Quantitative Comparison against Experiments Reveals Imperfections in Force Fields' Descriptions of POPC-Cholesterol Interactions

. 2023 Sep 26 ; 19 (18) : 6342-6352. [epub] 20230824

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid37616238

Cholesterol is a central building block in biomembranes, where it induces orientational order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular dynamics (MD) simulations have played a crucial role in resolving these effects at the molecular level; yet, it has recently become evident that different MD force fields predict quantitatively different behavior. Although easily neglected, identifying such limitations is increasingly important as the field rapidly progresses toward simulations of complex membranes mimicking the in vivo conditions: pertinent multicomponent simulations must capture accurately the interactions between their fundamental building blocks, such as phospholipids and cholesterol. Here, we define quantitative quality measures for simulations of binary lipid mixtures in membranes against the C-H bond order parameters and lateral diffusion coefficients from NMR spectroscopy as well as the form factors from X-ray scattering. Based on these measures, we perform a systematic evaluation of the ability of commonly used force fields to describe the structure and dynamics of binary mixtures of palmitoyloleoylphosphatidylcholine (POPC) and cholesterol. None of the tested force fields clearly outperforms the others across the tested properties and conditions. Still, the Slipids parameters provide the best overall performance in our tests, especially when dynamic properties are included in the evaluation. The quality evaluation metrics introduced in this work will, particularly, foster future force field development and refinement for multicomponent membranes using automated approaches.

Zobrazit více v PubMed

Lorent J. H.; Levental K.; Ganesan L.; Rivera-Longsworth G.; Sezgin E.; Doktorova M.; Lyman E.; Levental I. Plasma Membranes Are Asymmetric in Lipid Unsaturation, Packing and Protein Shape. Nat. Chem. Biol. 2020, 16, 644–652. 10.1038/s41589-020-0529-6. PubMed DOI PMC

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

Wang H.-Y.; Bharti D.; Levental I. Membrane Heterogeneity Beyond the Plasma Membrane. Front. Cell Dev. Biol. 2020, 8, 58081410.3389/fcell.2020.580814. PubMed DOI PMC

Kinnun J. J.; Bolmatov D.; Lavrentovich M. O.; Katsaras J. Lateral Heterogeneity and Domain Formation in Cellular Membranes. Chem. Phys. Lipids 2020, 232, 10497610.1016/j.chemphyslip.2020.104976. PubMed DOI PMC

Mouritsen O. G.; Zuckermann M. J. What’s So Special About Cholesterol?. Lipids 2004, 39, 1101–1113. 10.1007/s11745-004-1336-x. PubMed DOI

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

Kinnunen P. K. On the Principles of Functional Ordering in Biological Membranes. Chem. Phys. Lipids 1991, 57, 375–399. 10.1016/0009-3084(91)90087-R. PubMed DOI

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

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

Cebecauer M.; Amaro M.; Jurkiewicz P.; Sarmento M. J.; Sachl R.; Cwiklik L.; Hof M. Membrane Lipid Nanodomains. Chem. Rev. 2018, 118, 11259–11297. 10.1021/acs.chemrev.8b00322. PubMed DOI

Milovanovic D.; Honigmann A.; Koike S.; Göttfert F.; Pähler G.; Junius M.; Müllar S.; Diederichsen U.; Janshoff A.; Grubmüller H.; Risselada H. J.; Eggeling C.; Hell S. W.; van den Bogaart G.; Jahn R. Hydrophobic Mismatch Sorts SNARE Proteins Into Distinct Membrane Domains. Nat. Commun. 2015, 6, 598410.1038/ncomms6984. PubMed DOI PMC

Kelkar D. A.; Chattopadhyay A. Modulation of Gramicidin Channel Conformation and Organization by Hydrophobic Mismatch in Saturated Phosphatidylcholine Bilayers. Biochim. Biophys. Acta, Biomembr. 2007, 1768, 1103–1113. 10.1016/j.bbamem.2007.01.016. PubMed DOI

