Mechanistics of Enzyme Catalysis: From Small to Large Active-Site Models

Quantum Biochemistry

Volumn , Issue , 2010, Pages 643-666

  Llano, Jorge ^a   Gauld, James W ^a  

^a UNIVERSITY OF WINDSOR   (Canada)

Author keywords

Acid base catalysis; Active site models; Computational enzymology; Enzyme catalysis; Metalloenzyme; Quantum mechanics

Indexed keywords

EID: 80855124632     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527629213.ch23     Document Type: Chapter

References (170)

1. Pauling, L. (1946) Chem. & Eng. News, 24, 1375-1377.
2. Pauling, L. (1948) Nature, 161, 707-709.
3. Bruice, T.C. (1976) Annu. Rev. Biochem., 45, 331-373.
4. Jencks, W.P. (1986) Catalysis in Chemistry and Enzymology, Dover Publication, New York.
5. Warshel, A. (1998) J. Biol. Chem., 273, 27035-27038.
6. Villa, J., Strajbl, M., Glennon, T.M., Sham, Y.Y., Chu, Z.T., and Warshel, A. (2000) Proc. Natl. Acad. Sci. U.S.A., 97, 11899-11904.
7. Villa, J. and Warshel, A. (2001) J. Phys. Chem. B, 105, 7887-7907.
8. Crosby, J., Stone, R., and Lienhard, G.E. (1970) J. Am. Chem. Soc., 92, 2891-2900.
9. Warshel, A., Aqvist, J., and Creighton, S. (1989) Proc. Natl. Acad. Sci. U.S.A., 86, 5820-5824.
10. Lee, J.K. and Houk, K.N. (1997) Science, 276, 942-945.
11. Shurki, A., Strajbl, M., Villà, J., and Warshel, A. (2002) J. Am. Chem. Soc., 124, 4097-4107.
12. Devi-Kesavan, L.S. and Gao, J.L. (2003) J. Am. Chem. Soc., 125, 1532-1540.
13. Page, M.I. and Jencks, W.P. (1971) Proc. Natl. Acad. Sci. U.S.A., 68, 1678-1683.
14. Lau, E.Y. and Bruice, T.C. (1998) J. Am. Chem. Soc., 120, 12387-12394.
15. Hur, S. and Bruice, T.C. (2003) J. Am. Chem. Soc., 125, 1472-1473.
16. Kollman, P.A., Kuhn, B., and Perakyla, M. (2002) J. Phys. Chem. B, 106, 1537-1542.
17. Bruice, T.C. (2002) Acc. Chem. Res., 35, 139-148.
18. Warshel, A. and Levitt, M. (1976) J. Mol. Biol., 103, 227-249.
19. Warshel, A. (1978) Proc. Natl. Acad. Sci. U.S.A., 75, 5250-5254.
20. Warshel, A. (1987) Nature, 330, 15-16.
21. Warshel, A. (1991) Computer Modeling of Chemical Reactions in Enzymes and Solutions, John Wiley & Sons Inc., New York.
22. Warshel, A. and Papazyan, A. (1998) Curr. Opin. Struct. Biol., 8, 211-217.
23. Schutz, C.N. and Warshel, A. (2001) Proteins, 44, 400-417.
24. Warshel, A. (2002) Acc. Chem. Res., 35, 385-395.
25. Warshel, A. (2003) Annu. Rev. Biophys. Biomol. Struct., 32, 425-443.
26. Warshel, A., Sharma, P.K., Kato, M., and Parson, W.W. (2006) Biochim. Biophys. Acta, 1764, 1647-1676.
27. Warshel, A., Sharma, P.K., Kato, M., Xiang, Y., Liu, H.B., and Olsson, M.H.M. (2006) Chem. Rev., 106, 3210-3235.
28. Hammes, G.G. (2002) Biochemistry, 41, 8221-8228.
29. Eisenmesser, E.Z., Bosco, D.A., Akke, M., and Kern, D. (2002) Science, 295, 1520-1523.
30. Benkovic, S.J. and Hammes-Schiffer, S. (2003) Science, 301, 1196-1202.
31. Palmer, A.G. (2004) Chem. Rev., 104, 3623-3640.
32. Eisenmesser, E.Z., Millet, O., Labeikovsky, W., Korzhnev, D.M., Wolf-Watz, M., Bosco, D.A., Skalicky, J.J., Kay, L.E., and Kern, D. (2005) Nature, 438, 117-121.
