Hybrid schemes based on quantum mechanics/molecular mechanics simulations: Goals to success, problems, and perspectives

Advances in Protein Chemistry and Structural Biology

Volumn 85, Issue , 2011, Pages 81-142

  Ferrer, Silvia ^a   Ruiz Pernía, Javier ^a   Martí, Sergio ^a   Moliner, Vicent ^a   Tuñón, Iñaki ^b   Bertrán, Juan ^c   Andrés, Juan ^a  

^a UNIVERSITAT JAUME I   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80052797384     PISSN: 18761623     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-386485-7.00003-X     Document Type: Chapter

References (243)

1. O. Acevedo, and W.L. Jorgensen Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions Acc. Chem. Res. 43 1 2010 142 151
2. A. Aemissegger, and B. Jaun Investigation of the enzymatic and nonenzymatic cope rearrangement of carbaprephenate to carbachorismate J. Org. Chem. 67 19 2002 6725 6730
3. A. Aharoni, and L. Gaidukov The 'evolvability' of promiscuous protein functions Nat. Genet. 37 1 2005 73 76 (Pubitemid 40070942)
4. A.N. Alexandrova, and D. Rothlisberger Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination J. Am. Chem. Soc. 130 47 2008 15907 15915
5. H. Alonso, and A.A. Bliznyuk Combining docking and molecular dynamic simulations in drug design Med. Res. Rev. 26 5 2006 531 568 (Pubitemid 44230412)
6. A. Amadei, and A.B.M. Linssen Essential dynamics of proteins Proteins Struct. Funct. Bioinform. 17 4 1993 412 425 (Pubitemid 23358549)
7. P.R. Andrews, and G.D. Smith Transition-state stabilization and enzymic catalysis. Kinetic and molecular orbital studies of the rearrangement of chorismate to prephenate Biochemistry 12 18 1973 3492 3498
8. F.H. Arnold Design by directed evolution Acc. Chem. Res. 31 3 1998 125 131 (Pubitemid 128473641)
9. A. Babtie, and N. Tokuriki What makes an enzyme promiscuous? Curr. Opin. Chem. Biol. 14 2 2010 200 207
10. A.C. Backes, and K. Hotta Promiscuity in antibody catalysis: esterolytic activity of the decarboxylase 21D8 Helv. Chim. Acta 86 4 2003 1167 1174 (Pubitemid 36644470)
11. D. Bakowies, and W. Thiel Hybrid models for combined quantum mechanical and molecular mechanical approaches J. Phys. Chem. 100 25 1996 10580 10594 (Pubitemid 126788646)
12. 2 (rutile) (110) surface: a comparison of periodic and embedded cluster calculations J. Phys. Chem. B 108 23 2004 7844 7853
13. M. Barbany, and H. Gutiérrez-de-Terán On the generation of catalytic antibodies by transition state analogues Chembiochem 4 4 2003 277 285 (Pubitemid 36505198)
14. S.J. Benkovic, and S. Hammes-Schiffer A perspective on enzyme catalysis Science 301 5637 2003 1196 1202 (Pubitemid 37052200)
15. S. Bershtein, and D.S. Tawfik Ohno's Model revisited: measuring the frequency of potentially adaptive mutations under various mutational drifts Mol. Biol. Evol. 25 11 2008 2311 2318
16. T. Bligaard Linear energy relations and the computational design of selective hydrogenation/dehydrogenation catalysts Angew. Chem. Int. Ed. 48 52 2009 9782 9784
17. D.D. Boehr, and R. Nussinov The role of dynamic conformational ensembles in biomolecular recognition Nat. Chem. Biol. 5 11 2009 789 796
18. D.N. Bolon, and S.L. Mayo Enzyme-like proteins by computational design Proc. Natl. Acad. Sci. USA 98 2001 14274 14279 (Pubitemid 33121382)
19. U.T. Bornscheuer, and R.J. Kazlauskas Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways Angew. Chem. Int. Ed. Engl. 43 45 2004 6032 6040 (Pubitemid 39611872)
20. R. Brent, and J. Bruck 2020 computing: can computers help to explain biology? Nature 440 7083 2006 416 417
21. T.C. Bruice A view at the millennium: the efficiency of enzymatic catalysis Acc. Chem. Res. 35 3 2002 139 148
22. B.D. Bursulaya, and M. Totrov Comparative study of several algorithms for flexible ligand docking J. Comput. Aided Mol. Des. 17 11 2003 755 763 (Pubitemid 38418287)
