Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step

Archives of Biochemistry and Biophysics

Volumn 582, Issue , 2015, Pages 42-55

  Tuñón, Iñaki ^a   Laage, Damien ^b   Hynes, James T ^b,c  

^a UNIVERSITY OF VALENCIA   (Spain)

^b ECOLE NORMALE SUPÉRIEURE   (France)

^c UNIVERSITY OF COLORADO   (United States)

Author keywords

Dynamical effects; Enzyme catalysis; Transition State Theory

Indexed keywords

ARTICLE; ENZYME MECHANISM; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; QUANTUM MECHANICS; REACTION ANALYSIS; THEORETICAL MODEL; BIOCATALYSIS; BIOLOGICAL MODEL; CHEMISTRY; DIFFUSION; ENZYME ACTIVATION; ENZYMOLOGY; ESCHERICHIA COLI; KINETICS; METABOLISM; PROTEIN CONFORMATION; QUANTUM THEORY; VIBRATION;

DIHYDROFOLATE REDUCTASE; ENZYME; PROTON;

BIOCATALYSIS; DIFFUSION; ENZYME ACTIVATION; ENZYMES; ESCHERICHIA COLI; KINETICS; MODELS, BIOLOGICAL; PROTEIN CONFORMATION; PROTONS; QUANTUM THEORY; TETRAHYDROFOLATE DEHYDROGENASE; VIBRATION;

EID: 84940447481     PISSN: 00039861     EISSN: 10960384     Source Type: Journal    
DOI: 10.1016/j.abb.2015.06.004     Document Type: Article

References (95)

