Hamiltonian replica exchange method study of Escherichia coli and Yersinia pestis HPPK

Journal of Physical Chemistry B

Volumn 113, Issue 50, 2009, Pages 16197-16208

  Su, Li ^a   Cukier, Robert I ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIMICROBIAL AGENTS; CRYSTAL STRUCTURE; ESCHERICHIA COLI; MOLECULAR DYNAMICS; REACTION KINETICS;

BINDING POCKETS; BIOSYNTHETIC PATHWAY; CLUSTERING CRITERIA; CONFORMATIONAL SAMPLINGS; HAMILTONIAN REPLICA EXCHANGE METHODS; POTENTIAL TARGETS; ROOT MEAN SQUARE; SELECTIVE INHIBITORS;

HAMILTONIANS;

EID: 73449096452     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp903861a     Document Type: Article

References (50)

1. Berg, B. A.; Neuhaus, T. Phys. Lett. B 1991, 267, 249.
2. Hansmann, U. H. E.; Okamoto, Y.; Eisenmenger, F. Chem. Phys. Lett. 1996, 259, 321.
3. Lyubartsev, A. P.; Martsinovski, A. A.; Shevkunov, S. V.; Vorontsov-Velyaminov, P. N. J. Chem. Phys. 1992, 96, 1776.
4. Lyubartsev, A.; Laaksonen, A. Appl. Paralled Comput. 1998, 1541, 296.
5. Swendsen, R. H.; Wang, J. S. Phys. Rev. Lett. 1986, 57, 2607.
6. Geyer, C. J. Markov Chain Monte Carlo Maximum Likelihood. In Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface; Keramidas, E. M., Ed.; Interface Foundation: Fairfax Station, 1991.
7. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141.
8. Hansmann, U. H. E. Chem. Phys. Lett. 1997, 281, 140.
9. Wang, J. S.; Swendsen, R. H. Prog. Theor. Phys. Suppl. 2005, 317.
10. Hukushima, K.; Nemoto, K. J. Phys. Soc. Jpn. 1996, 65, 1604.
11. Lei, H. X.; Duan, Y. Curr. Opin. Struct. Biol. 2007, 17, 187.
12. Fukunishi, H.; Watanabe, O.; Takada, S. J. Chem. Phys. 2002, 116, 9058.
13. Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to Applications; Academic: San Diego, 1996.
14. Predescu, C.; Predescu, M.; Ciobanu, C. V. J. Phys. Chem. B 2005, 109, 4189.
15. Su, L.; Cukier, R. I. J. Phys. Chem. B 2007, 111, 12310.
16. Kumar, S.; Ma, B. Y.; Tsai, C. J.; Sinha, N.; Nussinov, R. Protein Sci. 2000, 9, 10.
17. James, L. C.; Tawfik, D. S. Trends Biochem. Sci. 2003, 28, 361.
18. Goh, C. S.; Milburn, D.; Gerstein, M. Curr. Opin. Struct. Biol. 2004, 14, 104.
19. Bahar, I.; Chennubhotla, C.; Tobi, D. Curr. Opin. Struct. Biol. 2007, 17, 633.
20. Tsai, C. J.; Ma, B. Y.; Nussinov, R. Proc. Natl. Acad. Sci. USA. 1999, 96, 9970.
21. Ma, B. Y.; Kumar, S.; Tsai, C. J.; Nussinov, R. Protein Eng. 1999, 12, 713.
22. Bosshard, H. R. News Physiol. Sci. 2001, 16, 171.
23. Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Proteins: Struct. Funct. Genet. 1995, 21, 167.
24. Dill, K. A.; Chan, H. S. Nat. Struct. Biol. 1997, 4, 10.
25. Taniuchi, H.; Anfinsen, C. B. J. Biol. Chem. 1966, 241, 4366.
26. Markley, J. L.; Williams, M. N.; Jardetzky, O. Proc. Natl. Acad. Sci. USA. 1970, 65, 645.
27. Chazin, W. J.; Kordel, J.; Drakenberg, T.; Thulin, E.; Brodin, P.; Grundstrom, T.; Forsen, S. Proc. Natl. Acad. Sci. USA. 1989, 86, 2195.
28. Han, Y.; Li, X.; Pan, X. M. FEBS Lett. 2002, 528, 161.
29. Zhang, H. J.; Sheng, X. R.; Niu, W. D.; Pan, X. M.; Zhou, J. M. J. Biol. Chem. 1998, 273, 7448.
30. Lou, H. F.; Cukier, R. I. J. Phys. Chem. B 2006, 110, 24121.
31. Henzler-Wildman, K. A.; Thai, V.; Lei, M.; Ott, M.; Wolf-Watz, M.; Fenn, T.; Pozharski, E.; Wilson, M. A.; Petsko, G. A.; Karplus, M.; Hubner, C. G.; Kern, D. Nature 2007, 450, 838.
32. Cukier, R. I. J. Phys. Chem. B 2009, 113, 1662.
33. Wilson, M. A.; Brunger, A. T. J. Mol. Biol. 2000, 301, 1237.
34. Lange, O. F.; Lakomek, N. A.; Fares, C.; Schroder, G. F.; Walter, K. F. A.; Becker, S.; Meiler, J.; Grubmuller, H.; Griesinger, C.; de Groot, B. L. Science 2008, 320, 1471.
35. Boehr, D. D.; Wright, P. E. Science 2008, 320, 1429.
36. Blakley, R. L., Benkovic, S. J. Chemistry and Biochemistry of Folates; John Wiley & Sons, Inc.: New York, 1984; Vol.1.
37. Walsh, C. Enzymatic Reaction Mechanisms; W. H. Freeman: San Francisco, 1979.
38. Blaszczyk, J.; Shi, G.; Yan, H.; Ji, X. Structure 2000, 8, 1049.
39. Blaszczyk, J.; Li, Y.; Cherry, S.; Alexandratos, J.; Wu, Y.; Shaw, G.; Tropea, J. E.; Waugh, D. S.; Yan, H. G.; Ji, X. H. Acta Crystallogr. Sect. D: Biol. Crystallogr. 2007, 63, 1169.
40. Li, Y.; Gong, Y. C.; Shi, G. B.; Blaszczyk, J.; Ji, X. H.; Yan, H. G. Biochemistry 2002, 41, 8777.
41. Blaszczyk, J.; Shi, G. B.; Li, Y.; Yan, H. G.; Ji, X. H. Structure 2004, 12, 467.
42. Xiao, B.; Shi, G. B.; Chen, X.; Yan, H. G.; Ji, X. H. Structure 1999, 7, 489.
43. Brubaker, R. R. Clin. Microbiol. Rev. 1991, 4, 309.
44. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P. Biomolecular Simulation: the GROMOS96 Manual and User Guide; Vdf hochschulverlag AG an der ETH: Zürich, 1996.
45. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
46. Berendsen, H. H. C.; Postma, J. P. M.; Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
47. Wang, P. M.; Izatt, R. M.; Oscarson, J. L.; Gillespie, S. E. J. Phys. Chem. 1996, 100, 9556.
48. McCammon, A.; Harvey, S. C. Dynamics of Proteins and Nucleic Acids; Cambridge University Press: Cambridge, 1987.
49. Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. Angew. Chem. Int. Ed. 1999, 38, 236.
50. Su, L.; Cukier, R. I. J. Phys. Chem. A 2009, 113, 2025.