedt J. O.; Cavigiolio G.; Budamagunta M. S.; Pagani I.; Voss J. C.; Oda M. N. Structure of Apolipoprotein A-I N Terminus on Nascent High Density Lipoproteins. J. Biol. Chem. 2011, 286, 2966–2975. 10.1074/jbc.M110.163097. PubMed DOI PMC

Jones M. K.; Gu F.; Catte A.; Li L.; Segrest J. P. Sticky” and “Promiscuous”, the Yin and Yang of Apolipoprotein A-I Termini in Discoidal High-Density Lipoproteins: A Combined Computational–Experimental Approach. Biochemistry 2011, 50, 2249–2263. 10.1021/bi101301g. PubMed DOI PMC

Segrest J. P.; Jones M. K.; Catte A.; Thirumuruganandham S. P. Validation of Previous Computer Models and MD Simulations of Discoidal HDL by a Recent Crystal Structure of ApoA-I. J. Lipid Res. 2012, 53, 1851–1863. 10.1194/jlr.M026229. PubMed DOI PMC

Pourmousa M.; Song H. D.; He Y.; Heinecke J. W.; Segrest J. P.; Pastor R. W. Tertiary Structure of Apolipoprotein A-I in Nascent High-Density Lipoproteins. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, 5163–5168. 10.1073/pnas.1721181115. PubMed DOI PMC

Segrest J. P.; Jones M. K.; Catte A.; Manchekar M.; Datta G.; Zhang L.; Zhang R.; Li L.; Patterson J. C.; Palgunachari M. N.; et al. Surface Density-Induced Pleating of a Lipid Monolayer Drives Nascent High-Density Lipoprotein Assembly. Structure 2015, 23, 1214–1226. 10.1016/j.str.2015.05.010. PubMed DOI PMC

Koivuniemi A.; Vattulainen I. Biogenesis of Nascent High Density Lipoprotein Particles. Structure 2015, 23, 1153–1154. 10.1016/j.str.2015.06.006. PubMed DOI

Islam R. M.; Pourmousa M.; Sviridov D.; Gordon S. M.; Neufeld E. B.; Freeman L. A.; Perrin B. S.; Pastor R. W.; Remaley A. T. Structural Properties of Apolipoprotein A-I Mimetic Peptides That Promote ABCA1-Dependent Cholesterol Efflux. Sci. Rep. 2018, 8, 2956.10.1038/s41598-018-20965-2. PubMed DOI PMC

Pourmousa M.; Pastor R. W. Molecular Dynamics Simulations of Lipid Nanodiscs. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 2094–2107. 10.1016/j.bbamem.2018.04.015. PubMed DOI PMC

Sei Y. J.; Ahn J.; Kim T.; Shin E.; Santiago-Lopez A. J.; Jang S. S.; Jeon N. L.; Jang Y. C.; Kim Y. Detecting the Functional Complexities between High-Density Lipoprotein Mimetics. Biomaterials 2018, 170, 58–69. 10.1016/j.biomaterials.2018.04.011. PubMed DOI PMC

Gogonea V.; Wu Z.; Lee X.; Pipich V.; Li X.-M.; Ioffe A. I.; DiDonato J. A.; Hazen S. L. Congruency between Biophysical Data from Multiple Platforms and Molecular Dynamics Simulation of the Double-Super Helix Model of Nascent High-Density Lipoprotein. Biochemistry 2010, 49, 7323–7343. 10.1021/bi100588a. PubMed DOI PMC

Jones M. K.; Zhang L.; Catte A.; Li L.; Oda M. N.; Ren G.; Segrest J. P. Assessment of the Validity of the Double Superhelix Model for Reconstituted High Density Lipoproteins: A Combined Computational-Experimental Approach. J. Biol. Chem. 2010, 285, 41161–41171. 10.1074/jbc.M110.187799. PubMed DOI PMC

Yetukuri L.; Söderlund S.; Koivuniemi A.; Seppänen-Laakso T.; Niemelä P. S.; Hyvönen M.; Taskinen M.-R.; Vattulainen I.; Jauhiainen M.; Orešič M. Composition and Lipid Spatial Distribution of HDL Particles in Subjects with Low and High HDL-Cholesterol. J. Lipid Res. 2010, 51, 2341–2351. 10.1194/jlr.M006494. PubMed DOI PMC

Yetukuri L.; Huopaniemi I.; Koivuniemi A.; Maranghi M.; Hiukka A.; Nygren H.; Kaski S.; Taskinen M.-R.; Vattulainen I.; Jauhiainen M.; et al. High Density Lipoprotein Structural Changes and Drug Response in Lipidomic Profiles Following the Long-Term Fenofibrate Therapy in the FIELD Substudy. PLoS One 2011, 6, e23589.10.1371/journal.pone.0023589. PubMed DOI PMC

Vuorela T.; Catte A.; Niemelä P. S.; Hall A.; Hyvönen M. T.; Marrink S.-J.; Karttunen M.; Vattulainen I. Role of Lipids in Spheroidal High Density Lipoproteins. PLoS Comput. Biol. 2010, 6, e1000964.10.1371/journal.pcbi.1000964. PubMed DOI PMC

Segrest J. P.; Jones M. K.; Catte A. MD Simulations Suggest Important Surface Differences between Reconstituted and Circulating Spherical HDL. J. Lipid Res. 2013, 54, 2718–2732. 10.1194/jlr.M039206. PubMed DOI PMC

Lähdesmäki K.; Ollila O. H. S.; Koivuniemi A.; Kovanen P. T.; Hyvönen M. T. Membrane Simulations Mimicking Acidic PH Reveal Increased Thickness and Negative Curvature in a Bilayer Consisting of Lysophosphatidylcholines and Free Fatty Acids. Biochim. Biophys. Acta, Biomembr. 2010, 1798, 938–946. 10.1016/j.bbamem.2010.01.020. PubMed DOI

Koivuniemi A.; Sysi-Aho M.; Orešič M.; Ollila S. Interfacial Properties of High-Density Lipoprotein-like Lipid Droplets with Different Lipid and Apolipoprotein A-I Compositions. Biophys. J. 2013, 104, 2193–2201. 10.1016/j.bpj.2013.02.058. PubMed DOI PMC

Inazu A.; Brown M. L.; Hesler C. B.; Agellon L. B.; Koizumi J.; Takata K.; Maruhama Y.; Mabuchi H.; Tall A. R. Increased High-Density Lipoprotein Levels Caused by a Common Cholesteryl-Ester Transfer Protein Gene Mutation. N. Engl. J. Med. 1990, 323, 1234–1238. 10.1056/NEJM199011013231803. PubMed DOI

Zhong S.; Sharp D. S.; Grove J. S.; Bruce C.; Yano K.; Curb J. D.; Tall A. R. Increased Coronary Heart Disease in Japanese-American Men with Mutation in the Cholesteryl Ester Transfer Protein Gene despite Increased HDL Levels. J. Clin. Invest. 1996, 97, 2917–2923. 10.1172/JCI118751. PubMed DOI PMC

Äijänen T.; Koivuniemi A.; Javanainen M.; Rissanen S.; Rog T.; Vattulainen I. How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations. PLoS Comput. Biol. 2014, 10, e1003987.10.1371/journal.pcbi.1003987. PubMed DOI PMC

Cilpa-Karhu G.; Jauhiainen M.; Riekkola M.-L. Atomistic MD Simulation Reveals the Mechanism by Which CETP Penetrates into HDL Enabling Lipid Transfer from HDL to CETP. J. Lipid Res. 2015, 56, 98–108. 10.1194/jlr.M054288. PubMed DOI PMC

Zhang M.; Charles R.; Tong H.; Zhang L.; Patel M.; Wang F.; Rames M. J.; Ren A.; Rye K.-A.; Qiu X.; et al. HDL Surface Lipids Mediate CETP Binding as Revealed by Electron Microscopy and Molecular Dynamics Simulation. Sci. Rep. 2015, 5, 8741.10.1038/srep08741. PubMed DOI PMC

Karilainen T.; Vuorela T.; Vattulainen I. How Well Does BODIPY-Cholesteryl Ester Mimic Unlabeled Cholesteryl Esters in High Density Lipoprotein Particles?. J. Phys. Chem. B 2015, 119, 15848–15856. 10.1021/acs.jpcb.5b10188. PubMed DOI

Karilainen T.; Timr Š.; Vattulainen I.; Jungwirth P. Oxidation of Cholesterol Does Not Alter Significantly Its Uptake into High-Density Lipoprotein Particles. J. Phys. Chem. B 2015, 119, 4594–4600. 10.1021/acs.jpcb.5b00240. PubMed DOI

Neuroscience, 2nd ed.; Purves D., Augustine G. J., Fitzpatrick D., Katz L. C., LaMantia A.-S., McNamara J. O., Williams S. M., Eds.; Sinauer Associates: Sunderland, Mass, 2001.

Wikström M.; Sharma V.; Kaila V. R. I.; Hosler J. P.; Hummer G. New Perspectives on Proton Pumping in Cellular Respiration. Chem. Rev. 2015, 115, 2196–2221. 10.1021/cr500448t. PubMed DOI

Wikström M.; Sharma V. Proton Pumping by Cytochrome c Oxidase – A 40 Year Anniversary. Biochim. Biophys. Acta, Bioenerg. 2018, 1859, 692–698. 10.1016/j.bbabio.2018.03.009. PubMed DOI

Musatov A.; Sedlák E. Role of Cardiolipin in Stability of Integral Membrane Proteins. Biochimie 2017, 142, 102–111. 10.1016/j.biochi.2017.08.013. PubMed DOI

Lemmin T.; Bovigny C.; Lançon D.; Dal Peraro M. Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes. J. Chem. Theory Comput. 2013, 9, 670–678. 10.1021/ct300590v. PubMed DOI

Dahlberg M.; Marini A.; Mennucci B.; Maliniak A. Quantum Chemical Modeling of the Cardiolipin Headgroup. J. Phys. Chem. A 2010, 114, 4375–4387. 10.1021/jp9110019. PubMed DOI

Aguayo D.; González-Nilo F. D.; Chipot C. Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field. J. Chem. Theory Comput. 2012, 8, 1765–1773. 10.1021/ct200849k. PubMed DOI

Pöyry S.; Róg T.; Karttunen M.; Vattulainen I. Mitochondrial Membranes with Mono- and Divalent Salt: Changes Induced by Salt Ions on Structure and Dynamics. J. Phys. Chem. B 2009, 113, 15513–15521. 10.1021/jp905915m. PubMed DOI

Róg T.; Martinez-Seara H.; Munck N.; Orešič M.; Karttunen M.; Vattulainen I. Role of Cardiolipins in the Inner Mitochondrial Membrane: Insight Gained through Atom-Scale Simulations. J. Phys. Chem. B 2009, 113, 3413–3422. 10.1021/jp8077369. PubMed DOI

Dahlberg M.; Maliniak A. Molecular Dynamics Simulations of Cardiolipin Bilayers. J. Phys. Chem. B 2008, 112, 11655–11663. 10.1021/jp803414g. PubMed DOI

Dahlberg M.; Maliniak A. Mechanical Properties of Coarse-Grained Bilayers Formed by Cardiolipin and Zwitterionic Lipids. J. Chem. Theory Comput. 2010, 6, 1638–1649. 10.1021/ct900654e. PubMed DOI

Boyd K. J.; Alder N. N.; May E. R. Buckling Under Pressure: Curvature-Based Lipid Segregation and Stability Modulation in Cardiolipin-Containing Bilayers. Langmuir 2017, 33, 6937–6946. 10.1021/acs.langmuir.7b01185. PubMed DOI PMC

Pan J.; Cheng X.; Sharp M.; Ho C.-S.; Khadka N.; Katsaras J. Structural and Mechanical Properties of Cardiolipin Lipid Bilayers Determined Using Neutron Spin Echo, Small Angle Neutron and X-Ray Scattering, and Molecular Dynamics Simulations. Soft Matter 2015, 11, 130–138. 10.1039/C4SM02227K. PubMed DOI

Boscia A. L.; Treece B. W.; Mohammadyani D.; Klein-Seetharaman J.; Braun A. R.; Wassenaar T. A.; Klösgen B.; Tristram-Nagle S. X-Ray Structure, Thermodynamics, Elastic Properties and MD Simulations of Cardiolipin/Dimyristoylphosphatidylcholine Mixed Membranes. Chem. Phys. Lipids 2014, 178, 1–10. 10.1016/j.chemphyslip.2013.12.010. PubMed DOI PMC

Kaurola P.; Sharma V.; Vonk A.; Vattulainen I.; Róg T. Distribution and Dynamics of Quinones in the Lipid Bilayer Mimicking the Inner Membrane of Mitochondria. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2116–2122. 10.1016/j.bbamem.2016.06.016. PubMed DOI

Wolf M. G.; Grubmüller H.; Groenhof G. Anomalous Surface Diffusion of Protons on Lipid Membranes. Biophys. J. 2014, 107, 76–87. 10.1016/j.bpj.2014.04.062. PubMed DOI PMC

Yamashita T.; Voth G. A. Properties of Hydrated Excess Protons near Phospholipid Bilayers. J. Phys. Chem. B 2010, 114, 592–603. 10.1021/jp908768c. PubMed DOI

Pöyry S.; Cramariuc O.; Postila P. A.; Kaszuba K.; Sarewicz M.; Osyczka A.; Vattulainen I.; Róg T. Atomistic Simulations Indicate Cardiolipin to Have an Integral Role in the Structure of the Cytochrome bc1 Complex. Biochim. Biophys. Acta, Bioenerg. 2013, 1827, 769–778. 10.1016/j.bbabio.2013.03.005. PubMed DOI

Zhang M.; Mileykovskaya E.; Dowhan W. Gluing the Respiratory Chain Together: Cardiolipin Is Required For Supercomplex Formation In The Inner Mitochondrial Membrane. J. Biol. Chem. 2002, 277, 43553–43556. 10.1074/jbc.C200551200. PubMed DOI

Lange C. Specific Roles of Protein-Phospholipid Interactions in the Yeast Cytochrome bc1 Complex Structure. EMBO J. 2001, 20, 6591–6600. 10.1093/emboj/20.23.6591. PubMed DOI PMC

Arnarez C.; Marrink S. J.; Periole X. Identification of Cardiolipin Binding Sites on Cytochrome c Oxidase at the Entrance of Proton Channels. Sci. Rep. 2013, 3, 1263.10.1038/srep01263. PubMed DOI PMC

