How does pin1 catalyze the cis-trans prolyl peptide bond isomerization? A QM/MM and mean reaction force study

Journal of Physical Chemistry B

Volumn 116, Issue 43, 2012, Pages 12972-12979

  Vöhringer Martinez, Esteban ^a   Duarte, Fernanda ^b   Toro Labbé, Alejandro ^b  

^a UNIVERSITY OF CONCEPCIÓN   (Chile)

^b PONTIFICIA UNIVERSIDAD CATÓLICA DE CHILE   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION FREE ENERGY; ALZHEIMER DISEASE; BIOLOGICAL PROCESS; CATALYTIC CAVITIES; CIS-TRANS; ELECTRONIC CONTRIBUTIONS; INTRAMOLECULAR HYDROGEN BOND; MOLECULAR DYNAMICS SIMULATIONS; PEPTIDE BONDS; REACTION COORDINATES; REACTION FORCES; REACTION FREE ENERGY; REACTION MECHANISM; REVERSE REACTIONS; ROOM TEMPERATURE; SERINE RESIDUES; SMALL ENERGY; STILL MISSING; STRUCTURAL REARRANGEMENT; TRANSITION STATE;

AMINO ACIDS; CATALYSIS; ENERGY BARRIERS; FREE ENERGY; HYDROGEN BONDS; ISOMERIZATION; ISOMERS; MOLECULAR DYNAMICS; PEPTIDES; PHOSPHORYLATION;

ENZYMES;

NIMA INTERACTING PEPTIDYLPROLYL ISOMERASE; NIMA-INTERACTING PEPTIDYLPROLYL ISOMERASE; PEPTIDYLPROLYL ISOMERASE; PROLINE; WATER;

ARTICLE; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; QUANTUM THEORY; STEREOISOMERISM;

HUMANS; MOLECULAR DYNAMICS SIMULATION; PEPTIDYLPROLYL ISOMERASE; PROLINE; PROTEIN CONFORMATION; QUANTUM THEORY; STEREOISOMERISM; WATER;

EID: 84868225874     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp307946h     Document Type: Article

References (56)