33. McElheny, D., Schnell, J.R., Lansing, J.C., Dyson, H.J., and Wright, P.E. (2005) Proc. Natl. Acad. Sci. U.S.A., 102, 5032-5037.
34. Smiley, R.D. and Hammes, G.G. (2006) Chem. Rev., 106, 3080-3094.
35. Hammes-Schiffer, S. and Benkovic, S.J. (2006) Annu. Rev. Biochem., 75, 519-541.
36. Liu, H.B. and Warshel, A. (2007) Biochemistry, 46, 6011-6025.
37. Henzler-Wildman, K.A., Thai, V., Lei, M., Ott, M., Wolf-Watz, M., Fenn, T., Pozharski, E., Wilson, M.A., Petsko, G.A., Karplus, M., Hubner, C.G., and Kern, D. (2007) Nature, 450, 838-844.
38. Watt, E.D., Shimada, H., Kovrigin, E.L., and Loria, J.P. (2007) Proc. Natl. Acad. Sci. U.S.A., 104, 11981-11986.
39. Benkovic, S.J., Hammes, G.G., and Hammes-Schiffer, S. (2008) Biochemistry, 47, 3317-3321.
40. Roca, M., Messer, B., Hilvert, D., and Warshel, A. (2008) Proc. Natl. Acad. Sci. U.S.A., 105, 13877-13882.
41. Dafforn, A. and Koshland, D.E. (1971) Proc. Natl. Acad. Sci. U.S.A., 68, 2463-2467.
42. Bruice, T.C., Brown, A., and Harris, D.O. (1971) Proc. Natl. Acad. Sci. U.S.A., 68, 658-661.
43. Mesecar, A.D., Stoddard, B.L., and Koshland, D.E. (1997) Science, 277, 202-206.
44. Scott, W.G. (2001) J. Mol. Biol., 311, 989-999.
45. Masgrau, L., Roujeinikova, A., Johannissen, L.O., Hothi, P., Basran, J., Ranaghan, K.E., Mulholland, A.J., Sutcliffe, M.J., Scrutton, N.S., and Leys, D. (2006) Science, 312, 237-241.