Sharma V.; Ala-Vannesluoma P.; Vattulainen I.; Wikström M.; Róg T. Role of Subunit III and Its Lipids in the Molecular Mechanism of Cytochrome c Oxidase. Biochim. Biophys. Acta, Bioenerg. 2015, 1847, 690–697. 10.1016/j.bbabio.2015.04.007. PubMed DOI

Mileykovskaya E.; Dowhan W. Cardiolipin-Dependent Formation of Mitochondrial Respiratory Supercomplexes. Chem. Phys. Lipids 2014, 179, 42–48. 10.1016/j.chemphyslip.2013.10.012. PubMed DOI PMC

Arnarez C.; Mazat J.-P.; Elezgaray J.; Marrink S.-J.; Periole X. Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc1. J. Am. Chem. Soc. 2013, 135, 3112–3120. 10.1021/ja310577u. PubMed DOI

Arnarez C.; Marrink S. J.; Periole X. Molecular Mechanism of Cardiolipin-Mediated Assembly of Respiratory Chain Supercomplexes. Chem. Sci. 2016, 7, 4435–4443. 10.1039/C5SC04664E. PubMed DOI PMC

Mohammadyani D.; Yanamala N.; Samhan-Arias A. K.; Kapralov A. A.; Stepanov G.; Nuar N.; Planas-Iglesias J.; Sanghera N.; Kagan V. E.; Klein-Seetharaman J. Structural Characterization of Cardiolipin-Driven Activation of Cytochrome c into a Peroxidase and Membrane Perturbation. Biochim. Biophys. Acta, Biomembr. 2018, 1860, 1057–1068. 10.1016/j.bbamem.2018.01.009. PubMed DOI

Sui X.; Arlt H.; Brock K. P.; Lai Z. W.; DiMaio F.; Marks D. S.; Liao M.; Farese R. V.; Walther T. C. Cryo–Electron Microscopy Structure of the Lipid Droplet–Formation Protein Seipin. J. Cell Biol. 2018, 217, 4080–4091. 10.1083/jcb.201809067. PubMed DOI PMC

Yan R.; Qian H.; Lukmantara I.; Gao M.; Du X.; Yan N.; Yang H. Human SEIPIN Binds Anionic Phospholipids. Dev. Cell 2018, 47, 248–256.e4. 10.1016/j.devcel.2018.09.010. PubMed DOI

Segrest J. P.; Jones M. K.; Loof H. D.; Dashti N. Structure of Apolipoprotein B-100 in Low Density Lipoproteins. J. Lipid Res. 2001, 42, 1346–1367. PubMed

Sherman M. B.; Orlova E. V.; Decker G. L.; Chiu W.; Pownall H. J. Structure of Triglyceride-Rich Human Low-Density Lipoproteins According to Cryoelectron Microscopy. Biochemistry 2003, 42, 14988–14993. 10.1021/bi0354738. PubMed DOI

Kumar V.; Butcher S. J.; Öörni K.; Engelhardt P.; Heikkonen J.; Kaski K.; Ala-Korpela M.; Kovanen P. T. Three-Dimensional CryoEM Reconstruction of Native LDL Particles to 16Å Resolution at Physiological Body Temperature. PLoS One 2011, 6, e18841.10.1371/journal.pone.0018841. PubMed DOI PMC

Li D.; Stansfeld P. J.; Sansom M. S. P.; Keogh A.; Vogeley L.; Howe N.; Lyons J. A.; Aragao D.; Fromme P.; Fromme R.; et al. Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase. Nat. Commun. 2015, 6, 10140.10.1038/ncomms10140. PubMed DOI PMC

Gustafsson C.; Vassiliev S.; Kürten C.; Syrén P.-O.; Brinck T. MD Simulations Reveal Complex Water Paths in Squalene–Hopene Cyclase: Tunnel-Obstructing Mutations Increase the Flow of Water in the Active Site. ACS Omega 2017, 2, 8495–8506. 10.1021/acsomega.7b01084. PubMed DOI PMC

Haapanen O.; Sharma V. A Modeling and Simulation Perspective on the Mechanism and Function of Respiratory Complex I. Biochim. Biophys. Acta, Bioenerg. 2018, 1859, 510–523. 10.1016/j.bbabio.2018.04.001. PubMed DOI

Liang R.; Swanson J. M. J.; Peng Y.; Wikström M.; Voth G. A. Multiscale Simulations Reveal Key Features of the Proton-Pumping Mechanism in Cytochrome c Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 7420–7425. 10.1073/pnas.1601982113. PubMed DOI PMC

Oliveira A. S. F.; Damas J. M.; Baptista A. M.; Soares C. M. Exploring O2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site. PLoS Comput. Biol. 2014, 10, e1004010.10.1371/journal.pcbi.1004010. PubMed DOI PMC

Oteri F.; Baaden M.; Lojou E.; Sacquin-Mora S. Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex Aeolicus and Desulfovibrio Fructosovorans. J. Phys. Chem. B 2014, 118, 13800–13811. 10.1021/jp5089965. PubMed DOI

Padayatti P. S.; Leung J. H.; Mahinthichaichan P.; Tajkhorshid E.; Ishchenko A.; Cherezov V.; Soltis S. M.; Jackson J. B.; Stout C. D.; Gennis R. B.; et al. Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase. Structure 2017, 25, 1111–1119. 10.1016/j.str.2017.05.022. PubMed DOI PMC

Sharma V.; Enkavi G.; Vattulainen I.; Róg T.; Wikström M. Proton-Coupled Electron Transfer and the Role of Water Molecules in Proton Pumping by Cytochrome c Oxidase. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 2040–2045. 10.1073/pnas.1409543112. PubMed DOI PMC

Sharma V.; Jambrina P. G.; Kaukonen M.; Rosta E.; Rich P. R. Insights into Functions of the H Channel of Cytochrome c Oxidase from Atomistic Molecular Dynamics Simulations. Proc. Natl. Acad. Sci. U. S. A. 2017, 114, E10339–E10348. 10.1073/pnas.1708628114. PubMed DOI PMC

Terasaka E.; Yamada K.; Wang P.-H.; Hosokawa K.; Yamagiwa R.; Matsumoto K.; Ishii S.; Mori T.; Yagi K.; Sawai H.; et al. Dynamics of Nitric Oxide Controlled by Protein Complex in Bacterial System. Proc. Natl. Acad. Sci. U. S. A. 2017, 114, 9888.10.1073/pnas.1621301114. PubMed DOI PMC

Wikström M.; Krab K.; Sharma V. Oxygen Activation and Energy Conservation by Cytochrome c Oxidase. Chem. Rev. 2018, 118, 2469–2490. 10.1021/acs.chemrev.7b00664. PubMed DOI PMC

Yang L.; Skjevik Å. A.; Han Du W.-G.; Noodleman L.; Walker R. C.; Götz A. W. Water Exit Pathways and Proton Pumping Mechanism in B-Type Cytochrome c Oxidase from Molecular Dynamics Simulations. Biochim. Biophys. Acta, Bioenerg. 2016, 1857, 1594–1606. 10.1016/j.bbabio.2016.06.005. PubMed DOI PMC

Zhou W.; Marinelli F.; Nief C.; Faraldo-Gómez J. D. Atomistic Simulations Indicate the C-Subunit Ring of the F1Fo ATP Synthase Is Not the Mitochondrial Permeability Transition Pore. eLife 2017, 6, e23781.10.7554/eLife.23781. PubMed DOI PMC

Sharma V.; Belevich G.; Gamiz-Hernandez A. P.; Róg T.; Vattulainen I.; Verkhovskaya M. L.; Wikström M.; Hummer G.; Kaila V. R. I. Redox-Induced Activation of the Proton Pump in the Respiratory Complex I. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 11571–11576. 10.1073/pnas.1503761112. PubMed DOI PMC

Postila P. A.; Kaszuba K.; Kuleta P.; Vattulainen I.; Sarewicz M.; Osyczka A.; Róg T. Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome bc1 Complex. Sci. Rep. 2016, 6, 33607.10.1038/srep33607. PubMed DOI PMC

Haapanen O.; Sharma V. Role of Water and Protein Dynamics in Proton Pumping by Respiratory Complex I. Sci. Rep. 2017, 7, 7747.10.1038/s41598-017-07930-1. PubMed DOI PMC

Postila P. A.; Kaszuba K.; Sarewicz M.; Osyczka A.; Vattulainen I.; Róg T. Key Role of Water in Proton Transfer at the Qo-Site of the Cytochrome bc1 Complex Predicted by Atomistic Molecular Dynamics Simulations. Biochim. Biophys. Acta, Bioenerg. 2013, 1827, 761–768. 10.1016/j.bbabio.2013.02.005. PubMed DOI

Manikandan P.; Nagini S. Cytochrome P450 Structure, Function and Clinical Significance: A Review. Curr. Drug Targets 2018, 19, 38–54. 10.2174/1389450118666170125144557. PubMed DOI

Hasler J. A.; Estabrook R.; Murray M.; Pikuleva I.; Waterman M.; Capdevila J.; Holla V.; Helvig C.; Falck J. R.; Farrell G.; et al. Human Cytochromes P450. Mol. Aspects Med. 1999, 20, 1–137. 10.1016/S0098-2997(99)00005-9. DOI

Burkina V.; Rasmussen M. K.; Pilipenko N.; Zamaratskaia G. Comparison of Xenobiotic-Metabolising Human, Porcine, Rodent, and Piscine Cytochrome P450. Toxicology 2017, 375, 10–27. 10.1016/j.tox.2016.11.014. PubMed DOI

Shalan H.; Kato M.; Cheruzel L. Keeping the Spotlight on Cytochrome P450. Biochim. Biophys. Acta, Proteins Proteomics 2018, 1866, 80–87. 10.1016/j.bbapap.2017.06.002. PubMed DOI PMC

Zanger U. M.; Schwab M. Cytochrome P450 Enzymes in Drug Metabolism: Regulation of Gene Expression, Enzyme Activities, and Impact of Genetic Variation. Pharmacol. Ther. 2013, 138, 103–141. 10.1016/j.pharmthera.2012.12.007. PubMed DOI

Backman J. T.; Filppula A. M.; Niemi M.; Neuvonen P. J. Role of Cytochrome P450 2C8 in Drug Metabolism and Interactions. Pharmacol. Rev. 2016, 68, 168–241. 10.1124/pr.115.011411. PubMed DOI

Monk B. C.; Tomasiak T. M.; Keniya M. V.; Huschmann F. U.; Tyndall J. D. A.; O’Connell J. D.; Cannon R. D.; McDonald J. G.; Rodriguez A.; Finer-Moore J. S.; et al. Architecture of a Single Membrane Spanning Cytochrome P450 Suggests Constraints That Orient the Catalytic Domain Relative to a Bilayer. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 3865–3870. 10.1073/pnas.1324245111. PubMed DOI PMC

Yousefpour A.; Modarress H.; Goharpey F.; Amjad-Iranagh S. Interaction of Drugs Amlodipine and Paroxetine with the Metabolizing Enzyme CYP2B4: A Molecular Dynamics Simulation Study. J. Mol. Model. 2018, 24, 1–11. 10.1007/s00894-018-3617-8. PubMed DOI

Lonsdale R.; Rouse S. L.; Sansom M. S. P.; Mulholland A. J. A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes. PLoS Comput. Biol. 2014, 10, e1003714.10.1371/journal.pcbi.1003714. PubMed DOI PMC

Yu X.; Nandekar P.; Mustafa G.; Cojocaru V.; Lepesheva G. I.; Wade R. C. Ligand Tunnels in T. Brucei and Human CYP51: Insights for Parasite-Specific Drug Design. Biochim. Biophys. Acta, Gen. Subj. 2016, 1860, 67–78. 10.1016/j.bbagen.2015.10.015. PubMed DOI PMC

Jeřábek P.; Florián J.; Martínek V. Lipid Molecules Can Induce an Opening of Membrane-Facing Tunnels in Cytochrome P450 1A2. Phys. Chem. Chem. Phys. 2016, 18, 30344–30356. 10.1039/C6CP03692A. PubMed DOI PMC

Cui Y.-L.; Xue Q.; Zheng Q.-C.; Zhang J.-L.; Kong C.-P.; Fan J.-R.; Zhang H.-X. Structural Features and Dynamic Investigations of the Membrane-Bound Cytochrome P450 17A1. Biochim. Biophys. Acta, Biomembr. 2015, 1848, 2013–2021. 10.1016/j.bbamem.2015.05.017. PubMed DOI

Hackett J. C. Membrane-Embedded Substrate Recognition by Cytochrome P450 3A4. J. Biol. Chem. 2018, 293, 4037–4046. 10.1074/jbc.RA117.000961. PubMed DOI PMC

Navrátilová V.; Paloncýová M.; Berka K.; Otyepka M. Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4. J. Phys. Chem. B 2016, 120, 11205–11213. 10.1021/acs.jpcb.6b10108. PubMed DOI

Navrátilová V.; Paloncýová M.; Kajšová M.; Berka K.; Otyepka M. Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4. J. Chem. Inf. Model. 2015, 55, 628–635. 10.1021/ci500645k. PubMed DOI

Cui Y.-L.; Wu R.-L. Molecular Dynamics Investigations of Membrane-Bound CYP2C19 Polymorphisms Reveal Distinct Mechanisms for Peripheral Variants by Long-Range Effects on the Enzymatic Activity. Mol. BioSyst. 2017, 13, 1070–1079. 10.1039/C6MB00827E. PubMed DOI

Navrátilová V.; Paloncýová M.; Berka K.; Mise S.; Haga Y.; Matsumura C.; Sakaki T.; Inui H.; Otyepka M. Molecular Insights into the Role of a Distal F240A Mutation That Alters CYP1A1 Activity towards Persistent Organic Pollutants. Biochim. Biophys. Acta, Gen. Subj. 2017, 1861, 2852–2860. 10.1016/j.bbagen.2017.08.002. PubMed DOI

Martin L. L.; Holien J. K.; Mizrachi D.; Corbin C. J.; Conley A. J.; Parker M. W.; Rodgers R. J. Evolutionary Comparisons Predict That Dimerization of Human Cytochrome P450 Aromatase Increases Its Enzymatic Activity and Efficiency. J. Steroid Biochem. Mol. Biol. 2015, 154, 294–301. 10.1016/j.jsbmb.2015.09.006. PubMed DOI

Jeřábek P.; Florián J.; Martínek V. Membrane-Anchored Cytochrome P450 1A2–Cytochrome b5 Complex Features an X-Shaped Contact between Antiparallel Transmembrane Helices. Chem. Res. Toxicol. 2016, 29, 626–636. 10.1021/acs.chemrestox.5b00349. PubMed DOI

