Abstract
Studying phase coexistence in lipid bilayers and monolayers is important for understanding lipid–lipid interactions underlying lateral organization in biological membranes. Computer simulations follow experimental approaches and use model lipid mixtures of simplified composition. Atomistic simulations give detailed information on the specificity of intermolecular interactions, while coarse-grained simulations achieve large time and length scales and provide a bridge towards state-of-the-art experimental techniques. Computer simulations allow characterizing the structure and composition of domains during phase transformations at Angstrom and picosecond resolution, and bring new insights into phase behavior of lipid membranes.
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Fahy E, Subramaniam S, Brown HA, Glass CK, Merrill AH, Murphy RC, Raetz CRH, Russell DW, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G, VanNieuwenhze MS, White SH, Witztum JL, Dennis EA (2005) A comprehensive classification system for lipids. Eur J Lipid Sci Technol 107(5):337–364
Mouritsen OG (2005) Life - as a matter of fat, The frontiers collection. Springer, Heidelberg
Tanford C (1980) The hydrophobic effect. Wiley, New York, NY
Seddon JM, Templer RH (1995) Chapter 3: Polymorphism of lipid-water systems. In: Lipowsky R, Sackmann E (eds) Handbook of biological physics, vol 1. Elsevier, North-Holland, pp 97–160
Vargaftik NB, Volkov BN, Voljak LD (1983) International tables of the surface tension of water. J Phys Chem Ref Data 12(3):817–820
Knobler CM, Desai RC (1992) Phase-transitions in monolayers. Annu Rev Phys Chem 43:207–236
Kaganer VM, Mohwald H, Dutta P (1999) Structure and phase transitions in Langmuir monolayers. Rev Mod Phys 71(3):779–819
Jahnig F (1996) What is the surface tension of a lipid bilayer membrane? Biophys J 71(3):1348–1349
Hames D, Hooper N (2006) Instant notes in biochemistry. Taylor & Francis, New York, NY
Clements JA (1957) Surface tension of lung extracts. Proc Soc Exp Biol Med 95(1): 170–172
Bachofen H, Schurch S (2001) Alveolar surface forces and lung architecture. Comp Biochem Physiol A Comp Physiol 129(1): 183–193
van Meer G, Voelker DR, Feigenson GW (2008) Membrane lipids: where they are and how they behave. Nat Rev Mol Cell Biol 9(2):112–124
Engelman DM (2005) Membranes are more mosaic than fluid. Nature 438(7068): 578–580
Plasencia I, Norlen L, Bagatolli LA (2007) Direct visualization of lipid domains in human skin stratum corneum’s lipid membranes: effect of pH and temperature. Biophys J 93(9):3142–3155
Simons K, Ikonen E (1997) Functional rafts in cell membranes. Nature 387(6633): 569–572
Lingwood D, Simons K (2010) Lipid rafts as a membrane-organizing principle. Science 327(5961):46–50
Pike LJ (2006) Rafts defined: a report on the keystone symposium on lipid rafts and cell function. J Lipid Res 47(7):1597–1598
Simons K, Toomre D (2000) Lipid rafts and signal transduction. Nat Rev Mol Cell Biol 1(1):31–39
Brown DA, London E (1998) Functions of lipid rafts in biological membranes. Annu Rev Cell Dev Biol 14:111–136
Mayor S, Rao M (2004) Rafts: scale-dependent, active lipid organization at the cell surface. Traffic 5(4):231–240
Parton RG, Richards AA (2003) Lipid rafts and caveolae as portals for endocytosis: new insights and common mechanisms. Traffic 4(11):724–738
Bernardino de la Serna J, Perez-Gil J, Simonsen AC, Bagatolli LA (2004) Cholesterol rules: direct observation of the coexistence of two fluid phases in native pulmonary surfactant membranes at physiological temperatures. J Biol Chem 279(39): 40715–40722
Nag K, Perez-Gil J, Ruano MLF, Worthman LAD, Stewart J, Casals C, Keough KMW (1998) Phase transitions in films of lung surfactant at the air-water interface. Biophys J 74(6):2983–2995
Piknova B, Schram V, Hall SB (2002) Pulmonary surfactant: phase behavior and function. Curr Opin Struct Biol 12(4): 487–494
