Curvature Matters: Modeling Calcium Binding to Neutral and Anionic Phospholipid Bilayers
Language English Country United States Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
37191140
PubMed Central
PMC10226117
DOI
10.1021/acs.jpcb.3c01962
Knihovny.cz E-resources
- MeSH
- Phosphatidylcholines chemistry MeSH
- Phospholipids * chemistry MeSH
- Ions MeSH
- Lipid Bilayers * chemistry MeSH
- Molecular Dynamics Simulation MeSH
- Calcium chemistry MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Phosphatidylcholines MeSH
- Phospholipids * MeSH
- Ions MeSH
- Lipid Bilayers * MeSH
- Calcium MeSH
In this work, the influence of membrane curvature on the Ca2+ binding to phospholipid bilayers is investigated by means of molecular dynamics simulations. In particular, we compared Ca2+ binding to flat, elastically buckled, or uniformly bent zwitterionic and anionic phospholipid bilayers. We demonstrate that Ca2+ ions bind preferably to the concave membrane surfaces in both types of bilayers. We also show that the membrane curvature leads to pronounced changes in Ca2+ binding including differences in free ion concentrations, lipid coordination distributions, and the patterns of ion binding to different chemical groups of lipids. Moreover, these effects differ substantially for the concave and convex membrane monolayers. Comparison between force fields with either full or scaled charges indicates that charge scaling results in reduction of the Ca2+ binding to curved phosphatidylserine bilayers, while for phosphatidylcholine membranes, calcium binds only weakly for both force fields.
See more in PubMed
Duboué-Dijon E.; Javanainen M.; Delcroix P.; Jungwirth P.; Martinez-Seara H. A Practical Guide to Biologically Relevant Molecular Simulations with Charge Scaling for Electronic Polarization. J. Chem. Phys. 2020, 153, 050901.10.1063/5.0017775. PubMed DOI
Binder H.; Zschörnig O. The Effect of Metal Cations on the Phase Behavior and Hydration Characteristics of Phospholipid Membranes. Chem. Phys. Lipids 2002, 115, 39–61. 10.1016/s0009-3084(02)00005-1. PubMed DOI
Pedersen U. R.; Leidy C.; Westh P.; Peters G. H. The Effect of Calcium on the Properties of Charged Phospholipid Bilayers. Biochim. Biophys. Acta, Biomembr. 2006, 1758, 573–582. 10.1016/j.bbamem.2006.03.035. PubMed DOI
Boettcher J. M.; Davis-Harrison R. L.; Clay M. C.; Nieuwkoop A. J.; Ohkubo Y. Z.; Tajkhorshid E.; Morrissey J. H.; Rienstra C. M. Atomic View of Calcium-Induced Clustering of Phosphatidylserine in Mixed Lipid Bilayers. Biochemistry 2011, 50, 2264–2273. 10.1021/bi1013694. PubMed DOI PMC
Mirza M.; Guo Y.; Arnold K.; Oss C. J. v.; Ohki S. Hydrophobizing Effect of Cations on Acidic Phospholipid Membranes. J. Dispersion Sci. Technol. 1998, 19, 951–962. 10.1080/01932699808913225. DOI
Tadross M. R.; Tsien R. W.; Yue D. T. Ca2+ Channel Nanodomains Boost Local Ca2+ Amplitude. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 15794–15799. 10.1073/pnas.1313898110. PubMed DOI PMC
Shi X.; Bi Y.; Yang W.; Guo X.; Jiang Y.; Wan C.; Li L.; Bai Y.; Guo J.; Wang Y.; Chen X.; Wu B.; Sun H.; Liu W.; Wang J.; Xu C. Ca2+ Regulates T-Cell Receptor Activation by Modulating the Charge Property of Lipids. Nature 2013, 493, 111–115. 10.1038/nature11699. PubMed DOI
Nielsen R. D.; Che K.; Gelb M. H.; Robinson B. H. A Ruler for Determining the Position of Proteins in Membranes. J. Am. Chem. Soc. 2005, 127, 6430–6442. 10.1021/ja042782s. PubMed DOI
Lemmon M. A. Membrane Recognition by Phospholipid-Binding Domains. Nat. Rev. Mol. Cell Biol. 2008, 9, 99–111. 10.1038/nrm2328. PubMed DOI
Melcrová A.; Pokorna S.; Pullanchery S.; Kohagen M.; Jurkiewicz P.; Hof M.; Jungwirth P.; Cremer P. S.; Cwiklik L. The Complex Nature of Calcium Cation Interactions with Phospholipid Bilayers. Sci. Rep. 2016, 6, 38035.10.1038/srep38035. PubMed DOI PMC
Martens S.; McMahon H. T. Mechanisms of Membrane Fusion: Disparate Players and Common Principles. Nat. Rev. Mol. Cell Biol. 2008, 9, 543–556. 10.1038/nrm2417. PubMed DOI