Ramsay R. R. Molecular Aspects of Monoamine Oxidase B. Prog. Neuro-Psychopharmacol. Biol. Psychiatry 2016, 69, 81–89. 10.1016/j.pnpbp.2016.02.005. PubMed DOI

Fišar Z. Drugs Related to Monoamine Oxidase Activity. Prog. Neuro-Psychopharmacol. Biol. Psychiatry 2016, 69, 112–124. 10.1016/j.pnpbp.2016.02.012. PubMed DOI

Apostolov R.; Yonezawa Y.; Standley D. M.; Kikugawa G.; Takano Y.; Nakamura H. Membrane Attachment Facilitates Ligand Access to the Active Site in Monoamine Oxidase A. Biochemistry 2009, 48, 5864–5873. 10.1021/bi900493n. PubMed DOI

Allen W. J.; Bevan D. R. Steered Molecular Dynamics Simulations Reveal Important Mechanisms in Reversible Monoamine Oxidase B Inhibition. Biochemistry 2011, 50, 6441–6454. 10.1021/bi200446w. PubMed DOI

Larit F.; Elokely K. M.; Chaurasiya N. D.; Benyahia S.; Nael M. A.; León F.; Abu-Darwish M. S.; Efferth T.; Wang Y. H.; Belouahem-Abed D.; et al. Inhibition of Human Monoamine Oxidase A and B by Flavonoids Isolated from Two Algerian Medicinal Plants. Phytomedicine 2018, 40, 27–36. 10.1016/j.phymed.2017.12.032. PubMed DOI PMC

Riessland M.; Kolisnyk B.; Greengard P. Reactive Dopamine Leads to Triple Trouble in Nigral Neurons. Biochemistry 2017, 56, 6409–6410. 10.1021/acs.biochem.7b01057. PubMed DOI

Orłowski A.; St-Pierre J.-F.; Magarkar A.; Bunker A.; Pasenkiewicz-Gierula M.; Vattulainen I.; Róg T. Properties of the Membrane Binding Component of Catechol-O-Methyltransferase Revealed by Atomistic Molecular Dynamics Simulations. J. Phys. Chem. B 2011, 115, 13541–13550. 10.1021/jp207177p. PubMed DOI

Magarkar A.; Parkkila P.; Viitala T.; Lajunen T.; Mobarak E.; Licari G.; Cramariuc O.; Vauthey E.; Róg T.; Bunker A. Membrane Bound COMT Isoform Is an Interfacial Enzyme: General Mechanism and New Drug Design Paradigm. Chem. Commun. 2018, 54, 3440–3443. 10.1039/C8CC00221E. PubMed DOI

Dzieciuch-Rojek M.; Poojari C.; Bednar J.; Bunker A.; Kozik B.; Nowakowska M.; Vattulainen I.; Wydro P.; Kepczynski M.; Róg T. Effects of Membrane PEGylation on Entry and Location of Antifungal Drug Itraconazole and Their Pharmacological Implications. Mol. Pharmaceutics 2017, 14, 1057–1070. 10.1021/acs.molpharmaceut.6b00969. PubMed DOI

Wilkosz N.; Rissanen S.; Cyza M.; Szybka R.; Nowakowska M.; Bunker A.; Róg T.; Kepczynski M. Effect of Piroxicam on Lipid Membranes: Drug Encapsulation and Gastric Toxicity Aspects. Eur. J. Pharm. Sci. 2017, 100, 116–125. 10.1016/j.ejps.2017.01.007. PubMed DOI

Markiewicz M.; Pasenkiewicz-Gierula M. Comparative Model Studies of Gastric Toxicity of Nonsteroidal Anti-Inflammatory Drugs. Langmuir 2011, 27, 6950–6961. 10.1021/la200499p. PubMed DOI

Lajunen T.; Kontturi L.-S.; Viitala L.; Manna M.; Cramariuc O.; Róg T.; Bunker A.; Laaksonen T.; Viitala T.; Murtomäki L.; et al. Indocyanine Green-Loaded Liposomes for Light-Triggered Drug Release. Mol. Pharmaceutics 2016, 13, 2095–2107. 10.1021/acs.molpharmaceut.6b00207. PubMed DOI

Cramariuc O.; Rog T.; Javanainen M.; Monticelli L.; Polishchuk A. V.; Vattulainen I. Mechanism for Translocation of Fluoroquinolones across Lipid Membranes. Biochim. Biophys. Acta, Biomembr. 2012, 1818, 2563–2571. 10.1016/j.bbamem.2012.05.027. PubMed DOI

Dzieciuch M.; Rissanen S.; Szydłowska N.; Bunker A.; Kumorek M.; Jamróz D.; Vattulainen I.; Nowakowska M.; Róg T.; Kepczynski M. Pegylated Liposomes as Carriers of Hydrophobic Porphyrins. J. Phys. Chem. B 2015, 119, 6646–6657. 10.1021/acs.jpcb.5b01351. PubMed DOI

Stepniewski M.; Kepczynski M.; Jamróz D.; Nowakowska M.; Rissanen S.; Vattulainen I.; Róg T. Interaction of Hematoporphyrin with Lipid Membranes. J. Phys. Chem. B 2012, 116, 4889–4897. 10.1021/jp300899b. PubMed DOI

Khandelia H.; Witzke S.; Mouritsen O. G. Interaction of Salicylate and a Terpenoid Plant Extract with Model Membranes: Reconciling Experiments and Simulations. Biophys. J. 2010, 99, 3887–3894. 10.1016/j.bpj.2010.11.009. PubMed DOI PMC

Rissanen S.; Kumorek M.; Martinez-Seara H.; Li Y. C.; Jamróz D.; Bunker A.; Nowakowska M.; Vattulainen I.; Kepczynski M.; Róg T. Effect of PEGylation on Drug Entry into Lipid Bilayer. J. Phys. Chem. B 2014, 118, 144–151. 10.1021/jp4105745. PubMed DOI

Kopeć W.; Telenius J.; Khandelia H. Molecular Dynamics Simulations of the Interactions of Medicinal Plant Extracts and Drugs with Lipid Bilayer Membranes. FEBS J. 2013, 280, 2785–2805. 10.1111/febs.12286. PubMed DOI

Cramariuc O.; Róg T.; Vattulainen I. Drug-Lipid Membrane Interaction Mechanisms Revealed Through Molecular Simulations. Curr. Phys. Chem. 2012, 2, 379–400. 10.2174/1877946811202040379. DOI

Jodko-Piorecka K.; Litwinienko G. First Experimental Evidence of Dopamine Interactions with Negatively Charged Model Biomembranes. ACS Chem. Neurosci. 2013, 4, 1114–1122. 10.1021/cn4000633. PubMed DOI PMC

Matam Y.; Ray B. D.; Petrache H. I. Direct Affinity of Dopamine to Lipid Membranes Investigated by Nuclear Magnetic Resonance Spectroscopy. Neurosci. Lett. 2016, 618, 104–109. 10.1016/j.neulet.2016.02.052. PubMed DOI

Drolle E.; Kučerka N.; Hoopes M. I.; Choi Y.; Katsaras J.; Karttunen M.; Leonenko Z. Effect of Melatonin and Cholesterol on the Structure of DOPC and DPPC Membranes. Biochim. Biophys. Acta, Biomembr. 2013, 1828, 2247–2254. 10.1016/j.bbamem.2013.05.015. PubMed DOI

Choi Y.; Attwood S. J.; Hoopes M. I.; Drolle E.; Karttunen M.; Leonenko Z. Melatonin Directly Interacts with Cholesterol and Alleviates Cholesterol Effects in Dipalmitoylphosphatidylcholine Monolayers. Soft Matter 2014, 10, 206–213. 10.1039/C3SM52064A. PubMed DOI

Huang X.; Gu H. H.; Zhan C. G. Mechanism for Cocaine Blocking the Transport of Dopamine: Insights from Molecular Modeling and Dynamics Simulations. J. Phys. Chem. B 2009, 113, 15057–15066. 10.1021/jp900963n. PubMed DOI PMC

Riedlová K.; Nekardová M.; Kačer P.; Syslová K.; Vazdar M.; Jungwirth P.; Kudová E.; Cwiklik L. Distributions of Therapeutically Promising Neurosteroids in Cellular Membranes. Chem. Phys. Lipids 2017, 203, 78–86. 10.1016/j.chemphyslip.2016.12.004. PubMed DOI

Juhola H.; Postila P. A.; Rissanen S.; Lolicato F.; Vattulainen I.; Rog T. Negatively Charged Gangliosides Promote Membrane Association of Amphipathic Neurotransmitters. Neuroscience 2018, 384, 214–223. 10.1016/j.neuroscience.2018.05.035. PubMed DOI

Mouchlis V. D.; Bucher D.; McCammon J. A.; Dennis E. A. Membranes Serve as Allosteric Activators of Phospholipase A 2, Enabling It to Extract, Bind, and Hydrolyze Phospholipid Substrates. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, E516–E525. 10.1073/pnas.1424651112. PubMed DOI PMC

Mouchlis V. D.; Chen Y.; McCammon J. A.; Dennis E. A. Membrane Allostery and Unique Hydrophobic Sites Promote Enzyme Substrate Specificity. J. Am. Chem. Soc. 2018, 140, 3285–3291. 10.1021/jacs.7b12045. PubMed DOI PMC

Riccardi L.; Arencibia J. M.; Bono L.; Armirotti A.; Girotto S.; De Vivo M. Lid Domain Plasticity and Lipid Flexibility Modulate Enzyme Specificity in Human Monoacylglycerol Lipase. Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2017, 1862, 441–451. 10.1016/j.bbalip.2017.01.002. PubMed DOI

Willems N.; Lelimousin M.; Koldsø H.; Sansom M. S. P. Interfacial Activation of M37 Lipase: A Multi-Scale Simulation Study. Biochim. Biophys. Acta, Biomembr. 2017, 1859, 340–349. 10.1016/j.bbamem.2016.12.012. PubMed DOI PMC

Cozza G.; Rossetto M.; Bosello-Travain V.; Maiorino M.; Roveri A.; Toppo S.; Zaccarin M.; Zennaro L.; Ursini F. Glutathione Peroxidase 4-Catalyzed Reduction of Lipid Hydroperoxides in Membranes: The Polar Head of Membrane Phospholipids Binds the Enzyme and Addresses the Fatty Acid Hydroperoxide Group toward the Redox Center. Free Radical Biol. Med. 2017, 112, 1–11. 10.1016/j.freeradbiomed.2017.07.010. PubMed DOI

Chatron N.; Chalmond B.; Trouvé A.; Benoît E.; Caruel H.; Lattard V.; Tchertanov L. Identification of the Functional States of Human Vitamin K Epoxide Reductase from Molecular Dynamics Simulations. RSC Adv. 2017, 7, 52071–52090. 10.1039/C7RA07463H. DOI

Gumbart J. C.; Chipot C. Decrypting Protein Insertion through the Translocon with Free-Energy Calculations. Biochim. Biophys. Acta, Biomembr. 2016, 1858, 1663–1671. 10.1016/j.bbamem.2016.02.017. PubMed DOI

Bonardi F.; Halza E.; Walko M.; Du Plessis F.; Nouwen N.; Feringa B. L.; Driessen A. J. M. Probing the SecYEG Translocation Pore Size with Preproteins Conjugated with Sizable Rigid Spherical Molecules. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 7775–7780. 10.1073/pnas.1101705108. PubMed DOI PMC

Gumbart J.; Chipot C.; Schulten K. Free-Energy Cost for Translocon-Assisted Insertion of Membrane Proteins. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 3596–3601. 10.1073/pnas.1012758108. PubMed DOI PMC

Mori T.; Ishitani R.; Tsukazaki T.; Nureki O.; Sugita Y. Molecular Mechanisms Underlying the Early Stage of Protein Translocation through the Sec Translocon. Biochemistry 2010, 49, 945–950. 10.1021/bi901594w. PubMed DOI

Wickles S.; Singharoy A.; Andreani J.; Seemayer S.; Bischoff L.; Berninghausen O.; Soeding J.; Schulten K.; van der Sluis E. O.; Beckmann R. A Structural Model of the Active Ribosome-Bound Membrane Protein Insertase YidC. eLife 2014, 3, e03035.10.7554/eLife.03035. PubMed DOI PMC

Bondar A. N.; del Val C.; Freites J. A.; Tobias D. J.; White S. H. Dynamics of SecY Translocons with Translocation-Defective Mutations. Structure 2010, 18, 847–857. 10.1016/j.str.2010.04.010. PubMed DOI PMC

Nilsson O. B.; Hedman R.; Marino J.; Wickles S.; Bischoff L.; Johansson M.; Müller-Lucks A.; Trovato F.; Puglisi J. D.; O’Brien E. P.; et al. Cotranslational Protein Folding inside the Ribosome Exit Tunnel. Cell Rep. 2015, 12, 1533–1540. 10.1016/j.celrep.2015.07.065. PubMed DOI PMC

Ulmschneider M. B.; Koehler Leman J.; Fennell H.; Beckstein O. Peptide Folding in Translocon-Like Pores. J. Membr. Biol. 2015, 248, 407–417. 10.1007/s00232-015-9808-7. PubMed DOI

Gumbart J. C.; Teo I.; Roux B.; Schulten K. Reconciling the Roles of Kinetic and Thermodynamic Factors in Membrane-Protein Insertion. J. Am. Chem. Soc. 2013, 135, 2291–2297. 10.1021/ja310777k. PubMed DOI PMC

Rychkova A.; Warshel A. Exploring the Nature of the Translocon-Assisted Protein Insertion. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 495–500. 10.1073/pnas.1220361110. PubMed DOI PMC

Niesen M. J. M.; Wang C. Y.; Van Lehn R. C.; Miller T. F. Structurally Detailed Coarse-Grained Model for Sec-Facilitated Co-Translational Protein Translocation and Membrane Integration. PLoS Comput. Biol. 2017, 13, e1005427.10.1371/journal.pcbi.1005427. PubMed DOI PMC

Crespo-Otero R.; Barbatti M. Recent Advances and Perspectives on Nonadiabatic Mixed Quantum–Classical Dynamics. Chem. Rev. 2018, 118, 7026–7068. 10.1021/acs.chemrev.7b00577. PubMed DOI

