Statistical Thermodynamics Through Computer Simulation to Characterize Phospholipid Interactions in Membranes
| Abstract |
|
|
This chapter describes the major issues thDepartment of Physiat are involved in the statistical thermodynamics of phospholipid
membranes at the atomic level. The ingredients going into models of lipid bilayers are summarized: force fields, representation
of long-range interactions, and boundary conditions. Next, the choice of thermodynamic ensembles, and the two main options
for the generation of a representative sample of configurations: molecular dynamics and Monte Carlo are discussed. The final
issue that is dealt with describes the various ways the generated ensembles can be analyzed.
Affiliation(s): (2) Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, New York, NY, USA
(3) Department of Colloid Chemistry, Eötvös Loránd University, Budapest, Hungary
(3) Department of Colloid Chemistry, Eötvös Loránd University, Budapest, Hungary
Book Title: Methods in Membrane Lipids
Series: Methods in Molecular Biology | Volume: 400 | Pub. Date: Aug-30-2007 | Page Range: 127-144 | DOI: 10.1007/978-1-59745-519-0_9
Subject: Biochemistry
Key Words: Ewald sum - force field - free-energy profile - molecular dynamics - Monte Carlo - Voronoi tesselation
| References |
|
| 1. | Jorgensen, W. L., Maxwell, D. S., and Tirado-Rives, J. (1996) Development and Testing of the OPLS All-Atom Force Field on
Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc.
118, 11,225–11,236.
|
| 2. | Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: A program
for macromolecular energy, minimization and dynamics calculation. J. Comp. Chem.
4, 187–217, URL:http://www.charmm.org. April 1, 2007.
|
| 3. | AMBER: Assisted model building with energy refinement, URL:http://www.amber.ucsf.edu/amber/amber.htm. April 1, 2007. |
| 4. | Gasteiger, J. and Marsali, M. (1980) Iterative partial equalization of orbital electronegativity—a rapid access to atomic
charges. Tetrahedron
36, 3219–3229.
|
| 5. | GROMACS: The world’s fastest molecular dynamics, URL:http://www.gromacs.org/. April 1, 2007. |
| 6. | Goetz, R. and Lipowsky, R. (1998) Computer simulation of bilayer membranes: Self-assembly and interfacial tension. J. Chem. Phys.
108, 7397–7409.
|
| 7. | Shelley, J. C., Shelley, M. Y., Reeder, R. C., Bandyopadhyay, S., and Klein, M. L. (2001) A Coarse Grain Model for Phospholipid
Simulations. J. Phys. Chem. B
105, 4464–4470.
|
| 8. | MartÍ, J. (2004) A molecular dynamics transition path sampling study of model lipid bilayer membranes in aqueous environment.
J. Phys. Condens. Matter.
16, 5669–5678.
|
| 9. | Marrink, S. J., de Vries, A. H., and Mark, A. E. (2004) Coarse Grained Model for Semiquantitative Lipid Simulations. J. Phys. Chem. B
108, 750–760.
|
| 10. | Jedlovszky, P. and Mezei, M. (1999) Grand canonical ensemble Monte Carlo simulation of a lipid bilayer using extension biased
rotations. J. Chem. Phys.
111, 10,770–10,773.
|
| 11. | Dolan, E. A., Venable, R. M., Pastor, R. W., and Brooks, B. R. (2002) Simulations of membranes and other interfacial systems
using P21 and Pc periodic boundary conditions. Biophys. J.
82, 2317–2325.
|
| 12. | Gumbart, J., Wang, Y., Aksimentiev, A., Tajkhorshid, E., and Schulten, K. (2005) Molecular dynamics simulations of proteins
in lipid bilayers. Curr. Opin. Struct. Biol.
15, 423–431.
|
| 13. | Neumann, M. (1985) The dielectric constant of water. Computer simulations with the MCY potential. J. Chem. Phys.
82, 5663–5672.
|
| 14. | Ewald, P. (1924) Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys. 64, 253–287. |
| 15. | Campbell, E. S. (1963) Existence of a “well defined” specific energy for an ionic crystal; justification of Ewald’s formulae
and their use to deduce equations for multipole lattices. J. Phys. Chem. Solids.
24, 197–208.
|
| 16. | Essman, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle mesh Ewald method.
J. Chem. Phys.
103, 8577–8593.
|
| 17. | Yeh, I. C. and Berkowitz, M. L. (1999) Ewald summation for systems with slab geometry. J. Chem. Phys.