Tsai H.-H. G.; Lai W.-X.; Lin H.-D.; Lee J.-B.; Juang W.-F.; Tseng W.-H. Molecular Dynamics Simulation of Cation–Phospholipid Clustering in Phospholipid Bilayers: Possible Role in Stalk Formation during Membrane Fusion. Biochim. Biophys. Acta, Biomembr. 2012, 1818, 2742–2755. 10.1016/j.bbamem.2012.05.029. PubMed DOI
Deplazes E.; Tafalla B. D.; Murphy C.; White J.; Cranfield C. G.; Garcia A. Calcium Ion Binding at the Lipid–Water Interface Alters the Ion Permeability of Phospholipid Bilayers. Langmuir 2021, 37, 14026–14033. 10.1021/acs.langmuir.1c02016. PubMed DOI
Ito T.; Ohnishi S.-I. Ca2+-Induced Lateral Phase Separations in Phosphatidic Acid-Phosphatidylcholine Membranes. Biochim. Biophys. Acta, Biomembr. 1974, 352, 29–37. 10.1016/0005-2736(74)90176-x. PubMed DOI
Papahadjopoulos D.; Vail W. J.; Jacobson K.; Poste G. Cochleate Lipid Cylinders: Formation by Fusion of Unilamellar Lipid Vesicles. Biochim. Biophys. Acta, Biomembr. 1975, 394, 483–491. 10.1016/0005-2736(75)90299-0. PubMed DOI
Dluhy R.; Cameron D. G.; Mantsch H. H.; Mendelsohn R. Fourier Transform Infrared Spectroscopic Studies of the Effect of Calcium Ions on Phosphatidylserine. Biochemistry 1983, 22, 6318–6325. 10.1021/bi00295a043. DOI
Naga K.; Rich N. H.; Keough K. M. W. Interaction between Dipalmitoylphosphatidylglycerol and Phosphatidylcholine and Calcium. Thin Solid Films 1994, 244, 841–844. 10.1016/0040-6090(94)90583-5. DOI
Moradi S.; Nowroozi A.; Shahlaei M. Shedding Light on the Structural Properties of Lipid Bilayers Using Molecular Dynamics Simulation: A Review Study. RSC Adv. 2019, 9, 4644–4658. 10.1039/c8ra08441f. PubMed DOI PMC
Leontyev I. V.; Stuchebrukhov A. A. Electronic Continuum Model for Molecular Dynamics Simulations of Biological Molecules. J. Chem. Theory Comput. 2010, 6, 1498–1508. 10.1021/ct9005807. PubMed DOI PMC
Kohagen M.; Lepšík M.; Jungwirth P. Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization. J. Phys. Chem. Lett. 2014, 5, 3964–3969. 10.1021/jz502099g. PubMed DOI
Duboué-Dijon E.; Delcroix P.; Martinez-Seara H.; Hladílková J.; Coufal P.; Křížek T.; Jungwirth P. Binding of Divalent Cations to Insulin: Capillary Electrophoresis and Molecular Simulations. J. Phys. Chem. B 2018, 122, 5640–5648. 10.1021/acs.jpcb.7b12097. PubMed DOI
Tolmachev D. A.; Boyko O. S.; Lukasheva N. V.; Martinez-Seara H.; Karttunen M. Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections. J. Chem. Theory Comput. 2020, 16, 677–687. 10.1021/acs.jctc.9b00813. PubMed DOI
Ahmed M. C.; Papaleo E.; Lindorff-Larsen K. How Well Do Force Fields Capture the Strength of Salt Bridges in Proteins?. PeerJ 2018, 6, e496710.7717/peerj.4967. PubMed DOI PMC
Debiec K. T.; Gronenborn A. M.; Chong L. T. Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields. J. Phys. Chem. B 2014, 118, 6561–6569. 10.1021/jp500958r. PubMed DOI PMC
Kim S.; Patel D. S.; Park S.; Slusky J.; Klauda J. B.; Widmalm G.; Im W. Bilayer Properties of Lipid A from Various Gram-Negative Bacteria. Biophys. J. 2016, 111, 1750–1760. 10.1016/j.bpj.2016.09.001. 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
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
Han K.; Venable R. M.; Bryant A.-M.; Legacy C. J.; Shen R.; Li H.; Roux B.; Gericke A.; Pastor R. W. Graph–Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions. J. Phys. Chem. B 2018, 122, 1484–1494. 10.1021/acs.jpcb.7b10730. PubMed DOI PMC
Yoo J.; Wilson J.; Aksimentiev A. Improved Model of Hydrated Calcium Ion for Molecular Dynamics Simulations Using Classical Biomolecular Force Fields. Biopolymers 2016, 105, 752–763. 10.1002/bip.22868. PubMed DOI PMC
Lipfert J.; Doniach S.; Das R.; Herschlag D. Understanding Nucleic Acid–Ion Interactions. Annu. Rev. Biochem. 2014, 83, 813–841. 10.1146/annurev-biochem-060409-092720. PubMed DOI PMC
Klauda J. B.; Venable R. M.; Freites J. A.; O’Connor J. W.; Tobias D. J.; Mondragon-Ramirez C.; Vorobyov I.; MacKerell A. D. Jr.; Pastor R. W. Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. J. Phys. Chem. B 2010, 114, 7830–7843. 10.1021/jp101759q. PubMed DOI PMC
