Computer simulations of fusion, fission and shape deformation in lipid membranes

Fusion and fission are two kinds of crucial cellular activities related to cell membranes. Therefore, the studies on fusion and fission are particularly important for the understanding of the nature of cell membranes. In this review, the recent studies on fusion, fission and shape deformation in the lipid membrane investigated by computer simulations are presented. Emphases are put on the causes, possible changes on the molecular level and the evolution pathways of fusion and fission processes. Furthermore, the relationship between fission (or fusion) and membrane deformation is also highlighted.

[1]  B. Lentz,et al.  Secretory and viral fusion may share mechanistic events with fusion between curved lipid bilayers. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Herman J. C. Berendsen,et al.  MOLECULAR-DYNAMICS SIMULATION OF A BILAYER-MEMBRANE , 1982 .

[3]  Hiroshi Noguchi,et al.  Fusion pathways of vesicles: A Brownian dynamics simulation , 2001 .

[4]  J. Zimmerberg,et al.  Synaptic Membranes Bend to the Will of a Neurotoxin , 2005, Science.

[5]  N. Destainville Cluster phases of membrane proteins. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[6]  M. Lindau,et al.  The fusion pore. , 2003, Biochimica et biophysica acta.

[7]  J. Joanny,et al.  Mechanochemical action of the dynamin protein. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[8]  A. J. Markvoort,et al.  A detailed look at vesicle fusion. , 2006, The journal of physical chemistry. B.

[9]  Kai Simons,et al.  Lipid rafts and signal transduction , 2000, Nature Reviews Molecular Cell Biology.

[10]  A Kusumi,et al.  Fast lipid disorientation at the onset of membrane fusion revealed by molecular dynamics simulations. , 2001, Biophysical journal.

[11]  Gernot Guigas,et al.  Cluster formation of transmembrane proteins due to hydrophobic mismatching. , 2008, Physical review letters.

[12]  Sarah L Veatch,et al.  Organization in lipid membranes containing cholesterol. , 2002, Physical review letters.

[13]  M. Lindau,et al.  The role of the C terminus of the SNARE protein SNAP-25 in fusion pore opening and a model for fusion pore mechanics , 2008, Proceedings of the National Academy of Sciences.

[14]  D. Siegel The modified stalk mechanism of lamellar/inverted phase transitions and its implications for membrane fusion. , 1999, Biophysical journal.

[15]  J. Hoh,et al.  Splaying of aliphatic tails plays a central role in barrier crossing during liposome fusion. , 2010, The journal of physical chemistry. B.

[16]  Yuqiang Ma,et al.  Computer simulations of vesicle fission induced by external amphipathic inclusions. , 2009, The journal of physical chemistry. B.

[17]  Ole G. Mouritsen,et al.  Life - As a Matter of Fat , 2004 .

[18]  Reinhard Lipowsky,et al.  Tension-induced fusion of bilayer membranes and vesicles , 2005, Nature materials.

[19]  Erik Lindahl,et al.  Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel , 2009, PLoS Comput. Biol..

[20]  Marcus Mueller,et al.  Biological and synthetic membranes: What can be learned from a coarse-grained description? , 2006 .

[21]  Alexander P. Lyubartsev,et al.  Recent development in computer simulations of lipid bilayers , 2011 .

[22]  Frank L. H. Brown,et al.  Implicit solvent simulation models for biomembranes , 2005, European Biophysics Journal.

[23]  A. Shevchenko,et al.  Lipid rafts function in biosynthetic delivery of proteins to the cell surface in yeast. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[24]  P S Kim,et al.  Mechanisms of viral membrane fusion and its inhibition. , 2001, Annual review of biochemistry.

[25]  M. Yamazaki,et al.  La(3+) and Gd(3+) induce shape change of giant unilamellar vesicles of phosphatidylcholine. , 2002, Biochimica et biophysica acta.

[26]  Yonathan Kozlovsky,et al.  Stalk model of membrane fusion: solution of energy crisis. , 2002, Biophysical journal.

[27]  Watt W. Webb,et al.  Imaging coexisting fluid domains in biomembrane models coupling curvature and line tension , 2003, Nature.

[28]  D. Siegel,et al.  Energetics of intermediates in membrane fusion: comparison of stalk and inverted micellar intermediate mechanisms. , 1993, Biophysical journal.

[29]  A. Spang Membrane traffic in the secretory pathway , 2008, Cellular and Molecular Life Sciences.

[30]  Klaus Schulten,et al.  Four-scale description of membrane sculpting by BAR domains. , 2008, Biophysical journal.

[31]  M. Kozlov,et al.  Protein-driven membrane stresses in fusion and fission. , 2010, Trends in biochemical sciences.

[32]  Klaus Schulten,et al.  Simulations of membrane tubulation by lattices of amphiphysin N-BAR domains. , 2009, Structure.

[33]  Guohua Lei,et al.  Lipid bilayer vesicle fusion: intermediates captured by high-speed microfluorescence spectroscopy. , 2003, Biophysical journal.