46. Nagel, Z.D. and Klinman, J.P. (2006) Chem. Rev., 106, 3095-3118.
47. Garcia-Viloca, M., Gao, J., Karplus, M., and Truhlar, D.G. (2004) Science, 303, 186-195.
48. Pu, J.Z., Gao, J.L., and Truhlar, D.G. (2006) Chem. Rev., 106, 3140-3169.
49. Olsson, M.H.M., Mavri, J., and Warshel, A. (2006) Philos. Trans. R. Soc. London, Ser. B, 361, 1417-1432.
50. Hay, S. and Scrutton, N.S. (2008) Photosynth. Res., 98, 169-177.
51. Marcus, R.A. (2006) J. Chem. Phys., 125, 194504.
52. Marcus, R.A. (2006) Philos. Trans. R. Soc. London, Ser. B, 361, 1445-1455.
53. Marcus, R.A. (2007) J. Phys. Chem. B, 111, 6643-6654.
54. Heyes, D.J., Sakuma, M., de Visser, S.P., and Scrutton, N.S. (2009) J. Biol. Chem., 284, 3762-3767.
55. Olsson, M.H.M., Parson, W.W., and Warshel, A. (2006) Chem. Rev., 106, 1737-1756.
56. Frey, P.A., Whitt, S.A., and Tobin, J.B. (1994) Science, 264, 1927-1930.
57. Warshel, A., Papazyan, A., and Kollman, P.A. (1995) Science, 269, 102-104.
58. Tuckerman, M.E., Marx, D., Klein, M.L., and Parrinello, M. (1997) Science, 275, 817-820.
59. Feierberg, I. and Aqvist, J. (2002) Theor. Chem. Acc., 108, 71-84.
60. Gerlt, J.A. and Gassman, P.G. (1993) Biochemistry, 32, 11943-11952.
61. Gerlt, J.A. and Gassman, P.G. (1993) J. Am. Chem. Soc., 115, 11552-11568.
62. Yu, Y.B. (2003) J. Phys. Chem. B, 107, 1721.
63. Borman, S. (2004) Chem. & Eng. News, 82, 35-39.
64. Zhang, X.Y. and Houk, K.N. (2005) Acc. Chem. Res., 38, 379-385.
65. Braun-Sand, S., Olsson, M.H.M., and Warshel, A. (2005) Adv. Phys. Org. Chem., 40, 201-245.
66. Bearne, S.L. and Wolfenden, R. (1995) J. Am. Chem. Soc., 117, 9588-9589.
67. Radzicka, A. and Wolfenden, R. (1995) Science, 267, 90-93.
68. Wolfenden, R., Lu, X.D., and Young, G. (1998) J.Am. Chem. Soc., 120, 6814-6815.
69. Wolfenden, R. and Snider, M.J. (2001) Acc. Chem. Res., 34, 938-945.
70. Miller, B.G. and Wolfenden, R. (2002) Annu. Rev. Biochem., 71, 847-885.
71. Callahan, B.P. and Wolfenden, R. (2003) J. Am. Chem. Soc., 125, 310-311.
72. Lad, C., Williams, N.H., and Wolfenden, R. (2003) Proc. Natl. Acad. Sci. U.S.A., 100, 5607-5610.
73. Wolfenden, R. (2003) Biophys. Chem., 105, 559-572.
74. Sievers, A., Beringer, M., Rodnina, M.V., and Wolfenden, R. (2004) Proc. Natl. Acad. Sci. U.S.A., 101, 7897-7901.
75. Snider, M.G., Temple, B.S., and Wolfenden, R. (2004) J. Phys. Org. Chem., 17, 586-591.
76. Callahan, B.P., Yuan, Y, and Wolfenden, R. (2005) J. Am. Chem. Soc., 127, 10828-10829.
77. Schroeder, G.K., Lad, C., Wyman, P., Williams, N.H., and Wolfenden, R. (2006) Proc. Natl. Acad. Sci. U.S.A., 103, 4052-4055.