111, 3155–3162.
|
| 18. | Chiu, S. W., Clark, M., Balaji, V., Subramaniam, S., Scott, H. L., and Jakobsson, E. (1995) Incorporation of Surface Tension
into Molecular Dynamics Simulation of an Interface. A Fluid Phase Lipid Bilayer Membrane. Biophys. J.
69, 1230–1245.
|
| 19. | Tieleman, D. P. and Berendsen, H. J. C. (1996) Molecular dynamics simulation of a fully hydrated dipalmitoylphosphatidylcholine
bilayer with different macroscopic boundary conditions and parameters. J. Chem. Phys.
103, 4871–4880.
|
| 20. | Mezei, M. (1980) A cavity-biased (T,V,μ) Monte Carlo method for the computer simulation of fluids. Mol. Phys.
40, 901–906.
|
| 21. | Mezei, M. (1987) Grand-canonical ensemble Monte Carlo simulation of dense fluids: Lennard-Jones, soft spheres and water. Mol. Phys.
61, 565–582. Erratum (1989) 67, 1207–1208.
|
| 22. | Mezei, M. (2002) On the potential of Monte Carlo methods for simulating macromolecular assemblies, in Third International Workshop for Methods for Macromolecular Modeling Conference Proceedings, (Gan, H. H. and Schlick, T., eds.), Springer, New York, pp. 177–196. |
| 23. | Chiu, S. W., Jakobsson, E., and Scott, H. L. (2001) Combined Monte Carlo and Molecular Dynamics Simulation of Hydrated Lipid-Cholesterol
Lipid Bilayers at Low Cholesterol Concentration. Biophys. J.
80, 1104–1114.
|
| 24. | Chiu, S. W., Jakobsson, E., and Scott, H. L. (2001) Combined Monte Carlo and molecular dynamics simulation of hydrated dipalmitoyl-phosphatidylcholine-cholesterol
lipid bilayers. J. Chem. Phys.
114, 5435–5443.
|
| 25. | Ebersole, B. J., Visiers, I., Weinstein, H., and Sealfon, S. C. (2003) Molecular basis of partial agonism: orientation of
indoleamine ligands in the binding pocket of the human serotonin 5-HT2A receptor determines relative efficacy. Mol. Pharm.
63, 36–43.
|
| 26. | Allen, M. P. and Tildesley, D. J. (1986) Computer simulation of liquids. Clarendon Press, Oxford. |
| 27. | Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of cartesian equation of motion of a system
with constraints; molecular dynamics of n-alkanes. J. Comp. Phys.
23, 327–341.
|
| 28. | Metropolis, N. A., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., and Teller, E. (1953) Equation of state calculation
by fast computing machines. J. Chem. Phys.
21, 1087–1092.
|
| 29. | Rosenbluth, M. N. and Rosenbluth, A. W. (1955) Monte Carlo calculation of the average extension of molecular chains. J. Chem. Phys.
23, 356–359.
|
| 30. | Siepman, I. and Frenkel, D. (1992) Configurational bias Monte Carlo: a new sampling scheme for flexible chains. Mol. Phys.
75, 59–70.
|
| 31. | Dodd, L. R., Boone, T. D., and Theodorou, D. N. (1993) A concerted rotation algorithm for atomistic Monte Carlo simulation
of polymer melts and glasses. Mol. Phys.
78, 961–996.
|
| 32. | Mezei, M. (2003) Efficient Monte Carlo sampling for long molecular chains using local moves, tested on a solvated lipid bilayer.
J. Chem. Phys.
118, 3874–3879.
|
| 33. | Noguti, T. and Go, N. (1985) Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins.
Biopolymers
24, 527–546.
|
| 34. | Marrink, S. J., Tieleman, D. P., and Mark, A. E. (2000) Molecular Dynamics Simulations of the Kinetics of Spontaneous Micelle
Formation. J. Phys. Chem. B
104, 12,165–12,173.
|
| 35. | URL:http://thallium.bsd.uchicago.edu/Roux Lab/; April 1, 2007. |
| 36. | De Loof, H. D., Harvey, S. C., Segrest, J. P., and Pastor, R. W. (1991) Mean field stochastic boundary molecular dynamics
simulation of a phospholipid in a membrane. Biochemistry
30, 2099–2113.
|
| 37. | Pastor, R. W., Venable, R. M., and Karplus, M. (1991) Model for the structure of the lipid bilayer. Proc. Natl. Acad. Sci. USA
88, 892–896.
|
| 38. | Smondyrev, A. M. and Berkowitz, M. L. (1999) Structure of Dipalmitoylphosphatidylcholine/ Cholesterol Bilayer at Low and High
Cholesterol Concentrations: Molecular Dynamics Simulation. Biophys. J.