Gimpl G. Interaction of G Protein Coupled Receptors and Cholesterol. Chem. Phys. Lipids 2016, 199, 61–73. 10.1016/j.chemphyslip.2016.04.006. PubMed DOI

Guixà-González R.; Albasanz J. L.; Rodriguez-Espigares I.; Pastor M.; Sanz F.; Martí-Solano M.; Manna M.; Martinez-Seara H.; Hildebrand P. W.; Martín M.; Selent J. Membrane Cholesterol Access Into a G-Protein-Coupled Receptor. Nat. Commun. 2017, 8, 1450510.1038/ncomms14505. 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, e1843210.7554/eLife.18432. PubMed DOI PMC

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

Berkowitz M. L. Detailed Molecular Dynamics Simulations of Model Biological Membranes Containing Cholesterol. Biochim. Biophys. Acta, Biomembr. 2009, 1788, 86–96. 10.1016/j.bbamem.2008.09.009. PubMed DOI

Enkavi G.; Javanainen M.; Kulig W.; Róg T.; Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge to Understand Biological Phenomena in a Living Substance. Chem. Rev. 2019, 119, 5607–5774. 10.1021/acs.chemrev.8b00538. PubMed DOI PMC

Marrink S. J.; Corradi V.; Souza P. C.; Ingolfsson H. I.; Tieleman D. P.; Sansom M. S. Computational Modeling of Realistic Cell Membranes. Chem. Rev. 2019, 119, 6184–6226. 10.1021/acs.chemrev.8b00460. PubMed DOI PMC

Brooks B. R.; Bruccoleri R. E.; Olafson B. D.; States D. J.; Swaminathan Sa.; Karplus M. CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 1983, 4, 187–217. 10.1002/jcc.540040211. DOI

Cornell W. D.; Cieplak P.; Bayly C. I.; Gould I. R.; Merz K. M.; Ferguson D. M.; Spellmeyer D. C.; Fox T.; Caldwell J. W.; Kollman P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179–5197. 10.1021/ja00124a002. DOI

Jorgensen W. L.; Tirado-Rives J. The OPLS Force Field for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin. J. Am. Chem. Soc. 1988, 110, 1657–1666. 10.1021/ja00214a001. PubMed DOI

Harder E.; Damm W.; Maple J.; Wu C.; Reboul M.; Xiang J. Y.; Wang L.; Lupyan D.; Dahlgren M. K.; Knight J. L.; Kaus J. W.; Cerutti D. S.; Krilov G.; Jorgensen W. L.; Abel R.; Friesner R. A. OPLS3: A Force Field Providing Broad Coverage of Drug-Like Small Molecules and Proteins. J. Chem. Theory Comput. 2016, 12, 281–296. 10.1021/acs.jctc.5b00864. PubMed DOI

Klauda J. B.; Kučerka N.; Brooks B. R. Simulation-Based Methods for Interpreting X-Ray Data from Lipid Bilayers. Biophys. J. 2006, 90, 2796–2807. 10.1529/biophysj.105.075697. PubMed DOI PMC

Lim J. B.; Rogaski B.; Klauda J. B. Update of the Cholesterol Force Field Parameters in CHARMM. J. Phys. Chem. B 2012, 116, 203–210. 10.1021/jp207925m. PubMed DOI

Dickson C. J.; Madej B. D.; Skjevik A. A.; Betz R. M.; Teigen K.; Gould I. R.; Walker R. C. Lipid14: The Amber Lipid Force Field. J. Chem. Theory Comput. 2014, 10, 865–879. 10.1021/ct4010307. PubMed DOI PMC

Madej B. D.; Gould I. R.; Walker R. C. A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field. J. Phys. Chem. B 2015, 119, 12424–12435. 10.1021/acs.jpcb.5b04924. PubMed DOI PMC