[34]  P. B. Warren,et al.  DISSIPATIVE PARTICLE DYNAMICS : BRIDGING THE GAP BETWEEN ATOMISTIC AND MESOSCOPIC SIMULATION , 1997 .

[35]  Thomas B Woolf,et al.  Insights into the molecular mechanism of membrane fusion from simulation: evidence for the association of splayed tails. , 2003, Physical review letters.

[36]  Yuliang Yang,et al.  Budding dynamics of multicomponent tubular vesicles. , 2005, Journal of the American Chemical Society.

[37]  Mohamed Laradji,et al.  Dynamics of domain growth in self-assembled fluid vesicles. , 2004, Physical review letters.

[38]  Zhi‐Wu Yu,et al.  Structural characterization on the gel to liquid-crystal phase transition of fully hydrated DSPC and DSPE bilayers. , 2009, The journal of physical chemistry. B.

[39]  W. Helfrich,et al.  The curvature elasticity of fluid membranes : A catalogue of vesicle shapes , 1976 .

[40]  Younan Xia,et al.  Nanomaterials at work in biomedical research. , 2008, Nature materials.

[41]  Satoru Yamamoto,et al.  Budding and fission dynamics of two-component vesicles , 2003 .

[42]  Shuangyang Li,et al.  The relationship between membrane curvature generation and clustering of anchored proteins: a computer simulation study , 2010 .

[43]  Ole G. Mouritsen,et al.  Life - as a matter of fat : the emerging science of lipidomics , 2005 .

[44]  Berend Smit,et al.  Mesoscopic models of biological membranes , 2006 .

[45]  Da-Wei Li,et al.  Examination of membrane fusion by dissipative particle dynamics simulation and comparison with continuum elastic models. , 2005, The Journal of chemical physics.

[46]  Paj Peter Hilbers,et al.  Vesicle shapes from molecular dynamics simulations. , 2006, The journal of physical chemistry. B.

[47]  Reinhard Jahn,et al.  SNAREs — engines for membrane fusion , 2006, Nature Reviews Molecular Cell Biology.

[48]  Kai Yang,et al.  Computer simulation of the translocation of nanoparticles with different shapes across a lipid bilayer. , 2010, Nature nanotechnology.

[49]  J. Shillcock,et al.  The fusion of membranes and vesicles: pathway and energy barriers from dissipative particle dynamics. , 2009, Biophysical journal.

[50]  Paj Peter Hilbers,et al.  Lipid-based mechanisms for vesicle fission. , 2007, The journal of physical chemistry. B.

[51]  K. Kremer,et al.  Aggregation and vesiculation of membrane proteins by curvature-mediated interactions , 2007, Nature.

[52]  Mun'delanji C. Vestergaard,et al.  Dynamic processes in endocytic transformation of a raft-exhibiting giant liposome. , 2007, The journal of physical chemistry. B.

[53]  Sandra L. Schmid,et al.  Regulated portals of entry into the cell , 2003, Nature.

[54]  Edwin R Chapman,et al.  SNARE-driven, 25-millisecond vesicle fusion in vitro. , 2005, Biophysical journal.

[55]  M. Kozlov Fission of Biological Membranes: Interplay Between Dynamin and Lipids , 2001, Traffic.

[56]  Gregory A. Voth,et al.  Direct observation of Bin/amphiphysin/Rvs (BAR) domain-induced membrane curvature by means of molecular dynamics simulations , 2006, Proceedings of the National Academy of Sciences.

[57]  B. Peter,et al.  BAR Domains as Sensors of Membrane Curvature: The Amphiphysin BAR Structure , 2004, Science.

[58]  Yonathan Kozlovsky,et al.  Membrane fission: model for intermediate structures. , 2003, Biophysical journal.

[59]  Petra Schwille,et al.  Sterol structure determines the separation of phases and the curvature of the liquid-ordered phase in model membranes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Udo Seifert,et al.  Configurations of fluid membranes and vesicles , 1997 .

[61]  S. Ramachandran,et al.  Lipid flip-flop driven mechanical and morphological changes in model membranes. , 2008, The Journal of chemical physics.

[62]  F. Pincet,et al.  Hemifusion and fusion of giant vesicles induced by reduction of inter-membrane distance , 2004, The European physical journal. E, Soft matter.

[63]  A. Shaw Lipid rafts: now you see them, now you don't , 2006, Nature Immunology.

[64]  Nicolas Destainville,et al.  Clusters of proteins in biomembranes: insights into the roles of interaction potential shapes and of protein diversity. , 2011, The journal of physical chemistry. B.

[65]  Reinhard Lipowsky,et al.  Pathway of membrane fusion with two tension-dependent energy barriers. , 2007, Physical review letters.

[66]  Herman J. C. Berendsen,et al.  MOLECULAR-DYNAMICS OF A BILAYER-MEMBRANE , 1983 .

[67]  Anna C Balazs,et al.  Designing synthetic vesicles that engulf nanoscopic particles. , 2007, The Journal of chemical physics.