Zuo YY, Tadayyon SM, Keating E, Zhao L, Veldhuizen RAW, Petersen NO, Amrein MW, Possmayer F (2008) Atomic force microscopy studies of functional and dysfunctional pulmonary surfactant films, II: albumin-inhibited pulmonary surfactant films and the effect of SP-A. Biophys J 95(6):2779–2791
Keating E, Zuo YY, Tadayyon SM, Petersen NO, Possmayer F, Veldhuizen RAW (2012) A modified squeeze-out mechanism for generating high surface pressures with pulmonary surfactant. Biochim Biophys Acta 1818(5): 1225–1234
Fan J, Sammalkorpi M, Haataja M (2010) Formation and regulation of lipid microdomains in cell membranes: theory, modeling, and speculation. FEBS Lett 584(9):1678–1684
Jacobson K, Mouritsen OG, Anderson RGW (2007) Lipid rafts: at a crossroad between cell biology and physics. Nat Cell Biol 9(1):7–14
Ziolkowska NE, Christiano R, Walther TC (2012) Organized living: formation mechanisms and functions of plasma membrane domains in yeast. Trends Cell Biol 22(3): 151–158
Honerkamp-Smith AR, Veatch SL, Keller SL (2009) An introduction to critical points for biophysicists; observations of compositional heterogeneity in lipid membranes. Biochim Biophys Acta Biomembr 1788(1):53–63
van Meer G (2005) Cellular lipidomics. EMBO J 24(18):3159–3165
Konyakhina TM, Wu J, Mastroianni JD, Heberle FA, Feigenson GW (2013) Phase diagram of a 4-component lipid mixture: DSPC/DOPC/POPC/chol. Biochim Biophys Acta Biomembr 1828(9):2204–2214
Davis JH, Clair JJ, Juhasz J (2009) Phase equilibria in DOPC/DPPC-d(62)/cholesterol mixtures. Biophys J 96(2):521–539
Feigenson GW (2009) Phase diagrams and lipid domains in multicomponent lipid bilayer mixtures. Biochim Biophys Acta Biomembr 1788(1):47–52
Veatch SL, Keller SL (2005) Seeing spots: complex phase behavior in simple membranes. Biochim Biophys Acta 1746(3):172–185
Elson EL, Fried E, Dolbow JE, Genin GM (2010) Phase separation in biological membranes: integration of theory and experiment. Annu Rev Biophys 39:207–226
Eggeling C, Ringemann C, Medda R, Schwarzmann G, Sandhoff K, Polyakova S, Belov VN, Hein B, von Middendorff C, Schoenle A, Hell SW (2009) Direct observation of the nanoscale dynamics of membrane lipids in a living cell. Nature 457(7233): 1159–U1121
Frisz JF, Lou KY, Klitzing HA, Hanafin WP, Lizunov V, Wilson RL, Carpenter KJ, Kim R, Hutcheon ID, Zimmerberg J, Weber PK, Kraft ML (2013) Direct chemical evidence for sphingolipid domains in the plasma membranes of fibroblasts. Proc Natl Acad Sci U S A 110(8):E613–E622
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102(18): 3586–3616
Klauda JB, Venable RM, Freites JA, O’Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD Jr, Pastor RW (2010) Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B 114(23): 7830–7843
Feller SE, MacKerell AD (2000) An improved empirical potential energy function for molecular simulations of phospholipids. J Phys Chem B 104(31):7510–7515
Klauda JB, Brooks BR, MacKerell AD, Venable RM, Pastor RW (2005) An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. J Phys Chem B 109(11):5300–5311
Jambeck JPM, Lyubartsev AP (2012) An extension and further validation of an All-atomistic force field for biological membranes. J Chem Theor Comput 8(8):2938–2948
Jambeck JPM, Lyubartsev AP (2012) Derivation and systematic validation of a refined All-atom force field for phosphatidylcholine lipids. J Phys Chem B 116(10): 3164–3179
Jambeck JPM, Lyubartsev AP (2013) Another piece of the membrane puzzle: extending slipids further. J Chem Theor Comput 9(1):774–784
Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The amber biomolecular simulation programs. J Comput Chem 26(16):1668–1688
Dickson CJ, Madej BD, Skjevik AA, Betz RM, Teigen K, Gould IR, Walker RC (2014) Lipid14: the amber lipid force field. J Chem Theor Comput 10(2):865–879
Hermans J, Berendsen HJC, Vangunsteren WF, Postma JPM (1984) A consistent empirical potential for water-protein interactions. Biopolymers 23(8):1513–1518