Saxena A.; Sept D. Multisite Ion Models That Improve Coordination and Free Energy Calculations in Molecular Dynamics Simulations. J. Chem. Theory Comput. 2013, 9, 3538–3542. 10.1021/ct400177g. PubMed DOI
Zhang A.; Yu H.; Liu C.; Song C. The Ca2+ Permeation Mechanism of the Ryanodine Receptor Revealed by a Multi-Site Ion Model. Nat. Commun. 2020, 11, 922.10.1038/s41467-020-14573-w. PubMed DOI PMC
Nencini R.; Tempra C.; Biriukov D.; Polák J.; Ondo D.; Heyda J.; Ollila S. O.; Javanainen M.; Martinez-Seara H. Prosecco: Polarization Reintroduced by Optimal Scaling of Electronic Continuum Correction Origin in MD Simulations. Biophys. J. 2022, 121, 157a.10.1016/j.bpj.2021.11.1935. 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
Membrane curvature and mechanisms of dynamic cell membrane remodelling|Nature. https://www.nature.com/articles/nature04396 (accessed Feb 17, 2023). PubMed
Mim C.; Unger V. M. Membrane Curvature and Its Generation by BAR Proteins. Trends Biochem. Sci. 2012, 37, 526–533. 10.1016/j.tibs.2012.09.001. PubMed DOI PMC
McMahon H. T.; Boucrot E. Membrane Curvature at a Glance. J. Cell Sci. 2015, 128, 1065–1070. 10.1242/jcs.114454. PubMed DOI PMC
Noguchi H. Anisotropic Surface Tension of Buckled Fluid Membranes. Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2011, 83, 061919.10.1103/physreve.83.061919. PubMed DOI
Yesylevskyy S.; Khandelia H. Encurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations. J. Chem. Theory Comput. 2021, 17, 1181–1193. 10.1021/acs.jctc.0c00800. PubMed DOI
Yesylevskyy S. O.; Kraszewski S.; Ramseyer C. Determination of the Shape and Curvature of Nonplanar Lipid Bilayers That Are Bent in a Single Plane in Molecular Dynamics Simulations. J. Mol. Model. 2014, 20, 2176.10.1007/s00894-014-2176-x. PubMed DOI
Yesylevskyy S. O.; Ramseyer C. Determination of Mean and Gaussian Curvatures of Highly Curved Asymmetric Lipid Bilayers: The Case Study of the Influence of Cholesterol on the Membrane Shape. Phys. Chem. Chem. Phys. 2014, 16, 17052–17061. 10.1039/c4cp01544d. PubMed DOI
Bhatia H.; Ingólfsson H. I.; Carpenter T. S.; Lightstone F. C.; Bremer P.-T. MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes. J. Chem. Theory Comput. 2019, 15, 6411–6421. 10.1021/acs.jctc.9b00453. PubMed DOI
Lee J.; Cheng X.; Jo S.; MacKerell A. D.; Klauda J. B.; Im W.; Wei S.; Buckner J.; Jeong J. C.; Qi Y.; Jo S.; Pande V. S.; Case D. A.; Brooks C. L. I.; MacKerell A. D. Jr.; 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, 110, 641a.10.1016/j.bpj.2015.11.3431. PubMed DOI PMC
Jo S.; Kim T.; Iyer V. G.; Im W. CHARMM-GUI: A Web-Based Graphical User Interface for CHARMM. J. Comput. Chem. 2008, 29, 1859–1865. 10.1002/jcc.20945. PubMed DOI
Abraham M. J.; Murtola T.; Schulz R.; Páll S.; Smith J. C.; Hess B.; Lindahl E. GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers. SoftwareX 2015, 1–2, 19–25. 10.1016/j.softx.2015.06.001. DOI
Parrinello M.; Rahman A. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method. J. Appl. Phys. 1981, 52, 7182–7190. 10.1063/1.328693. DOI
Bussi G.; Donadio D.; Parrinello M. Canonical Sampling through Velocity Rescaling. J. Chem. Phys. 2007, 126, 014101.10.1063/1.2408420. PubMed DOI
Verlet L. Computer “Experiments” on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Phys. Rev. 1967, 159, 98–103. 10.1103/physrev.159.98. DOI
Darden T.; York D.; Pedersen L. Particle Mesh Ewald: An N·log(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98, 10089–10092. 10.1063/1.464397. DOI
Hess B.; Bekker H.; Berendsen H. J. C.; Fraaije J. G. E. M. LINCS: A Linear Constraint Solver for Molecular Simulations. J. Comput. Chem. 1997, 18, 1463–1472. 10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.0.co;2-h. DOI
Yesylevskyy S. O. Pteros: Fast and Easy to Use Open-source C++ Library for Molecular Analysis. J. Comput. Chem. 2012, 33, 1632–1636. 10.1002/jcc.22989. PubMed DOI
Yesylevskyy S. O. Pteros 2.0: Evolution of the Fast Parallel Molecular Analysis Library for C++ and Python. J. Comput. Chem. 2015, 36, 1480–1488. 10.1002/jcc.23943. PubMed DOI