Elucidation of the proton transport mechanism in human carbonic anhydrase II

Journal of the American Chemical Society

Volumn 131, Issue 22, 2009, Pages 7598-7608

  Maupin, C Mark ^a   McKenna, Robert ^b   Silverman, David N ^b   Voth, Gregory A ^a  

^a UNIVERSITY OF UTAH   (United States)

^b UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; AREAS OF INTERESTS; ATOMISTIC LEVELS; BUFFER CONCENTRATIONS; CHEMICAL RESCUE; ENZYMATIC REACTION; HUMAN CARBONIC ANHYDRASE II; MULTISTATE EMPIRICAL VALENCE BOND METHOD; PROTON TRANSPORT; PROTON TRANSPORTERS; RATE LIMITING; RATE-LIMITING STEPS; WATER CLUSTER;

CATALYSTS; ELECTRON TRANSITIONS; ENZYMES; PHOTOTRANSISTORS; PROTONS; ZINC;

PLATINUM COMPOUNDS;

BUFFER; CARBONATE DEHYDRATASE II; HISTIDINE; HYDROXIDE; WATER; ZINC; PROTON;

ARTICLE; CATALYSIS; CHEMICAL BOND; CONFORMATION; ENZYME ACTIVE SITE; ENZYME STABILITY; HUMAN; MOLECULAR DYNAMICS; OSCILLATION; PROTON TRANSPORT; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROTEIN CONFORMATION; THERMODYNAMICS;

CARBONIC ANHYDRASE II; CATALYTIC DOMAIN; ENZYME STABILITY; HUMANS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTONS; THERMODYNAMICS; WATER; ZINC;

EID: 67650513577     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja8091938     Document Type: Article

References (84)