77, 2075–2089.
|
| 39. | Jedlovszky, P. and Mezei, M. (2003) Effect of Cholesterol on the Properties of Phospholipid Membranes. 1. Structural Features.
J. Phys. Chem. B
107, 5311–5321.
|
| 40. | Marrink, S. J. and Berendsen, H. J. C. (1994) Simulation of Water Transport through a Lipid Membrane. J. Phys. Chem.
98, 4155–4168.
|
| 41. | Rabinovich, A. L., Balabaev, N. K., Alinchenko, M. G., Voloshin, V. P., Medvedev, N. N., and Jedlovszky, P. (2005) Computer simulation study of intermolecular voids in unsaturated phosphatidylcholine lipid bilayers. J. Chem. Phys. 122, 084906. 12 pages. |
| 42. | Hyvönen, M. T., Rantala, T. T., and Ala-Korpela, M. (1997) Structure and Dynamic Properties of Diunsaturated 1-Palmitoyl-2-Linoleoyl-sn-Glycero-3-Phosphatidylcholine Lipid Bilayer from Molecular Dynamics Simulation. Biophys. J.
73, 2907–2923.
|
| 43. | Heller, H., Schaefer, M., and Schulten, K. (1993) Molecular Dynamics Simulation of a Bilayer of 200 Lipids in the Gel and
Liquid-Crystal Phases. J. Phys. Chem.
97, 8343–8360.
|
| 44. | Tu, K., Tobias, D. J., and Klein, M. L. (1995) Constant Pressure and Temperature Molecular Dynamics Simulation of a Fully
Hydrated Liquid Crystal Phase Dipalmitoylphosphatidylcholine Bilayer. Biophys. J.
69, 2558–2562.
|
| 45. | Tu, K., Klein, M. L., and Tobias, D. J. (1998) Constant-Pressure Molecular Dynamics Investigation of Cholesterol Effects in
a Dipalmitoylphosphatidylcholine Bilayer. Biophys. J.
75, 2147–2156.
|
| 46. | Zubrzycki, I. Z., Xu, Y., Madrid, M., and Tang, P. (2000) Molecular dynamics simulation of a fully hydrated dimyristoylphosphatidylcholine
membrane in liquid-crystalline phase. J. Chem. Phys.
112, 3437–3441.
|
| 47. | Saiz, L. and Klein, M. L. (2001) Structural Properties of a Highly Polyunsaturated Lipid Bilayer from Molecular Dynamics Simulations.
Biophys. J.
81, 204–216.
|
| 48. | Husslein, T., Newns, D. M., Pattnaik, P. C., Zhong, Q., Moore, P. B., and Klein, M. L. (1998) Constant pressure and temperature
molecular-dynamics simulation of the hydrated diphytanolphosphatidylcholine lipid bilayer. J. Chem. Phys.
109, 2826–2832.
|
| 49. | Pasenkiewicz-Gierula, M., Takaoka, Y., Miyagawa, H., Kitamura, K., and Kusumi, A. (1999) Charge Pairing of Headgroups in Phosphatidylcholine
Membranes: A Molecular Dynamics Simulation Study. Biophys. J.
76, 1228–1240.
|
| 50. | Saiz, L. and Klein, M. L. (2002) Electrostatic interactions in neutral model phospholipid bilayer by molecular dynamics simulations.
J. Chem. Phys.
116, 3052–3057.
|
| 51. | Åman, K., Lindahl, E., Edholm, O., Håkansson, P., and Westlund, P. O. (2003) Structure and Dynamics of Interfacial Water in
an L
α Phase Lipid Bilayer from Molecular Dynamics Simulations. Biophys. J.
84, 102–115.
|
| 52. | Rabinovich, A. L., Ripatti, P. O., Balabaev, N. K., and Leermakers, F. A. M. (2003) Molecular dynamics simulations of hydrated unsaturated lipid bilayers in the liquid-crystal phase and comparison to self-consistent field modelling. Phys. Rev. E 67, 011909. 14 pages. |
| 53. | Snyder, R. G., Tu, K., Klein, M. L., Mendelssohn, R., Strauss, H. L., and Sun, W. (2002) Acyl Chain Conformation and Packing
in Dipalmitoylphosphatidylcholine Bilayers from MD Simulation and IR Spectroscopy. J. Phys. Chem. B.