23. E. Busto, and V. Gotor-Fernandez ChemInform abstract: hydrolases: catalytically promiscuous enzymes for non-conventional reactions in organic synthesis ChemInform 42 8 2011 4504 4523
24. C. Canepa A stationary-wave model of enzyme catalysis J. Comput. Chem. 31 2 2010 343 350
25. W.R. Cannon, and S.J. Benkovic Solvation, reorganization energy, and biological catalysis J. Biol. Chem. 273 41 1998 26257 26260 (Pubitemid 28471620)
26. H.A. Carlson, and W.L. Jorgensen Monte Carlo investigations of solvent effects on the chorismate to prephenate rearrangement J. Am. Chem. Soc. 118 35 1996 8475 8484 (Pubitemid 26305271)
27. E.A. Carter, and P. Rossky Computational and theoretical chemistry J. Acc. Chem. Res. 39 2006 71 72
28. R. Catlow Modelling of catalysts and catalysis J. Comput. Aided Mater. Des. 3 1 1996 56 60 (Pubitemid 126707362)
29. K.-B. Cho, and W. Lai The reaction mechanism of allene oxide synthase: interplay of theoretical QM/MM calculations and experimental investigations Arch. Biochem. Biophys. 507 1 2011 14 25
30. Y.M. Chook, and H. Ke Crystal structures of the monofunctional chorismate mutase from BaciUus subtilis and its complex with a transition state analog Proc. Natl. Acad. Sci. USA 90 1993 8600
31. C.H. Christensen, and J.K. Norskov A molecular view of heterogeneous catalysis J. Chem. Phys. 128 18 2008 182503
32. Y. Chuang, and J.C. Corchado Mapped interpolation scheme for single-point energy corrections in reaction rate calculations and a critical evaluation of dual-level reaction path dynamics methods J. Phys. Chem. A 103 1999 1140
33. T. Clark Quo Vadis semiempirical MO-theory? J. Mol. Struct.: THEOCHEM 530 1-2 2000 1 10
34. D.E. Clark What has virtual screening ever done for drug discovery? Expert Opin. Drug Discov. 3 8 2008 841 851
35. W.W. Cleland, and P.A. Frey The low barrier hydrogen bond in enzymatic catalysis J. Biol. Chem. 273 40 1998 25529 25532 (Pubitemid 28475766)
36. M.C. Colombo, and L. Guidoni Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions Chimia 56 1-2 2002 13 19
37. S.D. Copley, and J.R. Knowles The conformational equilibrium of chorismate in solution: implications for the mechanism of the non-enzymic and the enzyme-catalyzed rearrangement of chorismate to prephenate J. Am. Chem. Soc. 109 1987 5008
38. J.C. Corchado, and E.L. Coitiño Interpolated variational transition-state theory by mapping J. Phys. Chem. A 102 1998 2424
39. C.J. Cramer, and D.G. Truhlar Continuum solvation models: classical and quantum mechanical implementations K.B. Lipkowitz, D.B. Boyd, Reviews in Computational Chemistry 6 1995 VCH Publishers New York 1 72
40. Q. Cui, and M. Karplus Molecular properties from combined QM/MM methods. 2. Chemical shifts in large molecules J. Phys. Chem. B 104 15 2000 3721 3743
41. Q. Cui, and M. Karplus Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations J. Chem. Phys. 112 3 2000 1133 1149
42. B.I. Dahiyat, and S.L. Mayo Protein design automation Protein Sci. 5 5 1996 895 903 (Pubitemid 26139177)
43. E.E. Dahlke, and D.G. Truhlar Electrostatically embedded many-body correlation energy, with applications to the calculation of accurate second-order Moller-Plesset perturbation theory energies for large water clusters J. Chem. Theory Comput. 3 4 2007 1342 1348
44. E.E. Dahlke, and D.G. Truhlar Electrostatically embedded many-body expansion for large systems, with applications to water clusters J. Chem. Theory Comput. 3 1 2007 46 53
45. M. Dal Peraro, and L.I. Llarrull Water-assisted reaction mechanism of monozinc beta-lactamases J. Am. Chem. Soc. 126 39 2004 12661 12668 (Pubitemid 39310535)
46. J. Damborsky, and J. Brezovsky Computational tools for designing and engineering biocatalysts Curr. Opin. Chem. Biol. 13 1 2009 26 34
47. O. Danyliv, and L. Kantorovich Treating periodic systems using embedding: Adams-Gilbert approach Phys. Rev. B 76 4 2007 045107
