Differential role of the protein matrix on the binding of a catalytic aspartate to Mg2+ vs Ca2+: Application to ribonuclease H

Journal of the American Chemical Society

Volumn 135, Issue 17, 2013, Pages 6541-6548

  Babu, C Satheesan ^a   Dudev, Todor ^a   Lim, Carmay ^a,b  

^a INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

^b NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

AQUEOUS ENVIRONMENT; CLASSICAL FORCE FIELDS; COORDINATION SHELLS; DIVALENT METAL CATIONS; METAL-BINDING SITES; POLARIZATION EFFECT; PROTEIN ARCHITECTURES; SELF-CONSISTENT REACTION FIELDS;

BINDING ENERGY; CHARGE TRANSFER; DENSITY FUNCTIONAL THEORY; ENERGY BARRIERS; ENZYMES; FREE ENERGY; METALS; PROTEINS;

CALCIUM;

ASPARTIC ACID; CALCIUM ION; MAGNESIUM ION; RIBONUCLEASE H; WATER;

ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; ENTROPY; ENZYME ACTIVITY; HYDROGEN BOND; METAL BINDING; POLARIZATION; PROTEIN INTERACTION; PROTEIN STRUCTURE; SELF CONCEPT; SIMULATION; STATIC ELECTRICITY; THERMODYNAMICS;

ASPARTIC ACID; CALCIUM; CARBOXYLIC ACIDS; CATALYSIS; COMPUTER SIMULATION; ESCHERICHIA COLI; MAGNESIUM; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTONS; RIBONUCLEASE H; THERMODYNAMICS; WATER;

EID: 84877054524     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja4006095     Document Type: Article

References (56)

1. Sigel, H. Metal Ions in Biological Systems; Marcel Dekker: New York, 1974.
2. Cowan, J. A. Biological Chemistry of Magnesium; VCH: New York, 1995.
3. Nicholson, A. W. Ribonucleases: Structures and Functions; Academic Press: 1997.
4. Cowan, J. A. Chem. Rev. 1998, 98, 1067
5. Bertini, I.; Sigel, A.; Sigel, H., Eds. Handbook on Metalloproteins; Marcel Dekker: New York, 2001.
6. Nucleases; Hostomsky, Z.; Hostomska, Z.; Matthews, D. A., Eds.; Cold Spring Harbor Laboratory: Cold Spring Harbor, NY, 1994.
7. Yang, W.; Lee, J. Y.; Nowotny, M. Mol. Cell 2006, 22, 5
8. Black, C. B.; Cowan, J. A. Inorg. Chem. 1994, 33, 5805
9. Casareno, R., L. B.; Li, D.; Cowan, J. A. J. Am. Chem. Soc. 1995, 117, 11011
10. Babu, C. S.; Dudev, T.; Casareno, R.; Cowan, J. A.; Lim, C. J. Am. Chem. Soc. 2003, 125, 9318
11. Yang, W.; Steitz, T. A. Structure 1995, 3, 131
12. Venclovas, C.; Siksnys, V. Nat. Struct. Biol. 1995, 2, 838
13. Casareno, R. L. B.; Cowan, J. A. Chem. Commun. 1996, 1813
14. Kanaya, S.; Kohara, A.; Miura, Y.; Sekiguchi, A.; Iwai, S.; Inoue, H.; Ohtsuka, E.; Ikehara, M. J. Biol. Chem. 1990, 265, 4615
15. Katayanagi, K.; Ishikawa, M.; Morikawa, K. Proteins: Struct., Funct., Genet. 1993, 17, 337
16. Pari, K.; Mueller, G. A.; DeRose, E. F.; Kirby, T. W.; London, R. E. Biochemistry 2003, 42, 639
17. Lim, D.; Gregorio, G.; Bingman, C.; Martinez-Hackert, E.; Hendrickson, W. A.; Goff, S. P. J. Virol. 2006, 80, 8379
18. Nowotny, M.; Yang, W. EMBO J. 2006, 25, 1924
19. Marcus, Y. Chem. Rev. 1988, 88, 1475
20. Ohtaki, H.; Radnai, T. Chem. Rev. 1993, 93, 1157
21. Dudev, T.; Lim, C. J. Phys. Chem. B 2004, 108, 4546
22. Dudev, T.; Lim, C. J. Am. Chem. Soc. 2006, 128, 1553
23. Dudev, T.; Lim, C. Annu. Rev. Biophys. 2008, 37, 97
24. Babu, C. S.; Lim, C. J. Phys. Chem. A 2006, 110, 691
25. Dudev, T.; Chang, L.-Y.; Lim, C. J. Am. Chem. Soc. 2005, 127, 4091
26. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187
27. Oda, Y.; Yoshida, M.; Kanaya, S. J. Biol. Chem. 1993, 268, 88
28. MacKerell, J. A. D. J. Phys. Chem. B 1998, 102, 3586
29. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926
30. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: New York, 1987.
31. Åqvist, J. J. Phys. Chem. 1990, 94, 8021
32. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327
33. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089
34. Maksimiak, K.; Rodziewicz-Motowidlo, S.; Czaplewski, C.; Liwo, A.; Scheraga, H. A. J. Phys. Chem. B 2003, 107, 13496
35. Mezei, M. J. Comput. Chem. 1997, 18, 812
36. Babu, C. S.; Lim, C. J. Am. Chem. Soc. 2010, 132, 6290
37. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. J. Comput. Chem. 1992, 13, 1011
38. Boczko, E. M.; Brooks, C. L., III. J. Phys. Chem. 1993, 97, 4509
39. Grossfield, A. WHAM: the weighted histogram analysis method, version 2.0.6; http://membrane.urmc.rochester.edu/content/wham.
40. Kottalam, J.; Case, D. A. J. Am. Chem. Soc. 1988, 110, 7690
41. Yang, T.-Y.; Dudev, T.; Lim, C. J. Am. Chem. Soc. 2008, 130, 3844
42. Onsager, L. J. Am. Chem. Soc. 1936, 58, 1486
43. Kirkwood, J. G. J. Chem. Phys. 1939, 7, 911
44. Gilson, M. K.; Honig, B. H. J. Comput. Chem. 1988, 9, 327
45. Lim, C.; Bashford, D.; Karplus, M. J. Phys. Chem. 1991, 95, 5610
46. Bashford, D. In Scientific Computing in Object-Oriented Parallel Environments; Ishikawa, Y.; Oldehoeft, R. R.; Reynders, V. W.; Tholburn, M., Eds.; Springer: Berlin, 1997; Vol. 1343, p 233.
47. Shao, Y. Phys. Chem. Chem. Phys. 2006, 8, 3172
48. Frisch, M. J. Gaussian 09, revision A.02; Gaussian, Inc.: Wallingford, CT, 2009.
49. Kuppuraj, G.; Dudev, M.; Lim, C. J. Phys. Chem. B 2009, 113, 2952
50. Rosta, E.; Nowotny, M.; Yang, W.; Hummer, G. J. Am. Chem. Soc. 2011, 133, 8934
51. De Vivo, M.; Dal Peraro, M.; Klein, M. L. J. Am. Chem. Soc. 2008, 130, 10955
52. Dudev, T.; Lim, C. Acc. Chem. Res. 2007, 40, 85-93
53. Sakharov, D.; Lim, C. J. Am. Chem. Soc. 2005, 127, 4923
54. Shannon, R. D. Acta Crystallogr., Sect. A 1976, 32, 751
55. Friedman, H. L.; Krishnan, C. V. In Water: A Comprehensive Treatise; Franks, F., Ed.; Plenum Press: New York, 1973; Vol. 3, p 1.
56. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33