A molecular mechanism of hydrolysis of peptide bonds at neutral pH using a model compound

Journal of Physical Chemistry B

Volumn 115, Issue 19, 2011, Pages 5958-5970

  Pan, Bin ^a   Ricci, Margaret S ^b   Trout, Bernhardt L ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b AMGEN INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; MECHANICS; MOLECULAR DYNAMICS; PEPTIDES; REACTION INTERMEDIATES; SAMPLING; TRAJECTORIES;

AB INITIO MOLECULAR DYNAMICS; AQUEOUS CONDITION; BIOLOGICAL CHEMISTRY; BREAKING PROCESS; CHEMICAL SPECIES; COMPUTATIONAL STUDIES; COMPUTATIONAL SYSTEM; DEGREES OF FREEDOM; FINITE TEMPERATURES; GEOMETRIC QUANTITIES; HYDROLYTIC REACTIONS; MODEL COMPOUND; MOLECULAR MECHANISM; NEUTRAL PH; ONE-DIMENSIONAL REACTION COORDINATES; PATH SAMPLING METHOD; PEPTIDE BONDS; REACTION COORDINATES; REACTION PATHWAYS; REACTION PROCESS; STATISTICAL WEIGHT; THERAPEUTIC PROTEIN; TRAJECTORY SPACE; WATER NETWORKS;

REACTION KINETICS;

EID: 79956121908     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp1076802     Document Type: Article

References (48)

1. Kahne, D.; Still, W. C. J. Am. Chem. Soc. 1988, 110, 7529-7534
2. Cohen, S. L.; Price, C.; Vlasak, J. J. Am. Chem. Soc. 2007, 129, 6976-+
3. Cordoba, A. J.; Shyong, B. J.; Breen, D.; Harris, R. J. J. Chromatogr., B: Anal. Technol. Biomed. Life Sci. 2005, 818, 115-121
4. Dillon, T. M.; Bondarenko, P. V.; Rehder, D. S.; Pipes, G. D.; Kleemann, G. R.; Ricci, M. S. J. Chromatogr., A 2006, 1120, 112-120
5. Brown, R. S.; Bennet, A. J.; Slebockatilk, H. Acc. Chem. Res. 1992, 25, 481-488
6. Bryant, R. A. R.; Hansen, D. E. J. Am. Chem. Soc. 1996, 118, 5498-5499
7. Radzicka, A.; Wolfenden, R. J. Am. Chem. Soc. 1996, 118, 6105-6109
8. Smith, R. M.; Hansen, D. E. J. Am. Chem. Soc. 1998, 120, 8910-8913
9. Krug, J. P.; Popelier, P. L. A.; Bader, R. F. W. J. Phys. Chem. 1992, 96, 7604-7616
10. Antonczak, S.; Ruizlopez, M. F.; Rivail, J. L. J. Am. Chem. Soc. 1994, 116, 3912-3921
11. Bakowies, D.; Kollman, P. A. J. Am. Chem. Soc. 1999, 121, 5712-5726
12. Stanton, R. V.; Perakyla, M.; Bakowies, D.; Kollman, P. A. J. Am. Chem. Soc. 1998, 120, 3448-3457
13. Cascella, M.; Raugei, S.; Carloni, P. J. Phys. Chem. B 2004, 108, 369-375
14. Zahn, D. J. Phys. Chem. B 2003, 107, 12303-12306
15. Zahn, D. Chem. Phys. Lett. 2004, 383, 134-137
16. Zahn, D. Chem. Phys. 2004, 300, 79-83
17. Zahn, D. Eur. J. Org. Chem. 2004, 4020-4023
18. Zahn, D.; Schmidt, K. F.; Kast, S. M.; Brickmann, J. J. Phys. Chem. A 2002, 106, 7807-7812
19. Gorb, L.; Asensio, A.; Tunon, I.; Ruiz-Lopez, M. F. Chem.-Eur. J. 2005, 11, 6743-6753
20. Buren, N. V.; Rehder, D.; Matsumura, H. G. M.; Jacob, J. J. Pharm. Sci. 2009, 98, 3013-3030
21. Perico, N.; Purtell, J.; Dillon, T.; Ricci, M. S. J. Pharm. Sci. 2009, 98, 3031-3042
22. Pan, B.; Ricci, M. S.; Trout, B. L. J. Phys. Chem. B 2010, 114, 4389-4399
23. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Annu. Rev. Phys. Chem. 2002, 53, 291-318
24. Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. J. Chem. Phys. 1998, 108, 1964-1977
25. Dellago, C.; Bolhuis, P. G.; Geissler, P. L. Adv. Chem. Phys. 2002, 123, 1-78
26. Peters, B.; Beckham, G. T.; Trout, B. L. J. Chem. Phys. 2007, 127, 034109
27. Peters, B.; Trout, B. L. J. Chem. Phys. 2006, 125, 054108
28. Peters, B. J. Chem. Phys. 2006, 125, 241101
29. Weinan, E.; Ren, W. Q.; Vanden-Eijnden, E. Chem. Phys. Lett. 2005, 413, 242-247
30. Metzner, P.; Schutte, C.; Vanden-Eijnden, E. J. Chem. Phys. 2006, 125, 084110
31. E, W.; Vanden-Eijnden, E. J. Stat. Phys. 2006, 123, 503-523
32. Geissler, P. L.; Dellago, C.; Chandler, D.; Hutter, J.; Parrinello, M. Science 2001, 291, 2121-2124
33. Ma, A.; Dinner, A. R. J. Phys. Chem. B 2005, 109, 6769-6779
34. Blumberger, J.; Ensing, B.; Klein, M. L. Angew. Chem. 2006, 118, 2959-2963
35. Gunaydin, H.; Houk, K. N. J. Am. Chem. Soc. 2008, 130, 15232-15233
36. Frisch, M. J.; et al. Gaussian 03, revision B.05; Gaussian, Inc.: Wallingford, CT, 2004.
37. MacKerell, A. D., Jr. J. Phys. Chem. B 1998, 102, 3586-3616
38. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217
39. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
40. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474
41. (Please see http://www.scc.acad.bg/downloads/programs/CPMD/CPMD-V3.13.2- Manuel.pdf page 8): CPMD, http://www.cpmd.org/, Copyright IBM Corp 1990-2008, Copyright MPI fur Festkorperforschung Stuttgart 1997-2001.
42. Beckham, G. T.; Peters, B.; Starbuck, C.; Variankaval, N.; Trout, B. L. J. Am. Chem. Soc. 2007, 129, 4714-4723
43. Troullier, N.; Martins, J. L. Phys. Rev. B 1991, 43, 1993-2006
44. Radhakrishnan, R.; Schlick, T. J. Chem. Phys. 2004, 121, 2436-2444
45. Pelmenschikov, V.; Blomberg, M. R.; Siegbahn, P. E. J. Biol. Inorg. Chem. 2002, 7, 284-298
46. Bolhuis, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12129-12134
47. Miller, T. F.; Vanden-Eijnden, E.; Chandle, D. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14559-14564
48. van Erp, S. T.; Meijier, J. E. Angew. Chem., Int. Ed. 2004, 43, 1660-1662