106, 6273–6288.
|
| 54. | Hofsäß, C., Lindahl, E., and Edholm, O. (2003) Molecular Dynamics Simulations of Phospholipid Bilayers with Cholesterol. Biophys. J.
84, 2192–2206.
|
| 55. | Shinoda, W., Mikami, M., Baba, T., and Hato M. (2003) Molecular Dynamics Study on the Effect of Chain Branching on the Physical
Properties of Lipid Bilayers: Structural Stability. J. Phys. Chem. B
107, 14,030–14,035.
|
| 56. | López-Cascales, J. J., GarcÍa de la Torre, J., Marrink, S. J., and Berendsen, H. J. C. (1996) Molecular dynamics simulations
of a charged biological membrane. J. Chem. Phys.
104, 2713–2720.
|
| 57. | van der Ploeg, P. and Berendsen, H. J. C. (1982) Molecular dynamics simulation of a bilayer membrane. J. Chem. Phys.
76, 3271–3276.
|
| 58. | Jedlovszky, P. and Mezei, M. (2001) Orientational Order of the Water Molecules Across a Fully Hydrated DMPC Bilayer. A Monte
Carlo Simulation Study. J. Phys. Chem. B
105, 3614–3623.
|
| 59. | Pandit, S. A., Bostick, D., and Berkowitz, M. L. (2003) An algorithm to describe molecular scale rugged surfaces and its application
to the study of a water/lipid bilayer interface. J. Chem. Phys.
119, 2199–2205.
|
| 60. | Gawrisch, K., Ruston, D., Zimmemberg, J., Parsegian, V. A., Rand, R. P., and Fuller, N. (1992) Membrane dipole potentials,
hydration forces, and the ordering of water at membrane surfaces. Biophys. J.
61, 1213–1223.
|
| 61. | Pasenkiewicz-Gierula, M., Takaoka, Y., Miyagawa, H., Kitamura, K., and Kusumi, A. (1997) Hydrogen Bonding of Water to Phosphatidylcholine
in the Membrane As Studied by a Molecular Dynamics Simulation: Location, Geometry, and Lipid-Lipid Bridging via Hydrogen-Bonded
Water. J. Phys. Chem. A
101, 3677–3691.
|
| 62. | Pasenkiewicz-Gierula, M., Róg, T., Kitamura, K., and Kusumi, A. (2000) Cholesterol Effects on the Phosphatidylcholine Bilayer Polar Region: A Molecular Simulation Study. Biophys. J. 78, 1517–1521. |
| 63. | Chiu, S. W., Jakobsson, E., Mashl, R. J., and Scott, H. L. (2002) Cholesterol-Induced Modifications in Lipid Bilayers: A Simulation
Study. Biophys. J.
83, 1842–1853.
|
| 64. | Shinoda, K., Shinoda, W., Baba, T., and Mikami, M. (2004) Comparative molecular dynamics study of ether-and esther-linked
phospholipid bilayers. J. Chem. Phys.
121, 9648–9654.
|
| 65. | Jedlovszky, P., Medvedev, N. N., and Mezei, M. (2004) Effect of Cholesterol on the Properties of Phospholipid Membranes. 3.
Local Lateral Structure. J. Phys. Chem. B
108, 465–472.
|
| 66. | Jedlovszky, P., Pártay, L., and Mezei, M. (2007) The structure of the zwitterionic headgroups in a DMPC bilayer as seen from
Monte Carlo simulation: Comparisons with ionic solutions. J. Mol. Liquids, 131–132, 225–234.
|
| 67. | Shinoda, W. and Okazaki, S. (1998) A Voronoi analysis of lipid area fluctuation in a bilayer. J. Chem. Phys.
109, 2199–2205.
|
| 68. | Falck, E., Patra, M., Karttunen, M., Hyvönen, M. T., and Vattulainen, I. (2004) Lessons of Slicing Membranes: Interplay of
Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers. Biophys. J.
87, 1076–1091.
|
| 69. | Jedlovszky, P., Vincze, á., and Horvai, G. (2002) New insight into the orientational order of water molecules at the water/1,2-dichloroethane
interface: a Monte Carlo simulation study. J. Chem. Phys.
117, 2271–2280.
|
| 70. | Jedlovszky, P., Vincze, á., and Horvai, G. (2004) Full description of the orientational statistics of molecules near interfaces.