Yu L.-J.; Suga M.; Wang-Otomo Z.-Y.; Shen J.-R. Structure of Photosynthetic LH1–RC Supercomplex at 1.9 Å Resolution. Nature 2018, 556, 209–213. 10.1038/s41586-018-0002-9. PubMed DOI

Qian P.; Siebert C. A.; Wang P.; Canniffe D. P.; Hunter C. N. Cryo-EM Structure of the Blastochloris Viridis LH1–RC Complex at 2.9 Å. Nature 2018, 556, 203–208. 10.1038/s41586-018-0014-5. PubMed DOI

Niwa S.; Yu L.-J.; Takeda K.; Hirano Y.; Kawakami T.; Wang-Otomo Z.-Y.; Miki K. Structure of the LH1–RC Complex from Thermochromatium Tepidum at 3.0 Å. Nature 2014, 508, 228–232. 10.1038/nature13197. PubMed DOI

Gisriel C.; Sarrou I.; Ferlez B.; Golbeck J. H.; Redding K. E.; Fromme R. Structure of a Symmetric Photosynthetic Reaction Center–Photosystem. Science 2017, 357, 1021–1025. 10.1126/science.aan5611. PubMed DOI

Nogi T.; Fathir I.; Kobayashi M.; Nozawa T.; Miki K. Crystal Structures of Photosynthetic Reaction Center and High-Potential Iron-Sulfur Protein from Thermochromatium Tepidum: Thermostability and Electron Transfer. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 13561–13566. 10.1073/pnas.240224997. PubMed DOI PMC

Saer R. G.; Pan J.; Hardjasa A.; Lin S.; Rosell F.; Mauk A. G.; Woodbury N. W.; Murphy M. E. P.; Beatty J. T. Structural and Kinetic Properties of Rhodobacter Sphaeroides Photosynthetic Reaction Centers Containing Exclusively Zn-Coordinated Bacteriochlorophyll as Bacteriochlorin Cofactors. Biochim. Biophys. Acta, Bioenerg. 2014, 1837, 366–374. 10.1016/j.bbabio.2013.11.015. PubMed DOI

Koepke J.; Krammer E.-M.; Klingen A. R.; Sebban P.; Ullmann G. M.; Fritzsch G. pH Modulates the Quinone Position in the Photosynthetic Reaction Center from Rhodobacter Sphaeroides in the Neutral and Charge Separated States. J. Mol. Biol. 2007, 371, 396–409. 10.1016/j.jmb.2007.04.082. PubMed DOI

Katona G.; Andréasson U.; Landau E. M.; Andréasson L.-E.; Neutze R. Lipidic Cubic Phase Crystal Structure of the Photosynthetic Reaction Centre from Rhodobacter Sphaeroides at 2.35 Å Resolution. J. Mol. Biol. 2003, 331, 681–692. 10.1016/S0022-2836(03)00751-4. PubMed DOI

Stowell M. H. Light-Induced Structural Changes in Photosynthetic Reaction Center: Implications for Mechanism of Electron-Proton Transfer. Science 1997, 276, 812–816. 10.1126/science.276.5313.812. PubMed DOI

Chirino A. J.; Lous E. J.; Huber M.; Allen J. P.; Schenck C. C.; Paddock M. L.; Feher G.; Rees D. C. Crystallographic Analyses of Site-Directed Mutants of the Photosynthetic Reaction Center from Rhodobacter Sphaeroides. Biochemistry 1994, 33, 4584–4593. 10.1021/bi00181a020. PubMed DOI

Chang C. H.; El-Kabbani O.; Tiede D.; Norris J.; Schiffer M. Structure of the Membrane-Bound Protein Photosynthetic Reaction Center from Rhodobacter Sphaeroides. Biochemistry 1991, 30, 5352–5360. 10.1021/bi00236a005. PubMed DOI

Johansson L. C.; Arnlund D.; Katona G.; White T. A.; Barty A.; DePonte D. P.; Shoeman R. L.; Wickstrand C.; Sharma A.; Williams G. J.; et al. Structure of a Photosynthetic Reaction Centre Determined by Serial Femtosecond Crystallography. Nat. Commun. 2013, 4, 2911.10.1038/ncomms3911. PubMed DOI PMC

Wöhri A. B.; Wahlgren W. Y.; Malmerberg E.; Johansson L. C.; Neutze R.; Katona G. Lipidic Sponge Phase Crystal Structure of a Photosynthetic Reaction Center Reveals Lipids on the Protein Surface. Biochemistry 2009, 48, 9831–9838. 10.1021/bi900545e. PubMed DOI

Deisenhofer J.; Epp O.; Sinning I.; Michel H. Crystallographic Refinement at 2.3 Å Resolution and Refined Model of the Photosynthetic Reaction Centre FromRhodopseudomonas Viridis. J. Mol. Biol. 1995, 246, 429–457. 10.1006/jmbi.1994.0097. PubMed DOI

Standfuss J.; Terwisscha van Scheltinga A. C.; Lamborghini M.; Kühlbrandt W. Mechanisms of Photoprotection and Nonphotochemical Quenching in Pea Light-Harvesting Complex at 2.5 Å Resolution. EMBO J. 2005, 24, 919–928. 10.1038/sj.emboj.7600585. PubMed DOI PMC

Pan X.; Li M.; Wan T.; Wang L.; Jia C.; Hou Z.; Zhao X.; Zhang J.; Chang W. Structural Insights into Energy Regulation of Light-Harvesting Complex CP29 from Spinach. Nat. Struct. Mol. Biol. 2011, 18, 309–315. 10.1038/nsmb.2008. PubMed DOI

Liu Z.; Yan H.; Wang K.; Kuang T.; Zhang J.; Gui L.; An X.; Chang W. Crystal Structure of Spinach Major Light-Harvesting Complex at 2.72 Å Resolution. Nature 2004, 428, 287–292. 10.1038/nature02373. PubMed DOI

Koepke J.; Hu X.; Muenke C.; Schulten K.; Michel H. The Crystal Structure of the Light-Harvesting Complex II (B800–850) from Rhodospirillum Molischianum. Structure 1996, 4, 581–597. 10.1016/S0969-2126(96)00063-9. PubMed DOI

Papiz M. Z.; Prince S. M.; Howard T.; Cogdell R. J.; Isaacs N. W. The Structure and Thermal Motion of the B800–850 LH2 Complex from Rps. Acidophila at 2.0 Å Resolution and 100 K: New Structural Features and Functionally Relevant Motions. J. Mol. Biol. 2003, 326, 1523–1538. 10.1016/S0022-2836(03)00024-X. PubMed DOI

Prince S. M.; Papiz M. Z.; Freer A. A.; McDermott G.; Hawthornthwaite-Lawless A. M.; Cogdell R. J.; Isaacs N. W. Apoprotein Structure in the LH2 Complex from Rhodopseudomonas Acidophila Strain 10050: Modular Assembly and Protein Pigment Interactions 1 1Edited by R. Huber. J. Mol. Biol. 1997, 268, 412–423. 10.1006/jmbi.1997.0966. PubMed DOI

Ago H.; Adachi H.; Umena Y.; Tashiro T.; Kawakami K.; Kamiya N.; Tian L.; Han G.; Kuang T.; Liu Z.; et al. Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga. J. Biol. Chem. 2016, 291, 5676–5687. 10.1074/jbc.M115.711689. PubMed DOI PMC

Suga M.; Akita F.; Sugahara M.; Kubo M.; Nakajima Y.; Nakane T.; Yamashita K.; Umena Y.; Nakabayashi M.; Yamane T.; et al. Light-Induced Structural Changes and the Site of O = O Bond Formation in PSII Caught by XFEL. Nature 2017, 543, 131–135. 10.1038/nature21400. PubMed DOI

Suga M.; Akita F.; Hirata K.; Ueno G.; Murakami H.; Nakajima Y.; Shimizu T.; Yamashita K.; Yamamoto M.; Ago H.; et al. Native Structure of Photosystem II at 1.95 Å Resolution Viewed by Femtosecond X-Ray Pulses. Nature 2015, 517, 99–103. 10.1038/nature13991. PubMed DOI

Koua F. H. M.; Umena Y.; Kawakami K.; Shen J.-R. Structure of Sr-Substituted Photosystem II at 2.1 Å Resolution and Its Implications in the Mechanism of Water Oxidation. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 3889–3894. 10.1073/pnas.1219922110. PubMed DOI PMC

Umena Y.; Kawakami K.; Shen J.-R.; Kamiya N. Crystal Structure of Oxygen-Evolving Photosystem II at a Resolution of 1.9 Å. Nature 2011, 473, 55–60. 10.1038/nature09913. PubMed DOI

Wiwczar J. M.; LaFountain A. M.; Wang J.; Frank H. A.; Brudvig G. W. Chlorophyll a with a Farnesyl Tail in Thermophilic Cyanobacteria. Photosynth. Res. 2017, 134, 175–182. 10.1007/s11120-017-0425-4. PubMed DOI PMC

Kupitz C.; Basu S.; Grotjohann I.; Fromme R.; Zatsepin N. A.; Rendek K. N.; Hunter M. S.; Shoeman R. L.; White T. A.; Wang D.; et al. Serial Time-Resolved Crystallography of Photosystem II Using a Femtosecond X-Ray Laser. Nature 2014, 513, 261–265. 10.1038/nature13453. PubMed DOI PMC

Kawakami K.; Umena Y.; Kamiya N.; Shen J.-R. Location of Chloride and Its Possible Functions in Oxygen-Evolving Photosystem II Revealed by X-Ray Crystallography. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 8567–8572. 10.1073/pnas.0812797106. PubMed DOI PMC

Kamiya N.; Shen J.-R. Crystal Structure of Oxygen-Evolving Photosystem II from Thermosynechococcus Vulcanus at 3.7-Å Resolution. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 98–103. 10.1073/pnas.0135651100. PubMed DOI PMC

Young I. D.; Ibrahim M.; Chatterjee R.; Gul S.; Fuller F. D.; Koroidov S.; Brewster A. S.; Tran R.; Alonso-Mori R.; Kroll T.; et al. Structure of Photosystem II and Substrate Binding at Room Temperature. Nature 2016, 540, 453–457. 10.1038/nature20161. PubMed DOI PMC

Ayyer K.; Yefanov O. M.; Oberthür D.; Roy-Chowdhury S.; Galli L.; Mariani V.; Basu S.; Coe J.; Conrad C. E.; Fromme R.; et al. Macromolecular Diffractive Imaging Using Imperfect Crystals. Nature 2016, 530, 202–206. 10.1038/nature16949. PubMed DOI PMC

Guskov A.; Kern J.; Gabdulkhakov A.; Broser M.; Zouni A.; Saenger W. Cyanobacterial Photosystem II at 2.9-Å Resolution and the Role of Quinones, Lipids, Channels and Chloride. Nat. Struct. Mol. Biol. 2009, 16, 334–342. 10.1038/nsmb.1559. PubMed DOI

Loll B.; Kern J.; Saenger W.; Zouni A.; Biesiadka J. Towards Complete Cofactor Arrangement in the 3.0 Å Resolution Structure of Photosystem II. Nature 2005, 438, 1040–1044. 10.1038/nature04224. PubMed DOI

Ferreira K. N. Architecture of the Photosynthetic Oxygen-Evolving Center. Science 2004, 303, 1831–1838. 10.1126/science.1093087. PubMed DOI

Qin X.; Suga M.; Kuang T.; Shen J.-R. Structural Basis for Energy Transfer Pathways in the Plant PSI-LHCI Supercomplex. Science 2015, 348, 989–995. 10.1126/science.aab0214. PubMed DOI

Amunts A.; Toporik H.; Borovikova A.; Nelson N. Structure Determination and Improved Model of Plant Photosystem I. J. Biol. Chem. 2010, 285, 3478–3486. 10.1074/jbc.M109.072645. PubMed DOI PMC

Jordan P.; Fromme P.; Witt H. T.; Klukas O.; Saenger W.; Krauß N. Three-Dimensional Structure of Cyanobacterial Photosystem I at 2.5 Å Resolution. Nature 2001, 411, 909–917. 10.1038/35082000. PubMed DOI

Brunger A. T.; Adams P. D.; Fromme P.; Fromme R.; Levitt M.; Schröder G. F. Improving the Accuracy of Macromolecular Structure Refinement at 7 Å Resolution. Structure 2012, 20, 957–966. 10.1016/j.str.2012.04.020. PubMed DOI PMC

Chapman H. N.; Fromme P.; Barty A.; White T. A.; Kirian R. A.; Aquila A.; Hunter M. S.; Schulz J.; DePonte D. P.; Weierstall U.; et al. Femtosecond X-Ray Protein Nanocrystallography. Nature 2011, 470, 73–77. 10.1038/nature09750. PubMed DOI PMC

Pan X.; Ma J.; Su X.; Cao P.; Chang W.; Liu Z.; Zhang X.; Li M. Structure of the Maize Photosystem I Supercomplex with Light-Harvesting Complexes I and II. Science 2018, 360, 1109–1113. 10.1126/science.aat1156. PubMed DOI

Pi X.; Tian L.; Dai H.-E.; Qin X.; Cheng L.; Kuang T.; Sui S.-F.; Shen J.-R. Unique Organization of Photosystem I–Light-Harvesting Supercomplex Revealed by Cryo-EM from a Red Alga. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, 4423–4428. 10.1073/pnas.1722482115. PubMed DOI PMC

Lyons J. A.; Aragão D.; Slattery O.; Pisliakov A. V.; Soulimane T.; Caffrey M. Structural Insights into Electron Transfer in caa3-Type Cytochrome Oxidase. Nature 2012, 487, 514–518. 10.1038/nature11182. PubMed DOI PMC

Harrenga A.; Michel H. The Cytochrome c Oxidase from Paracoccus Denitrificans Does Not Change the Metal Center Ligation upon Reduction. J. Biol. Chem. 1999, 274, 33296–33299. 10.1074/jbc.274.47.33296. PubMed DOI

Ishigami I.; Zatsepin N. A.; Hikita M.; Conrad C. E.; Nelson G.; Coe J. D.; Basu S.; Grant T. D.; Seaberg M. H.; Sierra R. G.; et al. Crystal Structure of CO-Bound Cytochrome c Oxidase Determined by Serial Femtosecond X-Ray Crystallography at Room Temperature. Proc. Natl. Acad. Sci. U. S. A. 2017, 114, 8011–8016. 10.1073/pnas.1705628114. PubMed DOI PMC