48. R. Das, and D. Baker Macromolecular modeling with Rosetta Annu. Rev. Biochem. 77 2008 363 382
49. M.S. DeClue, and K.K. Baldridge Isochorismate pyruvate lyase: a pericyclic reaction mechanism? J. Am. Chem. Soc. 127 43 2005 15002 15003 (Pubitemid 41547348)
50. R.J. Deeth Computational bioinorganic chemistry Principles and Applications of Density in Inorganic Chemistry II 113 2004 Springer Berlin pp. 37-69
51. P.J. Deuss, and R. den Heeten Bioinspired catalyst design and artificial metalloenzymes Chem. Eur. J 17 2011 4680 4698
52. M.J.S. Dewar, and E.G. Zoebisch Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model J. Am. Chem. Soc. 107 1985 3902
53. S. Difley, and L.-P. Wang Electronic properties of disordered organic semiconductors via QM/MM simulations Acc. Chem. Res. 43 7 2010 995 1004
54. M.A. Dwyer, and L.L. Looger Computational design of a biologically active enzyme Science 304 5679 2004 1967 1971 (Pubitemid 38822189)
55. M. Elstner, and D. Porezag Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties Phys. Rev. B 58 11 1998 7260
56. M. Faiella, and C. Andreozzi An artificial di-iron oxo-protein with phenol oxidase activity Nat. Chem. Biol. 5 12 2009 882 884
57. P. Feibelman DFT versus the "real world" (or, waiting for Godft) Top. Catal. 53 5 2010 417 422
58. K.N. Ferreira, and T.M. Iverson Architecture of the photosynthetic oxygen-evolving center Science 303 5665 2004 1831 1838 (Pubitemid 38374869)
59. S. Ferrer, and S. Martí Molecular mechanism of chorismate mutase activity of promiscuous MbtI Theor. Chem. Acc. Theory Comput. Model. (Theor. Chim. Acta) 128 4 2011 601 607
60. R. Feynman Feynman's office; the last blackboards Phys. Today 42 2 1989 88
61. M.J. Field, and P.A. Bash A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations J. Comput. Chem. 11 1990 700 733
62. C. Gaille, and P. Kast Salicylate biosynthesis in pseudomonas aeruginosa J. Biol. Chem. 277 24 2002 21768 21775
63. J. Gao Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials 2007 John Wiley & Sons, Inc. Hoboken, NJ
64. J. Gao, and M. Freindorf Hybrid ab initio QM/MM simulation of N-Methylacetamide in aqueous solution J. Phys. Chem. A 101 17 1997 3182 3188 (Pubitemid 127587609)
65. J. Gao, and X. Xia A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations Science 258 5082 1992 631 635
66. M. Garcia-Viloca, and J. Gao How enzymes work: analysis by modern rate theory and computer simulations Science 303 5655 2004 186 195 (Pubitemid 38057561)
67. J.A. Gerlt, and P.C. Babbitt Enzyme (re)design: lessons from natural evolution and computation Curr. Opin. Chem. Biol. 13 1 2009 10 18
68. M.E. Glasner, and J.A. Gerlt Evolution of enzyme superfamilies Curr. Opin. Chem. Biol. 10 5 2006 492 497 (Pubitemid 44375064)
69. M.V. Golynskiy, and B. Seelig De novo enzymes: from computational design to mRNA display Trends Biotechnol. 28 2010 340 345
70. H. Guo, and Q. Cui Substrate conformational transitions in the active site of chorismate mutase: their role in the catalytic mechanism Proc. Natl. Acad. Sci. USA 98 16 2001 9032 9037 (Pubitemid 32743864)
71. D.J. Gustin, and P. Mattei Heavy atom isotope effects reveal a highly polarized transition state for chorismate mutase J. Am. Chem. Soc. 121 1999 1756
72. R.J. Hall, and S.A. Hindle Aspects of hybrid QM/MM calculations: the treatment of the QM/MM interface region and geometry optimization with an application to chorismate mutase J. Comput. Chem. 21 16 2000 1433 1441
73. D. Hamelberg, and J. Mongan Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules J. Chem. Phys. 120 24 2004 11919 11929
74. E. Haslam Shikimic Acid: Metabolism and Metabolites 1993 Wiley New York
75. M. Haynes, and E. Stura Routes to catalysis: structure of a catalytic antibody and comparison with its natural counterpart Science 263 5147 1994 646 652 (Pubitemid 24076285)