Jämbeck J. P. M.; Lyubartsev A. P. Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids. J. Phys. Chem. B 2012, 116, 3164–3179. 10.1021/jp212503e. PubMed DOI PMC

Jämbeck J. P. M.; Lyubartsev A. P. An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. J. Chem. Theory Comput. 2012, 8, 2938–2948. 10.1021/ct300342n. PubMed DOI

Jämbeck J. P. M.; Lyubartsev A. P. Another Piece of the Membrane Puzzle: Extending Slipids Further. J. Chem. Theory Comput. 2013, 9, 774–784. 10.1021/ct300777p. PubMed DOI

Grote F.; Lyubartsev A. P. Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids. J. Phys. Chem. B 2020, 124, 8784–8793. 10.1021/acs.jpcb.0c06386. PubMed DOI PMC

Maciejewski A.; Pasenkiewicz-Gierula M.; Cramariuc O.; Vattulainen I.; Róg T. Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration. J. Phys. Chem. B 2014, 118, 4571–4581. 10.1021/jp5016627. PubMed DOI

Kulig W.; Tynkkynen J.; Javanainen M.; Manna M.; Róg T.; Vattulainen I.; Jungwirth P. How Well Does Cholesteryl Hemisuccinate Mimic Cholesterol in Saturated Phospholipid Bilayers. J. Mol. Model. 2014, 20, 212110.1007/s00894-014-2121-z. PubMed DOI

Kulig W.; Jurkiewicz P.; Olżyńska A.; Tynkkynen J.; Javanainen M.; Manna M.; Róg 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.; 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

Lee J.; Cheng X.; Swails J. M.; Yeom M. S.; Eastman P. K.; Lemkul J. A.; Wei S.; Buckner J.; Jeong J. C.; Qi Y.; Jo S.; Pande V. S.; Case D. A.; Brooks C. L.; MacKerell A. D.; Klauda J. B.; Im W. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J. Chem. Theory Comput. 2016, 12, 405–413. 10.1021/acs.jctc.5b00935. PubMed DOI PMC

Lee J.; Hitzenberger M.; Rieger M.; Kern N. R.; Zacharias M.; Im W. CHARMM-GUI Supports the Amber Force Fields. J. Chem. Phys. 2020, 153, 03510310.1063/5.0012280. 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.; Monticelli L.; Määttä J.; Ollila O. H. S.; Retegan M.; Róg T.; Santuz H.; Tynkkynen J. 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

Ollila O. 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

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

Antila H.; Buslaev P.; Favela-Rosales F.; Ferreira T. M.; Gushchin I.; Javanainen M.; Kav B.; Madsen J. J.; Melcr J.; Miettinen M. S.; Määttä J.; Nencini R.; Ollila O. H. S.; Piggot T. J. Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers. J. Phys. Chem. B 2019, 123, 9066–9079. 10.1021/acs.jpcb.9b06091. PubMed DOI

Bacle A.; Buslaev P.; Garcia-Fandino R.; Favela-Rosales F.; Mendes Ferreira T.; Fuchs P. F.; Gushchin I.; Javanainen M.; Kiirikki A. M.; Madsen J. J.; Melcr J.; Milán Rodriguez P.; Miettinen M. S.; Ollila O. H. S.; Papadopoulos C. G.; Peón A.; Piggot T. J.; Piñeiro A.; Virtanen S. I. Inverse Conformational Selection in Lipid–Protein Binding. J. Am. Chem. Soc. 2021, 143, 13701–13709. 10.1021/jacs.1c05549. PubMed DOI

Kurki M.; Poso A.; Bartos P.; Miettinen M. S. Structure of POPC Lipid Bilayers in OPLS3e Force Field. J. Chem. Inf. Model. 2022, 62, 6462–6474. 10.1021/acs.jcim.2c00395. PubMed DOI PMC

