Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H

Journal of Computational Chemistry

Volumn 30, Issue 11, 2009, Pages 1634-1641

  Rosta, Edina ^a   Woodcock, H Lee ^b   Brooks, Bernard R ^b   Hummer, Gerhard ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

Catalysis; Enzyme; Free energy; Proton transfer; QM MM; Reaction coordinate; RNase H; Umbrella sampling

Indexed keywords

BACILLUS HALODURANS; CATALYTIC REACTIONS; DEGREES OF FREEDOM; DIESTER; ENERGY PROFILE; FREE-ENERGY CALCULATIONS; HYBRID DUPLEX; HYDROXIDE IONS; MOLECULAR MECHANICALS; PHOSPHATE GROUP; QM/MM; REACTION COORDINATE; REACTION COORDINATES; REACTION PATHS; RNASE H; TRANSITION STATE; UMBRELLA SAMPLING; WATER MOLECULE;

BACTERIOLOGY; CATALYSIS; ENZYMES; FREE ENERGY; MOLECULAR MECHANICS; NUCLEIC ACIDS; OXYGEN; PHOSPHORUS; PROTON TRANSFER; REACTION RATES; RNA;

COORDINATION REACTIONS;

BACTERIAL DNA; BACTERIAL RNA; RIBONUCLEASE H;

ARTICLE; BACILLUS; BIOCATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYMOLOGY; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION; QUANTUM THEORY; THERMODYNAMICS;

BACILLUS; BIOCATALYSIS; COMPUTER SIMULATION; DNA, BACTERIAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; QUANTUM THEORY; RIBONUCLEASE H; RNA, BACTERIAL; THERMODYNAMICS;

EID: 67650433782     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21312     Document Type: Article

References (44)

