Membrane-protein interactions in a generic coarse-grained model for lipid bilayers

Biophysical Journal

Volumn 96, Issue 1, 2009, Pages 101-115

  West, Beate ^a   Brown, Frank L H ^b   Schmid, Friederike ^a  

^a BIELEFELD UNIVERSITY   (Germany)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIPID BILAYER; PROTEIN;

ALGORITHM; CELL INCLUSION; CHEMICAL MODEL; CHEMICAL PHENOMENA; CHEMISTRY; COMPUTER SIMULATION; ELASTICITY; FOURIER ANALYSIS; LIPID BILAYER; METABOLISM; MONTE CARLO METHOD; SURFACE TENSION;

ALGORITHMS; COMPUTER SIMULATION; ELASTICITY; FOURIER ANALYSIS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; INCLUSION BODIES; LIPID BILAYERS; MODELS, CHEMICAL; MONTE CARLO METHOD; PROTEINS; SURFACE TENSION;

EID: 58849140540     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.138677     Document Type: Article

References (84)

1. Gennis, R. B. 1989. Biomembranes - Molecular Structure and Function. Springer Verlag, New York.
2. Rasband, M. N., and J. S. Trimmer. 2001. Developmental clustering of ion channels at and near the node of Ranvier. Dev. Biol. 236:5-16.
3. Elliott, J., D. Needham, J. Dilger, and D. Haydon. 1983. The effects of bilayer thickness and tension on gramicidin single-channel lifetimes. Biochim. Biophys. Acta. 735:95-103.
4. Botelho, A. V., T. Huber, T. P. Sakmar, and M. F. Brown. 2006. Curvature and hydrophobic forces drive oligomerization and modulate activity of rhodopsin in membranes. Biophys. J. 91:4464 - 4477.
5. Mouritsen, O. G., and M. Bloom. 1993. Models of lipid-protein interactions in membranes. Annu. Rev. Biophys. Biomol. Struct. 22:145 - 171.
6. Gil, T., J. H. Ipsen, O. G. Mouritsen, M. C. Sabra, M. M. Sperotto, et al. 1998. Theoretical analysis of protein organization in lipid membranes. Biochim. Biophys. Acta. Rev. Biomembr. 1376:245 - 266.
7. Sperotto, M. M., S. May, and A. Baumgärtner. 2006. Modeling of proteins in membranes. Chem. Phys. Lipids. 141: - 29.
8. Edidin, M. 2003. The state of lipid rafts: from model membranes to cells. Annu. Rev. Biophys. Biomol. Struct. 32:257 - 283.
9. Bloom, M., E. Evans, and O. G. Mouritsen. 1991. Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective. Q. Rev. Biophys. 24:293 - 397.
10. Killian, J. A. 1998. Hydrophobic mismatch between proteins and lipids in membranes. Biochim. Biophys. Acta Rev. Biomembr. 1376:401 - 416.
11. Dumas, F., M. C. Lebrun, and J. F. Tocanne. 1999. Is the protein/lipid hydrophobic matching principle relevant to membrane organization and functions? FEBS Lett. 458:271 - 277.
12. Harroun, T. A., W. T. Heller, T. M. Weiss, L. Yang, and H. W. Huang. 1999. Experimental evidence for hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin. Biophys. J. 76:937-945.
13. Sharpe, S., K. R. Barber, C. W. M. Grant, D. Goodyear, and M. R. Marrow. 2002. Organization of model helical peptides in lipid bilayers:
14. insight into the behavior of single-span protein transmembrane domains. Biophys. J. 83:345-358.
15. De Planque, M. R. R., and J. A. Killian. 2003. Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Review. Mol. Membr. Biol. 20:271-284.
16. Owicki, J. C., M. W. Springgate, and H. M. McConnell. 1978. Theoretical study of protein-lipid interactions in bilayer membranes. Proc. Natl. Acad. Sci. USA. 75:1616-1619.
17. Owicki, J. C., and H. M. McConnell. 1979. Theory of protein-lipid and protein-protein interactions in bilayer membranes. Proc. Natl. Acad. Sci. USA. 76:4750-4754.
