Single molecule conformational dynamics of adenylate kinase: Energy landscape, structural correlations, and transition state ensembles

Journal of the American Chemical Society

Volumn 130, Issue 14, 2008, Pages 4772-4783

  Lu, Qiang ^a   Wang, Jin ^a,b  

^a STONY BROOK UNIVERSITY   (United States)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; COMPUTATIONAL METHODS; CONFORMATIONS; KINETIC ENERGY; MATHEMATICAL MODELS; THERMAL EFFECTS;

ADENYLATE KINASE; CONFORMATIONAL ENERGY; ENERGY LANDSCAPE; TRANSITION STATE ENSEMBLES;

ENZYME KINETICS;

ADENOSINE TRIPHOSPHATE; ADENYLATE CYCLASE; NUCLEOSIDE MONOPHOSPHATE KINASE;

ARTICLE; CONFORMATIONAL TRANSITION; ENERGY; ENZYME BINDING; ENZYME CONFORMATION; ENZYME KINETICS; ENZYME STRUCTURE; MICROSCOPY; MODEL; MOLECULAR DYNAMICS; PROTEIN DOMAIN; SIGNAL TRANSDUCTION; STRUCTURE ANALYSIS;

ADENOSINE TRIPHOSPHATE; ADENYLATE KINASE; BINDING SITES; COMPUTER SIMULATION; KINETICS; MODELS, MOLECULAR; NUCLEOTIDES; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 41849107614     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0780481     Document Type: Article

References (31)

1. McCammon, J. A.; Wolynes, P. G.; Karplus, M. Biochemistry 1979, 18, 927-942.
2. Wang, J.; Wolynes, P. Phys. Rev. Lett. 1995, 74, 4317-4320.
3. Lu, H. P.; Xun, L. Y.; Xie, X. S. Science 1998, 282, 1877-1882.
4. Leite, V. B.; Onuchic, J. N.; Stell, G.; Wang, J. Biophys. J. 2004, 87, 3633-3641.
5. Lu, Q.; Lu, H. P.; Wang, J. Phys. Rev. Lett. 2007, 98, 128105-128108.
6. Lipman, E. A; Schuler, B.; Bakajin, O.; Eaton, W. A. Science 2003, 301, 1233-1235.
7. Zhuang, X. W. Annu. Rev. Biophy. Biomol. Struct. 2005, 34, 399-414.
8. Geva, E.; Skinner, J. L. Chem. Phys. Lett. 1998, 288, 225-229.
9. Yang, S. L.; Cao, J. J. Chem. Phys. 2004, 121, 572-581.
10. Miyashita, O.; Onuchic, J. N.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12570-12575.
11. Zuckerman, D. M. J. Phys. Chem. B 2004, 108, 5127-5137.
12. Okazaki, K.; Koga, N.; Takada, S.; Onuchic, J. N.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 11844-11849.
13. Whitford, P. C.; Miyashita, O.; Levy, Y.; Onuchic, J. N. J. Mol. Biol. 2007, 366, 1661-1671.
14. Best, R. B.; Chen, Y. G.; Hummer, G. Structure 2005, 13, 1755-1763.
15. Maragakis, P.; Karplus, M. J. Mol. Biol. 2005, 352, 807-822.
16. Temiz, N. A.; Meirovitch, E.; Bahar, I. Proteins 2004, 57, 468-480.
17. Arora, K.; Brooks, C. L. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18496-18501.
18. 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.; Hübner, C. G.; Kern, D. Nature 2007, 450, 838-844.
19. Henzler-Wildman, K. A.; Lei, M.; Thai, V.; Kerns, S. J.; Karplus, M.; Kern, D. Nature 2007, 450, 913-916.
20. Wolf-Watz, M.; Thai, V.; Henzler-Wildman, K.; Hadjipavlou, G.; Eisenmesser, E. Z.; Kern, D. Nat. Struct. Mol. Biol. 2004, 11, 945-949.
21. Hanson, J. A.; Duderstadt, K.; Bhattacharyya, S.; Brokaw, J.; Chu, J. W.; Yang, H. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18055-18060.
22. Muller, C. W.; Schulz, G. E. J. Mol. Biol. 1992, 224, 159-177.
23. Ådén, J.; Wolf-Watz, M. J. Am. Chem. Soc. 2007, 129, 14003-14012.
24. Muller, C. W.; Schlauderer, G. J.; Reinstein, J.; Schulz, G. E. Structure 1996, 4, 147-156.
25. Ma, J. Structure 2005, 13, 373-380.
26. Levy, Y.; Wolynes, P. G.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 511-516.
27. Cheung, M. D.; Garcia, A. E.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 685-690.
28. Sobolev, V.; Wade, R. C.; Vriend, G.; Edelman, M. Proteins: Struct., Funct., Genet. 1996, 25, 120-129.
29. Papoian, G. A.; Ulander, J.; Eastwook, M. P.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 3352-3357.
30. Wang, J.; Lu, Q. Abstr. Pap., 234th ACS Natl. Meet. 2007.
31. Chu, J. W.; Voth, G. A. Biophys. J. 2007, 97, 3860-3871.