Poger D, Van Gunsteren WF, Mark AE (2010) A new force field for simulating phosphatidylcholine bilayers. J Comput Chem 31(6):1117–1125
Poger D, Mark AE (2010) On the validation of molecular dynamics simulations of saturated and cis-monounsaturated phosphatidylcholine lipid bilayers: a comparison with experiment. J Chem Theor Comput 6(1): 325–336
Berger O, Edholm O, Jahnig F (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J 72(5): 2002–2013
de Joannis J, Coppock PS, Yin F, Mori M, Zamorano A, Kindt JT (2011) Atomistic simulation of cholesterol effects on miscibility of saturated and unsaturated phospholipids: implications for liquid-ordered/liquid-disordered phase coexistence. J Am Chem Soc 133(10):3625–3634
Tjörnhammar R, Edholm O (2014) Atomistic simulations of gel and liquid crystalline lipid bilayers. Biophys J 106(2):403
Sodt AJ, Sandar ML, Gawrisch K, Pastor RW, Lyman E (2014) The molecular structure of the liquid-ordered phase of lipid bilayers. J Am Chem Soc 136(2):725–732
Hakobyan D, Heuer A (2013) Phase separation in a lipid/cholesterol system: comparison of coarse-grained and united-atom simulations. J Phys Chem B 117(14):3841–3851
Polley A, Vemparala S, Rao M (2012) Atomistic simulations of a multicomponent asymmetric lipid bilayer. J Phys Chem B 116(45):13403–13410
Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, Vries AH (2007) The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111(27): 7812–7824
Bennett WFD, Tieleman DP (2013) Computer simulations of lipid membrane domains. Biochim Biophys Acta Biomembr 1828(8):1765–1776
Shinoda W, DeVane R, Klein ML (2010) Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. J Phys Chem B 114(20):6836–6849
Shinoda W, Devane R, Klein ML (2007) Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants. Mol Simul 33(1–2):27–36
Lenz O, Schmid F (2005) A simple computer model for liquid lipid bilayers. J Mol Liq 117(1–3):147–152
Venturoli M, Sperotto MM, Kranenburg M, Smit B (2006) Mesoscopic models of biological membranes. Phys Rep Rev Sec Phys Lett 437(1–2):1–54
Marrink SJ, de Vries AH, Tieleman DP (2009) Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochim Biophys Acta Biomembr 1788(1): 149–168
Mueller M, Katsov K, Schick M (2006) Biological and synthetic membranes: what can be learned from a coarse-grained description? Phys Rep Rev Sec Phys Lett 434(5–6):113–176
Brannigan G, Lin LCL, Brown FLH (2006) Implicit solvent simulation models for biomembranes. Eur Biophys J 35(2):104–124
Deserno M (2009) Mesoscopic membrane physics: concepts, simulations, and selected applications. Macromol Rapid Commun 30(9–10):752–771
Jo S, Lim JB, Klauda JB, Im W (2009) CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes. Biophys J 97(1):50–58
Herrera FE, Pantano S (2012) Structure and dynamics of nano-sized raft-like domains on the plasma membrane. J Chem Phys 136(1):015103
Marrink SJ, Risselada J, Mark AE (2005) Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chem Phys Lipids 135(2):223–244
de Vries AH, Yefimov S, Mark AE, Marrink SJ (2005) Molecular structure of the lecithin ripple phase. Proc Natl Acad Sci U S A 102(15):5392–5396
Rodgers JM, Sorensen J, de Meyer FJM, Schiott B, Smit B (2012) Understanding the phase behavior of coarse-grained model lipid bilayers through computational calorimetry. J Phys Chem B 116(5):1551–1569
Coppock PS, Kindt JT (2010) Determination of phase transition temperatures for atomistic models of lipids from temperature-dependent stripe domain growth kinetics. J Phys Chem B 114(35):11468–11473
Revalee JD, Laradji M, Kumar PBS (2008) Implicit-solvent mesoscale model based on soft-core potentials for self-assembled lipid membranes. J Chem Phys 128(3):035102
Baoukina S, Monticelli L, Marrink SJ, Tieleman DP (2007) Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations. Langmuir 23(25):12617–12623