Melcr J.; Martinez-Seara H.; Nencini R.; Kolafa J.; Jungwirth P.; Ollila O. H. S. Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization. J. Phys. Chem. B 2018, 122, 4546–4557. 10.1021/acs.jpcb.7b12510. PubMed DOI

Melcr J.; Mendes Ferreira T.; Jungwirth P.; Ollila O. S. Improved Cation Binding to Lipid Bilayer with Negatively Charged POPS by Effective Inclusion of Electronic Polarization. J. Chem. Theory Comput. 2019, 16, 738–748. 10.1021/acs.jctc.9b00824. PubMed DOI

Nencini R.; Ollila O. H. S. Charged Small Molecule Binding to Membranes in MD Simulations Evaluated against NMR Experiments. J. Phys. Chem. B 2022, 126, 6955–6963. 10.1021/acs.jpcb.2c05024. PubMed DOI PMC

Antila H. S.; Kav B.; Miettinen M. S.; Martinez-Seara H.; Jungwirth P.; Ollila O. S. Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks. J. Phys. Chem. B 2022, 126, 4169–4183. 10.1021/acs.jpcb.2c01954. DOI

Kiirikki A. M.; Antila H. S.; Bort L.; Buslaev P.; Favela F.; Ferreira T. M.; Fuchs P. F.; Garcia-Fandino R.; Gushchin I.; Kav B.; Kula P.; Kurki M.; Kuzmin A.; Madsen J. J.; Miettinen M. S.; Nencini R.; Piggot T.; Pineiro A.; Samantray S.; Suarez-Leston F.; Ollila O. H. S.. NMRlipids Databank: Making Data-Driven Analyses of Membrane Properties Accessible for All 2023, 10.26434/chemrxiv-2023-jrpwm-v2. DOI

Antila H. S.; Wurl A.; Ollila O. S.; Miettinen M. S.; Ferreira T. M. Rotational Decoupling Between the Hydrophilic and Hydrophobic Regions in Lipid Membranes. Biophys. J. 2022, 121, 68–78. 10.1016/j.bpj.2021.12.003. PubMed DOI PMC

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

Filippov A.; Orädd G.; Lindblom G. Influence of Cholesterol and Water Content on Phospholipid Lateral Diffusion in Bilayers. Langmuir 2003, 19, 6397–6400. 10.1021/la034222x. DOI

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

Vögele M.; Köfinger J.; Hummer G. Hydrodynamics of Diffusion in Lipid Membrane Simulations. Phys. Rev. Lett. 2018, 120, 26810410.1103/PhysRevLett.120.268104. PubMed DOI

Rieder A.; Koller D.; Lohner K.; Pabst G. Optimizing Rapid Solvent Exchange Preparation of Multilamellar Vesicles. Chem. Phys. Lipids 2015, 186, 39–44. 10.1016/j.chemphyslip.2014.12.001. PubMed DOI

Belička M.; Weitzer A.; Pabst G. High-Resolution Structure of Coexisting Nanoscopic and Microscopic Lipid Domains. Soft Matter 2017, 13, 1823–1833. 10.1039/C6SM02727J. PubMed DOI

Buboltz J. T.; Feigenson G. W. A Novel Strategy for the Preparation of Liposomes: Rapid Solvent Exchange. Biochim. Biophys. Acta, Biomembr. 1999, 1417, 232–245. 10.1016/S0005-2736(99)00006-1. PubMed DOI

Heftberger P.; Kollmitzer B.; Heberle F. A.; Pan J.; Rappolt M.; Amenitsch H.; Kučerka N.; Katsaras J.; Pabst G. Global Small-Angle X-Ray Scattering Data Analysis for Multilamellar Vesicles: The Evolution of the Scattering Density Profile Model. J. Appl. Crystallogr. 2014, 47, 173–180. 10.1107/S1600576713029798. PubMed DOI PMC