Luo F.; Shinzawa-Itoh K.; Hagimoto K.; Shimada A.; Shimada S.; Yamashita E.; Yoshikawa S.; Tsukihara T. Structure of Bovine Cytochrome c Oxidase in the Ligand-Free Reduced State at Neutral pH. Acta Crystallogr., Sect. F: Struct. Biol. Commun. 2018, 74, 92–98. 10.1107/S2053230X17018532. PubMed DOI PMC

Shimada A.; Hatano K.; Tadehara H.; Yano N.; Shinzawa-Itoh K.; Yamashita E.; Muramoto K.; Tsukihara T.; Yoshikawa S. X-Ray Structural Analyses of Azide-Bound Cytochrome c Oxidases Reveal That the H-Pathway Is Critically Important for the Proton-Pumping Activity. J. Biol. Chem. 2018, 293, 14868–14879. 10.1074/jbc.RA118.003123. PubMed DOI PMC

Tsukihara T.; Shimokata K.; Katayama Y.; Shimada H.; Muramoto K.; Aoyama H.; Mochizuki M.; Shinzawa-Itoh K.; Yamashita E.; Yao M.; et al. The Low-Spin Heme of Cytochrome c Oxidase as the Driving Element of the Proton-Pumping Process. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 15304–15309. 10.1073/pnas.2635097100. PubMed DOI PMC

Hasan S. S.; Yamashita E.; Baniulis D.; Cramer W. A. Quinone-Dependent Proton Transfer Pathways in the Photosynthetic Cytochrome b6f Complex. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 4297–4302. 10.1073/pnas.1222248110. PubMed DOI PMC

Stroebel D.; Choquet Y.; Popot J.-L.; Picot D. An Atypical Haem in the Cytochrome B6f Complex. Nature 2003, 426, 413–418. 10.1038/nature02155. PubMed DOI

Yamashita E.; Zhang H.; Cramer W. A. Structure of the Cytochrome b6f Complex: Quinone Analogue Inhibitors as Ligands of Heme cn. J. Mol. Biol. 2007, 370, 39–52. 10.1016/j.jmb.2007.04.011. PubMed DOI PMC

Yan J.; Kurisu G.; Cramer W. A. Intraprotein Transfer of the Quinone Analogue Inhibitor 2,5-Dibromo-3-Methyl-6-Isopropyl-p-Benzoquinone in the Cytochrome b6f Complex. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 69–74. 10.1073/pnas.0504909102. PubMed DOI PMC

Kurisu G. Structure of the Cytochrome b6f Complex of Oxygenic Photosynthesis: Tuning the Cavity. Science 2003, 302, 1009–1014. 10.1126/science.1090165. PubMed DOI

Esser L.; Gong X.; Yang S.; Yu L.; Yu C.-A.; Xia D. Surface-Modulated Motion Switch: Capture and Release of Iron-Sulfur Protein in the Cytochrome bc1 Complex. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 13045–13050. 10.1073/pnas.0601149103. PubMed DOI PMC

Solmaz S. R. N.; Hunte C. Structure of Complex III with Bound Cytochrome c in Reduced State and Definition of a Minimal Core Interface for Electron Transfer. J. Biol. Chem. 2008, 283, 17542–17549. 10.1074/jbc.M710126200. PubMed DOI

Zhang Z.; Huang L.; Shulmeister V. M.; Chi Y.-I.; Kim K. K.; Hung L.-W.; Crofts A. R.; Berry E. A.; Kim S.-H. Electron Transfer by Domain Movement in Cytochrome bc1. Nature 1998, 392, 677–684. 10.1038/33612. PubMed DOI

Crowley P. J.; Berry E. A.; Cromartie T.; Daldal F.; Godfrey C. R. A.; Lee D.-W.; Phillips J. E.; Taylor A.; Viner R. The Role of Molecular Modeling in the Design of Analogues of the Fungicidal Natural Products Crocacins A and D. Bioorg. Med. Chem. 2008, 16, 10345–10355. 10.1016/j.bmc.2008.10.030. PubMed DOI PMC

Huang L.; Cobessi D.; Tung E. Y.; Berry E. A. Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial Bc1 Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-Bonding Pattern. J. Mol. Biol. 2005, 351, 573–597. 10.1016/j.jmb.2005.05.053. PubMed DOI PMC

Huang L.; Sun G.; Cobessi D.; Wang A. C.; Shen J. T.; Tung E. Y.; Anderson V. E.; Berry E. A. 3-Nitropropionic Acid Is a Suicide Inhibitor of Mitochondrial Respiration That, upon Oxidation by Complex II, Forms a Covalent Adduct with a Catalytic Base Arginine in the Active Site of the Enzyme. J. Biol. Chem. 2006, 281, 5965–5972. 10.1074/jbc.M511270200. PubMed DOI PMC

Huang L.-S.; Shen J. T.; Wang A. C.; Berry E. A. Crystallographic Studies of the Binding of Ligands to the Dicarboxylate Site of Complex II, and the Identity of the Ligand in the “Oxaloacetate-Inhibited” State. Biochim. Biophys. Acta, Bioenerg. 2006, 1757, 1073–1083. 10.1016/j.bbabio.2006.06.015. PubMed DOI PMC

Sun F.; Huo X.; Zhai Y.; Wang A.; Xu J.; Su D.; Bartlam M.; Rao Z. Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex II. Cell 2005, 121, 1043–1057. 10.1016/j.cell.2005.05.025. PubMed DOI

Horsefield R.; Yankovskaya V.; Sexton G.; Whittingham W.; Shiomi K.; O̅mura S.; Byrne B.; Cecchini G.; Iwata S. Structural and Computational Analysis of the Quinone-Binding Site of Complex II (Succinate-Ubiquinone Oxidoreductase): A MECHANISM OF ELECTRON TRANSFER AND PROTON CONDUCTION DURING UBIQUINONE REDUCTION. J. Biol. Chem. 2006, 281, 7309–7316. 10.1074/jbc.M508173200. PubMed DOI

Yankovskaya V. Architecture of Succinate Dehydrogenase and Reactive Oxygen Species Generation. Science 2003, 299, 700–704. 10.1126/science.1079605. PubMed DOI

Jormakka M. Molecular Basis of Proton Motive Force Generation: Structure of Formate Dehydrogenase-N. Science 2002, 295, 1863–1868. 10.1126/science.1068186. PubMed DOI

Agip A.-N. A.; Blaza J. N.; Bridges H. R.; Viscomi C.; Rawson S.; Muench S. P.; Hirst J. Cryo-EM Structures of Complex I from Mouse Heart Mitochondria in Two Biochemically Defined States. Nat. Struct. Mol. Biol. 2018, 25, 548–556. 10.1038/s41594-018-0073-1. PubMed DOI PMC

Parey K.; Brandt U.; Xie H.; Mills D. J.; Siegmund K.; Vonck J.; Kühlbrandt W.; Zickermann V. Cryo-EM Structure of Respiratory Complex I at Work. eLife 2018, 7, e39213.10.7554/eLife.39213. PubMed DOI PMC

Rothery R. A.; Bertero M. G.; Cammack R.; Palak M.; Blasco F.; Strynadka N. C. J.; Weiner J. H. The Catalytic Subunit of Escherichia Coli Nitrate Reductase A Contains a Novel [4Fe-4S] Cluster with a High-Spin Ground State. Biochemistry 2004, 43, 5324–5333. 10.1021/bi049938l. PubMed DOI

Bertero M. G.; Rothery R. A.; Palak M.; Hou C.; Lim D.; Blasco F.; Weiner J. H.; Strynadka N. C. J. Insights into the Respiratory Electron Transfer Pathway from the Structure of Nitrate Reductase A. Nat. Struct. Mol. Biol. 2003, 10, 681–687. 10.1038/nsb969. PubMed DOI

Abe K.; Irie K.; Nakanishi H.; Suzuki H.; Fujiyoshi Y. Crystal Structures of the Gastric Proton Pump. Nature 2018, 556, 214–218. 10.1038/s41586-018-0003-8. PubMed DOI

Andersson M.; Mattle D.; Sitsel O.; Klymchuk T.; Nielsen A. M.; Møller L. B.; White S. H.; Nissen P.; Gourdon P. Copper-Transporting P-Type ATPases Use a Unique Ion-Release Pathway. Nat. Struct. Mol. Biol. 2014, 21, 43–48. 10.1038/nsmb.2721. PubMed DOI PMC

Ogawa H.; Cornelius F.; Hirata A.; Toyoshima C. Sequential Substitution of K+ Bound to Na+,K+-ATPase Visualized by X-Ray Crystallography. Nat. Commun. 2015, 6, 8004.10.1038/ncomms9004. PubMed DOI PMC

Ogawa H.; Shinoda T.; Cornelius F.; Toyoshima C. Crystal Structure of the Sodium-Potassium Pump (Na+,K+-ATPase) with Bound Potassium and Ouabain. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 13742–13747. 10.1073/pnas.0907054106. PubMed DOI PMC

Shinoda T.; Ogawa H.; Cornelius F.; Toyoshima C. Crystal Structure of the Sodium–Potassium Pump at 2.4 Å Resolution. Nature 2009, 459, 446–450. 10.1038/nature07939. PubMed DOI

Laursen M.; Gregersen J. L.; Yatime L.; Nissen P.; Fedosova N. U. Structures and Characterization of Digoxin- and Bufalin-Bound Na+,K+-ATPase Compared with the Ouabain-Bound Complex. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 1755–1760. 10.1073/pnas.1422997112. PubMed DOI PMC

Kanai R.; Ogawa H.; Vilsen B.; Cornelius F.; Toyoshima C. Crystal Structure of a Na+-Bound Na+,K+-ATPase Preceding the E1P State. Nature 2013, 502, 201–206. 10.1038/nature12578. PubMed DOI

Nyblom M.; Poulsen H.; Gourdon P.; Reinhard L.; Andersson M.; Lindahl E.; Fedosova N.; Nissen P. Crystal Structure of Na+, K +-ATPase in the Na+-Bound State. Science 2013, 342, 123–127. 10.1126/science.1243352. PubMed DOI

Laursen M.; Yatime L.; Nissen P.; Fedosova N. U. Crystal Structure of the High-Affinity Na+,K+-ATPase-Ouabain Complex with Mg2+ Bound in the Cation Binding Site. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 10958–10963. 10.1073/pnas.1222308110. PubMed DOI PMC

Morth J. P.; Pedersen B. P.; Toustrup-Jensen M. S.; Sørensen T. L.-M.; Petersen J.; Andersen J. P.; Vilsen B.; Nissen P. Crystal Structure of the Sodium–Potassium Pump. Nature 2007, 450, 1043–1049. 10.1038/nature06419. PubMed DOI

Norimatsu Y.; Hasegawa K.; Shimizu N.; Toyoshima C. Protein–Phospholipid Interplay Revealed with Crystals of a Calcium Pump. Nature 2017, 545, 193–198. 10.1038/nature22357. PubMed DOI

Clausen J. D.; Bublitz M.; Arnou B.; Montigny C.; Jaxel C.; Møller J. V.; Nissen P.; Andersen J. P.; le Maire M. SERCA Mutant E309Q Binds Two Ca 2+ Ions but Adopts a Catalytically Incompetent Conformation: Structure and Function of SERCA Mutant E309Q. EMBO J. 2013, 32, 3231–3243. 10.1038/emboj.2013.250. PubMed DOI PMC

Toyoshima C.; Iwasawa S.; Ogawa H.; Hirata A.; Tsueda J.; Inesi G. Crystal Structures of the Calcium Pump and Sarcolipin in the Mg2+-Bound E1 State. Nature 2013, 495, 260–264. 10.1038/nature11899. PubMed DOI

Obara K.; Miyashita N.; Xu C.; Toyoshima I.; Sugita Y.; Inesi G.; Toyoshima C. Structural Role of Countertransport Revealed in Ca2+ Pump Crystal Structure in the Absence of Ca2+. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 14489–14496. 10.1073/pnas.0506222102. PubMed DOI PMC

Saroussi S.; Schushan M.; Ben-Tal N.; Junge W.; Nelson N. Structure and Flexibility of the C-Ring in the Electromotor of Rotary FoF1-ATPase of Pea Chloroplasts. PLoS One 2012, 7, e43045.10.1371/journal.pone.0043045. PubMed DOI PMC

Murata T. Structure of the Rotor of the V-Type Na+-ATPase from Enterococcus Hirae. Science 2005, 308, 654–659. 10.1126/science.1110064. PubMed DOI

Huang C.-S.; Pedersen B. P.; Stokes D. L. Crystal Structure of the Potassium-Importing KdpFABC Membrane Complex. Nature 2017, 546, 681–685. 10.1038/nature22970. PubMed DOI PMC

Johnson Z. L.; Chen J. ATP Binding Enables Substrate Release from Multidrug Resistance Protein 1. Cell 2018, 172, 81–89.e10. 10.1016/j.cell.2017.12.005. PubMed DOI

Shintre C. A.; Pike A. C. W.; Li Q.; Kim J.-I.; Barr A. J.; Goubin S.; Shrestha L.; Yang J.; Berridge G.; Ross J.; et al. Structures of ABCB10, a Human ATP-Binding Cassette Transporter in Apo- and Nucleotide-Bound States. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 9710–9715. 10.1073/pnas.1217042110. PubMed DOI PMC

Oldham M. L.; Chen S.; Chen J. Structural Basis for Substrate Specificity in the Escherichia Coli Maltose Transport System. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 18132–18137. 10.1073/pnas.1311407110. PubMed DOI PMC

Chen S.; Oldham M. L.; Davidson A. L.; Chen J. Carbon Catabolite Repression of the Maltose Transporter Revealed by X-Ray Crystallography. Nature 2013, 499, 364–368. 10.1038/nature12232. PubMed DOI PMC

Oldham M. L.; Chen J. Snapshots of the Maltose Transporter during ATP Hydrolysis. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 15152–15156. 10.1073/pnas.1108858108. PubMed DOI PMC

Ho H.; Miu A.; Alexander M. K.; Garcia N. K.; Oh A.; Zilberleyb I.; Reichelt M.; Austin C. D.; Tam C.; Shriver S.; et al. Structural Basis for Dual-Mode Inhibition of the ABC Transporter MsbA. Nature 2018, 557, 196–201. 10.1038/s41586-018-0083-5. PubMed DOI

Hu N.-J.; Iwata S.; Cameron A. D.; Drew D. Crystal Structure of a Bacterial Homologue of the Bile Acid Sodium Symporter ASBT. Nature 2011, 478, 408–411. 10.1038/nature10450. PubMed DOI PMC