18. Jensen, M. O., and O. G. Mouritsen. 2004. Lipids do influence protein function - the hydrophobic matching hypothesis revisited. Biochim. Biophys. Acta. 1666:205-226.
19. Mouritsen, O. G., and M. Bloom. 1984. Mattress model of lipid-protein interactions in membranes. Biophys. J. 36:141-153.
20. Fattal, D. R., and A. Ben-Shaul. 1993. A molecular model for lipid-protein interaction in membranes: the role of hydrophobic mismatch. Biophys. J. 65:1795-1809.
21. Fattal, D. R., and A. Ben-Shaul. 1995. Lipid chain packing and lipid-protein interaction in membranes. Physica A. 220:192-216.
22. Kralchevski, P. A., V. N. Paunov, N. D. Denkov, and K. Nagayama. 1995. Stresses in lipid membranes and interactions between inclusions. Faraday Trans. 91:3415-3432.
23. Bohinc, K., V. Kralj-Iglic, and S. May. 2003. Interaction between two cylindrical inclusions in a symmetric lipid bilayer. J. Chem. Phys. 119:7435-7444.
24. Huang, H. W. 1986. Deformation free energy of bilayer membrane and its effect on gramicidin channel lifetime. Biophys. J. 50:1061-1070.
25. Huang, H. W. 1995. Elasticity of lipid bilayer interacting with amphophilic helical peptides. J. Physique II Fr. 5:1427-1431.
26. Harroun, T. A., W. T. Heller, T. M. Weiss, L. Yang, and H. W. Huang. 1999. Theoretical analysis of hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin. Biophys. J. 76:3176-3185.
27. Nielsen, C., M. Goulian, and O. S. Andersen. 2000. Energetics of inclusion-induced bilayer deformations. Biophys. J. 74:1966-1983.
28. Nielsen, C., and O. S. Andersen. 2000. Inclusion-induced bilayer deformations: effects of monolayer equilibrium curvature. Biophys. J. 79:2583-2604.
29. Dan, N., P. Pincus, and S. A. Safran. 1993. Membrane induced interactions between inclusions. Langmuir. 9:2768-2771.
30. Dan, N., A. Berman, P. Pincus, and S. A. Safran. 1994. Membrane induced interactions between inclusions. Journal de Physique II.Fr. 4:1713-1725.
31. Aranda-Espinoza, H., A. Berman, N. Dan, P. Pincus, and S. Safran. 1996. Interaction between inclusions embedded in membranes. Biophys.J. 71:648-656.
32. Brannigan, G., and F. L. H. Brown. 2006. A consistent model for thermal fluctuations and protein-induced deformations in lipid bilayer. Biophys. J. 90:1501-1520.
33. Brannigan, G., and F. L. H. Brown. 2007. Contributions of Gaussian curvature and nonconstant lipid volume to protein deformations of lipid bilayers. Biophys. J. 92:864-876.
34. van Duyl, B. Y., D. T. S. Rijkers, B. De Kruijff, and J. A. Killian. 2002. Influence of hydrophobic mismatch and palmitoylation on the association of transmembrane α-helical peptides with detergent-resistant membranes. FEBS Lett. 523:79-84.
35. De Planque, M. R. R., B. B. Bonev, J. A. A. Demmers, D. V. Greathouse, R. E. Koeppe, et al. 2003. Interfacial anchor properties of tryptophan residues in transmembrane peptides dominate over hydrophobic matching effects in peptide-lipid interactions. Biochemistry. 42:5341-5348.
36. Ben-Shaul, A., N. Ben-Tal, and B. Honig. 1996. Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes. Biophys. J. 71:130-137.
37. Lagüe, P., M. J. Zuckermann, and B. Roux. 1998. Protein inclusion in lipid membranes: a theory based on the hypernetted chain integral equation. Faraday Discuss. 111:165-172.