1. Stewart, D. E.; Sarkar, A.; Wampler, J. E. J. Mol. Biol. 1990, 214, 253-260
2. Weiss, M. S.; Jabs, A.; Hilgenfeld, R. Nat. Struct. Biol. 1998, 5, 676
3. Levitt, M. J. Mol. Biol. 1981, 145, 251-263
4. Kiefhaber, T.; Grunert, H. P.; Hahn, U.; Schmid, F. X. Biochemistry 1990, 29, 6475-6480
5. Sarkar, P.; Reichman, C.; Saleh, T.; Birge, R. B.; Kalodimos, C. G. Mol. Cell 2007, 25, 413-426
6. Lummis, S. C. R.; Beene, D. L.; Lee, L. W.; Lester, H. A.; Broadhurst, R. W.; Dougherty, D. A. Nature 2005, 438, 248-252
7. Wu, X.; Wilcox, C.; Devasahayam, G.; Hackett, R.; Arevalo-Rodriguez, M.; Cardenas, M.; Heitman, J.; Hanes, S. EMBO J. 2000, 919, 3727-3738
8. Nelson, C. J.; Santos-Rosa, H.; Kouzarides, T. Cell 2006, 126, 905-916
9. Ryo, A.; Liou, Y.; Wulf, G.; Nakamura, M.; Lee, S.; Lu, K. Mol. Cell. Biol. 2002, 22, 5281-5295
10. Suizu, F.; Ryo, A.; Wulf, G.; Lim, J.; Lu, K. Mol. Cell. Biol. 2006, 26, 1463-1479
11. Lu, K. P.; Finn, G.; Lee, T. H.; Nicholson, L. K. Nat. Chem. Biol. 2007, 3, 619-629
12. Butterfield, D.; Abdul, H. M.; Opii, W.; Newman, S. F.; Joshi, G.; Ansari, M. A.; Sultana, R. J. Neurochem. 2006, 98, 1697-1706
13. Schutkowski, M.; Bernhardt, A.; Zhou, X. Z.; Shen, M.; Reimer, U.; Rahfeld, J.-U.; Lu, K. P.; Fischer, G. Biochemistry 1998, 37, 5566-5575
14. Hamelberg, D.; Shen, T.; McCammon, J. A. J. Am. Chem. Soc. 2005, 127, 1969-1974
15. Cohen, P. Trends Biochem. Sci. 2000, 25, 596-601
16. Lu, K.; Hanes, S.; Hunter, T. Nature 1996, 380, 544-547
17. Yaffe, M. Science 1997, 278, 1957-1960
18. Zhou, X.; Kops, O.; Werner, A.; Lu, P.; Shen, M.; Stoller, G.; Kullertz, G.; Stark, M.; Fischer, G.; Lu, K. P. Mol. Cell 2000, 6, 873-883
19. Ranganathan, R.; Lu, K. P.; Hunter, T.; Noel, J. P. Cell 1997, 89, 875-886
20. Schroeder, O. E.; Carper, E.; Wind, J. J.; Poutsma, J. L.; Etzkorn, F. A.; Poutsma, J. C. J. Phys. Chem. A 2006, 110, 6522-6530
21. Behrsin, C.; Bailey, M.; Bateman, K.; Hamilton, K.; Wahl, L.; Brandl, C.; Shilton, B.; Litchfield, D. J. Mol. Biol. 2007, 365, 1143-1162
22. Bailey, M.; Shilton, B.; Brandl, C.; Litchfield, D. Biochemistry 2008, 47, 11481
23. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447
24. Bussi, G.; Donadio, D.; Parrinello, M. J. Chem. Phys. 2007, 126, 014101
25. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Nola, A. D.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690
26. Hess, B.; Bekker, H.; Berendsen, H.; Fraaije, J. J. Comput. Chem. 1997, 18, 1463-1472
27. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J.; Vreven, T.; Kudin, K. N.; Burant, J. C.; et al. Gaussian 03, revision D.02; Gaussian, Inc.: Wallingford, CT, 2004.
28. Zhang, Y.; Daum, S.; Wildemann, D.; Zhou, X. Z.; Verdecia, M. A.; Bowman, M. E.; Lücke, C.; Hunter, T.; Lu, K.-P.; Fischer, G. ACS Chem. Biol. 2007, 2, 320-328
29. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins: Struct., Funct., Bioinf. 2006, 65, 712-725
30. Craft, J. W., Jr; Legge, G. B. J. Biomol. NMR 2005, 33, 15-24
31. Bayer, E.; Goettsch, S.; Mueller, J. W.; Griewel, B.; Guiberman, E.; Mayr, L. M.; Bayer, P. J. Biol. Chem. 2003, 278, 26183-26193
32. Jacobs, D. M.; Saxena, K.; Vogtherr, M.; Bernado, P.; Pons, M.; Fiebig, K. M. J. Biol. Chem. 2003, 278, 26174-26182
33. Hermans, J.; Berendsen, H. J. C.; Van Gunsteren, W. F.; Postma, J. P. M. Biopolymers 1984, 23, 1513-1518
34. Fischer, S.; Michnick, S.; Karplus, M. Biochemistry 1993, 32, 13830-13837
35. Fischer, S.; Dunbrack, R. L.; Karplus, M. J. Am. Chem. Soc. 1994, 116, 11931-11937
36. Velazquez, H. A.; Hamelberg, D. Biochemistry 2011, 50, 9605-9615
37. Jhon, J.; Kang, Y. J. Phys. Chem. A 1999, 103, 5436-5439
38. Vöhringer-Martinez, E.; Toro-Labbé, A. J. Chem. Phys. 2011, 135, 64505
39. Toro-Labbé, A. J. Phys. Chem. A 1999, 103, 4398-4403
40. Herrera, B.; Toro-Labbé, A. J. Chem. Phys. 2004, 121, 7096-7102
41. Rincón, E.; Jaque, P.; Toro-Labbé, A. J. Phys. Chem. A 2006, 110, 9478-9485
42. Burda, J. V.; Toro-Labbé, A.; Gutiérrez-Oliva, S.; Murray, J. S.; Politzer, P. J. Phys. Chem. A 2007, 111, 2455-2457
43. Vöhringer-Martinez, E.; Toro-Labbé, A. J. Comput. Chem. 2010, 31, 2642-2649
44. Duarte, F.; Vöhringer-Martinez, E.; Toro-Labbé, A. Phys. Chem. Chem. Phys. 2011, 13, 7773-7782
45. Kästner, J.; Thiel, W. J. Chem. Phys. 2005, 123, 144104
46. Kästner, J.; Thiel, W. J. Chem. Phys. 2006, 124, 234106
47. Kästner, J. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 932-942
48. Yonezawa, Y.; Nakata, K.; Sakakura, K.; Takada, T.; Nakamura, H. J. Am. Chem. Soc. 2009, 131, 4535-4540
49. Cox, C.; Lectka, T. J. Am. Chem. Soc. 1998, 120, 10660-10668
50. Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 1978, 5250-5254
51. Holst, M.; McCammon, J. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10037-10041
52. Fischer, G. Chem. Soc. Rev. 2000, 29, 119-127
53. Greenwood, A. I.; Rogals, M. J.; De, S.; Lu, K.-P.; Kovrigin, E. L.; Nicholson, L. K. J. Biomol. NMR 2011, 51, 21-34
54. Labeikovsky, W.; Eisenmesser, E. Z.; Bosco, D. A.; Kern, D. J. Mol. Biol. 2007, 367, 1370-1381
55. Pisliakov, A. V.; Cao, J.; Kamerlin, S. C. L.; Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 17359-17364
56. Johansson, D. G. A.; Wallin, G.; Sandberg, A.; Macao, B.; Qvist, J.; Härd, T. J. Am. Chem. Soc. 2012, 131, 9475-9477