1. C. Walsh Enzymatic Reaction Mechanisms 1979 W. H. Freeman San Francisco
2. D.E. Koshland Proc. Natl. Acad. Sci. USA 44 1958 98 104
3. A. Warshel J. Biol. Chem. 273 1998 27035 27038
4. M. Garcia-Viloca, J. Gao, M. Karplus, and D.G. Truhlar Science 303 2004 186 195
5. X. Zhang, and K.N. Houk Acc. Chem. Res. 38 2005 379 385
6. G.G. Hammes, S.J. Benkovic, and S. Hammes-Schiffer Biochemistry 50 2011 10422 10430
7. L. Pauling C&E News 24 1946 1375 1377
8. A. Kohen, and J.P. Klinman Acc. Chem. Res. 31 1998 397 404
9. A. Warshel, P.K. Sharma, M. Kato, Y. Xiang, H. Liu, and M.H.M. Olsson Chem. Rev. 106 2006 3210 3235
10. S. Hay, and N.S. Scrutton Nat. Chem. 4 2012 161 168
11. D.R. Glowacki, J.N. Harvey, and A.J. Mulholland Nat. Chem. 4 2012 169
12. M. Karplus, and J.A. McCammon Annu. Rev. Biochem. 52 1983 263 300
13. E.Z. Eisenmesser, O. Millet, W. Labeikovsky, D.M. Korzhnev, M. Wolf-Watz, D.A. Bosco, J.J. Skalicky, L.E. Kay, and D. Kern Nature 438 2005 117 121
14. S. Hammes-Schiffer Acc. Chem. Res. 39 2006 93 100
15. M.H.M. Olsson, W.W. Parson, and A. Warshel Chem. Rev. 106 2006 1737 1756
16. D. Antoniou, J. Basner, S. Núñez, and S.D. Schwartz Chem. Rev. 106 2006 3170 3187
17. S.C. Kamerlin, and A. Warshel Proteins 78 2010 1339 1375
18. V.C. Nashine, S. Hammes-Schiffer, and S.J. Benkovic Curr. Opin. Chem. Biol. 14 2010 644 651
19. L.Y. Luk Proc. Natl. Acad. Sci. USA 110 2013 16344 16349
20. D. Antoniou, and S.D. Schwartz J. Phys. Chem. B 115 2011 15147 15158
21. Virtual special issue on "Protein Motion in Catalysis". Acc. Chem. Res. (2015) 48.
22. S.D. Schwartz Top. Curr. Chem. 337 2013 189 208
23. S.D. Schwartz, and V.L. Schramm Nat. Chem. Biol. 5 2009 551 558
24. Z.D. Nagel, and J.P. Klinman Nat. Chem. Biol. 5 2009 543 550
25. K. Henzler-Wildman, and D. Kern Nature 450 2007 964 972
26. R. Jimenez, G.R. Fleming, P.V. Kumar, and M. Maroncelli Nature 369 1994 471 473
27. J.T. Hynes Crossing the transition state in solution Solvent Effects and Chemical Reactivity 1996 Kluwer Amsterdam 231 258
28. E. Wigner Trans. Faraday Soc. 34 1938 29 41
29. H.S. Johnston Gas Phase Reaction Rate Theory 1966 Ronald New York
30. J.T. Hynes The theory of reactions in solution Theory of Chemical Reaction Dynamics vol. 4 1985 CRC Press Boca Raton, FL 171 234
31. H.A. Kramers Physica 7 1940 284 304
32. P. Hänggi, P. Talkner, and M. Borkovec Rev. Mod. Phys. 62 1990 251
33. R.F. Grote, and J.T. Hynes J. Chem. Phys. 73 1980 2715 2732
34. M. Roca, V. Moliner, I. Tuñón, and J.T. Hynes J. Am. Chem. Soc. 128 2006 6186 6193
35. J.J. Ruiz-Pernía, I. Tuñón, V. Moliner, J.T. Hynes, and M. Roca J. Am. Chem. Soc. 130 2008 7477 7488
36. G. Van der Zwan, and J.T. Hynes J. Chem. Phys. 76 1982 2993 3001
37. J.P. Bergsma, B.J. Gertner, K.R. Wilson, and J.T. Hynes J. Chem. Phys. 86 1987 1356 1376
38. B.J. Gertner, J.P. Bergsma, K.R. Wilson, S. Lee, and J.T. Hynes J. Chem. Phys. 86 1987 1377 1386
39. B.J. Gertner, R.M. Whitnell, K.R. Wilson, and J.T. Hynes J. Am. Chem. Soc. 113 1991 74 87
40. D.G. Truhlar, and B.C. Garrett Annu. Rev. Phys. Chem. 35 1984 159 189
41. G. Van der Zwan, and J.T. Hynes J. Chem. Phys. 78 1983 4174 4185
42. R.G. Mullen, J.-E. Shea, and B. Peters J. Chem. Theory Comput. 2014
43. R.G. Mullen, J.-E. Shea, and B. Peters J. Chem. Phys. 140 2014 041104
44. M.F. Hegazi, R.T. Borchardt, and R.L. Schowen J. Am. Chem. Soc. 101 1979 4359 4365
45. J. Zhang, and J.P. Klinman J. Am. Chem. Soc. 133 2011 17134 17137
46. S. Hammes-Schiffer Biochemistry 52 2013 2012 2020
47. B.J. Gertner, K.R. Wilson, and J.T. Hynes J. Chem. Phys. 90 1989 3537 3558
48. R.G. Silva, A.S. Murkin, and V.L. Schramm Proc. Natl. Acad. Sci. USA 108 2011 18661 18665
49. D. Antoniou, X. Ge, V.L. Schramm, and S.D. Schwartz J. Phys. Chem. Lett. 3 2012 3538 3544
50. K. Swiderek, J.J. Ruiz-Pernía, V. Moliner, and I. Tuñón Curr. Opin. Chem. Biol. 21 2014 11 18
51. J. Ulstrup Charge Transfer Processes in Condensed Media 1979 Springer-Verlag Berlin, New York