1. 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., Eds.; VCH: Weinheim, Germany, 1991; pp 1-13.
2. Fersht, A. Enzyme Structure and Mechanism;WH. Freeman and Sons: New York, 1985.
3. Silverman, D. N.; Lindskog, S. Acc. Chem. Res. 1988, 21, 30-36.
4. Davies, D. R. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 189-215.
5. Maren, T. H. Physiol. Rev. 1967, 47, 595-781.
6. Tashian, R. E. BioEssays 1989, 10, 186-192.
7. Fisher, S. Z.; Tu, C.; Bhatt, D.; Govindasamy, L.; Agbandje-McKenna, M.; McKenna, R.; Silverman, D. N. Biochemistry 2007, 46, 3803-3813.
8. Nair, S. K.; Christianson, D. W. J. Am. Chem. Soc. 1991, 113, 9455-9458.
9. Christianson, D. W. Adv. Protein Chem. 1991, 42, 281-335.
10. Lesburg, C. A.; Christianson, D. W. J. Am. Chem. Soc. 1995, 117, 6838-6844.
11. Erikson, A. E.; Jones, A. T.; Liljas, A. Proteins 1988, 4, 274-282.
12. Liljas, A.; Kannan, K. K.; Bergsten, P. C.; Waara, I. Nature 1972, 235, 131-137.
13. Duda, D.; Tu, C.; Qian, M.; Laipis, P.; Agvandje-McKenna, A.; Silverman, D. N.; McKenna, R. Biochemistry 2001, 40, 1741-1748.
14. Håkansson, K.; Carlsson, M.; Svensson, L. A.; Liljas, A. J. Mol. Biol. 1992, 227, 1192-1204.
15. Kannan, K. K.; Ramanadham, M.; Jones, T. A. Ann. N.Y. Acad. Sci. 1984, 429, 49-60.
16. Maupin, C. M.; Voth, G. A. Biochemistry 2007, 46, 2938-2947.
17. Fisher, Z.; Hernandez, Prada, J. A.; Tu, C.; Duda, D.; Yoshioka, C.; An, H.; Govindasamy, L.; Silverman, D. N.; McKenna, R. Biochemistry 2005, 44, 1097-1105.
18. Duda, D.; Govindasamy, L.; Agbandje-McKenna, Tu, C.; Silverman, D. N.; McKenna, R. Acta. Crystallogr., Sect. D 2003, 59, 93-104.
19. Schimara, H.; Yoshida, T.; Shibata, Y.; Shimizu, M.; Kyogoku, Y.; Sakiyama, F.; Nakazawa, T.; Tate, S.; Ohki, S.; Kato, T.; Moriyama, H.; Kishida, K.; Tano, Y.; Ohkubo, T.; Kobayashi, Y. J. Biol. Chem. 2007, 282, 9646-9656.
20. Marino, S.; Hayakawa, K.; Hatada, K.; Benfatto, M.; Rizzello, A.; Maffia, M.; Bubacco, L. Biophys. J. 2007, 93, 2781-2790.
21. Roy, A.; Taraphder, S. J. Phys. Chem. B. 2007, 111, 10563-10576.
22. Silverman, D. N.; McKenna, R. Acc. Chem. Res. 2007, 40.
23. 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, 4300-4314.
24. Silverman, D. N.; Vincent, S. H. CRC Crit. Rev. Biochem. 1983, 14, 207-255.
25. Lindskog, S.; Coleman, J. E. Proc. Natl. Acad. Sci. U.S.A. 1973, 70, 2505-2508.
26. Lindskog, S. In Zinc enzymes; Spiro, T. G., Ed.; John Wiley & Sons: New York, 1983; pp 78-121.
27. Erikson, A. E.; Kylsten, P. M.; Jones, T. A.; Liljas, A. Proteins: Struct., Funct., Genet. 1988, 4, 283-293.
28. Tu, C.; Silverman, D. N.; Forsman, C.; Jonsson, B.-H.; Lindskog, S. Biochemistry 1989, 28, 7913-7918.
29. Qian, M.; Tu, C.; Earnhardt, N.; Laipis, P. J.; Silverman, D. N. Biochemistry 1997, 36, 15758-15764.
30. Haiqian, A.; Tu, C.; Duda, D.; Montanez-Clemente, I.; Math, K.; Laipis, P. J.; McKenna, R.; Silverman, D. N. Biochemistry 2002, 41, 3235-3242.
31. Bhatt, D.; Fisher, S. Z.; Tu, C.; McKenna, R.; Silverman, D. N. Biophys. J. 2007, 92, 562-570.
32. Cui, Q.; Karplus, K. J. Phys. Chem. B. 2003, 107, 1071-1078.
33. Riccardi, D.; Schaefer, P.; Yang, Y.; Yu, H.; Ghosh, N.; Prat-Resina, X.; Konig, P.; Li, G.; Xu, D.; Guo, H.; Elstner, M.; Cui, Q. J. Phys. Chem. B. 2006, 110, 6458-6469.
34. Toba, S.; Colombo, G.; Merz, K. M., Jr. J. Am. Chem. Soc. 1999, 121, 2290-2302.
35. Lu, D.; Voth, G. A. Proteins 1998, 33, 119-134.
36. Lu, D.; Voth, G. A. J. Am. Chem. Soc. 1998, 120, 4006-4014.
37. König, P. H.; Ghosh, N.; Hoffmann, M.; Elstner, M.; Tajkhorshid, E.; Frauenheim, Th.; Cui, Q. J. Phys. Chem. A. 2006, 110, 548-563.
38. Riccardi, D.; Konig, P.; Prat-Resina, X.; Yu, H.; Elstner, M.; Frauehneim, T.; Cui, Q. J. Am. Chem. Soc. 2006, 128, 16302-16311.
39. Riccardi, D.; Konig, P.; Guo, H.; Cui, Q. Biochemistry 2008, 47, 2369-2378.
