Molecular Simulations Suggest Protein Salt Bridges Are Uniquely Suited to Life at High Temperatures

Journal of the American Chemical Society

Volumn 126, Issue 7, 2004, Pages 2208-2214

  Thomas, Andrew S ^a   Elcock, Adrian H ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ASSOCIATION REACTIONS; COMPUTER SIMULATION; DISSOCIATION; HIGH TEMPERATURE EFFECTS; HYDROPHOBICITY; MOLECULAR DYNAMICS; RAPID PROTOTYPING;

POLAR CONTACTS; SALT BRIDGES;

PROTEINS;

AMINO ACID; INORGANIC SALT; PROTEIN;

ARTICLE; ATOM; DISSOCIATION; ENTROPY; FORCE; HIGH TEMPERATURE; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; POLARIZATION; PROTEIN CONFORMATION; PROTEIN STABILITY; RIGIDITY; SIMULATION; TEMPERATURE DEPENDENCE; THERMODYNAMICS;

COMPUTER SIMULATION; GLUTAMIC ACID; HEAT; HYDROPHOBICITY; LYSINE; MODELS, MOLECULAR; PROTEINS; SALTS; THERMODYNAMICS;

EID: 1242319481     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja039159c     Document Type: Article

References (49)

1. Yip, K. S. P.; Stillman, T. J.; Britton, K. L.; Artymiuk, P. J.; Baker, P. J.; Sedelnikova, S. E.; Engel, P. C.; Pasquo, A.; Chiaraluce, R.; Consalvi, V.; Scandurra, R.; Rice, D. W. Structure 1995, 3, 1147-1158.
2. Hennig, M.; Darimont, B.; Sterner, R.; Kirschner, K.; Jansonius, J. N. Science 1995, 3, 1295-1306.
3. Chan, M. K.; Mukund, S.; Kletzin, A.; Adams, M. W. W.; Rees, D. C. Science 1995, 267, 1463-1469.
4. Thompson, M. J.; Eisenberg, D. J. Mol. Biol. 1999, 290, 595-604.
5. Vogt, G.; Woell, S.; Argos, P. J. Mol. Biol. 1997, 269, 631-643.
6. England, J. L.; Shakhnovich, B. E.; Shakhnovich, E. I. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 8727-8731.
7. Perutz, M. F. Science 1978, 201, 1187-1191.
8. Fersht, A. R. J. Mol. Biol. 1972, 64, 497-509,
9. Szilágyi, A.; Závodszky, P. Structure 2000, 8, 493-504.
10. Kumar, S.; Nussinov, R. Cell. Mol. Life Sci. 2001, 58, 1216-1233.
11. Karshikoff, A.; Ladenstein, R. Trends Biochem. Sci. 2001, 26, 550-556.
12. Spassov, V. Z.; Karshikoff, A. D.; Ladenstein, R. Protein Sci. 1995, 4, 1516-1527.
13. Xiao, L.; Honig, B. J. Mol. Biol. 1999, 289, 1435-1444.
14. Dominy, B. N.; Perl, D.; Schmid, F. X.; Broks, C. L., III J. Mol. Biol. 2002, 319, 541-554.
15. Cambillau, C.; Claverie, J. M. J. Biol. Chem. 2000, 275, 32 383-32 386.
16. Strop, P.; Mayo, S. L. Biochemistry 2000, 39, 1251-1255.
17. Takano, K.; Tsuchimori, K.; Yamagata, Y.; Yutani, K. Biochemistry 2000, 39, 12375-12381.
18. Makhatadze, G. I.; Loladze, V. V.; Ermolenko, D. N.; Chen, X.; Thomas. S. T. J. Mol. Biol. 2003, 27, 1135-1148.
19. Hendsch, Z. X.; Tidor, B. Protein Sci. 1994, 3, 211-226.
20. Kumar, S.; Nussinov, R. J. Mol. Biol. 1999, 29, 1241-1255.
21. Kumar, S.; Ma, B.; Tsai, C.-J.; Nussinov, R. Proteins 2000. 38, 368-383.
22. Lounnas, V.; Wade, R. C. Biochemistry 1997, 6, 5402-5417.
23. Luo, R.; David, L.; Hung, H.; Devaney, J.; Gilson, M. K. J. Phys. Chem. B 1999, 103, 727-736.
24. Elcock, A. H. J. Mol. Biol. 1998, 284, 489-502.
25. Elcock, A. H.; McCammon, J. A. I. Phys. Chem. B 1997, 101, 9624-9634.
26. Zhong R.; Berne. B. J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12 777-12 782.
27. de Bakker, P. I. W.; Hünenberger, P. H.; McCammon, J. A. J. Mol. Biol. 1999, 285, 1811-1830.
28. Masunov, A.; Lazaridis, T. J. Am. Chem. Soc. 2003, 125, 1722-1730.
29. Yang, H.; Elcock, A. H. J. Am. Chem. Soc. 2003, 125, 13 968-13 969.
30. Zhang, Y.; McCammon, J. A. J. Chem. Phys. 2003, 118. 1821-1827.
31. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Interaction Models for Water in Relalion to Protein Hydration: Pullman. B., Ed.; Reidel Publishing Company: Dordrecht. The Netherlands. 1981: p 331.
32. Nosé, S. J. Chem. Phys. 1984, 81, 511-519.
33. Hoover, W. G. Phys. Rev. A 1985, 31, 1695-1697.
34. Parrinello, M.; Rahman, A. J. Appl. Phys. 1981, 52, 7182-7190.
35. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952-962.
36. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fnmije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463-1472.
37. Essman, U.; Perela, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedemen, L. G. J. Chem. Phys. 1995, 103, 8577-8592.
38. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Mod. 2001, 7, 306-317.
39. Dang, L. X.; Pettitt, B. M. J. Phys. Chem. 1990, 94, 4303-4308.
40. Del Buono, G. S.; Figueirido, F. E.; Levy, R. M. Chem. Phys. Lett. 1996, 263, 521-529.
41. Lide, D. R. CRC Handbook of Chemistry and Physics, 83rd ed.; CRC Press Inc.; Boca Raton, FL, 2003.
42. Lüdemann, S.; Schreiber, H.; Abseher, R.; Steinhauser, O. J. Chem. Phys 1996, 104, 286-295.
43. Shimizu, S.; Chan, H. S. J. Chem. Phys. 2000, 113, 4683-4700.
44. Southall, N. T.; Dill, K. A. Biophys. Chem. 2002, 101, 295-307.
45. Sanchez-Ruiz, J. M.; Makhaladze, G. I. Trends Biotech. 2001, 19, 132-135.
46. Mahoney, W. M.; Jorgensen, W. L. J. Chem. Phys. 2000, 112, 8910-8922.
47. Jorgensen, W. L.; Jensen, C. J. Comput. Chem. 1998, 19, 1179-1186.
48. Hünenberger, P. H.; McCammon, J. A. J. Chem. Phys. 1999, 110, 1856-1872.
49. Weber, W.; Hünenberger, P. H.; McCammon, J. A. J. Phys. Chem. B 2000, 104, 3668-3675.