Modelling and simulation of light-activated membrane proteins: Dynamical transitions in bacteriorhodopsin

Abstract

Many of the functions of membranes are carried out by proteins associated with them. A knowledge of atomic-detail membrane protein structures and dynamics is required for a full understanding of these functions. We briefly discuss recent progress in this field using modelling and simulation. One of the best characterised membrane proteins, bacteriorhodopsin, undergoes dynamical transitions with temperature. Here we present preliminary results of molecular dynamics simulation of this protein as a function of temperature, indicating the presence of dynamical transitions at approximately the temperatures seen experimentally.

References

1. J. Deisenhofer, O. Epp, K. Miki, R. Huber and H. Michel, Nature (London), 1985, 318, 618.
2. R. Henderson, J. M. Baldwin, T. A. Caska., F. Zemlin, E. Beckmann and K. H. Downing, J. Mol. Biol., 1990, 213, 899.
3. E. Pebay-Peyrouola, G. Rummel, J. P. Rosenbusch and E. M. Landau, Science, 1997, 277, 1676.
4. Y. Kimura, D. G. Vassylyev, A. Miyazawa, A. Kidera, M. Matsushima, K. Mitsuoka, K. Murata, T. Hirai and Y. Fujiyoshi, Nature (London), 1997, 389, 206.
5. N. Foloppe, M. Ferrand, J. Breton and J. C. Smith, Proteins: Structure, Function Genetics, 1995, 22(3), 226.
6. J. Breton, E. J. Bylina and D. C. Youvan, Biochemistry, 1989, 28, 6423.
7. T. Mattioli, personal communication.
8. M. H. Vos, F. Rappaport, J. C. Lambry, J. Breton and J. L. Martin, Nature (London), 1993, 363, 320.
9. S. J. Robles, J. Breton and D. C. Youvan, Science, 1990, 248, 1402.
10. N. Foloppe, M. Ferrand and J. C. Smith, Chem. Phys. Lett., 1995, 242, 238.
11. B. Svensson, C. Etchebest, P. Tuffery, P. van Kan, J. C. Smith and S. Styring, Biochemistry, 1996, 35, 14486.
12. D. Oesterhelt and W. Stoeckenius, Nature (London), New Biol., 1971, 233, 149.
13. K. J. Rothschild, P. V. Argade, T. N. Earnest, K.-S. Huang, E. London, M.-J. Liao, H. Bayley, H. G. Khorana and J. Herzfeld, J. Biol. Chem., 1982, 257, 8592.
14. R. A. Mathies, S. W. Lin, J. B. Ames and W. T. Pollard, Annu. Rev. Biophys. Biophys. Chem., 1991, 20, 491.
15. T. Mogi, L. J. Stern, N. R. Hackett and H. G. Khorana, Proc. Natl. Acad. Sci. USA, 1987, 85, 5595.
16. T. Mogi, L. J. Stern, T. Marti, B. H. Chao and H. G. Khorana, Proc. Natl. Acad. Sci. USA, 1988, 84, 5595.
17. L. J. Stern and H. G. Khorana, J. Biol. Chem., 1989, 264, 14202.
18. T. Marti, H. Otto, T. Mogi, S. J. Rösselet, M. P. Heyn and H. G. Khorana, J. Biol. Chem., 1991, 266, 6919.
19. G. Papadopoulos, N. Dencher, G. Zaccaï and G. Büldt, J. Mol. Biol., 1990, 214, 15.
20. P. Hildebrandt and M. Stockburger, Biochemistry, 1984, 23, 5539.
21. H. J. M. De Groot, S. O. Smith, J. Courtin, E. van der Berg, C. Winkel, J. Lugtenburg, R. G. Griffin and J. Herzfeld, Biochemistry, 1990, 29, 6873.
22. G. S. Harbison, J. E. Roberts, J. Herzfeld and R. G. Griffin, J. Am. Chem. Soc., 1988, 110, 7221.
23. H. Deng, L. Huang, R. Callender and T. Ebrey, Biophys. J., 1994, 66, 1129.
24. M. Nina, B. Roux and J. C. Smith, in Structures and Functions of Retinal Proteins, ed. J. L. Rigaud, Colloque INSERM/John Libbey Eurotext Ltd., 1992, vol. 221, pp. 17–20.
25. M. Nina, J. C. Smith and B. Roux, J. Mol. Struc. (THEOCHEM), 1993, 286, 231.
26. B. Roux, M. Nina, R. Pomes and J. C. Smith, Biophys. J., 1996, 670.
27. J. Baudry, S. Crouzy, B. Roux and J. C. Smith, J. Chem. Inf. Comp. Sci., 1997, 37(6), 1018.
28. M. Ferrand, G. Zaccaï, M. Nina, J. C. Smith, C. Etchebest and B. Roux, FEBS Lett., 1993, 327, 256.
29. W. Humphrey, I. Logunov, K. Schulten and M. Sheves, Biochemistry, 1994, 33, 3668.
30. W. Humphrey, E. Bamberg and K. Schulten, Biophys. J., 1997, 72(3), 1347.
31. I. Logunov and K. Schulten, J. Am. Chem. Soc., 1996, 118(40), 9727.
32. D. Xu, C. Martin and K. Schulten, Biophys. J., 1996, 70(1), 453.
33. D. Xu, M. Sheves and K. Schulten, Biophys. J., 1995, 69(6), 2745.
34. M. Ferrand, A. J. Dianoux, W. Petry and G. Zaccai, Proc. Natl. Acad. Sci. USA, 1993, 90, 9668.
35. V. Réat, H. Patzelt, M. Ferrand, C. Pfister, D. Oesterhelt and G. Zaccai, Proc. Natl. Acad. Sci. USA, 1998, 95, 4970.
36. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus., J. Comput. Chem., 1983, 4, 187.
37. A. D. MacKerell, Jr., D. Bashford, M. Bellot, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin and M. Karplus, J. Phys. Chem. B, 1998, 102, 3586.
38. M. Bée, Quasi Elastic Neutron Scattering: Principles and Applications in Solid State Chemistry, Biology and Materials Science, Adam Hilger, Bristol, 1998, UK.
39. A. Rahman, K. Singwi and A. Sjölander, Phys. Rev., 1962, 126(3), 986.
40. A. Rahman, Phys. Rev., 1963, 140(4), 1334.
41. V. Réat, G. Zaccai, M. Ferrand and C. Pfister, in Biological Macromolecular Dynamics. Proceedings of a Workshop on Inelastic and Quasielastic Neutron Scattering in Biology, ed. S. Cusack, H Büttner, M. Ferrand, P. Langan and P. Timmins, Adenine Pres, New York, 1996, p. 117.