38. Lagüe, P., M. J. Zuckermann, and B. Roux. 2000. Lipid-mediated interactions between intrinsic membrane proteins: a theoretical study based on integral equations. Biophys. J. 79:2867-2879.
39. Lagüe, P., M. J. Zuckermann, and B. Roux. 2001. Lipid-mediated interactions between intrinsic membrane proteins: dependence on protein size and lipid composition. Biophys. J. 81:276-284.
40. May, S., and A. Ben-Shaul. 2000. A molecular model for lipid-mediated interaction between proteins in membranes. Phys. Chem. Chem. Phys. 2:4494-4502.
41. Natali, F., A. Relini, A. Gliozzi, R. Rolandi, P. Cavatorta, et al. 2003. Protein-membrane interaction: effect of myelin basic protein on the dynamics of oriented lipids. Chem. Phys. 292:455-464.
42. Kota, Z., T. Pali, and D. Marsh. 2004. Orientation and lipid-peptide interactions of gramicidin a in lipid membranes: polarized attenuated total reflection infrared spectroscopy and spin-label electron spin resonance. Biophys. J. 86:1521-1531.
43. May, S. 2000. Theories on structural perturbations of lipid bilayers. Curr. Opin. Colloid Interface Sci. 5:244-249.
44. Goulian, M., R. Bruinsma, and P. Pincus. 1993. Long-range forces in heterogeneous fluid membranes. Europhys. Lett. 22:145-150.
45. Netz, R. R., and P. Pincus. 1995. Inhomogeneous fluid membranes - segregation, ordering and effective rigidity. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 52:4114-4128.
46. Golestanian, R., M. Goulian, and M. Kardar. 1996. Fluctuation-induced interactions between rods on membranes and interfaces. Europhys. Lett. 33:241-245.
47. Weikl, T. R. 2001. Fluctuation-induced aggregation of rigid membrane inclusions. Europhys. Lett. 54:547.
48. Reynwar, B. J., G. Illya, V. A. Harmandaris, M. M. Müller, K. Kremer, et al. 2007. Aggregation and vesiculation of membrane proteins by curvature-mediated interactions. Nature. 447:461-464.
49. Fournier, J.-B. 1999. Microscopic membrane elasticity and interactions among membrane inclusions: interplay between the shape, dilation, tilt and tilt-difference modes. Eur. Phys. J. B. 11:261-272.
50. Lenz, O., and F. Schmid. 2007. Structure of symmetric and asymmetric ripple phases in lipid bilayers. Phys. Rev. Lett. 98:058104.
51. Efremov, R. G., D. E. Nolde, A. G. Konshina, N. P. Syrtcev, and A. S. Arseniev. 2004. Peptides and proteins in membranes: what can we learn via computer simulations? Curr. Med. Chem. 11:2421-2442.
52. de Meyer, F., M. Venturoli, and B. Smit. 2008. Molecular simulations of lipid mediated protein-protein interactions. Biophys. J. 95:1851-1865.
53. Sintes, T., and A. Baumgärtner. 1997. Protein attraction in membranes induced by lipid fluctuations. Biophys. J. 73:2251-2259.
54. Smeijers, A. F., K. Pieterse, A. J. Markvoort, and P. A. J. Hilbers. 2006. Coarse-grained transmembrane proteins: hydrophobic matching, aggregation, and their effect on fusion. J. Phys. Chem. B. 110:13614-13623.
55. Marrink, S. J., H. J. Risselada, S. Yefimov, D. P. Tielemann, and A. H. de Vries. 2007. The MARTINI force field: coarse-grained model for biomolecular simulations. J. Phys. Chem. B. 111:7812-7823.
56. Schmid, F., D. Düchs, O. Lenz, and B. West. 2007. A generic model for lipid monolayers, bilayers, and membranes. Comput. Phys. Commun. 177:168-171.
57. Stadler, C., H. Lange, and F. Schmid. 1999. Short grafted chains: Monte Carlo simulations of a model for monolayers of amphiphiles. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 59:4248-4257.