Ruprecht J. J.; Hellawell A. M.; Harding M.; Crichton P. G.; McCoy A. J.; Kunji E. R. S. Structures of Yeast Mitochondrial ADP/ATP Carriers Support a Domain-Based Alternating-Access Transport Mechanism. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, E426–E434. 10.1073/pnas.1320692111. PubMed DOI PMC

Nury H.; Dahout-Gonzalez C.; Trézéguet V.; Lauquin G.; Brandolin G.; Pebay-Peyroula E. Structural Basis for Lipid-Mediated Interactions between Mitochondrial ADP/ATP Carrier Monomers. FEBS Lett. 2005, 579, 6031–6036. 10.1016/j.febslet.2005.09.061. PubMed DOI

Pebay-Peyroula E.; Dahout-Gonzalez C.; Kahn R.; Trézéguet V.; Lauquin G. J.-M.; Brandolin G. Structure of Mitochondrial ADP/ATP Carrier in Complex with Carboxyatractyloside. Nature 2003, 426, 39–44. 10.1038/nature02056. PubMed DOI

Wöhlert D.; Kühlbrandt W.; Yildiz Ö. Structure and Substrate Ion Binding in the Sodium/Proton Antiporter PaNhaP. eLife 2014, 3, e03579.10.7554/eLife.03579. PubMed DOI PMC

Baradaran R.; Wang C.; Siliciano A. F.; Long S. B. Cryo-EM Structures of Fungal and Metazoan Mitochondrial Calcium Uniporters. Nature 2018, 559, 580–584. 10.1038/s41586-018-0331-8. PubMed DOI PMC

Koshy C.; Schweikhard E. S.; Gärtner R. M.; Perez C.; Yildiz Ö.; Ziegler C. Structural Evidence for Functional Lipid Interactions in the Betaine Transporter BetP: Structural Evidence for Functional Lipid Interactions in the BetP. EMBO J. 2013, 32, 3096–3105. 10.1038/emboj.2013.226. PubMed DOI PMC

Perez C.; Koshy C.; Yildiz Ö.; Ziegler C. Alternating-Access Mechanism in Conformationally Asymmetric Trimers of the Betaine Transporter BetP. Nature 2012, 490, 126–130. 10.1038/nature11403. PubMed DOI

Li F.; Liu J.; Zheng Y.; Garavito R. M.; Ferguson-Miller S. Crystal Structures of Translocator Protein (TSPO) and Mutant Mimic of a Human Polymorphism. Science 2015, 347, 555–558. 10.1126/science.1260590. PubMed DOI PMC

Wöhlert D.; Grötzinger M. J.; Kühlbrandt W.; Yildiz Ö. Mechanism of Na+-Dependent Citrate Transport from the Structure of an Asymmetrical CitS Dimer. eLife 2015, 4, e09375.10.7554/eLife.09375. PubMed DOI PMC

Coleman J. A.; Gouaux E. Structural Basis for Recognition of Diverse Antidepressants by the Human Serotonin Transporter. Nat. Struct. Mol. Biol. 2018, 25, 170–175. 10.1038/s41594-018-0026-8. PubMed DOI PMC

Jungnickel K. E. J.; Parker J. L.; Newstead S. Structural Basis for Amino Acid Transport by the CAT Family of SLC7 Transporters. Nat. Commun. 2018, 9, 550.10.1038/s41467-018-03066-6. PubMed DOI PMC

Penmatsa A.; Wang K. H.; Gouaux E. X-Ray Structures of Drosophila Dopamine Transporter in Complex with Nisoxetine and Reboxetine. Nat. Struct. Mol. Biol. 2015, 22, 506–508. 10.1038/nsmb.3029. PubMed DOI PMC

Heng J.; Zhao Y.; Liu M.; Liu Y.; Fan J.; Wang X.; Zhao Y.; Zhang X. C. Substrate-Bound Structure of the E. Coli Multidrug Resistance Transporter MdfA. Cell Res. 2015, 25, 1060–1073. 10.1038/cr.2015.94. PubMed DOI PMC

Oswald C.; Tam H.-K.; Pos K. M. Transport of Lipophilic Carboxylates Is Mediated by Transmembrane Helix 2 in Multidrug Transporter AcrB. Nat. Commun. 2016, 7, 13819.10.1038/ncomms13819. PubMed DOI PMC

Bai X.; Yan C.; Yang G.; Lu P.; Ma D.; Sun L.; Zhou R.; Scheres S. H. W.; Shi Y. An Atomic Structure of Human γ-Secretase. Nature 2015, 525, 212–217. 10.1038/nature14892. PubMed DOI PMC

Quigley A.; Dong Y. Y.; Pike A. C. W.; Dong L.; Shrestha L.; Berridge G.; Stansfeld P. J.; Sansom M. S. P.; Edwards A. M.; Bountra C.; et al. The Structural Basis of ZMPSTE24-Dependent Laminopathies. Science 2013, 339, 1604–1607. 10.1126/science.1231513. PubMed DOI

Vinothkumar K. R. Structure of Rhomboid Protease in a Lipid Environment. J. Mol. Biol. 2011, 407, 232–247. 10.1016/j.jmb.2011.01.029. PubMed DOI PMC

Ben-Shem A.; Fass D.; Bibi E. Structural Basis for Intramembrane Proteolysis by Rhomboid Serine Proteases. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 462–466. 10.1073/pnas.0609773104. PubMed DOI PMC

Luo P.; Yu X.; Wang W.; Fan S.; Li X.; Wang J. Crystal Structure of a Phosphorylation-Coupled Vitamin C Transporter. Nat. Struct. Mol. Biol. 2015, 22, 238–241. 10.1038/nsmb.2975. PubMed DOI

Yang J.; Kulkarni K.; Manolaridis I.; Zhang Z.; Dodd R. B.; Mas-Droux C.; Barford D. Mechanism of Isoprenylcysteine Carboxyl Methylation from the Crystal Structure of the Integral Membrane Methyltransferase ICMT. Mol. Cell 2011, 44, 997–1004. 10.1016/j.molcel.2011.10.020. PubMed DOI

Mao G.; Zhao Y.; Kang X.; Li Z.; Zhang Y.; Wang X.; Sun F.; Sankaran K.; Zhang X. C. Crystal Structure of E. Coli Lipoprotein Diacylglyceryl Transferase. Nat. Commun. 2016, 7, 10198.10.1038/ncomms10198. PubMed DOI PMC

Diver M. M.; Pedi L.; Koide A.; Koide S.; Long S. B. Atomic Structure of the Eukaryotic Intramembrane RAS Methyltransferase ICMT. Nature 2018, 553, 526–529. 10.1038/nature25439. PubMed DOI PMC

Petrou V. I.; Herrera C. M.; Schultz K. M.; Clarke O. B.; Vendome J.; Tomasek D.; Banerjee S.; Rajashankar K. R.; Belcher Dufrisne M.; Kloss B.; et al. Structures of Aminoarabinose Transferase ArnT Suggest a Molecular Basis for Lipid A Glycosylation. Science 2016, 351, 608–612. 10.1126/science.aad1172. PubMed DOI PMC

Bai L.; Wang T.; Zhao G.; Kovach A.; Li H. The Atomic Structure of a Eukaryotic Oligosaccharyltransferase Complex. Nature 2018, 555, 328–333. 10.1038/nature25755. PubMed DOI PMC

Wild R.; Kowal J.; Eyring J.; Ngwa E. M.; Aebi M.; Locher K. P. Structure of the Yeast Oligosaccharyltransferase Complex Gives Insight into Eukaryotic N-Glycosylation. Science 2018, 359, 545–550. 10.1126/science.aar5140. PubMed DOI

Basak S.; Gicheru Y.; Samanta A.; Molugu S. K.; Huang W.; Fuente M. la de; Hughes T.; Taylor D. J.; Nieman M. T.; Moiseenkova-Bell V.; et al. Cryo-EM Structure of 5-HT3A Receptor in Its Resting Conformation. Nat. Commun. 2018, 9, 514.10.1038/s41467-018-02997-4. PubMed DOI PMC

Zhu S.; Noviello C. M.; Teng J.; Walsh R. M.; Kim J. J.; Hibbs R. E. Structure of a Human Synaptic GABAA Receptor. Nature 2018, 559, 67–72. 10.1038/s41586-018-0255-3. PubMed DOI PMC

Song X.; Jensen M. Ø.; Jogini V.; Stein R. A.; Lee C.-H.; Mchaourab H. S.; Shaw D. E.; Gouaux E. Mechanism of NMDA Receptor Channel Block by MK-801 and Memantine. Nature 2018, 556, 515–519. 10.1038/s41586-018-0039-9. PubMed DOI PMC

Walsh R. M.; Roh S.-H.; Gharpure A.; Morales-Perez C. L.; Teng J.; Hibbs R. E. Structural Principles of Distinct Assemblies of the Human Α4β2 Nicotinic Receptor. Nature 2018, 557, 261–265. 10.1038/s41586-018-0081-7. PubMed DOI PMC

Pan J.; Chen Q.; Willenbring D.; Mowrey D.; Kong X.-P.; Cohen A.; Divito C. B.; Xu Y.; Tang P. Structure of the Pentameric Ligand-Gated Ion Channel GLIC Bound with Anesthetic Ketamine. Structure 2012, 20, 1463–1469. 10.1016/j.str.2012.08.009. PubMed DOI PMC

Sauguet L.; Poitevin F.; Murail S.; Van Renterghem C.; Moraga-Cid G.; Malherbe L.; Thompson A. W.; Koehl P.; Corringer P.-J.; Baaden M.; et al. Structural Basis for Ion Permeation Mechanism in Pentameric Ligand-Gated Ion Channels. EMBO J. 2013, 32, 728–741. 10.1038/emboj.2013.17. PubMed DOI PMC

Fan C.; Choi W.; Sun W.; Du J.; Lu W. Structure of the Human Lipid-Gated Cation Channel TRPC3. eLife 2018, 7, e36852.10.7554/eLife.36852. PubMed DOI PMC

Strugatsky D.; McNulty R.; Munson K.; Chen C.-K.; Soltis S. M.; Sachs G.; Luecke H. Structure of the Proton-Gated Urea Channel from the Gastric Pathogen Helicobacter Pylori. Nature 2012, 493, 255–258. 10.1038/nature11684. PubMed DOI PMC

Levin E. J.; Cao Y.; Enkavi G.; Quick M.; Pan Y.; Tajkhorshid E.; Zhou M. Structure and Permeation Mechanism of a Mammalian Urea Transporter. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 11194–11199. 10.1073/pnas.1207362109. PubMed DOI PMC

Jiang J.; Daniels B. V.; Fu D. Crystal Structure of AqpZ Tetramer Reveals Two Distinct Arg-189 Conformations Associated with Water Permeation through the Narrowest Constriction of the Water-Conducting Channel. J. Biol. Chem. 2006, 281, 454–460. 10.1074/jbc.M508926200. PubMed DOI

Tani K.; Mitsuma T.; Hiroaki Y.; Kamegawa A.; Nishikawa K.; Tanimura Y.; Fujiyoshi Y. Mechanism of Aquaporin-4’s Fast and Highly Selective Water Conduction and Proton Exclusion. J. Mol. Biol. 2009, 389, 694–706. 10.1016/j.jmb.2009.04.049. PubMed DOI

Hite R. K.; Li Z.; Walz T. Principles of Membrane Protein Interactions with Annular Lipids Deduced from Aquaporin-0 2D Crystals. EMBO J. 2010, 29, 1652–1658. 10.1038/emboj.2010.68. PubMed DOI PMC

Gonen T.; Cheng Y.; Sliz P.; Hiroaki Y.; Fujiyoshi Y.; Harrison S. C.; Walz T. Lipid–Protein Interactions in Double-Layered Two-Dimensional AQP0 Crystals. Nature 2005, 438, 633–638. 10.1038/nature04321. PubMed DOI PMC

Jin P.; Bulkley D.; Guo Y.; Zhang W.; Guo Z.; Huynh W.; Wu S.; Meltzer S.; Cheng T.; Jan L. Y.; et al. Electron Cryo-Microscopy Structure of the Mechanotransduction Channel NOMPC. Nature 2017, 547, 118–122. 10.1038/nature22981. PubMed DOI PMC

Wilkes M.; Madej M. G.; Kreuter L.; Rhinow D.; Heinz V.; De Sanctis S.; Ruppel S.; Richter R. M.; Joos F.; Grieben M.; et al. Molecular Insights into Lipid-Assisted Ca2+ Regulation of the TRP Channel Polycystin-2. Nat. Struct. Mol. Biol. 2017, 24, 123–130. 10.1038/nsmb.3357. PubMed DOI

Hirschi M.; Herzik M. A. Jr; Wie J.; Suo Y.; Borschel W. F.; Ren D.; Lander G. C.; Lee S.-Y. Cryo-Electron Microscopy Structure of the Lysosomal Calcium-Permeable Channel TRPML3. Nature 2017, 550, 411–414. 10.1038/nature24055. PubMed DOI PMC

Zhang Z.; Tóth B.; Szollosi A.; Chen J.; Csanády L. Structure of a TRPM2 Channel in Complex with Ca2+ Explains Unique Gating Regulation. eLife 2018, 7, e36409.10.7554/eLife.36409. PubMed DOI PMC

Duan J.; Li J.; Zeng B.; Chen G.-L.; Peng X.; Zhang Y.; Wang J.; Clapham D. E.; Li Z.; Zhang J. Structure of the Mouse TRPC4 Ion Channel. Nat. Commun. 2018, 9, 3102.10.1038/s41467-018-05247-9. PubMed DOI PMC

Vinayagam D.; Mager T.; Apelbaum A.; Bothe A.; Merino F.; Hofnagel O.; Gatsogiannis C.; Raunser S. Electron Cryo-Microscopy Structure of the Canonical TRPC4 Ion Channel. eLife 2018, 7, e36615.10.7554/eLife.36615. PubMed DOI PMC

Tang L.; Gamal El-Din T. M.; Swanson T. M.; Pryde D. C.; Scheuer T.; Zheng N.; Catterall W. A. Structural Basis for Inhibition of a Voltage-Gated Ca2+ Channel by Ca2+ Antagonist Drugs. Nature 2016, 537, 117–121. 10.1038/nature19102. PubMed DOI PMC

Tang L.; Gamal El-Din T. M.; Payandeh J.; Martinez G. Q.; Heard T. M.; Scheuer T.; Zheng N.; Catterall W. A. Structural Basis for Ca2+ Selectivity of a Voltage-Gated Calcium Channel. Nature 2014, 505, 56–61. 10.1038/nature12775. PubMed DOI PMC