52. R.R. Dogonadze, A.M. Kuznetsov, M.G. Zaqaraya, and J. Ulstrup A quantum theory of low-temperature chemical and biological rate processes Tunneling in Biological Systems 1979 Academic Press New York 145 171
53. A. Kuznetsov Charge Transfer in Chemical Reactions Kinetics 1997 Press polytechniques et universitaires romandes Lausanne
54. P.M. Kiefer, and J.T. Hynes Proton transfer reactions in a polar environment Hydrogen Transfer Reactions vol. 1 2007 Wiley-VCH Weinheim 307 348
55. D. Borgis, and J.T. Hynes Chem. Phys. 170 1993 315 346
56. P.M. Kiefer, and J.T. Hynes J. Phys. Org. Chem. 23 2010 632 646
57. K. Ando, and J.T. Hynes J. Phys. Chem. B 101 1997 10464 10478
58. A. Staib, D. Borgis, and J.T. Hynes J. Chem. Phys. 102 1995 2487
59. S. Hammes-Schiffer, and S.R. Billeter Int. Rev. Phys. Chem. 20 2001 591 616
60. D.G. Truhlar J. Phys. Org. Chem. 23 2010 660 676
61. P.M. Kiefer, and J.T. Hynes J. Phys. Chem. A 108 2004 11809 11818
62. S. Hammes-Schiffer ChemPhysChem 3 2002 33 42
63. D.G. Truhlar, J. Gao, C. Alhambra, M. Garcia-Viloca, J. Corchado, M.L. Sánchez, and J. Villà Acc. Chem. Res. 35 2002 341 349
64. R.I. Cukier, and D.G. Nocera Annu. Rev. Phys. Chem. 49 1998 337 369
65. S. Hammes-Schiffer Acc. Chem. Res. 34 2001 273 281
66. S. Hammes-Schiffer, and A.V. Soudackov J. Phys. Chem. B 112 2008 14108 14123
67. V.K. Babamov, and R.A. Marcus J. Chem. Phys. 74 1981 1790
68. D. Antoniou, and S.D. Schwartz J. Phys. Chem. B 105 2001 5553 5558
69. Q. Cui, and M. Karplus J. Phys. Chem. B 106 2002 7927 7947
70. R.S. Sikorski, L. Wang, K.A. Markham, P.T. Rajagopalan, S.J. Benkovic, and A. Kohen J. Am. Chem. Soc. 126 2004 4778 4779
71. Z.D. Nagel, and J.P. Klinman Chem. Rev. 106 2006 3095 3118
72. P.M. Kiefer, and J.T. Hynes J. Phys. Chem. A 108 2004 11793 11808
73. J.P. Klinman, and A. Kohen Annu. Rev. Biochem. 82 2013 471 496
74. A. Kohen Acc. Chem. Res. 48 2015 466 473
75. S. Hu, S.C. Sharma, A.D. Scouras, A.V. Soudackov, C.A.M. Carr, S. Hammes-Schiffer, T. Alber, and J.P. Klinman J. Am. Chem. Soc. 136 2014 8157 8160
76. V. Stojković, L.L. Perissinotti, D. Willmer, S.J. Benkovic, and A. Kohen J. Am. Chem. Soc. 134 2012 1738 1745
77. J.P. Klinman Acc. Chem. Res. 48 2015 449 456
78. E. Hatcher, A.V. Soudackov, and S. Hammes-Schiffer J. Am. Chem. Soc. 129 2007 187 196
79. P.G. Bolhuis, D. Chandler, C. Dellago, and P.L. Geissler Annu. Rev. Phys. Chem. 53 2002 291 318
80. D.G. Truhlar Variational transition state theory and multidimensional tunneling for simple and complex reactions in the gas phase, solids, and liquids, and enzymes Isotope Effects in Chemistry and Biology 2006 Marcel Dekker Inc New York 579 620
81. D. Doron, A. Kohen, K. Nam, and D.T. Major J. Chem. Theory Comput. 10 2014 1863 1871
82. S.H. Northrup, and J.T. Hynes J. Chem. Phys. 73 1980 2700 2714
83. W. Min, X.S. Xie, and B. Bagchi J. Phys. Chem. B 112 2008 454 466
84. L. Li, P.E. Wright, S.J. Benkovic, and C.J. Falzone Biochemistry 31 1992 7826 7833
85. C.J. Falzone, P.E. Wright, and S.J. Benkovic Biochemistry 33 1994 439 442
86. G. Bhabha, J. Lee, D.C. Ekiert, J. Gam, I.A. Wilson, H.J. Dyson, S.J. Benkovic, and P.E. Wright Science 332 2011 234 238
87. E.J. Loveridge, E.M. Behiry, J. Guo, and R.K. Allemann Nat. Chem. 4 2012 292 297
88. E.J. Loveridge, L.H. Tey, E.M. Behiry, W.M. Dawson, R.M. Evans, S.B. Whittaker, U.L. Günther, C. Williams, M.P. Crump, and R.K. Allemann J. Am. Chem. Soc. 133 2011 20561 20570
89. A.J. Adamczyk, J. Cao, S.C.L. Kamerlin, and A. Warshel Proc. Natl. Acad. Sci. USA 108 2011 14115 14120
90. J.J. Ruiz-Pernia, L.Y.P. Luk, R. Garcia-Meseguer, S. Martí, E.J. Loveridge, I. Tuñón, V. Moliner, and R.K. Allemann J. Am. Chem. Soc. 135 2013 18689 18696
91. A.V. Pisliakov, J. Cao, S.C.L. Kamerlin, and A. Warshel Proc. Natl. Acad. Sci. USA 106 2009 17359 17364
92. S.J. Benkovic, G.G. Hammes, and S. Hammes-Schiffer Biochemistry 47 2008 3317 3321
93. M.R. Sawaya, and J. Kraut Biochemistry 36 1997 586 603
94. D.D. Boehr, D. McElheny, H.J. Dyson, and P.E. Wright Science 313 2006 1638 1642
95. H.P. Lu, L. Xun, and X.S. Xie Science 282 1998 1877 1882