78. Wolfenden, R. (2006) Chem. Rev., 106, 3379-3396.
79. Schroeder, G.K. and Wolfenden, R. (2007) Biochemistry, 46, 4037-4044.
80. Lewis, C.A. and Wolfenden, R. (2008) Proc. Natl. Acad. Sci. U.S.A., 105, 17328-17333.
81. Wolfenden, R. and Yuan, Y. (2008) J. Am. Chem. Soc., 130, 7548-7549.
82. Nelson, D.L. and Cox, M.M. (2004) Lehninger Principles of Biochemistry, 4th edn, W.H. Freeman.
83. Houk, K.N., Leach, A.G., Kim, S.P., and Zhang, X.Y. (2003) Angew. Chem. Int. Ed., 42, 4872-4897.
84. Wolfenden, R., Snider, M., Ridgway, C., and Miller, B. (1999) J. Am. Chem. Soc., 121, 7419-7420.
85. Sievers, A., Beringer, M., Rodnina, M.V., and Wolfenden, R. (2004) Proc. Natl. Acad. Sci. U.S.A., 101, 12397-12398.
86. Gao, J.L., Ma, S.H., Major, D.T., Nam, K., Pu, J.Z., and Truhlar, D.G. (2006) Chem. Rev., 106, 3188-3209.
87. Kuhn, B. and Kollman, P.A. (2000) J. Am. Chem. Soc., 122, 2586-2596.
88. Stanton, R.V., Perakyla, M., Bakowies, D., and Kollman, P.A. (1998) J. Am. Chem. Soc., 120, 3448-3457.
89. Marcus, R.A. and Sutin, N. (1985) Biochim. Biophys. Acta, 811, 265-322.
90. Siddarth, P. and Marcus, R.A. (1993) J. Phys. Chem., 97, 6111-6114.
91. Moser, C.C., Page, C.C., Farid, R., and Dutton, P.L. (1995) J. Bioenerg. Biomembr., 27, 263-274.
92. Mulholland, A.J. (2005) Drug Discov. Today, 10, 1393-1402.
93. Hu, H. and Yang, W.T. (2008) Annu. Rev. Phys. Chem., 59, 573-601.
94. Singh, U.C. and Kollman, P.A. (1986) J. Comput. Chem., 7, 718-730.
95. Field, M.J., Bash, P.A., and Karplus, M. (1990) J. Comput. Chem., 11, 700-733.
96. Maseras, F. and Morokuma, K. (1995) J. Comput. Chem., 16, 1170-1179.
97. Humbel, S., Sieber, S., and Morokuma, K. (1996) J. Chem. Phys., 105, 1959-1967.
98. Matsubara, T., Sieber, S., and Morokuma, K. (1996) Int. J. Quantum Chem., 60, 1101-1109.
99. Svensson, M., Humbel, S., Froese, R.D.J., Matsubara, T., Sieber, S., and Morokuma, K. (1996) J. Phys. Chem., 100, 19357-19363.
100. Svensson, M., Humbel, S., and Morokuma, K. (1996) J. Chem. Phys., 105, 3654-3661.
101. Dapprich, S., Komaromi, I., Byun, K.S., Morokuma, K., and Frisch, M.J. (1999) J. Mol. Struct. (THEOCHEM), 461, 1-21.
102. Vreven, T. and Morokuma, K. (2000) J. Comput. Chem., 21, 1419-1432.
103. Vreven, T., Mennucci, B., da Silva, C.O., Morokuma, K., and Tomasi, J. (2001) J. Chem. Phys., 115, 62-72.
104. Morokuma, K. (2002) Philos. Trans. R. Soc. London, Ser. A, 360, 1149-1164.
105. Vreven, T., Morokuma, K., Farkas, O., Schlegel, H.B., and Frisch, M.J. (2003) J. Comput. Chem., 24, 760-769.
106. Torrent, M., Vreven, T., Musaev, D.G., Morokuma, K., Farkas, O., and Schlegel, H.B. (2002) J. Am. Chem. Soc., 124, 192-193.
107. Lundberg, M. and Morokuma, K. (2007) J. Phys. Chem. B, 111, 9380-9389.
108. Åqvist, J. and Warshel, A. (1993) Chem. Rev., 93, 2523-2544.
