Molecular dynamics simulations of lipid bilayers

Current Opinion in Structural Biology

Volumn 7, Issue 4, 1997, Pages 511-517

  Merz Jr , Kenneth M ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOLIPID;

LIPID BILAYER; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; REVIEW;

EID: 0343118775     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80115-7     Document Type: Article

References (54)

1. Gennis RB. Biomembranes: Molecular Structure and Function. 1989;Springer-Verlag, New York.
2. Egberts E. Molecular dynamics simulations of multibilayer membranes. PhD Thesis. 1988;University of Groningen, Groningen.
3. Pastor RW. Molecular dynamics and Monte Carlo simulations of lipid bilayers. Curr Opin Struct Biol. 4:1994;486-492.
4. of outstanding interest Merz KM Jr, Roux B. Biological Membranes: a Molecular Perspective from Computation to Experiment. 1996;Birkhäuser, Boston, This book gives a broad overview of contemporary issues in membrane biophysics from both theoretical and experimental perspectives.
5. Egberts E, Marrink SJ, Berendsen HJC. Molecular dynamics simulation of a phospholipid bilayer. Eur Biophys J. 22:1994;423-436.
6. Huang P, Perez JJ, Loew GH. Molecular dynamics simulations of phospholipid bilayers. J Biomol Struct Dyn. 11:1994;927-956.
7. Shinoda W, Fukada T, Okazaki S, Okada I. Molecular dynamics simulation of the dipalmitoylphosphatidylcholine (DPPC) lipid bilayer in the fluid phase using the Nóse - Parrinello - Rahman NPT ensemble. Chem Phys Lett. 232:1995;308-322.
8. Tu K, Tobias DJ, Klein ML. Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystalline phase dipalmitoylphosphatidylcholine bilayer. Biophys J. 69:1995;2558-2562.
9. Chiu S-W, Clark M, Balaji V, Subramaniam S, Scott HL, Jakobsson E. Incorportion of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. Biophys J. 69:1995;1230-1245.
10. Feller SE, Zhang Y, Pastor RW. Computer simulation of liquid/liquid interfaces. II. Surface tension-area dependence of a bilayer and monolayer. J Chem Phys. 103:1995;10267-10276.
11. Jähnig F. What is the surface tension of a lipid bilayer membrane? Biophys J. 71:1996;1348-1349.
12. Tielman DP, Berendsen HJC. Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. J Chem Phys. 105:1996;4871-4880.
13. Feller SE, Pastor RW. On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations. Biophys J. 71:1996;1350-1355.
14. Allen MP, Tildesley DJ. Computer Simulation of Liquids. 1987;Clarendon Press, Oxford.
15. Darden T, York D, Pedersen L. Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems. J Chem Phys. 98:1993;10089-10092.
16. Luty BA, Tironi LG, van Gunsteren WF. Lattice-sum methods for calculating electrostatic interactions in molecular simulations. J Chem Phys. 103:1995;3014-3021.
17. Feller SE, Pastor RW, Rojnuckarin A, Bogusz S, Brooks BR. Effect of electrostatic force truncation on interfacial and transport properties of water. of special interest J Phys Chem. 100:1996;17011-17020 This paper gives a concise presentation of the problems associated with truncating long-range electrostatic interactions in the simulation of lipid bilayers.
18. Zhou F, Schulten K. Molecular dynamics study of a membrane - water interface. J Phys Chem. 99:1995;2194-2207.
19. Alper HE, Bassolino D, Stouch TR. Computer simulation of a phospholipid monolayer - water system: the influence of long-range forces of water structure and dynamics. J Chem Phys. 98:1993;9798-9807.
20. Cheatham TE III, Miller JL, Fox T, Darden TA, Kollman PA. Molecular dynamics simulations and solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J Am Chem Soc. 117:1996;4193-4194.
21. Israelachvili JN, Wennerstrom H. Entropic forces between amphiphilic surfaces in liquids. J Phys Chem. 96:1992;520-531.
22. Rand RP, Parsegian VA. The forces between interacting bilayer membranes and the hydration of phospholipid assemblies. Yeagle P. The Structure of Biological Membranes. 1992;251-306 CRC Press, Boca Raton.
23. Van Buren AR, Marrink S-J, Berendsen HJC. Characterisation of aqueous interfaces with different hydrophobicities by molecular dynamics. Colloid Surf A. 102:1995;143-157.
24. Essmann U, Purera L, Berkowitz ML. The origin of the hydration interaction of lipid bilayers from MD simulations of dipalmitoylphosphatidylcholine membranes in gel and liquid crystalline phases. Langmuir. 11:1995;4519-4531.
25. Damodaran KV, Merz KM Jr. Head group - water interactions in lipid bilayers: a comparison between DMPC and DLPE based lipid bilayers. Langmuir. 9:1993;1179-1183.
26. Damodaran KV, Merz KM Jr. A comparison between DMPC and DLPE based lipid bilayers. Biophys J. 66:1994;1076-1087.