1. Chandler, D. J Chem Phys 1978, 68, 2959.
2. Zwanzig, R. Nonequilibrium Statistical Mechanics; Oxford. University Press: New York, 2001.
3. Tome, G. M.; Valleau, J. P. J Comput Phys 1977, 23, 187.
4. Kirkwood, J. G. J Chem Phys 1935, 3, 300.
5. Kong, X.; Brooks, C. L., III. J Chem Phys 1996, 105, 2414.
6. Darve, E.; Pohorille, A. J Chem Phys 2001, 115, 9169.
7. Wigner, E. J Chem. Phys 1937, 5, 720.
8. Klahn, M.; Braun-Sand, S.; Rosta, E.; Warshel, A. J Phys Chem B 2005, 109, 15645.
9. Truhlař, D. G.; Garrett, B. C. Annu Rev Phys Chem. 1984, 35, 159.
10. Ensing, B.; Meijer, E. J.; Blochl, P. E.; Baerends, E. J. J Phys Chem A 2001, 105, 3300.
11. Henkelman, G.; Uberuaga, B. P.; Jónsson, H. J Chem Phys 2000, 113, 9901.
12. Henkelman, G.; Jónsson, H. J Chem Phys 2000, 113, 9978.
13. Woodcock, H. L.; Hodoscek, M.; Sherwood, P.; Lee, Y. S.; Schaefer, H. F., Ill; Brooks, B. R. Theor Chem Acc 2003, 109, 140.
14. Woodcock, H. L.; Hodoscek, M.; Brooks, B. R. J Phys Chem A 2007, 111, 5720.
15. Huber, T.; Torda, A. E.; van. Gunsteren, W. F. J Comput-Aided Mol. Des 1994, 8, 695.
16. Ensing, B.; Laio, A.; Parrinello, M.; Klein, M. L. J Phys Chem B 2005, 109, 6676.
17. Laio, A.; Parrinello, M. Proc Natl Acad Sci USA 2002, 99, 12562.
18. Ren, W.; E, W.; Vanden-Eijnden, E. Phys Rev B 2002, 66, 052301.
19. Zheng, L.; Chen, M.; Yang, W. Proc Natl Acad Sci USA 2008, 105, 20227.
20. Steitz, T. A.; Steitz, J. A. Proc Natl. Acad Sci USA 1993, 90, 6498.
21. Yang, W.; Lee, J. Y.; Nowotny, M. Mol Cell 2006, 22, 5.
22. Pingoud, A.; Fuxreiter, M.; Pingoud, V.; Wende, W. Cell Mol Life Sci 2005, 62, 685.
23. Kamerun, S. C. L.; Wilkie, J. Org Biomol Chem 2007, 5, 2098.
24. Williams, N. H. Biochim Biophys Acta 2004, 1697, 279.
25. Zalatan, J. G.; Herschlag, D. J Am Chem Soc 2006, 128, 1293.
26. Zhao, Y.; Zhang, Z.-Y. Biochemistry 1996, 35, 11797.
27. Admiraal, S. J.; Herschlag, D. Chem Biol 1995, 2, 729.
28. Wang, L.; Yu, X.; Hu, P.; Broyde, S.; Zhang, Y. J Am Chem Soc 2007, 129, 4731.
29. Cisneros, G. A.; Perera, L.; García-Díaz, M.; Bebenek, K.; Kunkel, T. A.; Pedersen, L. G. DNA Repair 2008, 7, 1824.
30. De Vivo, M.; Dal Peraro, M.; Klein, M. L. J Am Chem. Soc 2008, 130, 10955.
31. Cramer, C. J.; Truhlar, D. G. In Solvent Effects and Chemical Reactivity; Tapia, O.; Bertrán, J., Eds. Kluwer: Dordrecht, 1996, pp. 180.
32. Klahn, M.; Rosta, E.; Warshel, A. J Am Chem Soc 2006, 128, 15310.
33. Rosta, E.; Kamerlin, S. C. L.; Warshel, A. Biochemistry 2008, 47, 3725.
34. Rosta, E.; Klahn, M.; Warshel, A. J Phys Chem B 2006, 110, 2934.
35. Lima, W. F.; Wu, H.; Nichols, J. G.; Prakash, T. P.; Ravikumar, V.; Crooke, S. T. J Biol Chem 2003, 278, 49860.
36. Nowotny, M.; Gaidamakov, S. A.; Chirlando, R.; Ceiritelli, S. M.; Crouch, R. J.; Yang, W. Mol Cell 2007, 28, 264.
37. Nowotny, M.; Gaidamakov, S. A.; Crouch, R. J.; Yang, W. Cell 2005, 121, 1005.
38. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 1877.
39. Shao, Y.; Molnar, L. F.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.; Brown, S. T.; Gilbert, A. T. B.; Slipchenko, L. V.; Levchenko, S. V.; O'Neill, D. P.; DiStasio, R. A., Jr.; Lochan, R. C.; Wang, T.; Beran, G. J. O.; Besley, N. A.; Herbert, J. M.; Lin, C. Y.; Voorhis, T. V.; Chien, S. H.; Sodt, A.; Steele, R. P.; Rassolov, V. A.; Maslen, P. E.; Korambath, P. P.; Adamson, R. D.; Austin, B.; Baker, J.; Byrd, E. F. C.; Dachsel, H.; Doerksen, R. J.; Dreuw, A.; Dunietz, B. D.; Dutoi, A. D.; Furlani, T. R.; Gwaltney, S. R.; Heyden, A.; Hirata, S.; Hsu, C.-P.; Kedziora, G.; Khalliulin, R. Z.; Hunzinger, P.; Lee, A. M.; Lee, M. S.; Liang, W.; Lotan, I.; Nair, N.; Peters, B.; Proynov, E. I.; Pieniazek, P. A.; Rhee, Y. M.; Ritchie, J.; Rosta, E.; Sherrill, C. D.; Simmonett, A. C.; Subotnik, J. E.; Woodcock, H. L.; Zhang, W.; Bell, A. T.; Chakraborty, A. K.; Chipman, D. M.; Keil, F. J.; Warshel, A.; Hehre, W. J.; Schaefer, H. F.; Kong, J.; Krylov, A. I.; Gill, P. M. W.; HeadGordon, M. Phys Chem Chem Phys 2006, 8, 3172.
40. Becke, A. D. J Chem Phys 1993, 98, 5648.
41. Woodcock, H. L.; Hodoscek, M.; Gilbert, A. T. B.; Gill, P. M. W.; Schaefer, H. F., III; Brooks, B. R. J Comput Chem 2007, 28, 1485.
42. Fukunishi, H.; Watanabe, O.; Takada, S. J Chem Phys 2002,116,9058.
43. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. J Comput. Chem 1992, 13, 1011.
44. Thorpe, I. F.; Brooks, C. L., III. Proteins: Struct, Funct, Bioinform 2004, 57, 444.