109. Rosta, E., Klahn, M., and Warshel, A. (2006) J. Phys. Chem. B, 110, 2934-2941.
110. Stanton, R.V., Peräkylä, M., Bakowies, D., and Kollman, P.A. (1998) J. Am. Chem. Soc., 120, 3448-3457.
111. Laio, A., Van de Vondele, J., and Rothlisberger, U. (2002) J. Phys. Chem. B, 106, 7300-7307.
112. Carloni, P., Rothlisberger, U., and Parrinello, M. (2002) Acc. Chem. Res., 35, 455-464.
113. Rohrig, U.F., Guidoni, L., and Rothlisberger, U. (2005) ChemPhysChem, 6, 1836-1847.
114. Siegbahn, P.E.M. and Blomberg, M.R.A. (1999) Annu. Rev. Phys. Chem., 50, 221-249.
115. Siegbahn, P.E.M. (2001) J. Comput. Chem., 22, 1634-1645.
116. Himo, F. and Siegbahn, P.E.M. (2003) Chem. Rev., 103, 2421-2456.
117. Siegbahn, P.E.M. (2003) Q. Rev. Biophys., 36, 91-145.
118. Noodleman, L., Lovell, T., Han, W.G., Li, J., and Himo, F. (2004) Chem. Rev., 104, 459-508.
119. Siegbahn, P.E.M. and Blomberg, M.R.A. (2005) Philos. Trans. R. Soc. London, Ser. A, 363, 847-860.
120. Siegbahn, P.E.M. and Borowski, T. (2006) Acc. Chem. Res., 39, 729-738.
121. Blomberg, M.R.A. and Siegbahn, P.E.M. (2006) Biochim. Biophys. Acta, 1757, 969-980.
122. Siegbahn, P.E.M. (2006) J. Biol. Inorg. Chem., 11, 695-701.
123. Bassan, A., Blomberg, M.R.A., Borowski, T., and Siegbahn, P.E.M. (2006) J. Inorg. Biochem., 100, 727-743.
124. Siegbahn, P.E.M., Tye, J.W., and Hall, M.B. (2007) Chem. Rev., 107, 4414-4435.
125. Lundberg, M., Blomberg, M.R.A., and Siegbahn, P.E.M. (2004) Top. Curr. Chem., 238, 79-112.
126. Gauld, J.W. and Eriksson, L.A. (2000) J. Am. Chem. Soc., 122, 2035-2040.
127. Rankin, K.N., Gauld, J.W., and Boyd, R.J. (2001) J. Am. Chem. Soc., 123, 2047-2052.
128. Robinet, J.J., Baciu, C., Cho, K.B., and Gauld, J.W. (2007) J. Phys. Chem. A, 111, 1981-1989.
129. Becke, A.D. (1993) J. Chem. Phys., 98, 5648-5652.
130. Becke, A.D. (1993) J. Chem. Phys., 98, 1372-1377.
131. Lee, C.T., Yang, W.T., and Parr, R.G. (1988) Phys. Rev. B, 37, 785-789.
132. Frisch, M.J. et al.. (2004) Gaussian 03, Gaussian, Inc., Wallingford CT.
133. Schrödinger, L.L.C. (1991-2003) Jaguar 5.5, Portland, OR.
134. Melius, C.F. and Goddard, W.A. (1974) Phys. Rev. A, 10, 1528-1540.
135. Melius, C.F., Olafson, B.D., and Goddard, W.A. (1974) Chem. Phys. Lett., 28, 457-462.
136. Hay, P.J. and Wadt, W.R. (1985) J. Chem. Phys., 82, 270-283.
137. Harihara, P.C. and Pople, J.A. (1972) Chem. Phys. Lett., 16, 217-219.
138. Francl, M.M., Pietro, W.J., Hehre, W.J., Binkley, J.S., Gordon, M.S., Defrees, D.J., and Pople, J.A. (1982) J. Chem. Phys., 77, 3654-3665.
139. Cancès, E., Mennucci, B., and Tomasi, J. (1997) J. Chem. Phys., 107, 3032-3041.
140. Tomasi, J., Mennucci, B., and Cammi, R. (2005) Chem. Rev., 105, 2999-3093.
141. Tannor, D.J., Marten, B., Murphy, R., Friesner, R.A., Sitkoff,D., Nicholls, A., Ringnalda, M., Goddard, W.A., and Honig, B. (1994) J. Am. Chem. Soc., 116, 11875-11882.
142. Marten, B., Kim, K., Cortis, C., Friesner, R.A., Murphy, R.B., Ringnalda, M.N., Sitkoff, D., and Honig, B. (1996) J. Phys. Chem., 100, 11775-11788.