Yang H.; Hu M.; Guo J.; Ou X.; Cai T.; Liu Z. Pore Architecture of TRIC Channels and Insights into Their Gating Mechanism. Nature 2016, 538, 537–541. 10.1038/nature19767. PubMed DOI

Ahuja S.; Mukund S.; Deng L.; Khakh K.; Chang E.; Ho H.; Shriver S.; Young C.; Lin S.; Johnson J. P.; et al. Structural Basis of Nav1.7 Inhibition by an Isoform-Selective Small-Molecule Antagonist. Science 2015, 350, aac5464–aac5464. 10.1126/science.aac5464. PubMed DOI

Pan X.; Li Z.; Zhou Q.; Shen H.; Wu K.; Huang X.; Chen J.; Zhang J.; Zhu X.; Lei J.; et al. Structure of the Human Voltage-Gated Sodium Channel Nav1.4 in Complex with Β1. Science 2018, 362, eaau2486.10.1126/science.aau2486. PubMed DOI

Zhang X.; Ren W.; DeCaen P.; Yan C.; Tao X.; Tang L.; Wang J.; Hasegawa K.; Kumasaka T.; He J.; et al. Crystal Structure of an Orthologue of the NaChBac Voltage-Gated Sodium Channel. Nature 2012, 486, 130–134. 10.1038/nature11054. PubMed DOI PMC

Lenaeus M. J.; Gamal El-Din T. M.; Ing C.; Ramanadane K.; Pomès R.; Zheng N.; Catterall W. A. Structures of Closed and Open States of a Voltage-Gated Sodium Channel. Proc. Natl. Acad. Sci. U. S. A. 2017, 114, E3051–E3060. 10.1073/pnas.1700761114. PubMed DOI PMC

Payandeh J.; Gamal El-Din T. M.; Scheuer T.; Zheng N.; Catterall W. A. Crystal Structure of a Voltage-Gated Sodium Channel in Two Potentially Inactivated States. Nature 2012, 486, 135–139. 10.1038/nature11077. PubMed DOI PMC

Payandeh J.; Scheuer T.; Zheng N.; Catterall W. A. The Crystal Structure of a Voltage-Gated Sodium Channel. Nature 2011, 475, 353–358. 10.1038/nature10238. PubMed DOI PMC

Jiang D.; Gamal El-Din T. M.; Ing C.; Lu P.; Pomès R.; Zheng N.; Catterall W. A. Structural Basis for Gating Pore Current in Periodic Paralysis. Nature 2018, 557, 590–594. 10.1038/s41586-018-0120-4. PubMed DOI PMC

Duan J.; Li Z.; Li J.; Hulse R. E.; Santa-Cruz A.; Valinsky W. C.; Abiria S. A.; Krapivinsky G.; Zhang J.; Clapham D. E. Structure of the Mammalian TRPM7, a Magnesium Channel Required during Embryonic Development. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, E8201–E8210. 10.1073/pnas.1810719115. PubMed DOI PMC

Whorton M. R.; MacKinnon R. X-Ray Structure of the Mammalian GIRK2−Βγ G-Protein Complex. Nature 2013, 498, 190–197. 10.1038/nature12241. PubMed DOI PMC

Hansen S. B.; Tao X.; MacKinnon R. Structural Basis of PIP2 Activation of the Classical Inward Rectifier K+ Channel Kir2.2. Nature 2011, 477, 495–498. 10.1038/nature10370. PubMed DOI PMC

Hite R. K.; Tao X.; MacKinnon R. Structural Basis for Gating the High-Conductance Ca2+-Activated K+ Channel. Nature 2017, 541, 52–57. 10.1038/nature20775. PubMed DOI PMC

Tao X.; Hite R. K.; MacKinnon R. Cryo-EM Structure of the Open High-Conductance Ca2+-Activated K+ Channel. Nature 2017, 541, 46–51. 10.1038/nature20608. PubMed DOI PMC

Whicher J. R.; MacKinnon R. Structure of the Voltage-Gated K+ Channel Eag1 Reveals an Alternative Voltage Sensing Mechanism. Science 2016, 353, 664–669. 10.1126/science.aaf8070. PubMed DOI PMC

Pau V.; Zhou Y.; Ramu Y.; Xu Y.; Lu Z. Crystal Structure of an Inactivated Mutant Mammalian Voltage-Gated K+ Channel. Nat. Struct. Mol. Biol. 2017, 24, 857–865. 10.1038/nsmb.3457. PubMed DOI PMC

Tao X.; Lee A.; Limapichat W.; Dougherty D. A.; MacKinnon R. A Gating Charge Transfer Center in Voltage Sensors. Science 2010, 328, 67–73. 10.1126/science.1185954. PubMed DOI PMC

Long S. B.; Tao X.; Campbell E. B.; MacKinnon R. Atomic Structure of a Voltage-Dependent K+ Channel in a Lipid Membrane-like Environment. Nature 2007, 450, 376–382. 10.1038/nature06265. PubMed DOI

Rheinberger J.; Gao X.; Schmidpeter P. A.; Nimigean C. M. Ligand Discrimination and Gating in Cyclic Nucleotide-Gated Ion Channels from Apo and Partial Agonist-Bound Cryo-EM Structures. eLife 2018, 7, e39775.10.7554/eLife.39775. PubMed DOI PMC

She J.; Guo J.; Chen Q.; Zeng W.; Jiang Y.; Bai X. Structural Insights into the Voltage and Phospholipid Activation of the Mammalian TPC1 Channel. Nature 2018, 556, 130–134. 10.1038/nature26139. PubMed DOI PMC

Dong Y. Y.; Pike A. C. W.; Mackenzie A.; McClenaghan C.; Aryal P.; Dong L.; Quigley A.; Grieben M.; Goubin S.; Mukhopadhyay S.; et al. K2P Channel Gating Mechanisms Revealed by Structures of TREK-2 and a Complex with Prozac. Science 2015, 347, 1256–1259. 10.1126/science.1261512. PubMed DOI PMC

Kintzer A. F.; Green E. M.; Dominik P. K.; Bridges M.; Armache J.-P.; Deneka D.; Kim S. S.; Hubbell W.; Kossiakoff A. A.; Cheng Y.; et al. Structural Basis for Activation of Voltage Sensor Domains in an Ion Channel TPC1. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, E9095–E9104. 10.1073/pnas.1805651115. PubMed DOI PMC

Cuello L. G.; Cortes D. M.; Perozo E. The Gating Cycle of a K+ Channel at Atomic Resolution. eLife 2017, 6, e28032.10.7554/eLife.28032. PubMed DOI PMC

Matulef K.; Annen A. W.; Nix J. C.; Valiyaveetil F. I. Individual Ion Binding Sites in the K+ Channel Play Distinct Roles in C-Type Inactivation and in Recovery from Inactivation. Structure 2016, 24, 750–761. 10.1016/j.str.2016.02.021. PubMed DOI PMC

Lenaeus M. J.; Burdette D.; Wagner T.; Focia P. J.; Gross A. Structures of KcsA in Complex with Symmetrical Quaternary Ammonium Compounds Reveal a Hydrophobic Binding Site. Biochemistry 2014, 53, 5365–5373. 10.1021/bi500525s. PubMed DOI PMC

Matulef K.; Komarov A. G.; Costantino C. A.; Valiyaveetil F. I. Using Protein Backbone Mutagenesis to Dissect the Link between Ion Occupancy and C-Type Inactivation in K+ Channels. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 17886–17891. 10.1073/pnas.1314356110. PubMed DOI PMC

Thompson A. N.; Kim I.; Panosian T. D.; Iverson T. M.; Allen T. W.; Nimigean C. M. Mechanism of Potassium-Channel Selectivity Revealed by Na+ and Li+ Binding Sites within the KcsA Pore. Nat. Struct. Mol. Biol. 2009, 16, 1317–1324. 10.1038/nsmb.1703. PubMed DOI PMC

Zhou Y.; Morais-Cabral J. H.; Kaufman A.; MacKinnon R. Chemistry of Ion Coordination and Hydration Revealed by a K+ Channel–Fab Complex at 2.0 Å Resolution. Nature 2001, 414, 43–48. 10.1038/35102009. PubMed DOI

Labro A. J.; Cortes D. M.; Tilegenova C.; Cuello L. G. Inverted Allosteric Coupling between Activation and Inactivation Gates in K+ Channels. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, 5426–5431. 10.1073/pnas.1800559115. PubMed DOI PMC

Gong X.; Qian H.; Cao P.; Zhao X.; Zhou Q.; Lei J.; Yan N. Structural Basis for the Recognition of Sonic Hedgehog by Human Patched1. Science 2018, 361, eaas8935.10.1126/science.aas8935. PubMed DOI

Wu H.; Wang C.; Gregory K. J.; Han G. W.; Cho H. P.; Xia Y.; Niswender C. M.; Katritch V.; Meiler J.; Cherezov V.; et al. Structure of a Class C GPCR Metabotropic Glutamate Receptor 1 Bound to an Allosteric Modulator. Science 2014, 344, 58–64. 10.1126/science.1249489. PubMed DOI PMC

Hollenstein K.; Kean J.; Bortolato A.; Cheng R. K. Y.; Doré A. S.; Jazayeri A.; Cooke R. M.; Weir M.; Marshall F. H. Structure of Class B GPCR Corticotropin-Releasing Factor Receptor 1. Nature 2013, 499, 438–443. 10.1038/nature12357. PubMed DOI

Zhang D.; Gao Z.-G.; Zhang K.; Kiselev E.; Crane S.; Wang J.; Paoletta S.; Yi C.; Ma L.; Zhang W.; et al. Two Disparate Ligand-Binding Sites in the Human P2Y1 Receptor. Nature 2015, 520, 317–321. 10.1038/nature14287. PubMed DOI PMC

Zhang J.; Zhang K.; Gao Z.-G.; Paoletta S.; Zhang D.; Han G. W.; Li T.; Ma L.; Zhang W.; Müller C. E.; et al. Agonist-Bound Structure of the Human P2Y12 Receptor. Nature 2014, 509, 119–122. 10.1038/nature13288. PubMed DOI PMC

Zhang K.; Zhang J.; Gao Z.-G.; Zhang D.; Zhu L.; Han G. W.; Moss S. M.; Paoletta S.; Kiselev E.; Lu W.; et al. Structure of the Human P2Y12 Receptor in Complex with an Antithrombotic Drug. Nature 2014, 509, 115–118. 10.1038/nature13083. PubMed DOI PMC

Wacker D.; Wang S.; McCorvy J. D.; Betz R. M.; Venkatakrishnan A. J.; Levit A.; Lansu K.; Schools Z. L.; Che T.; Nichols D. E.; et al. Crystal Structure of an LSD-Bound Human Serotonin Receptor. Cell 2017, 168, 377–389.e12. 10.1016/j.cell.2016.12.033. PubMed DOI PMC

Liu W.; Wacker D.; Gati C.; Han G. W.; James D.; Wang D.; Nelson G.; Weierstall U.; Katritch V.; Barty A.; et al. Serial Femtosecond Crystallography of G Protein-Coupled Receptors. Science 2013, 342, 1521–1524. 10.1126/science.1244142. PubMed DOI PMC

Wacker D.; Wang C.; Katritch V.; Han G. W.; Huang X.-P.; Vardy E.; McCorvy J. D.; Jiang Y.; Chu M.; Siu F. Y.; et al. Structural Features for Functional Selectivity at Serotonin Receptors. Science 2013, 340, 615–619. 10.1126/science.1232808. PubMed DOI PMC

Hua T.; Vemuri K.; Nikas S. P.; Laprairie R. B.; Wu Y.; Qu L.; Pu M.; Korde A.; Jiang S.; Ho J.-H.; et al. Crystal Structures of Agonist-Bound Human Cannabinoid Receptor CB1. Nature 2017, 547, 468–471. 10.1038/nature23272. PubMed DOI PMC

Huang W.; Manglik A.; Venkatakrishnan A. J.; Laeremans T.; Feinberg E. N.; Sanborn A. L.; Kato H. E.; Livingston K. E.; Thorsen T. S.; Kling R. C.; et al. Structural Insights into Μ-Opioid Receptor Activation. Nature 2015, 524, 315–321. 10.1038/nature14886. PubMed DOI PMC

Manglik A.; Kruse A. C.; Kobilka T. S.; Thian F. S.; Mathiesen J. M.; Sunahara R. K.; Pardo L.; Weis W. I.; Kobilka B. K.; Granier S. Crystal Structure of the μ-Opioid Receptor Bound to a Morphinan Antagonist. Nature 2012, 485, 321–326. 10.1038/nature10954. PubMed DOI PMC

Che T.; Majumdar S.; Zaidi S. A.; Ondachi P.; McCorvy J. D.; Wang S.; Mosier P. D.; Uprety R.; Vardy E.; Krumm B. E.; et al. Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor. Cell 2018, 172, 55–67.e15. 10.1016/j.cell.2017.12.011. PubMed DOI PMC

Thal D. M.; Sun B.; Feng D.; Nawaratne V.; Leach K.; Felder C. C.; Bures M. G.; Evans D. A.; Weis W. I.; Bachhawat P.; et al. Crystal Structures of the M1 and M4Muscarinic Acetylcholine Receptors. Nature 2016, 531, 335–340. 10.1038/nature17188. PubMed DOI PMC

Shihoya W.; Nishizawa T.; Yamashita K.; Inoue A.; Hirata K.; Kadji F. M. N.; Okuta A.; Tani K.; Aoki J.; Fujiyoshi Y.; et al. X-Ray Structures of Endothelin ETB Receptor Bound to Clinical Antagonist Bosentan and Its Analog. Nat. Struct. Mol. Biol. 2017, 24, 758–764. 10.1038/nsmb.3450. PubMed DOI

Burg J. S.; Ingram J. R.; Venkatakrishnan A. J.; Jude K. M.; Dukkipati A.; Feinberg E. N.; Angelini A.; Waghray D.; Dror R. O.; Ploegh H. L.; et al. Structural Basis for Chemokine Recognition and Activation of a Viral G Protein-Coupled Receptor. Science 2015, 347, 1113–1117. 10.1126/science.aaa5026. PubMed DOI PMC

Oswald C.; Rappas M.; Kean J.; Doré A. S.; Errey J. C.; Bennett K.; Deflorian F.; Christopher J. A.; Jazayeri A.; Mason J. S.; et al. Intracellular Allosteric Antagonism of the CCR9 Receptor. Nature 2016, 540, 462–465. 10.1038/nature20606. PubMed DOI