58. Düchs, D., and F. Schmid. 2001. Phase behavior of amphiphilic mono-layers: theory and simulations. J. Phys. Condens. Matter. 13:4853-4862.
59. Lenz, O., and F. Schmid. 2005. A simple computer model for liquid lipid bilayers. J. Mol. Liq. 117:147-152.
60. Lenz, O. 2007. Computer simulations of lipid bilayers. Dissertation, Universität Bielefeld, Germany.
61. Sperotto, M. M., and O. G. Mouritsen. 1991. Monte Carlo simulation of lipid order parameter profiles near integral membrane proteins. Biophys. J. 59:261 - 270.
62. Venturoli, M., B. Smit, and M. M. Sperotto. 2005. Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins. Biophys.J. 88:1778-1798.
63. Venturoli, M. 2004. Mesoscopic models of lipid bilayers and bilayers with embedded proteins. PhD thesis, University of Amsterdam, The Netherlands.
64. Helfrich, P., and E. Jakobsson. 1990. Calculation of deformation energies and conformations in lipid membranes containing gramicidin channels. Biophys. J. 57:1075-1084.
65. Reference deleted in proof.
66. Reference deleted in proof.
67. Fournier, J.-B. 1998. Coupling between membrane tilt-difference and dilation: a new "ripple" instability and multiple crystalline inclusions phases. Europhys. Lett. 43:725-730.
68. Fošnariè, M., A. Igliè, and S. May. 2006. Influence of rigid inclusions on the bending elasticity of a lipid membrane. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 74:051503.
69. Harries, D., and A. Ben-Shaul. 1997. Conformational chain statistics in a model lipid bilayer: comparison between mean field and Monte Carlo calculations. J. Chem. Phys. 106:1609-1619.
70. Goetz, R., G. Gompper, and R. Lipowsky. 1999. Mobility and elasticity of self-assembled membranes. Phys. Rev. Lett. 82:221-224.
71. Lindahl, E., and O. Edholm. 2000. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys. J. 79:426-433.
72. Marrink, S. J., and A. E. Mark. 2001. Effect of undulations on surface tension in simulated bilayers. J. Phys. Chem. B. 105:6122-6127.
73. Loison, C., M. Mareschal, K. Kremer, and F. Schmid. 2003. Thermal fluctuations in a lamellar phase of a binary amphiphile-solvent mixture: a molecular-dynamics study. J. Chem. Phys. 119:13138-13148.
74. Safran, S. A. 1994. Statistical Thermodynamics of Surfaces, Interfaces, and Membranes. Perseus Books, Cambridge, MA.
75. Irving, J. H., and J. G. Kirkwood. 1950. The statistical mechanical theory of transport processes. IV. The equations of hydrodynamics. J. Chem. Phys. 18:817-829.
76. Goetz, R., and R. Lipowsky. 1998. Computer simulations of bilayer membranes: self-assembly and interfacial tension. J. Chem. Phys. 108:7397-7409.
77. Lindahl, E., and O. Edholm. 2000b. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. J. Chem. Phys. 113:3882-3893.
78. Reference deleted in proof.
79. Reference deleted in proof.
80. Marsh, D. 2006. Elastic curvature constants of lipid monolayers and bilayers. Chem. Phys. Lipids. 144:146-159.
81. Cordomi, A., and J. J. Perez. 2007. Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers. J. Phys. Chem. B. 111:7052-7063.
82. Kranenburg, M., M. Venturoli, and B. Smit. 2003. Phase behavior and induced interdigitation in bilayers studied with dissipative particle dynamics. J. Phys. Chem. B. 107:11491-11501.
83. Reference deleted in proof.
84. Schmid, F., and M. Schick. 1995. Liquid phases of Langmuir mono-layers. J. Chem. Phys. 102:2080-2091.