[68]  Siewert J Marrink,et al.  The mechanism of vesicle fusion as revealed by molecular dynamics simulations. , 2003, Journal of the American Chemical Society.

[69]  Klaus Schulten,et al.  Membrane-bending mechanism of amphiphysin N-BAR domains. , 2009, Biophysical journal.

[70]  P. Dommersnes,et al.  Dynamin recruitment by clathrin coats: a physical step? , 2003, Comptes rendus biologies.

[71]  H. Stenmark,et al.  Mechanisms and functions of endocytosis , 2008, The Journal of cell biology.

[72]  R. Rappuoli,et al.  Cell entry machines: a common theme in nature? , 2005, Nature Reviews Microbiology.

[73]  Siewert J. Marrink,et al.  The molecular face of lipid rafts in model membranes , 2008, Proceedings of the National Academy of Sciences.

[74]  Mark S P Sansom,et al.  Blocking of carbon nanotube based nanoinjectors by lipids: a simulation study. , 2008, Nano letters.

[75]  Kurt Kremer,et al.  Tunable generic model for fluid bilayer membranes. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[76]  Harvey T. McMahon,et al.  Membrane curvature and mechanisms of dynamic cell membrane remodelling , 2005, Nature.

[77]  Masahito Yamazaki,et al.  Vesicle fission of giant unilamellar vesicles of liquid-ordered-phase membranes induced by amphiphiles with a single long hydrocarbon chain. , 2007, Langmuir : the ACS journal of surfaces and colloids.

[78]  I. López-Montero,et al.  Proteins involved in lipid translocation in eukaryotic cells. , 2006, Chemistry and physics of lipids.

[79]  Peter M. Kasson,et al.  Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion , 2006, Proceedings of the National Academy of Sciences.

[80]  Feng Qiu,et al.  Budding dynamics of individual domains in multicomponent membranes simulated by N-varied dissipative particle dynamics. , 2007, The journal of physical chemistry. B.

[81]  Yonathan Kozlovsky,et al.  Lipid intermediates in membrane fusion: formation, structure, and decay of hemifusion diaphragm. , 2002, Biophysical journal.

[82]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[83]  Hiroshi Noguchi,et al.  Adhesion of nanoparticles to vesicles: a Brownian dynamics simulation. , 2002, Biophysical journal.

[84]  Reinhard Lipowsky,et al.  Tension-induced vesicle fusion: pathways and pore dynamics. , 2008, Soft matter.

[85]  A. Mayer,et al.  Mutual Control of Membrane Fission and Fusion Proteins , 2004, Cell.

[86]  Berend Smit,et al.  Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins. , 2005, Biophysical journal.

[87]  H. Grubmüller,et al.  Caught in the Act: Visualization of SNARE‐Mediated Fusion Events in Molecular Detail , 2011, Chembiochem : a European journal of chemical biology.

[88]  Paj Peter Hilbers,et al.  Vesicle deformation by draining: geometrical and topological shape changes. , 2009, The journal of physical chemistry. B.

[89]  A. Mark,et al.  Coarse grained model for semiquantitative lipid simulations , 2004 .

[90]  Reinhard Lipowsky,et al.  Solvent-exposed tails as prestalk transition states for membrane fusion at low hydration. , 2010, Journal of the American Chemical Society.

[91]  Jeremy B. A. Green Sophistications of cell sorting , 2008, Nature Cell Biology.

[92]  Seifert,et al.  Budding transitions of fluid-bilayer vesicles: The effect of area-difference elasticity. , 1994, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[93]  A. Bray Theory of phase-ordering kinetics , 1994, cond-mat/9501089.

[94]  A. Mark,et al.  Simulation of the spontaneous aggregation of phospholipids into bilayers. , 2001, Journal of the American Chemical Society.

[95]  J. Shillcock,et al.  Dissipative particle dynamics of tension-induced membrane fusion , 2009 .

[96]  Soichi Takeda,et al.  Endophilin BAR domain drives membrane curvature by two newly identified structure‐based mechanisms , 2006, The EMBO journal.

[97]  Siewert J Marrink,et al.  Lipids on the move: simulations of membrane pores, domains, stalks and curves. , 2009, Biochimica et biophysica acta.

[98]  Kai Yang,et al.  Wrapping and Internalization of Nanoparticles by Lipid Bilayers: a Computer Simulation Study , 2011 .

[99]  R. G. Anderson The caveolae membrane system. , 1998, Annual review of biochemistry.

[100]  Volker Knecht,et al.  Molecular dynamics simulations of lipid vesicle fusion in atomic detail. , 2007, Biophysical journal.

[101]  Jason D. Perlmutter,et al.  Interleaflet interaction and asymmetry in phase separated lipid bilayers: molecular dynamics simulations. , 2011, Journal of the American Chemical Society.

[102]  Hongxia Guo,et al.  Simulation study of protein-mediated vesicle fusion. , 2009, The journal of physical chemistry. B.

[103]  Berend Smit,et al.  Molecular simulations of lipid-mediated protein-protein interactions. , 2008, Biophysical journal.