Knecht V, Muller M, Bonn M, Marrink SJ, Mark AE (2005) Simulation studies of pore and domain formation in a phospholipid monolayer. J Chem Phys 122(2):024704
Baoukina S, Mendez-Villuendas E, Tieleman DP (2012) Molecular view of phase coexistence in lipid monolayers. J Am Chem Soc 134(42):17543–17553
Duncan SL, Dalal IS, Larson RG (2011) Molecular dynamics simulation of phase transitions in model lung surfactant monolayers. Biochim Biophys Acta Biomembr 1808(10): 2450–2465
Coppock PS, Kindt JT (2009) Atomistic simulations of mixed-lipid bilayers in gel and fluid phases. Langmuir 25(1):352–359
Stevens MJ (2005) Complementary matching in domain formation within lipid bilayers. J Am Chem Soc 127(44):15330–15331
Shi Q, Voth GA (2005) Multi-scale modeling of phase separation in mixed lipid bilayers. Biophys J 89(4):2385–2394
Faller R, Marrink SJ (2004) Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir 20(18):7686–7693
Bennun SV, Longo M, Faller R (2007) Phase and mixing behavior in two-component lipid bilayers: a molecular dynamics study in DLPC/DSPC mixtures. J Phys Chem B 111(32):9504–9512
Muddana HS, Chiang HH, Butler PJ (2012) Tuning membrane phase separation using nonlipid amphiphiles. Biophys J 102(3): 489–497
Laradji M, Kumar PBS (2005) Domain growth, budding, and fission in phase-separating self-assembled fluid bilayers. J Chem Phys 123(22):224902
Illya G, Lipowsky R, Shillcock JC (2006) Two-component membrane material properties and domain formation from dissipative particle dynamics. J Chem Phys 125(11): 114710
Hong B, Qiu F, Zhang H, Yang Y (2007) Budding dynamics of individual domains in multicomponent membranes simulated by N-varied dissipative particle dynamics. J Phys Chem B 111(21):5837–5849
Sugar IP, Chong PLG (2012) A statistical mechanical model of cholesterol/phospholipid mixtures: linking condensed complexes, superlattices, and the phase diagram. J Am Chem Soc 134(2):1164–1171
McMullen TPW, Lewis R, McElhaney RN (2004) Cholesterol-phospholipid interactions, the liquid-ordered phase and lipid rafts in model and biological membranes. Curr Opin Colloid Interface Sci 8(6):459–468
Waheed Q, Tjornhammar R, Edholm O (2012) Phase transitions in coarse-grained lipid bilayers containing cholesterol by molecular dynamics simulations. Biophys J 103(10): 2125–2133
Meinhardt S, Vink RLC, Schmid F (2013) Monolayer curvature stabilizes nanoscale raft domains in mixed lipid bilayers. Proc Natl Acad Sci U S A 110(12):4476–4481
de Meyer FJM, Benjamini A, Rodgers JM, Misteli Y, Smit B (2010) Molecular simulation of the DMPC-cholesterol phase diagram. J Phys Chem B 114(32):10451–10461
Martinez-Seara H, Rog T, Karttunen M, Vattulainen I, Reigada R (2010) Cholesterol induces specific spatial and orientational order in cholesterol/phospholipid membranes. PLoS One 5(6):e11162
Khelashvili G, Pabst G, Harries D (2010) Cholesterol orientation and tilt modulus in DMPC bilayers. J Phys Chem B 114(22):7524–7534
Mihailescu M, Vaswani RG, Jardon-Valadez E, Castro-Roman F, Freites JA, Worcester DL, Chamberlin AR, Tobias DJ, White SH (2011) Acyl-chain methyl distributions of liquid-ordered and -disordered membranes. Biophys J 100(6):1455–1462
Bennett WFD, MacCallum JL, Tieleman DP (2009) Thermodynamic analysis of the effect of cholesterol on dipalmitoylphosphatidylcholine lipid membranes. J Am Chem Soc 131(5):1972–1978
Rog T, Pasenkiewicz-Gierula M, Vattulainen I, Karttunen M (2009) Ordering effects of cholesterol and its analogues. Biochim Biophys Acta Biomembr 1788(1):97–121
Berkowitz ML (2009) Detailed molecular dynamics simulations of model biological membranes containing cholesterol. Biochim Biophys Acta Biomembr 1788(1):86–96
de Meyer F, Smit B (2009) Effect of cholesterol on the structure of a phospholipid bilayer. Proc Natl Acad Sci U S A 106(10): 3654–3658
Pandit SA, Jakobsson E, Scott HL (2004) Simulation of the early stages of nano-domain formation in mixed bilayers of sphingomyelin, cholesterol, and dioleylphosphatidylcholine. Biophys J 87(5):3312–3322
