Ab initio and molecular dynamics study of the active site of the reaction between ribonuclease A and cytidyl-3′,5′-adenosine

Journal of Physical Chemistry B

Volumn 107, Issue 20, 2003, Pages 4871-4878

  Peeters, Anik ^a   Swerts, Ben ^a   Van Alsenoy, Christian ^a  

^a UNIVERSITY OF ANTWERP   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CATALYSIS; CONFORMATIONS; ENZYMES; HYDROGEN BONDS; ORGANIC COMPOUNDS; PHOSPHATES; REACTION KINETICS; SUBSTRATES;

BOVINE PANCREATIC RIBONUCLEASE; CYTIDYL ADENOSINE; HARTREE-FOCK METHOD; RIBONUCLEASE;

MOLECULAR DYNAMICS;

EID: 0038621671     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp027648d     Document Type: Article

References (74)

1. Borkakoti, N. Eur. J. Biochem. 1983, 132, 89.
2. Wlodawer, A.; Miller, M.; Sjolin, L. Proc. Natl. Acad. Sci. U.S.A. 1983, 80, 3628.
3. Borah, B.; Chen, C. W.; Egan, W.; Miller, M.; Wlodawer, A.; Cohen, J. S. Biochemistry 1985, 24, 2058.
4. McPherson, A.; Brayer, G.; Cascio, D.; Williams, R. Science 1986, 232, 765.
5. Nachman, J.; Miller, M.; Gilliland, G. L.; Carty, R.; Pincus, M.; Wlodawer, A. Biochemistry 1990, 29, 928.
6. Aguilar, C. F.; Thomas, P. J.; Moss, D. S.; Mills, A.; Palmer, R. A. Biochim. Biophys. Acta 1991, 1118, 6.
7. Zegers, I.; Maes, D.; Daothi, M. H.; Poortmans, F.; Palmer, R.; Wyns, L. Protein Sci. 1994, 3, 2322.
8. Fontecilla-Camps, J. C,; de Llorens, R.; le Du, M. H.; Cuchillo, C. M. J. Biol. Chem. 1994, 269, 21526.
9. Leonidas, D. D.; Shapiro, R.; Irons, L. I.; Russo, N.; Acharya, K. R. Biochemistry 1997, 36, 5578.
10. Vitagliano, L.; Merlino, A.; Zagari, A.; Mazzarella, L. Protein Sci. 2000, 9, 1217-1225.
11. Chatani, E.; Hayashi, R.; Moriyama, H.; Ueki, T. Protein Sci. 2002, 11, 72-81.
12. Berisio, R.; Sica, F.; Lamzin, V. S.; Wilson, K. S.; Zagari, A.; Mazzarella, L. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2002, 58, 441-450.
13. Gorenste, Dg.; Wyrwicz, A. Biochem. Biophys. Res. Commun. 1973, 54, 976.
14. Jentoft, J. E.; Gerken, T. A.; Jentoft, N.; Dearborn, D. G. J. Biol. Chem. 1981, 256, 231-236.
15. Sportelli, L.; Viti, V. Stud. Biophys. 1984, 99, 35.
16. Hahn, U.; Ruterjans, H. Eur. J. Biochem. 1985, 152, 481.
17. Hahn, U.; Desaihahn, R.; Ruterjans, H. Eur. J. Biochem. 1985, 146, 705-712.
18. Dobson, C. M.; Lian, L. Y. FEBS Lett. 1987, 225, 183.
19. Alonso, J.; Paolillo, L.; Dauria, G.; Nogues, M. V.; Cuchillo, C. M. Int. J. Pept. Protein Res. 1988, 31, 537.
20. Veenstra, T. D.; Lee, L. Biophys. J. 1994, 67, 331.
21. Toiron, C.; Gonzalez, C.; Bruix, M.; Rico, M. Protein Sci. 1996, 5, 1633.
22. Brunger, A. T.; Brooks, C. L.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 8458.
23. Havdock, K.; Lim, C.; Brunger, A. T.; Karplus, M. J. Am. Chem. Soc. 1990, 112, 3826.
24. Seshadri, K.; Balaji, P. V.; Rao, V. S. R.; Vishveshwara, S. J. Biomol. Struct. Dyn. 1993, 11, 395.
25. Straub, J. E.; Thirumalai, D. Proteins 1993, 15, 360.
26. Seshadri, K.; Rao, V. S. R.; Vishveshwara, S. J. Biomol. Struct. Dyn. 1994, 12, 581.
27. Straub, J. E.; Lim, C.; Karplus, M. J. Am. Chem. Soc. 1994, 116, 2591.
28. Seshadri, K.; Rao, V. S. R.; Vishveshwara, S. Biophys. J. 1995, 69, 2185.
29. Nadig, G.; Vishveshwara, S. Biopolymers 1997, 42, 505.
30. Lopez, X.; York, D. M.; Dejaegere, A.; Karplus, M. Int. J. Quantum Chem. 2002, 86, 10.
31. Walter, B.; Wold, F. Biochemistry 1976, 15, 304.