143. Wink, D.A. and Mitchell, J.B. (1998) Free Radical Biol. Med., 25, 434-456.
144. Griffith, O.W. and Stuehr, D.J. (1995) Annu. Rev. Physiol., 57, 707-736.
145. Alderton, W.K., Cooper, C.E., and Knowles, R.G. (2001) Biochem. J., 357, 593-615.
146. Rosen, G.M., Tsai, P., and Pou, S. (2002) Chem. Rev., 102, 1191-1199.
147. Huang, H., Hah, J.M., and Silverman, R.B. (2001) J. Am. Chem. Soc., 123, 2674-2676.
148. Cho, K.B. and Gauld, J.W. (2004) J. Am. Chem. Soc., 126, 10267-10270.
149. Cho, K.B. and Gauld, J.W. (2005) J. Phys. Chem. B, 109, 23706-23714.
150. Robinet, J.J., Cho, K.B., and Gauld, J.W. (2008) J. Am. Chem. Soc., 130, 3328-3334.
151. Duncan, T., Trewick, S.C., Koivisto, P., Bates, P.A., Lindahl, T., and Sedgwick, B. (2002) Proc. Natl. Acad. Sci. U.S.A., 99, 16660-16665.
152. Koivisto, P., Duncan, T., Lindahl, T., and Sedgwick, B. (2003) J. Biol. Chem., 278, 44348-44354.
153. Mishina, Y., Yang, C.G., and He, C. (2005) J. Am. Chem. Soc., 127, 14594-14595.
154. Delaney, J.C., Smeester, L., Wong, C.Y., Frick, L.E., Taghizadeh, K., Wishnok, J.S., Drennan, C.L., Samson, L.D., and Essigmann, J.M. (2005) Nat. Struct. Mol. Biol., 12, 855-860.
155. Yang, C.-G., Yi, C., Duguid, E.M., Sullivan, C.T., Jian, X., Rice, P.A., and He, C. (2008) Nature, 452, 961-965.
156. Yu, B., Edstrom, W.C., Benach, J., Hamuro, Y., Weber, P.C., Gibney, B.R., and Hunt, J.F. (2006) Nature, 439, 879-884.
157. Trewick, S.C., Henshaw, T.F., Hausinger, R.P., Lindahl, T., and Sedgwick, B. (2002) Nature, 419, 174-178.
158. Falnes, P.Ø., Johansen, R.F., and Seeberg, E. (2002) Nature, 419, 178-182.
159. Liu, H., Llano, J., and Gauld, J.W. (2009) J. Phys. Chem. B, 113, 4887-4898.
160. Borowski, T., Bassan, A., and Siegbahn, P.E.M. (2004) Chem.-Eur. J., 10, 1031-1041.
161. Borowski, T., Bassan, A., and Siegbahn, P.E.M. (2004) Biochemistry, 43, 12331-12342.
162. Bassan, A., Blomberg, M.R.A., and Siegbahn, P.E.M. (2003) Chem.-Eur. J., 9, 106-115.
163. Lundberg, M., Siegbahn, P.E.M., and Morokuma, K. (2008) Biochemistry, 47, 1031-1042.
164. Raetz, C.R.H. and Whitfield, C. (2002) Annu. Rev. Biochem., 71, 635-700.
165. Raetz, C.R.H., Reynolds, C.M., Trent, M.S., and Bishop, R.E. (2007) Annu. Rev. Biochem., 76, 295-329.
166. Lipscomb, W.N. and Strater, N. (1996) Chem. Rev., 96, 2375-2433.
167. Hernick, M. and Fierke, C.A. (2005) Arch. Biochem. Biophys., 433, 71-84.
168. Whittington, D.A., Rusche, K.M., Shin, H., Fierke, C.A., and Christianson, D.W. (2003) Proc. Natl. Acad. Sci. U.S.A., 100, 8146-8150.
169. Hernick, M., Gennadios, H.A., Whittington, D.A., Rusche, K.M., Christianson, D.W., and Fierke, C.A. (2005) J. Biol. Chem., 280, 16969-16978.
170. Robinet, J.J. and Gauld, J.W. (2008) J. Phys. Chem. B, 112, 3462-3469.