Niemela PS, Ollila S, Hyvonen MT, Karttunen M, Vattulainen I (2007) Assessing the nature of lipid raft membranes. PLoS Comput Biol 3(2):e34
Risselada HJ, Marrink SJ (2008) The molecular face of lipid rafts in model membranes. Proc Natl Acad Sci U S A 105(45):17367–17372
Risselada HJ, Marrink SJ, Muller M (2011) Curvature-dependent elastic properties of liquid-ordered domains result in inverted domain sorting on uniaxially compressed vesicles. Phys Rev Lett 106(14):148102
Baoukina S, Mendez-Villuendas E, Bennett WFD, Tieleman DP (2013) Computer simulations of the phase separation in model membranes. Faraday Discuss 161:63–75
Perlmutter JD, Sachs JN (2011) Interleaflet interaction and asymmetry in phase separated lipid bilayers: molecular dynamics simulations. J Am Chem Soc 133(17):6563–6577
Piggot TJ, Holdbrook DA, Khalid S (2011) Electroporation of the E. coli and S. aureus membranes: molecular dynamics simulations of complex bacterial membranes. J Phys Chem B 115(45):13381–13388
Kiessling V, Wan C, Tamm LK (2009) Domain coupling in asymmetric lipid bilayers. Biochim Biophys Acta Biomembr 1788(1): 64–71
May S (2009) Trans-monolayer coupling of fluid domains in lipid bilayers. Soft Matter 5(17):3148–3156
Brewster R, Pincus PA, Safran SA (2009) Hybrid lipids as a biological surface-active component. Biophys J 97(4):1087–1094
Schäfer LV, Marrink SJ (2010) Partitioning of lipids at domain boundaries in model membranes. Biophys J 99(12):L91–L93
Rosetti C, Pastorino C (2012) Comparison of ternary bilayer mixtures with asymmetric or symmetric unsaturated phosphatidylcholine lipids by coarse grained molecular dynamics simulations. J Phys Chem B 116(11): 3525–3537
Hakobyan D, Heuer A (2014) Key molecular requirements for raft formation in lipid/cholesterol membranes. PLoS One 9(2):e87369
Marsh D (1996) Lateral pressure in membranes. Biochim Biophys Acta 1286(3): 183–223
Baoukina S, Marrink SJ, Tieleman DP (2010) Lateral pressure profiles in lipid monolayers. Faraday Discuss 144:393–409
Wu Z, Cui QA, Yethiraj A (2010) A new coarse-grained model for water: the importance of electrostatic interactions. J Phys Chem B 114(32):10524–10529
Abascal JLF, Vega C (2005) A general purpose model for the condensed phases of water: TIP4P/2005. J Chem Phys 123(23): 234505
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926–935
Yesylevskyy SO, Schafer LV, Sengupta D, Marrink SJ (2010) Polarizable water model for the coarse-grained MARTINI force field. PLoS Comput Biol 6(6):e1000810
Davis RS, Kumar PBS, Sperotto MM, Laradji M (2013) Predictions of phase separation in three-component lipid membranes by the MARTINI force field. J Phys Chem B 117(15):4072–4080
Domanski J, Marrink SJ, Schäfer LV (2012) Transmembrane helices can induce domain formation in crowded model membranes. Biochim Biophys Acta 1818(4):984–994
Camley BA, Brown FLH (2011) Dynamic scaling in phase separation kinetics for quasi-two-dimensional membranes. J Chem Phys 135(22):225106
Wassenaar TA, Pluhackova K, Bockmann RA, Marrink SJ, Tieleman DP (2014) Going backward: a flexible geometric approach to reverse transformation from coarse grained to atomistic models. J Chem Theor Comput 10(2):676–690
Acknowledgements
This work was supported by the Natural Sciences and Engineering Research Council (Canada). DPT is an Alberta Innovates Health Solutions Scientist and Alberta Innovates Technology Futures Strategic Chair in (Bio)Molecular Simulation.
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Baoukina, S., Tieleman, D.P. (2015). Computer Simulations of Phase Separation in Lipid Bilayers and Monolayers. In: Owen, D. (eds) Methods in Membrane Lipids. Methods in Molecular Biology, vol 1232. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1752-5_21
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