27. Alper HE, Bassolino D, Stouch TR. Computer simulation of a phospholipid monolayer-water system: the influence of long range forces on water structure and dynamics. J Chem Phys. 98:1993;9798-9807.
28. Damodaran KV, Merz KM Jr, Gaber BP. Structure and dynamics of the dilauroylphosphatidylethanolamine lipid bilayer. Biochemistry. 31:1992;7656-7664.
29. Heller H, Schaefer M, Schulten K. Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phases. J Phys Chem. 97:1993;8343-8360.
30. Israelachvili JN, Wennerstrom H. Role of hydration and water structure in biological and colloidal interactions. of special interest Nature. 379:1996;219-225 This paper reviews the current status of the hydration force problem. It highlights the fact that the constrained counterions between approaching bilayers may account for the observed hydration force.
31. Robinson AJ, Richards WG, Thomas PJ, Mann MM. Head group and chain behavior in biological membranes: a molecular dynamics computer simulation. Biophys J. 67:1994;2345-2354.
32. Wilson MA, Pohorille A. Mechanism of unassisted ion transport across membrane bilayers. of special interest J Am Chem Soc. 118:1996;6580-6587 Unique molecular level insights into unassisted ion transport across a membrane using MD simulations are provided.
33. Marrink SJ, Berendsen HJC. Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations. J Phys Chem. 100:1996;16729-16738.
34. Marrink SJ, Jähnig F, Berendsen HJC. Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. of special interest Biophys J. 71:1996;632-647 This paper tests the concept that transient water channels in a membrane facilitate proton transfer across a membrane.
35. Nagle JF. Theory of passive proton conductance in lipid bilayers. J Bioeng Biomembr. 19:1987;413-426.
36. Deisenhofer J, Michel H. The photosynthetic reaction center from the purple bacterium Rhodopseudomonas viridis. Science. 245:1989;1463-1473.
37. Cross TA, Opella SJ. Solid-state NMR structural studies of peptides and proteins in membranes. Curr Opin Struct Biol. 4:1994;574-581.
38. Woolf TB, Roux B. Structure, energetics, and dynamics of lipid - protein interactions: a molecular dynamics study of the gramicidin A channel in a DMPC bilayer. of special interest Proteins. 24:1996;92-114 A very thorough examination of the interactions between a biomembrane and the gramicidin A channel is presented.
39. Woolf TB, Roux B. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc Natl Acad Sci USA. 91:1994;11631-11635.
40. Jacobs RE, White SH. The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices. Biochemistry. 28:1989;3421-3437.
41. 1H NMR study. J Phys Chem. 97:1993;2967-2973.
42. Damodaran KV, Merz KM Jr, Gaber BP. Interaction of small peptides with lipid bilayers. Biophys J. 69:1995;1299-1308.
43. Turner DC, Straume M, Kasimova MR, Gaber BP. Thermodynamics of interaction of the fusion inhibiting peptide Z-D-Phe-D-Phe-Gly with dioleoylphosphatidylcholine vesicles: direct calorimetric determination. Biochemistry. 34:1995;9517-9525.
44. Damodaran KV, Merz KM Jr. Interaction of the fusion inhibiting peptide carbobenzoxy-D-Phe-L-Phe-Gly with N-methyldioleoylphosphatidylethanolamine lipid bilayers. J Am Chem Soc. 117:1995;6561-6571.
45. White JM. Membrane fusion. Science. 258:1992;917-924.
46. Huang P, Loew GH. Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study. J Biomol Struct Dyn. 12:1995;937-956.
47. Edholm O, Berger O, Jähnig F. Structure and fluctuations of bacteriorhodopsin in the purple membrane: a molecular dynamics study. J Mol Biol. 250:1995;94-111.
48. 2 on a membrane surface. Proteins. 25:1996;12-27.
49. Chipot C, Wilson MA, Pohorille A. Interactions of anesthetics with the water/hexane interface. A molecular dynamics study. J Phys Chem. 101:1997;782-791.
50. Pohorille A, Cieplak P, Wilson MA. Interactions of anesthetics with the membrane/water interface. Chem Phys. 204:1996;337-345.
51. Huang P, Bertaccini E, Loew GH. Molecular dynamics simulation of anesthetic - phospholipid bilayer interactions. J Biomol Struct Dyn. 12:1995;725-754.
52. McMullen TPW, McElhaney RN. Physical studies of cholesterol - phospholipid interactions. Curr Opin Colloid Interface Sci. 1:1996;83-90.
53. Gabdoulline RR, Vanderkooi G, Zheng C. Comparison of the structure of dimyristoylphosphatidylcholine in the presence and absence of cholesterol by molecular dynamics simulations. J Phys Chem. 100:1996;15942-15946.
54. Robinson AJ, Richards WG, Thomas PJ, Mann MM. Behavior of cholesterol and its effect on head group and chain conformations in lipid bilayers: a molecular dynamics study. Biophys J. 68:1995;164-170.