Role of water in the enzymatic catalysis: Study of ATP + AMP → 2ADP conversion by adenylate kinase

Journal of Physical Chemistry A

Volumn 115, Issue 16, 2011, Pages 3691-3697

  Adkar, Bharat V ^a   Jana, Biman ^a   Bagchi, Biman ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLATE KINASE; CATALYTIC CONVERSION; CATALYTIC CYCLES; CONFORMATIONAL FREE ENERGY; DOMAIN MOTIONS; ENZYMATIC CATALYSIS; EXPLICIT WATER; FREE ENERGY SURFACE; HISTIDINE RESIDUES; IMPLICIT SOLVENT MODEL; INTERMEDIATE STATE; PHOSPHATE TRANSFER; POLAR AMINO ACIDS; PRODUCT RELEASE; REACTION COORDINATES; ROLE OF WATER; SIDE CHAINS; SPECIFIC INTERACTION;

AMINO ACIDS; CONFORMATIONS; FREE ENERGY; MOLECULES; TWO DIMENSIONAL;

ENZYMES;

ADENOSINE DIPHOSPHATE; ADENOSINE PHOSPHATE; ADENOSINE TRIPHOSPHATE; ADENYLATE KINASE; WATER;

ARTICLE; BIOCATALYSIS; BIOSYNTHESIS; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; X RAY CRYSTALLOGRAPHY;

ADENOSINE DIPHOSPHATE; ADENOSINE MONOPHOSPHATE; ADENOSINE TRIPHOSPHATE; ADENYLATE KINASE; BIOCATALYSIS; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; WATER;

EID: 79551634832     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp104787s     Document Type: Article

References (35)

1. Hammes, G. G. Enzyme Catalysis and Regulation; Academic Press: New York, 1982.
2. Fersht, A. Structure and Mechanism in Protein Science. A Guide to Enzyme Catalysis and Protein Folding; Freeman: New York, 1999.
3. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; John Wiley and Sons, Inc.: New York, 1991.
4. Nagel, Z. D.; Klinman, J. P. Nat. Struct. Biol. 2009, 5, 543-550
5. Benkovic, S. J.; Hammes, G. G.; Hammes-Schiffer, S. Biochemistry 2008, 47, 3317-3321
6. English, B. P.; Min, W.; Van Oijen, A. M.; Lee, K. T.; Luo, G. B.; Sun, H. Y.; Cherayil, B. J.; Kou, S. C.; Xie, X. S. Nat. Chem. Biol. 2006, 2, 87-94
7. Min, W.; English, B. P.; Luo, G.; Cherayil, B. J.; Kou, S. C.; Xie, X. S. Acc. Chem. Res. 2005, 38, 923-931
8. Garcia-Viloca, M.; Gao, J.; Karplus, M.; Truhlar, D. G. Science 2004, 303, 186-195
9. Cross, A. J.; Chang, M. C.; Fleming, G. R. Primary Photoprocesses in Biology and Medicine; Bensasson, R. V., et al., Eds.; NATO-ASI A Series: Life Sciences, 85; Springer: Berlin, 1985.
10. Chang, M. C.; Cross, A. J.; Fleming, G. R. J. Biomol. Struct. Dyn. 1984, 1, 299
11. Cross, A. J.; Fleming, G. R. Biophys. J. 1986, 50, 507
12. Chen, L. X. Q.,; Engh, R. A.,; Brunger, A.; Nguyen, D. T.; Karplus, M.; Fleming, G. R. Biochemistry 1988, 27, 6908
13. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227
14. Warshel, A.; Sussman, F.; Hwang, J.-K. J. Mol. Biol. 201, 139
15. Singh, G.; Senapati, S. Biochemistry 2008, 47, 10657
16. Henzler-Wildman, K.; Kern, D. Nature 2007, 450, 913
17. Henzler-Wildman, K. Nature 2007, 450, 838
18. Henzler-Wildman, K.; Lei, M.; Thai, V.; Kerns, S. J.; Karplus, M.; Kern, D. Nature 2007, 450, 913
19. Miyashita, O.; Onuchic, J. N.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12570-12575
20. Whitford, P. C.; Miyashita, O.; Levy, Y.; Onuchic, J. N. J. Mol. Biol. 2007, 366, 1661-1671
21. Whitford, P. C.; Gosavi, S.; Onuchic, J. N. J. Biol. Chem. 2007, 283, 2042
22. Arora, K.; Brooks, C. L. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18496-18501
23. Pisliakov, A. V.; Cao, J.; Kamerlin, S. C. L.; Warshel, A. Proc Natl Acad Sci U.S.A. 2009, 106, 17359-17364
24. Torbeev, V.; Raghuraman, H.; Mandal, K.; Senapati, S.; Kent, S. J. Am. Chem. Soc. 2009, 131, 884
25. Min, W.; Xie, X. S.; Bagchi, B. J. Phys. Chem. B 2008, 112, 454
26. Min, W.; Xie, X. S.; Bagchi, B. J. Chem. Phys. 2009, 131 065104
27. Muller, C. W.; Schlauderer, G.; Reinstein, J.; Schulz, G. E. Structure 1996, 4, 147-156
28. Mueller, C. W.; Schulz, G. E. J. Mol. Biol. 1992, 224, 159-177
29. Schlauderer, G. J.; Schulz, G. E. Protein Sci. 1996, 5, 434-441
30. Warshel, A. Chem. Rev. 2006, 106, 3210-3235
31. Olsson, M. H. M.; Parson, W. W.; Warshel, A. Chem. Rev. 2006, 106, 1737-1756
32. Roca, M.; Messer, B.; Hilvert, D.; Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 13877-13882
33. Zwanzig, R. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 2029-2030
34. van der Spoel, D.; Lindahl, E.; Hess, B.; van Buuren, A. R.; Apol, E.; Meulenhoff, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Feenstra, K. A.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual, version 3.2, www.gromacs.org, 2004.
35. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Chem. Phys. 1987, 91, 6269