32. Katoh, H.; Yoshinaga, M.; Yanagita, T.; Ohgi, K.; Irie, M.; Beintema, J. J.; Meinsma, D. Biochim. Biophys. Acta 1986, 873, 367.
33. Trautwein, K.; Holliger, P.; Stackhouse, J.; Benner, S. A. FEBS Lett. 1991, 281, 275.
34. Tarragona-Fiol, A.; Eggelte, H. J.; Harbron, S.; Sanchez, E.; Taylorson, C. J.; Ward, J. M.; Rabin, B. R. Protein Eng. 1993, 6, 901.
35. Herschlag, D. J. Am. Chem. Soc. 1994, 116, 11631.
36. Delcardayre, S. B.; Raines, R. T. Biochemistry 1994, 33, 6031.
37. Messmore, J. M.; Fuchs, D. N.; Raines, R. T. J. Am. Chem. Soc. 1995, 117, 8057.
38. Delcardayre, S. B.; Raines, R. T. J. Mol. Biol. 1995, 252, 328.
39. Fisher, B. M.; Ha, J. H.; Raines, R. T. Biochemistry 1998, 37, 12121.
40. Fisher, B. M.; Schultz, L. W.; Raines, R. T. Biochemistry 1998, 37, 17386.
41. Schultz, L. W.; Quirk, D. J.; Raines, R. T. Biochemistry 1998, 37, 8886.
42. Raines, R. T. Chem. Rev. 1998, 98, 1045.
43. Chatani, E.; Hayashi, R. J. Biosci. Bioeng. 2001, 92, 98-107.
44. Richards, F. M.; Wyckoff, H. W. The enzymes; Academic Press: New York, 1971; Vol. 4.
45. Blackburn, P.; Moore, S. The enzymes; Academic Press: New York, 1982; Vol. 15.
46. Gerlt, J. A.; Gassman, P. G. Biochemistry 1993, 32, 11943.
47. Lim, C.; Tole, P. J. Am. Chem. Soc. 1992, 114, 7245.
48. Breslow, R.; Xu, R. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 1201.
49. Glennon, T. M.; Warshel, A. J. Am. Chem. Soc. 1998, 120, 10234.
50. Anslyn, E.; Breslow, R. J. Am. Chem. Soc. 1989, 111, 4473.
51. Breslow, R.; Huang, D. L.; Anslyn, E. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 1746.
52. Breslow, R.; Xu, R. J. Am. Chem. Soc. 1993, 115, 10705.
53. Chatfield, D. C.; Brooks, B. R. J. Am. Chem. Soc. 1995, 117, 5561.
54. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
55. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667-683.
56. Van Alsenoy, C. J. Comput. Chem. 1988, 9, 620.
57. Van Alsenoy, C.; Peeters, A. THEOCHEM 1993, 105, 19.
58. Ditchfield, R.; Hehre, W.; Pople, J. J. Chem. Phys. 1971, 54, 724.
59. Hehre, W.; Ditchfield, R.; Pople, J. J. Chem. Phys. 1972, 56, 2257.
60. Pares, X.; Nogues, M. V.; Dellorens, R.; Cuchillo, C. M. Essays Biochem. 1991, 26, 89.
61. Altona, C.; Sundaralingam, M. J. Am. Chem. Soc. 1972, 94, 8205.
62. Beintema, J. J.; Schuller, C.; Irie, M.; Carsana, A. Prog. Biophys. Mol. Biol. 1988, 51, 165.
63. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
64. Peeters, A.; Van Alsenoy, C. Biopolymers 1999, 50, 697.
65. Gutte, B. J. Biol. Chem. 1978, 253, 3837.
66. Thompson, J. E.; Raines, R. T. J. Am. Chem. Soc. 1994, 116, 5467.
67. Dantzman, C. L. Ph.D. Thesis, University of Wisconsin-Madison, Madison, WI, 1998.
68. Govil, G. Biopolymers 1976, 15, 2303-2307.
69. Srinivasan, A. R.; Yathindra, N.; Rao, V. S. R.; Prakash, S. Biopolymers 1980, 19, 165.
70. Boque, L.; Coll, M. G.; Ribo, M.; Cuchillo, C. M.; Fita, I.; Vilanova, M. Protein Pept. Lett. 1998, 5, 101-108.
71. Panov, K. I.; Kolbanovskaya, E. Y.; Okorokov, A. L.; Panova, T. B.; vanScheltinga, A. C. T.; Karpeisky, M. Y.; Beintema, J. J. FEBS Lett. 1996, 398, 57.
72. Witzel, H.; Barnard, E. A. Biochem. Biophys. Res. Commun. 1962, 7, 295.
73. Wladkowski, B. D.; Krauss, M.; Stevens, W. J. J. Phys. Chem. 1995, 99, 6273.
74. Vishveshwara, S.; Madhusudhan, M. S.; Maizel, J. V. Biophys. Chem. 2001, 89, 105.