Prediction of membrane protein structures by replica-exchange Monte Carlo simulations: Case of two helices

Journal of Chemical Physics

Volumn 120, Issue 22, 2004, Pages 10837-10847

  Kokubo, Hironori ^a   Okamoto, Yuko ^a,b  

^a GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^b INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; AMINO ACIDS; APPROXIMATION THEORY; BIOLOGICAL MEMBRANES; COMPUTER SIMULATION; DIMERS; ELECTROSTATICS; LIPIDS; MOLECULAR STRUCTURE; MONTE CARLO METHODS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; TORSIONAL STRESS; VAN DER WAALS FORCES;

HELIX-HELIX INTERACTIONS; PROTEIN STRUCTURES; TRANSMEMBRANE HELICES;

PROTEINS;

EID: 2942692122     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1712942     Document Type: Article

References (37)

1. A. Krogh, B. Larsson, G. v. Heijne, and E. L. L. Sonnhammer, J. Mol. Biol. 305, 567 (2001).
2. S. Mitaku, Biophysics (Engl. Transl.) 42, 104 (2002) (in Japanese).
3. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, Nucleic Acids Res. 28, 235 (2000).
4. W. R. Taylor, D. T. Jones, and N. M. Green, Proteins 18, 281 (1994).
5. M. Suwa, T. Hirokawa, and S. Mitaku, Proteins 22, 363 (1995).
6. P. D. Adams, D. M. Engelman, and A. T. Brünger, Proteins 26, 257 (1996).
7. R. V. Pappu, G. R. Marshall, and J. W. Ponder, Nat. Struct. Biol. 6, 50 (1999).
8. T. Hirokawa, J. Uechi, H. Sasamoto, M. Suwa, and S. Mitaku, Protein Eng. 13, 771 (2000).
9. N. Vaidehi, W. B. Floriano, R. Trabanino, S. E. Hall, P. Freddolino, E. J. Choi, G. Zamanakos, and W. A. Goddard III, Proc. Natl. Acad. Sci. U.S.A. 99, 12622 (2002).
10. J. L. Popot and D. M. Engelman, Annu. Rev. Biochem. 69, 881 (2000).
11. M. J. Liao, E. London, and H. G. Khorana, J. Biol. Chem. 258, 9949 (1983).
12. D. M. Engelman, B. D. Adair, J. F. Hunt, T. W. Kahn, and J. L. Popot, Curr. Topics Membr. Transport 36, 71 (1990).
13. P. Argos, J. K. Rao, and P. A. Hargrave, Eur. J. Biochem. 128, 565 (1982).
14. D. Eisenberg, R. M. Weiss, T. C. Terwilliger, and W. Wilcox, Faraday Symp. Chem. Soc. 17, 109 (1982).
15. K. Nakai and M. Kanehisa, Genomics 14, 897 (1992).
16. D. T. Jones, W. R. Taylor, and J. M. Thornton, Biochemistry 33, 3038 (1994).
17. B. Rost, R. Casadio, P. Fariselli, and C. Sander, Protein Sci. 4, 521 (1995).
18. T. Hirokawa, S. Boon-Chieng, and S. Mitaku, Bioinformatics 14, 378 (1998).
19. G. E. Tusnady and I. Simon, J. Mol. Biol. 283, 489 (1998).
20. U. H. E. Hansmann and Y. Okamoto, in Annual Reviews of Computational Physics VI, edited by D. Stauffer (World Scientific, Singapore, 1999), p. 129.
21. A. Mitsutake, Y. Sugita, and Y. Okamoto, Biopolymers (Pept. Sci.) 60, 96 (2001).
22. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996).
23. K. Hukushima, H. Takayama, and K. Nemoto, Int. J. Mod. Phys. C 7, 337 (1996).
24. C. J. Geyer, in Proceedings of the 23rd Symposium on the Interface, edited by E. Keramidas (Interface Foundation, Fairfax Station, 1991), p. 156.
25. E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo, in Spin Glasses and Ran-dom Fields, edited by A. P. Young (World Scientific, Singapore, 1998), p. 59.
26. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
27. S. Kumar, D. Bouzida, R. H. Swendesen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992).
28. H. Kokubo and Y. Okamoto, Chem. Phys. Lett. 383, 397 (2004).
29. W. Im, M. Feig, and C. L. Brooks III, Biophys. J. 85, 2900 (2003).
30. W. E. Reiher III, "Theoretical studies of hydrogen bonding," Ph.D. thesis, Department of Chemistry, Harvard University Cambridge, MA, 1985.
31. E. Neria, S. Fischer, and M. Karplus, J. Chem. Phys. 105, 1902 (1996).
32. A. Mitsutake, Y. Sugita, and Y. Okamoto, J. Chem. Phys. 118, 6664 (2003).
33. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
34. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
35. K. R. MacKenzie, J. H. Prestegard, and D. M. Engelman, Science 276, 131 (1997).
36. S. O. Smith, D. Song, S. Shekar, M. Groesbeek, M. Zilioz, and S. Aimoto, Biochemistry 40, 6553 (2001).
37. H. Kokubo and Y. Okamoto, Chem. Phys. Lett, (in press).