Water at the interface with CCl4. Phys. Chem. Chem. Phys.
6, 1874–1879.
|
| 71. | Cantor, R. S. (1999) Lipid Composition and the Lateral Pressure Profile in Bilayers. Biophys. J.
76, 2625–2639.
|
| 72. | Marrink, S. J., Sok, R. M., and Berendsen, H. J. C. (1996). Free volume properties of a simulated lipid membrane, J. Chem. Phys.
104, 9090–9099.
|
| 73. | Okabe, A., Boots, B., Sugihara, K., and Chiu, S. N. (2000) Spatial Tessellations: Concepts and Applications of Voronoi Diagrams. John Wiley, Chichester. |
| 74. | Jedlovszky, P. and Mezei, M. (2000) Calculation of the Free Energy Profile of H2O, O2, CO, CO2, NO, and CHCl3 in a Lipid Bilayer with a Cavity Insertion Variant of the Widom Method. J. Am. Chem. Soc.
122, 5125–5131.
|
| 75. | Jedlovszky, P. and Mezei, M. (2003) Effect of Cholesterol on the Properties of Phospholipid Membranes. 2. Free Energy Profile
of Small Molecules. J. Phys. Chem. B
107, 5322–5332.
|
| 76. | Falck, E., Patra, M., Karttunen, M., Hyvönen, M. T., and Vattulainen, I. (2004) Impact of cholesterol on voids in phospholipid
membranes. J. Chem. Phys.
121, 12,676–12,689.
|
| 77. | Alinchenko, M. G., Anikeenko, A. V., Medvedev, N. N., Voloshin, V. P., Mezei, M., and Jedlovszky, P. (2004) Morphology of
Voids in Molecular Systems. A Voronoi-Delaunay Analysis of a Simulated DMPC Membrane. J. Phys. Chem. B
108, 19,056–19,067.
|
| 78. | Alinchenko, M. G., Voloshin, V. P., Medvedev, N. N., Mezei, M., Pártay, L., and Jedlovszky, P. (2005) Effect of Cholesterol
on the Properties of Phospholipid Membranes. 4. Interatomic Voids. J. Phys. Chem. B
109, 16,490–16,502.
|
| 79. | Bassolino-Klimas, D., Alper, H. E., and Stouch, T. R. (1995) Mechanism of Solute Diffusion through Lipid Bilayer Membranes
by Molecular Dynamics Simulation. J. Am. Chem. Soc.
117, 4118–4129.
|
| 80. | López-Cascales, J. J., Hernández Cifre, J. G., and GarcÍa de la Torre, J. (1998) Anaesthetic Mechanism on a Model Biological
Membrane: A Molecular Dynamics Simulations Study. J. Phys. Chem. B
102, 625–631.
|
| 81. | Söderhäll, J. A. and Laaksonen, A. (2001) Molecular Dynamics Simulation of Ubiquinone inside a Lipid Bilayer. J. Phys. Chem. B
105, 9308–9315.
|
| 82. | Duong, T. H., Mehler, E. L., and Weinstein, H. (1999) Molecular Dynamics Simulation of Membranes and a Transmembrane Helix.
J. Comp. Phys.
151, 358–387.
|
| 83. | Bandyopadhyay, S., Tarek, M., and Klein, M. L. (1999) Molecular Dynamics Study of a Lipid-DNA Complex, J. Phys. Chem. B
103, 10,075–10,080.
|
| 84. | Pandit, S. A., Vasudevan, S., Chiu, S. W., Mashl, R. J., Jakobsson, E., and Scott, H. L. (2004) Sphingomyelin-Cholesterol
Domains in Phospholipid Membranes: Atomistic Simulation. Biophys. J.
87, 1092–1100.
|
| 85. | Marrink, S. J. and Berendsen, H. J. C. (1996) Permeation Process of Small Molecules across Lipid Membranes Studied by Molecular
Dynamics Simulations. J. Phys. Chem.
100, 16,729–16,738.
|
| 86. | Shinoda, W., Mikami, M., Baba, T., and Hato, M. (2004) Molecular Dynamics Study on the Effect of Chain Branching on the Physical
Properties of Lipid Bilayers: 2. Permeability. J. Phys. Chem. B
108, 9346–9356.
|
| 87. | Widom, B. (1963) Some Topics in the Theory of Fluids. J. Chem. Phys.
39, 2808–2812.
|
Comments (Loading...) |
||
 Loading... |