Cheng R. K. Y.; Segala E.; Robertson N.; Deflorian F.; Doré A. S.; Errey J. C.; Fiez-Vandal C.; Marshall F. H.; Cooke R. M. Structures of Human A1 and A2A Adenosine Receptors with Xanthines Reveal Determinants of Selectivity. Structure 2017, 25, 1275–1285.e4. 10.1016/j.str.2017.06.012. PubMed DOI

Liu X.; Ahn S.; Kahsai A. W.; Meng K.-C.; Latorraca N. R.; Pani B.; Venkatakrishnan A. J.; Masoudi A.; Weis W. I.; Dror R. O.; et al. Mechanism of Intracellular Allosteric β2AR Antagonist Revealed by X-Ray Crystal Structure. Nature 2017, 548, 480–484. 10.1038/nature23652. PubMed DOI PMC

Rosenbaum D. M.; Zhang C.; Lyons J. A.; Holl R.; Aragao D.; Arlow D. H.; Rasmussen S. G. F.; Choi H.-J.; DeVree B. T.; Sunahara R. K.; et al. Structure and Function of an Irreversible Agonist-β2 Adrenoceptor Complex. Nature 2011, 469, 236–240. 10.1038/nature09665. PubMed DOI PMC

Wacker D.; Fenalti G.; Brown M. A.; Katritch V.; Abagyan R.; Cherezov V.; Stevens R. C. Conserved Binding Mode of Human β2 Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-Ray Crystallography. J. Am. Chem. Soc. 2010, 132, 11443–11445. 10.1021/ja105108q. PubMed DOI PMC

Warne T.; Moukhametzianov R.; Baker J. G.; Nehmé R.; Edwards P. C.; Leslie A. G. W.; Schertler G. F. X.; Tate C. G. The Structural Basis for Agonist and Partial Agonist Action on a β1-Adrenergic Receptor. Nature 2011, 469, 241–244. 10.1038/nature09746. PubMed DOI PMC

Murakami M.; Kouyama T. Crystallographic Analysis of the Primary Photochemical Reaction of Squid Rhodopsin. J. Mol. Biol. 2011, 413, 615–627. 10.1016/j.jmb.2011.08.044. PubMed DOI

Murakami M.; Kouyama T. Crystal Structure of Squid Rhodopsin. Nature 2008, 453, 363–367. 10.1038/nature06925. PubMed DOI

Mattle D.; Kuhn B.; Aebi J.; Bedoucha M.; Kekilli D.; Grozinger N.; Alker A.; Rudolph M. G.; Schmid G.; Schertler G. F. X.; et al. Ligand Channel in Pharmacologically Stabilized Rhodopsin. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, 3640–3645. 10.1073/pnas.1718084115. PubMed DOI PMC

Standfuss J.; Edwards P. C.; D’Antona A.; Fransen M.; Xie G.; Oprian D. D.; Schertler G. F. X. The Structural Basis of Agonist-Induced Activation in Constitutively Active Rhodopsin. Nature 2011, 471, 656–660. 10.1038/nature09795. PubMed DOI PMC

Stenkamp R. E. Alternative Models for Two Crystal Structures of Bovine Rhodopsin. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2008, 64, 902–904. 10.1107/S0907444908017162. PubMed DOI PMC

Zimmerman B.; Kelly B.; McMillan B. J.; Seegar T. C. M.; Dror R. O.; Kruse A. C.; Blacklow S. C. Crystal Structure of a Full-Length Human Tetraspanin Reveals a Cholesterol-Binding Pocket. Cell 2016, 167, 1041–1051.e11. 10.1016/j.cell.2016.09.056. PubMed DOI PMC

Chen Y.; Clarke O. B.; Kim J.; Stowe S.; Kim Y.-K.; Assur Z.; Cavalier M.; Godoy-Ruiz R.; von Alpen D. C.; Manzini C.; et al. Structure of the STRA6 Receptor for Retinol Uptake. Science 2016, 353, aad8266–aad8266. 10.1126/science.aad8266. PubMed DOI PMC

Chan S. K.; Kitajima-Ihara T.; Fujii R.; Gotoh T.; Murakami M.; Ihara K.; Kouyama T. Crystal Structure of Cruxrhodopsin-3 from Haloarcula Vallismortis. PLoS One 2014, 9, e108362.10.1371/journal.pone.0108362. PubMed DOI PMC

Ran T.; Ozorowski G.; Gao Y.; Sineshchekov O. A.; Wang W.; Spudich J. L.; Luecke H. Cross-Protomer Interaction with the Photoactive Site in Oligomeric Proteorhodopsin Complexes. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2013, 69, 1965–1980. 10.1107/S0907444913017575. PubMed DOI

Wada T.; Shimono K.; Kikukawa T.; Hato M.; Shinya N.; Kim S. Y.; Kimura-Someya T.; Shirouzu M.; Tamogami J.; Miyauchi S.; et al. Crystal Structure of the Eukaryotic Light-Driven Proton-Pumping Rhodopsin, Acetabularia Rhodopsin II, from Marine Alga. J. Mol. Biol. 2011, 411, 986–998. 10.1016/j.jmb.2011.06.028. PubMed DOI

Luecke H.; Schobert B.; Stagno J.; Imasheva E. S.; Wang J. M.; Balashov S. P.; Lanyi J. K. Crystallographic Structure of Xanthorhodopsin, the Light-Driven Proton Pump with a Dual Chromophore. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 16561–16565. 10.1073/pnas.0807162105. PubMed DOI PMC

Kouyama T.; Fujii R.; Kanada S.; Nakanishi T.; Chan S. K.; Murakami M. Structure of Archaerhodopsin-2 at 1.8 Å Resolution. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2014, 70, 2692–2701. 10.1107/S1399004714017313. PubMed DOI PMC

Gushchin I.; Reshetnyak A.; Borshchevskiy V.; Ishchenko A.; Round E.; Grudinin S.; Engelhard M.; Bldt G.; Gordeliy V. Active State of Sensory Rhodopsin II: Structural Determinants for Signal Transfer and Proton Pumping. J. Mol. Biol. 2011, 412, 591–600. 10.1016/j.jmb.2011.07.022. PubMed DOI

Vogeley L. Anabaena Sensory Rhodopsin: A Photochromic Color Sensor at 2.0 Å. Science 2004, 306, 1390–1393. 10.1126/science.1103943. PubMed DOI PMC

Kouyama T.; Kanada S.; Takeguchi Y.; Narusawa A.; Murakami M.; Ihara K. Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas Pharaonis. J. Mol. Biol. 2010, 396, 564–579. 10.1016/j.jmb.2009.11.061. PubMed DOI

Nogly P.; Weinert T.; James D.; Carbajo S.; Ozerov D.; Furrer A.; Gashi D.; Borin V.; Skopintsev P.; Jaeger K.; et al. Retinal Isomerization in Bacteriorhodopsin Captured by a Femtosecond X-Ray Laser. Science 2018, eaat0094.10.1126/science.aat0094. PubMed DOI

Nango E.; Royant A.; Kubo M.; Nakane T.; Wickstrand C.; Kimura T.; Tanaka T.; Tono K.; Song C.; Tanaka R.; et al. A Three-Dimensional Movie of Structural Changes in Bacteriorhodopsin. Science 2016, 354, 1552–1557. 10.1126/science.aah3497. PubMed DOI

Nakane T.; Hanashima S.; Suzuki M.; Saiki H.; Hayashi T.; Kakinouchi K.; Sugiyama S.; Kawatake S.; Matsuoka S.; Matsumori N.; et al. Membrane Protein Structure Determination by SAD, SIR, or SIRAS Phasing in Serial Femtosecond Crystallography Using an Iododetergent. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 13039–13044. 10.1073/pnas.1602531113. PubMed DOI PMC

Nogly P.; James D.; Wang D.; White T. A.; Zatsepin N.; Shilova A.; Nelson G.; Liu H.; Johansson L.; Heymann M.; et al. Lipidic Cubic Phase Serial Millisecond Crystallography Using Synchrotron Radiation. IUCrJ 2015, 2, 168–176. 10.1107/S2052252514026487. PubMed DOI PMC

Wang T.; Sessions A. O.; Lunde C. S.; Rouhani S.; Glaeser R. M.; Duan Y.; Facciotti M. T. Deprotonation of D96 in Bacteriorhodopsin Opens the Proton Uptake Pathway. Structure 2013, 21, 290–297. 10.1016/j.str.2012.12.018. PubMed DOI PMC

Spudich E. N.; Ozorowski G.; Schow E. V.; Tobias D. J.; Spudich J. L.; Luecke H. A Transporter Converted into a Sensor, a Phototaxis Signaling Mutant of Bacteriorhodopsin at 3.0 Å. J. Mol. Biol. 2012, 415, 455–463. 10.1016/j.jmb.2011.11.025. PubMed DOI PMC

Borshchevskiy V. I.; Round E. S.; Popov A. N.; Büldt G.; Gordeliy V. I. X-Ray-Radiation-Induced Changes in Bacteriorhodopsin Structure. J. Mol. Biol. 2011, 409, 813–825. 10.1016/j.jmb.2011.04.038. PubMed DOI

Luecke H.; Schobert B.; Richter H.-T.; Cartailler J.-P.; Lanyi J. K. Structural Changes in Bacteriorhodopsin During Ion Transport at 2 Angstrom Resolution. Science 1999, 286, 255–260. 10.1126/science.286.5438.255. PubMed DOI

Luecke H.; Schobert B.; Richter H.-T.; Cartailler J.-P.; Lanyi J. K. Structure of Bacteriorhodopsin at 1.55 Å Resolution. J. Mol. Biol. 1999, 291, 899–911. 10.1006/jmbi.1999.3027. PubMed DOI

Belrhali H.; Nollert P.; Royant A.; Menzel C.; Rosenbusch J. P.; Landau E. M.; Pebay-Peyroula E. Protein, Lipid and Water Organization in Bacteriorhodopsin Crystals: A Molecular View of the Purple Membrane at 1.9 Å Resolution. Structure 1999, 7, 909–917. 10.1016/S0969-2126(99)80118-X. PubMed DOI

Facciotti M. T.; Rouhani S.; Burkard F. T.; Betancourt F. M.; Downing K. H.; Rose R. B.; McDermott G.; Glaeser R. M. Structure of an Early Intermediate in the M-State Phase of the Bacteriorhodopsin Photocycle. Biophys. J. 2001, 81, 3442–3455. 10.1016/S0006-3495(01)75976-0. PubMed DOI PMC

Schobert B.; Cupp-Vickery J.; Hornak V.; Smith S. O.; Lanyi J. K. Crystallographic Structure of the K Intermediate of Bacteriorhodopsin: Conservation of Free Energy after Photoisomerization of the Retinal. J. Mol. Biol. 2002, 321, 715–726. 10.1016/S0022-2836(02)00681-2. PubMed DOI

Tanaka K.; Caaveiro J. M. M.; Morante K.; González-Mañas J. M.; Tsumoto K. Structural Basis for Self-Assembly of a Cytolytic Pore Lined by Protein and Lipid. Nat. Commun. 2015, 6, 6337.10.1038/ncomms7337. PubMed DOI PMC

Choudhary O. P.; Paz A.; Adelman J. L.; Colletier J.-P.; Abramson J.; Grabe M. Structure-Guided Simulations Illuminate the Mechanism of ATP Transport through VDAC1. Nat. Struct. Mol. Biol. 2014, 21, 626–632. 10.1038/nsmb.2841. PubMed DOI PMC

Ujwal R.; Cascio D.; Colletier J.-P.; Faham S.; Zhang J.; Toro L.; Ping P.; Abramson J. The Crystal Structure of Mouse VDAC1 at 2.3 Å Resolution Reveals Mechanistic Insights into Metabolite Gating. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 17742–17747. 10.1073/pnas.0809634105. PubMed DOI PMC

Gruss F.; Zähringer F.; Jakob R. P.; Burmann B. M.; Hiller S.; Maier T. The Structural Basis of Autotransporter Translocation by TamA. Nat. Struct. Mol. Biol. 2013, 20, 1318–1320. 10.1038/nsmb.2689. PubMed DOI

Su C.-C.; Radhakrishnan A.; Kumar N.; Long F.; Bolla J. R.; Lei H.-T.; Delmar J. A.; Do S. V.; Chou T.-H.; Rajashankar K. R.; et al. Crystal Structure of the Campylobacter Jejuni CmeC Outer Membrane Channel: Crystal Structure of the C. Jejuni CmeC Outer Membrane Channel. Protein Sci. 2014, 23, 954–961. 10.1002/pro.2478. PubMed DOI PMC

Eren E.; Vijayaraghavan J.; Liu J.; Cheneke B. R.; Touw D. S.; Lepore B. W.; Indic M.; Movileanu L.; van den Berg B. Substrate Specificity within a Family of Outer Membrane Carboxylate Channels. PLoS Biol. 2012, 10, e1001242.10.1371/journal.pbio.1001242. PubMed DOI PMC

Monk B. C.; Tomasiak T. M.; Keniya M. V.; Huschmann F. U.; Tyndall J. D. A.; O’Connell J. D.; Cannon R. D.; McDonald J. G.; Rodriguez A.; Finer-Moore J. S.; et al. Architecture of a Single Membrane Spanning Cytochrome P450 Suggests Constraints That Orient the Catalytic Domain Relative to a Bilayer. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 3865–3870. 10.1073/pnas.1324245111. PubMed DOI PMC

Magotti P.; Bauer I.; Igarashi M.; Babagoli M.; Marotta R.; Piomelli D.; Garau G. Structure of Human N-Acylphosphatidylethanolamine-Hydrolyzing Phospholipase D: Regulation of Fatty Acid Ethanolamide Biosynthesis by Bile Acids. Structure 2015, 23, 598–604. 10.1016/j.str.2014.12.018. PubMed DOI PMC

Ray L. C.; Das D.; Entova S.; Lukose V.; Lynch A. J.; Imperiali B.; Allen K. N. Membrane Association of Monotopic Phosphoglycosyl Transferase Underpins Function. Nat. Chem. Biol. 2018, 14, 538–541. 10.1038/s41589-018-0054-z. PubMed DOI PMC

Ruan J.; Xia S.; Liu X.; Lieberman J.; Wu H. Cryo-EM Structure of the Gasdermin A3Membrane Pore. Nature 2018, 557, 62–67. 10.1038/s41586-018-0058-6. PubMed DOI PMC

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