Chemical rescue of enzymes: Proton transfer in mutants of human carbonic anhydrase II

Journal of the American Chemical Society

Volumn 133, Issue 16, 2011, Pages 6223-6234

  Maupin, C Mark ^a   Castillo, Norberto ^a   Taraphder, Srabani ^a,b   Tu, Chingkuang ^c   McKenna, Robert ^c   Silverman, David N ^c   Voth, Gregory A ^a,d  

^a UNIVERSITY OF UTAH   (United States)

^b INDIAN INSTITUTE OF TECHNOLOGY   (India)

^c UNIVERSITY OF FLORIDA   (United States)

^d UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; CATALYTIC ACTIVITY; CHEMICAL RESCUE; CRYSTALLOGRAPHIC STUDIES; HUMAN CARBONIC ANHYDRASE II; METHYLIMIDAZOLE; MODE OF ACTION; MULTI STATE; NMR SPECTROSCOPY; POTENTIAL OF MEAN FORCE; PROTON TRANSPORT; RATE LIMITING; SELF-RESCUE; SITE-SPECIFIC; VALENCE BONDS; WILD TYPES; WILD-TYPE ENZYMES; WILD-TYPE LEVELS;

AMINO ACIDS; BINDING ENERGY; BIOCHEMISTRY; CARBONIC ANHYDRASE; CATALYST ACTIVITY; ENZYME ACTIVITY; ENZYMES; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTON TRANSFER;

BINDING SITES;

4 METHYLIMIDAZOLE; BUFFER; CARBONATE DEHYDRATASE II; ENZYME; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CARBON NUCLEAR MAGNETIC RESONANCE; CATALYSIS; CHEMICAL PHENOMENA; CHEMICAL RESCUE PATHWAY; CONTROLLED STUDY; CRYSTALLOGRAPHY; ENZYME ACTIVITY; HUMAN; PROTEIN BINDING; PROTON TRANSPORT; SIMULATION;

BIOCATALYSIS; CARBONIC ANHYDRASE II; HUMANS; KINETICS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PROTONS;

EID: 79954992410     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja1097594     Document Type: Article

References (76)