Heftberger P.; Kollmitzer B.; Rieder A. A.; Amenitsch H.; Pabst G. In Situ Determination of Structure and Fluctuations of Coexisting Fluid Membrane Domains. Biophys. J. 2015, 108, 854–862. 10.1016/j.bpj.2014.11.3488. PubMed DOI PMC

Heberle F. A.; Pan J.; Standaert R.; Drazba P.; Kučerka N.; Katsaras J. Model-Based Approaches for the Determination of Lipid Bilayer Structure From Small-Angle Neutron and X-Ray Scattering Data. Eur. Biophys. J. 2012, 41, 875–890. 10.1007/s00249-012-0817-5. PubMed DOI

Kučerka N.; Nagle J. F.; Sachs J. N.; Feller S. E.; Pencer J.; Jackson A.; Katsaras J. Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-ray Scattering Data. Biophys. J. 2008, 95, 2356–2367. 10.1529/biophysj.108.132662. PubMed DOI PMC

Kučerka N.; Holland B. W.; Gray C. G.; Tomberli B.; Katsaras J. Scattering Density Profile Model of POPG Bilayers As Determined by Molecular Dynamics Simulations and Small-Angle Neutron and X-Ray Scattering Experiments. J. Phys. Chem. B 2012, 116, 232–239. 10.1021/jp208920h. PubMed DOI

Heftberger P.Structure and Elasticity of Fluid Membrane Domains. Ph.D. thesis, Graz University of Technology, 2015.

Fabian B.; Vattulainen I.; Javanainen M. Protein Crowding and Cholesterol Increase Cell Membrane Viscosity in a Temperature Dependent Manner. J. Chem. Theory Comput. 2023, 19, 2630–2643. 10.1021/acs.jctc.3c00060. PubMed DOI PMC

Páll S.; Zhmurov A.; Bauer P.; Abraham M.; Lundborg M.; Gray A.; Hess B.; Lindahl E. Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. J. Chem. Phys. 2020, 153, 13411010.1063/5.0018516. PubMed DOI

Ong E. E.; Liow J.-L. The Temperature-Dependent Structure, Hydrogen Bonding and Other Related Dynamic Properties of the Standard TIP3P and CHARMM-Modified TIP3P Water Models. Fluid Ph. Equilib. 2019, 481, 55–65. 10.1016/j.fluid.2018.10.016. DOI

Amidror I. Scattered Data Interpolation Methods for Electronic Imaging Systems: A Survey. J. Electron. Imaging 2002, 11, 157–176. 10.1117/1.1455013. DOI

Ferreira T. M.; Coreta-Gomes F.; Ollila O. H. S.; Moreno M. J.; Vaz W. L. C.; Topgaard D. Cholesterol and POPC Segmental Order Parameters in Lipid Membranes: Solid State 1H-13C NMR and MD Simulation Studies. Phys. Chem. Chem. Phys. 2013, 15, 1976–1989. 10.1039/C2CP42738A. PubMed DOI

Pan J.; Cheng X.; Heberle F. A.; Mostofian B.; Kučerka N.; Drazba P.; Katsaras J. Interactions between Ether Phospholipids and Cholesterol As Determined by Scattering and Molecular Dynamics Simulations. J. Phys. Chem. B 2012, 116, 14829–14838. 10.1021/jp310345j. PubMed DOI PMC

Marquardt D.; Heberle F. A.; Nickels J. D.; Pabst G.; Katsaras J. On Scattered Waves and Lipid Domains: Detecting Membrane Rafts With X-rays and Neutrons. Soft Matter 2015, 11, 9055–9072. 10.1039/C5SM01807B. PubMed DOI PMC

Doktorova M.; Kučerka N.; Kinnun J. J.; Pan J.; Marquardt D.; Scott H. L.; Venable R. M.; Pastor R. W.; Wassall S. R.; Katsaras J.; Heberle F. A. Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-Ray Scattering Data. J. Phys. Chem. B 2020, 124, 5186–5200. 10.1021/acs.jpcb.0c03389. PubMed DOI PMC

