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2003 | 50 | 3 | 789-798
Article title

Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions.

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Molecular dynamics (MD) simulations complement experimental methods in studies of the structure and dynamics of lipid bilayers. The choice of algorithms employed in this computational method represents a trade-off between the accuracy and real calculation time. The largest portion of the simulation time is devoted to calculation of long-range electrostatic interactions. To speed-up evaluation of these interactions, various approximations have been used. The most common ones are the truncation of long-range interactions with the use of cut-offs, and the particle-mesh Ewald (PME) method. In this study, several multi-nanosecond cut-off and PME simulations were performed to establish the influence of the simulation protocol on the bilayer properties. Two bilayers were used. One consisted of neutral phosphatidylcholine molecules. The other was a mixed lipid bilayer consisting of neutral phosphatidylethanolamine and negatively charged phosphatidylglycerol molecules. The study shows that the cut-off simulation of a bilayer containing charge molecules generates artefacts; in particular the mobility and order of the charged molecules are vastly different from those determined experimentally. In the PME simulation, the bilayer properties are in general agreement with experimental data. The cut-off simulation of bilayers containing only uncharged molecules does not generate artefacts, nevertheless, the PME simulation gives generally better agreement with experimental data.
Physical description
  • Department of Biophysics, Faculty of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
  • Department of Biophysics, Faculty of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
  • Department of Biophysics, Faculty of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
  • Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. (1984) Molecular dynamics with coupling to an external bath. J Chem Phys.; 81: 3684-90.
  • Case DA, Pearlman DA, Caldwell JW, Cheatham III TE, Ross WS, Simmerling C, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Ferguson DM, Radmer RJ, Seibel GL, Singh UC, Weiner PK, Kollman PA. (1997) AMBER 5.0. University of California, San Francisco.
  • Charifson PS, Hiskey RG, Pedersen LG. (1990) Construction and molecular modeling of phospholipid surfaces. J Comp Chem.; 11: 1181-6.
  • Egberts E, Marrik S-J, Berendsen HJC. (1994) Molecular dynamics simulation of phospholipid membrane. Eur Biophys J.; 22: 423-36.
  • Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. (1995) A smooth particle mesh Ewald method. J Chem Phys.; 103: 8577-93.
  • Haibel A, Nimtz G, Pelster R, Jaggi R. (1998) Translational diffusion in phospholipid bilayer membranes. Phys Rev E.; 57: 4838-41.
  • Huang C, Li S. (1999) Calorimetric and molecular mechanics studies of the thermotropic phase bahavior of membrane phospholipids. Biochim Biophys Acta.; 1422: 273-307.
  • Hubbell WL, McConnell HM. (1971) Molecular motion in spin-labeled phospholipids and membranes. J Am Chem Soc.; 93: 314-26.
  • Jorgensen WL, Tirado-Rives J. (1988) The OPLS potential functions for proteins: energy minimization for crystals of cyclic peptides and crambin. J Am Chem Soc.; 110: 1657-66.
  • Jorgensen WL, Chandrasekhar J, Madura JD, Impey R, Klein ML. (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys.; 79: 926-35.
  • Marsh D, Watts A, Smith ICP. (1983) Dynamic structure and phase behavior of dimyristoylphosphatidylethanolamine bilayers studied by deuterium nuclear magnetic resonance. Biochemistry.; 22: 3023-6.
  • Murzyn K, Pasenkiewicz-Gierula M. (1999) Construction and optimisation of a computer model for a bacterial membrane. Acta Biochim Polon.; 46: 631-9.
  • Murzyn K, Róg T, Pasenkiewicz-Gierula M. (1999) Comparison of the conformation and the dynamics of saturated and mono-unsaturated hydrocarbon chains of phosphatidylcholines. Curr Top Biophys.; 23: 87-94.
  • Murzyn K, Róg T, Jezierski G, Takaoka Y, Pasenkiewicz-Gierula M. (2001) Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study. Biophys J.; 81: 170-83.
  • Pasenkiewicz-Gierula M, Takaoka Y, Miyagawa H, Kitamura K, Kusumi A. (1999) Charge pairing of headgroups in phosphatidylcholine membranes: a molecular dynamics simulation study. Biophys J.; 76: 1228-40.
  • Patra M, Karttunen M, Hyvönen MT, Falck E, Linqvist P, Vattulainen I. (2003) Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. Biophys J.; 84: 3636-45.
  • Pearlman DA, Case DA, Caldwell JC, Seibel GL, Singh UC, Weiner PK, Kollman PA. (1991) Amber 4.0. University of California, San Francisco.
  • Róg T, Pasenkiewicz-Gierula M. (2001) Cholesterol effects on the phosphatidylcholine bilayer nonpolar region: A molecular simulation study. Biophys J.; 81: 2190-202.
  • Ryckaert JP, Cicotti G, Berendsen HJC. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Phys.; 22: 327-41.
  • Sagui C, Daren TA. (1999) Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu Rev Biophys Biomol Struct.; 28: 155-79.
  • Schreiber H, Steinhauser O. (1992) Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry.; 31: 5856-60.
  • Seelig J, Waespe-Šarčević N. (1978) Molecular order in cis and trans unsaturated phospholipid bilayers. Biochemistry.; 17: 3310-5.
  • Shinoda W, Okazaki S. (1998) A Voronoi analysis of lipid area fluctuation in a bilayer. J Chem Phys.; 109: 1517-21.
  • Tabony J, Perly B. (1991) Quasielastic neutron scattering measurements of fast local translational diffusion of lipid molecules in phospholipid bilayers. Biochim Biophys Acta.; 1063: 67-72.
  • Tieleman DP, Berendsen HJC. (1998) A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys J.; 74: 2786-801.
  • Trouard TP, Nevzorov AA, Alam TM, Job CC, Zajicek J, Brown MF. (1999) Influence of cholesterol on dynamics of dimyristoylphosphatidylcholine bilayers as studied by deuterium NMR relaxation. J Chem Phys.; 110: 8802-18.
  • York DM, Yang W, Lee H, Darden T, Pedersen LG. (1995) Toward the accurate modeling of DNA: the importance of long-range electrostatics. J Am Chem Soc.; 117: 5001-2.
  • Róg T, Murzyn K, Gurbiel R, Takaoka Y, Kusumi A, Pasenkiewicz-Gierula M. (2003) Effects of phospholipid unsaturation on the bilayer nonpolar region: a molecular simulation study. Submitted to J Lipid Res.
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