1. Decoursey, T. E. Physiol Rev 2002, 83, 475
2. Wraight, C. A. Biochim. Biophys. Acta 2006, 1757, 886
3. Voth, G. A. Acc. Chem. Res. 2006, 39, 143
4. Swanson, J. M. J.; Maupin, C. M.; Chen, H.; Petersen, M. K.; Xu, J.; Wu, Y.; Voth, G. A. J. Phys. Chem. B. 2007, 111, 4300
5. Warshel, A.; Hwang, J. K.; Åqvist, J. Faraday Discuss. 1992, 22
6. Lu, D.; Voth, G. A. Proteins 1998, 33, 119
7. Lu, D.; Voth, G. A. J. Am. Chem. Soc. 1998, 120, 4006
8. Toba, S.; Colombo, G.; Merz, K. M., Jr. J. Am. Chem. Soc. 1999, 121, 2290
9. Cui, Q.; Karplus, K. J. Phys. Chem. B. 2003, 107, 1071
10. Smedarchina, Z.; Siebrand, W.; Fernandez-Ramos, A.; Cui, Q. J. Am. Chem. Soc. 2003, 125, 243
11. Braun-Sand, S.; Strajbl, M.; Warshel, A. Biophys. J. 2004, 87, 2221
12. Schutz, C. N.; Warshel, A. J. Phys. Chem. B. 2004, 108, 2066
13. Riccardi, D.; Schaefer, P.; Yang, Y.; Yu, H.; Ghosh, N.; Prat-Resina, X.; König, P.; Li, G.; Xu, D.; Guo, H.; Elstner, M.; Cui, Q. J. Phys. Chem. B. 2006, 110, 6458
14. Silverman, D. N.; McKenna, R. Acc. Chem. Res. 2007, 40, 669
15. Fisher, S. Z.; Maupin, C. M.; Govindasamy, L.; Budayova-Spano, M.; Govindasamy, L.; Tu, C.; Agbandje-McKenna, M.; Silverman, D. N.; Voth, G. A.; McKenna, R. Biochemistry 2007, 46, 2930
16. Maupin, C. M.; Voth, G. A. Biochemistry 2007, 46, 2938
17. Maupin, C. M.; Voth, G. A. BBA Proteins and Proteomics 2009, 1804, 332
18. Maupin, C. M.; Saunders, M. G.; Thorpe, I. F.; McKenna, R.; Silverman, D. N.; Voth, G. A. J. Am. Chem. Soc. 2008, 130, 11399
19. Maupin, C. M.; McKenna, R.; Silverman, D. N.; Voth, G. A. J. Am. Chem. Soc. 2009, 131, 7598
20. Maupin, C. M.; Zheng, J.; Tu, C.; McKenna, R.; Silverman, D. N.; Voth, G. A. Biochemistry 2009, 48, 7996
21. Lindskog, S.; Behravan, G.; Engstrand, C.; Forsman, C.; Jonsson, B.; Liang, Z.; Ren, X.; Xue, Y. In Carbonic Anhydrase - From Biochemistry and Genetics to Physiology and Clinical Medicine; Botre, F.; Gros, G.; Storey, B. T., Ed.; VCH: Weinheim, Germany, 1991; p 1.
22. Silverman, D. N.; Lindskog, S. Acc. Chem. Res. 1988, 21, 30
23. Davies, D. R. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 189
24. Fersht, A. Enzyme Structure and Mechanism; W. H. Freeman and Sons: New York, 1985.
25. Tashian, R. E. BioEssays 1989, 10, 186
26. Maren, T. H. Physiol. Rev. 1967, 47, 595
27. Christianson, D. W. Adv. Protein Chem. 1991, 42, 281
28. Lindskog, S.; Coleman, J. E. Proc. Natl. Acad. Sci. U.S.A. 1973, 70, 2505
29. Lindskog, S. In Zinc enzymes; Spiro, T. G., Ed.; John Wiley & Sons: New York, 1983; p 78.
30. Liljas, A.; Kannan, K. K.; Bergsten, P. C.; Waara, I. Nature 1972, 235, 131
31. Nair, S. K.; Christianson, D. W. J. Am. Chem. Soc. 1991, 113, 9455
32. Fisher, Z.; Hernandez Prada, J. A.; Tu, C.; Duda, D.; Yoshioka, C.; An, H.; Govindasamy, L.; Silverman, D. N.; McKenna, R. Biochemistry 2005, 44, 1097
33. Steiner, H.; Jonsson, B.-H.; Lindskog, S. J. Eur. J. Biochem. 1975, 59, 253
34. Tu, C.; Silverman, D. N.; Forsman, C.; Jonsson, B.-H.; Lindskog, S. Biochemistry 1989, 28, 7913
35. Duda, D.; Tu, C.; Qian, M.; Laipis, P.; Agbandje-McKenna, M.; Silverman, D. N.; McKenna, R. Biochemistry 2001, 40, 1741
36. Silverman, D. N.; Vincent, S. H. CRC Crit. Rev. Biochem. 1983, 14, 207
37. Erikson, A. E.; Jones, A. T.; Liljas, A. Proteins 1988, 4, 274
