Determination of the shape and curvature of nonplanar lipid bilayers that are bent in a single plane in molecular dynamics simulations

Journal of Molecular Modeling

Volumn 20, Issue 4, 2014, Pages

  Yesylevskyy, S O ^a   Kraszewski, S ^b   Ramseyer, C ^b  

^a INSTITUTE OF PHYSICS   (Ukraine)

^b UNIVERSITÉ DE FRANCHE COMTÉ   (France)

Author keywords

Membrane curvature; Molecular dynamics; Nonplanar membranes

Indexed keywords

LIPID;

ALGORITHM; ARTICLE; BILAYER MEMBRANE; CHEMICAL STRUCTURE; GEOMETRY; LIPID BILAYER; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; CHEMISTRY;

ALGORITHMS; LIPID BILAYERS; MOLECULAR DYNAMICS SIMULATION;

EID: 84896587164     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-014-2176-x     Document Type: Article

References (27)

1. Hansson T, Oostenbrink C, van Gunsteren W (2002) Molecular dynamics simulations. Curr Opin Struct Biol 12(2):190-196 (Pubitemid 34327478)
2. Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Mol Biol 9(9):646-652 (Pubitemid 34977295)
3. Tieleman DP, Marrink SJ, Berendsen HJC (1997) A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta 1331:235-270 (Pubitemid 28015516)
4. Demchenko AP, Yesylevskyy SO (2009) Nanoscopic description of biomembrane electrostatics: results of molecular dynamics simulations and fluorescence probing. Chem Phys Lipids 160(2):63-84
5. McMahon HT, Gallop JL (2005) Membrane curvature and mechanisms of dynamic cell membrane remodelling. Nature 438(7068):590-596 (Pubitemid 41740562)
6. Chernomordik L, Kozlov MM, Zimmerberg J (1995) Lipids in biological membrane fusion. J Membr Biol 146(1):1-14
7. Kamal MM et al (2009) Measurement of the membrane curvature preference of phospholipids reveals only weak coupling between lipid shape and leaflet curvature. Proc Natl Acad Sci 106(52):22245-22250
8. Martens S, McMahon HT (2008) Mechanisms of membrane fusion: disparate players and common principles. Nat Rev Mol Cell Biol 9(7):543-556 (Pubitemid 351881838)
9. Mim C, Unger VM (2012) Membrane curvature and its generation by BAR proteins. Trends Biochem Sci 37(12):526-533
10. Ivankin A, Kuzmenko I, Gidalevitz D (2012) Cholesterol mediates membrane curvature during fusion events. Phys Rev Lett 108(23):238103
11. Antonny B (2011) Mechanisms of membrane curvature sensing. Annu Rev Biochem 80(1):101-123
12. Yesylevskyy SO, Klymchenko AS, Demchenko AP (2005) Semi-empirical study of two-color fluorescent dyes based on 3-hydroxychromone. J Mol Struct 755:229-239 (Pubitemid 41783348)
13. Tian A, Baumgart T (2009) Sorting of lipids and proteins in membrane curvature gradients. Biophys J 96(7):2676-2688
14. Knecht V, Marrink S-J (2007) Molecular dynamics simulations of lipid vesicle fusion in atomic detail. Biophys J 92(12):4254-4261 (Pubitemid 46910541)
15. Marrink SJ, Mark AE (2003) The mechanism of vesicle fusion as revealed by molecular dynamics simulations. J Am Chem Soc 125(37):11144-11145 (Pubitemid 37108020)
16. Meyer GR et al (2006) Molecular dynamics study of MscL interactions with a curved lipid bilayer. Biophys J 91(5):1630-1637 (Pubitemid 44352429)
17. Yesylevskyy S, Demchenko A (2012) How cholesterol is distributed between monolayers in asymmetric lipid membranes. Eur Biophys J 41(12):1043-1054
18. Yesylevskyy SO (2013) Cholesterol induces uneven curvature of asymmetric lipid bilayers. Sci World J 965230
19. Van Der Spoel D et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26(16):1701-1718 (Pubitemid 43076182)
20. Nelson MT et al (1996) NAMD: a parallel, object-oriented molecular dynamics program. Int J High Perform Comput Appl 10(4):251-268
21. Salomon-Ferrer R, Case DA, Walker RC (2012) An overview of the Amber biomolecular simulation package. Wiley Interdiscip Rev Comput Mol Sci 3:198-210
22. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33-38 (Pubitemid 26152973)
23. Delano WL (2002) The PyMOL molecular graphics system. http://www.pymol.org, last accessed 6/2/2013
24. Brigham E (1988) Fast Fourier transform and its applications, 1st edn. Prentice Hall, Englewood Cliffs, p 448
25. Coxeter HSM (1989) Introduction to geometry, 2nd edn. Wiley, New York
26. Yesylevskyy SO (2012) Pteros: fast and easy to use open-source C++ library for molecular analysis. J Comput Chem 33(19):1632-1636
27. Marrink SJ et al (2007) The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111(27):7812-7824 (Pubitemid 47169693)