Camley B. A.; Lerner M. G.; Pastor R. W.; Brown F. L. Strong Influence of Periodic Boundary Conditions on Lateral Diffusion in Lipid Bilayer Membranes. J. Chem. Phys. 2015, 143, 24311310.1063/1.4932980. PubMed DOI PMC

Fitzgerald J. E.; Venable R. M.; Pastor R. W.; Lyman E. R. Surface Viscosities of Lipid Bilayers Determined From Equilibrium Molecular Dynamics Simulations. Biophys. J. 2023, 122, 1094–1104. 10.1016/j.bpj.2023.01.038. PubMed DOI PMC

Faizi H. A.; Dimova R.; Vlahovska P. M. A Vesicle Microrheometer for High-Throughput Viscosity Measurements of Lipid and Polymer Membranes. Biophys. J. 2022, 121, 910–918. 10.1016/j.bpj.2022.02.015. PubMed DOI PMC

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

Höltje M.; Förster T.; Brandt B.; Engels T.; von Rybinski W.; Höltje H.-D. Molecular Dynamics Simulations of Stratum Corneum Lipid Models: Fatty Acids and Cholesterol. ACS Appl. Electron. Mater. 2001, 1511, 156–167. 10.1016/S0005-2736(01)00270-X. 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

Javanainen M.; Martinez-Seara H.; Vattulainen I. Nanoscale Membrane Domain Formation Driven by Cholesterol. Sci. Rep. 2017, 7, 114310.1038/s41598-017-01247-9. PubMed DOI PMC

Schachter I.; Paananen R. O.; Fábián B.; Jurkiewicz P.; Javanainen M. The Two Faces of the Liquid Ordered Phase. J. Phys. Chem. Lett. 2022, 13, 1307–1313. 10.1021/acs.jpclett.1c03712. PubMed DOI PMC

Edholm O.; Nagle J. F. Areas of Molecules in Membranes Consisting of Mixtures. Biophys. J. 2005, 89, 1827–1832. 10.1529/biophysj.105.064329. PubMed DOI PMC

Javanainen M.; Melcrová A.; Magarkar A.; Jurkiewicz P.; Hof M.; Jungwirth P.; Martinez-Seara H. Two Cations, Two Mechanisms: Interactions of Sodium and Calcium With Zwitterionic Lipid Membranes. Chem. Commun. 2017, 53, 5380–5383. 10.1039/C7CC02208E. PubMed DOI

Antila H. S.; M Ferreira T.; Ollila O. H. S.; Miettinen M. S. Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics. J. Chem. Inf. Model. 2021, 61, 938–949. 10.1021/acs.jcim.0c01299. PubMed DOI PMC

Leonard A. N.; Simmonett A. C.; Pickard F. C. IV; Huang J.; Venable R. M.; Klauda J. B.; Brooks B. R.; Pastor R. W. Comparison of Additive and Polarizable Models With Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations. J. Chem. Theory Comput. 2018, 14, 948–958. 10.1021/acs.jctc.7b00948. PubMed DOI PMC

Yu Y.; Kramer A.; Venable R. M.; Simmonett A. C.; MacKerell A. D. Jr; Klauda J. B.; Pastor R. W.; Brooks B. R. Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. J. Chem. Theory Comput. 2021, 17, 1562–1580. 10.1021/acs.jctc.0c01326. PubMed DOI PMC

Yu Y.; Kramer A.; Venable R. M.; Brooks B. R.; Klauda J. B.; Pastor R. W. CHARMM36 Lipid Force Field With Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids. J. Chem. Theory Comput. 2021, 17, 1581–1595. 10.1021/acs.jctc.0c01327. PubMed DOI PMC

Wennberg C. L.; Murtola T.; Hess B.; Lindahl E. Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties. J. Chem. Theory Comput. 2013, 9, 3527–3537. 10.1021/ct400140n. PubMed DOI

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...