38. Erikson, A. E.; Kylsten, P. M.; Jones, T. A.; Liljas, A. Prot. Struct. Funct. Gen. 1988, 4, 283
39. Duda, D.; Govindasamy, L.; Agbandje-McKenna, M.; Tu, C.; Silverman, D. N.; McKenna, R. Acta. Crystallogr., Sect. D 2003, 59, 93
40. An, H.; Tu, C.; Duda, D.; Montanez-Clemente, I.; Math, K.; Laipis, P. J.; McKenna, R.; Silverman, D. N. Biochemistry 2002, 41, 3235
41. Haiqian, A.; Tu, C.; Duda, D.; Montanez-Clemente, I.; Math, K.; Laipis, P. J.; McKenna, R.; Silverman, D. N. Biochemistry 2002, 41, 3235
42. Bhatt, D.; Fisher, S. Z.; Tu, C.; McKenna, R.; Silverman, D. N. Biophys. J. 2007, 92, 562
43. Elder, I.; Tu, C.; Ming, L.-J.; McKenna, R.; Silverman, D. N. Arch. Biochem. Biophys. 2005, 437, 106
44. Garcia, A. E.; Hummer, G.; Soumpasis, D. M. Prot. Struct. Funct. Gen. 1997, 27, 471
45. Roy, A.; Taraphder, S. Biopolymers 2006, 82, 623
46. Schmitt, U. W.; Voth, G. A. J. Phys. Chem. B. 1998, 102, 5547
47. Schmitt, U. W.; Voth, G. A. J. Chem. Phys. 1999, 111, 9361
48. Day, T. J.; Soudackov, A. V.; Cuma, M.; Schmitt, U. W.; Voth, G. A. J. Chem. Phys. 2002, 117, 5839
49. Kim, J.; Schmitt, U. W.; Gruetzmacher, J. A.; Voth, G. A. J. Chem. Phys. 2002, 116, 737
50. Wu, Y.; H., C.; F., W.; F., P.; Voth, G. A. J. Phys. Chem. B. 2008, 112, 467
51. Cuma, M.; Schmitt, U. W.; Voth, G. A. Chem. Phys. 2000, 258, 187
52. Cuma, M.; Schmitt, U. W.; Voth, G. A. J. Phys. Chem. A. 2001, 105, 2814
53. Maupin, C. M.; Wong, K. F.; Soudackov, A. V.; Kim, S.; Voth, G. A. J. Phys. Chem. A. 2006, 110, 631
54. Gao, J. Curr. Opin. Struct. Biol. 2003, 13, 184
55. Warshel, A.; Weiss, J. J. Am. Chem. Soc. 1980, 102, 6218
56. Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049
57. CRC Handbook of Chemistry and Physics, 90 th ed.; CRC Press/Taylor and Francis: Boca Raton, FL, 2010.
58. Bruice, T. C.; Schmir, G. L. J. Am. Chem. Soc. 1957, 80, 148
59. Chen, J.; Brooks, C. L., III; Scheraga, H. A. J. Phys. Chem. B. 2008, 112, 242
60. Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Phys. Chem. 1996, 100, 1206
61. Case, D. A.,; Amber, 10th edition; San Francisco, 2008.
62. Smith, W.; Forester, T. R. CCLRC; Daresbury Laboratory: Warrington, England, 1999.
63. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011
64. Roux, B. Comput. Phys. Commun. 1995, 91, 275
65. Khalifah, R. G.; Strader, D. J.; Bryant, S. H.; Gibson, S. M. Biochemistry 1977, 16, 2241
66. Silverman, D. N. Methods Enzymol. 1982, 87, 732
67. Riccardi, D.; König, P.; Guo, H.; Cui, Q. Biochemistry 2008, 47, 2369
68. Roy, A.; Taraphder, S. J. Phys. Chem. B. 2007, 111, 10563
69. Roy, A.; Taraphder, S. J. Phys. Chem. B. 2008, 112, 13597
70. Petersen, M. K.; Iyengar, S. S.; Day, T. J. F.; Voth, G. A. J. Phys. Chem. B. 2004, 108, 14804
71. Petersen, P. B.; Saykally, R. J. Annu. Rev. Phys. Chem. 2006, 57, 333
72. Petersen, P. B.; Saykally, R. J. J. Phys. Chem. B. 2005, 109, 7976
73. Tian, C.; Ji, N.; Waychunas, G. A.; Shen, Y. R. J. Am. Chem. Soc. 2008, 130, 13033
74. Petersen, M. K.; Voth, G. A. J. Phys. Chem. B. 2006, 110, 7085
75. Iuchi, S.; Chen, H.; Paesani, F.; Voth, G. A. J. Phys. Chem. B. 2009, 113, 4017
76. Fisher, Z. S.; Kovalevsky, A. Y.; Domsic, J. F.; Mustyakimov, M.; McKenna, R.; Silverman, D. N.; Langan, P. A. Biochemistry 2010, 49, 415