40. Voth, G. A. Acc. Chem. Res. 2006, 39, 143-150.
41. Schmitt, U. W.; Voth, G. A. J. Phys. Chem. B. 1998, 102, 5547-5551.
42. Schmitt, U. W.; Voth, G. A. J. Chem. Phys. 1999, 111, 9361-9381.
43. Day, T. J.; Soudackov, A. V.; Cuma, M.; Schmitt, U. W.; Voth, G. A. J. Chem. Phys. 2002, 117, 5839-5849.
44. Kim, J.; Schmitt, U. W.; Gruetzmacher, J. A.; Voth, G. A. J. Chem. Phys. 2002, 116, 737-746.
45. Cuma, M.; Schmitt, U. W.; Voth, G. A. J. Phys. Chem. A. 2001, 105, 2814-2823.
46. Cuma, M.; Schmitt, U. W.; Voth, G. A. Chem. Phys. 2000, 258, 187-199.
47. Maupin, C. M.; Wong, K. F.; Soudackov, A. V.; Kim, S.; Voth, G. A. J. Phys. Chem. A. 2006, 110, 631-639.
48. Warshel, A. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 425-443.
49. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; John Wiley and Sons: New York, 1991.
50. Warshel, A.; Weiss, R. M. J. Am. Chem. Soc. 1980, 102, 6218.
51. Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
52. Vreven, T.; Morkuma, K.; Farakas, O.; Schlegel, H. B.; Frish, M. J. J. Comput. Chem. 2003, 24, 760-769.
53. Dapprich, S.; Komaromi, I.; Byun, K. S.; Morokuma, K.; Frisch, M. J. J. Mol. Struct. Theochem 1999, 462, 1-21.
54. Humbel, S.; Sieber, S.; Morokuma, K. J. Chem. Phys. 1996, 105, 1959-1967.
55. Kuno, M.; Hannongbua, S.; Morokuma, K. Chem. Phys. Lett. 2003, 380, 456-463.
56. Maseras, F.; Morokuma, K. J. Comput. Chem. 1995, 16, 1170-1179.
57. Svensson, M.; Humbel, S.; Morokuma, K. J. Chem. Phys. 1996, 105, 3654-3661.
58. Svensson, M.; Humbel, S.; Froese, R. D. J.; Matsubara, T.; Sieber, S.; Morokuma, K. J. Phys. Chem. 1996, 100 (50), 19357-19363.
59. Vreven, T.; Morokuma, K. J. Comput. Chem. 2000, 21, 1419-1432.
60. Vreven, T.; Mennucci, B.; da Silva, C. O.; Morokuma, K.; Tomasi, J. J. Chem. Phys. 2001, 115, 62-72.
61. Frish, M. J.; et al. Gaussian03; Gaussian Inc.: Pittsburgh, PA, 2003.
62. Cieplak, P.; Cornell, W. D.; Bayly, C.; Kollman, P. A. J. Comput. Chem. 1995, 16, 1357-1376.
63. Rowan, T. Functional Stability Analysis of Numerical Algorithms. PhD thesis, Department of Computer Science, University of Texas at Austin, 1990.
64. Chen, J.; Brooks, C. L.; Scheraga, H. A. J. Phys. Chem. B. 2008, 112, 242-249.
65. 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, 2930-2937.
66. Kast, S. M.; Nicklas, K.; Bär, H.-J.; Brickmann, J. J. Chem. Phys. 1994, 100, 566-576.
67. Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Phys. Chem. 1996, 100, 1206-1215.
68. Case, D. A.; et al. AMBER 7th ed.; University of California: San Francisco, 2002.
69. Smith, W.; Forester, T. R. CCLRC; Daresbury Laboratory: Daresbury, Warrington, England, 1999.
70. Mezei, M. J. Comput. Phys. 1987, 68, 237-248.
71. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
72. Roux, B. Comput. Phys. Commun. 1995, 91, 275-282.
73. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38.
74. Reinhard, F.; Grubmüller, H. J. Chem. Phys. 2007, 126, 014102.
75. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. J. 1997, 72, 1047-1069.
76. Petersen, M. K.; Iyengar, S. S.; Day, T. J. F.; Voth, G. A. J. Phys. Chem. B. 2004, 108, 14804-14806.
77. Petersen, P. B.; Saykally, R. J. J. Phys. Chem. B. 2005, 109, 7976-7980.
78. Petersen, M. K.; Voth, G. A. J. Phys. Chem. B. 2006, 110, 7085-7089.
79. Iuchi, S.; Chen, H.; Paesani, F.; Voth, G. A. J. Phys. Chem. 2008, . in press.
80. Tian, C.; Ji, N.; Waychunas, G. A.; Shen, Y. R. J. Am. Chem. Soc. 2008, 130, 13033-13039.
81. Levering, L. M.; Sierra-Hernanadez, M. R.; Allen, H. C. J. Phys. Chem. C 2007, 111, 8814-8826.
82. Tarbuck, T. L.; Ota, S. T.; Richmond, G. L. J. Am. Chem. Soc. 2006, 128, 14519-14527.
83. Maupin, C. M.; Saunders, M. G.; Thorpe, I. F.; McKenna, R.; Silverman, D. N.; Voth, G. A. J. Am. Chem. Soc. 2008, 130, 11399-11408.
84. Roy, A.; Taraphder, S. J. Phys. Chem. B. 2008, 112, 13597-13607.