76. W.J. Hehre, and L. Radom Ab Initio Molecular Orbital Theory 1986 Wiley USA
77. H.W. Hellinga, and F.M. Richards Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry J. Mol. Biol. 222 3 1991 763 785
78. R.J. Hemley Effects of high pressure on molecules Annu. Rev. Phys. Chem. 51 1 2000 763 800
79. K. Heremans, and L. Smeller Protein structure and dynamics at high pressure Biochim. Biophys. Acta 1386 2 1998 353 370 (Pubitemid 28451537)
80. W.A. Herrmann, and B. Cornils Applied Homogeneous Catalysis with Organometallic Compounds 2002 Wiley New York
81. D. Hilvert, and S.H. Carpenter Catalysis of concerted reactions by antibodies: the Claisen rearrangement Proc. Natl. Acad. Sci. USA 85 14 1988 4953 4955
82. D. Hilvert, and K.D. Nared Stereospecific Claisen rearrangement catalyzed by an antibody J. Am. Chem. Soc. 110 16 1988 5593 5594
83. H. Hu, and W. Yang Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods Annu. Rev. Phys. Chem. 59 2008 573 601 (Pubitemid 351703398)
84. H. Hu, and W. Yang Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes J. Mol. Struct.: THEOCHEM 898 1-3 2009 17 30
85. K. Hult, and P. Berglund Enzyme promiscuity: mechanism and applications Trends Biotechnol. 25 5 2007 231 238 (Pubitemid 46589665)
86. L. Hung, and E.A. Carter Accurate simulations of metals at the mesoscale: explicit treatment of 1 million atoms with quantum mechanics Chem. Phys. Lett. 475 4-6 2009 163 170
87. S. Hur, and T.C. Bruice Enzymes do what is expected (chalcone isomerase versus chorismate mutase) J. Am. Chem. Soc. 125 2003 1472
88. R.A. Jensen Enzyme recruitment in evolution of new function Annu. Rev. Microbiol. 30 1 1976 409 425
89. L. Jiang, and E.A. Althoff De novo computational design of retro-aldol enzymes Science 319 5868 2008 1387 1391 (Pubitemid 351354873)
90. S. Jonas, and F. Hollfelder Mechanism and Catalytic Promiscuity: Emerging Mechanistic Principles for Identification and Manipulation of Catalytically Promiscuous Enzymes U. Bornscheuer, S. Lutz, The Protein Engineering Handbook Vol. 1 2008 Wiley Chichester
91. W.L. Jorgensen Efficient drug lead discovery and optimization Acc. Chem. Res. 42 6 2009 724 733
92. S.C. Kamerlin, and M. Haranczyk Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies J. Phys. Chem. B 113 5 2009 1253 1272
93. E. Kangas, and B. Tidor Electrostatic complementarity at ligand binding sites: application to chorismate mutase J. Phys. Chem. B 105 4 2001 880 888
94. J. Kaplan, and W.F. DeGrado De novo design of catalytic proteins Proc. Natl. Acad. Sci. USA 101 2004 11566 11570 (Pubitemid 39095336)
95. M. Karplus, and Y.Q. Gao Protein structural transitions and their functional role Philos. Transact. A Math. Phys. Eng. Sci. 363 1827 2005 331 355 discussion 355-336
96. M. Karplus, and J.A. McCammon Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 9 9 2002 646 652 (Pubitemid 34977295)
97. P. Kast, and M. Asif-Ullah Is chorismate mutase a prototypic entropy trap? - Activation parameters for the Bacillus subtilis enzyme Tetrahedron Lett. 37 1996 2691
98. P. Kast, and M. Asif-Ullah Exploring the active site of chorismate mutase by combinatorial mutagenesis and selection: the importance of electrostatic catalysis Proc. Natl. Acad. Sci. USA 93 10 1996 5043 5048 (Pubitemid 26162867)
99. J. Kastner, and H.M. Senn QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling: application to an enzymatic reaction J. Chem. Theory Comput. 2 2 2006 452 461
100. J. Kastner, and S. Thiel Exploiting QM/MM capabilities in geometry optimization: a microiterative approach using electrostatic embedding J. Chem. Theory Comput. 3 3 2007 1064 1072
101. M. Kato, and R. Hayashi Effects of high pressure on lipids and biomembranes for understanding high-pressure-induced biological phenomena Biosci. Biotechnol. Biochem. 63 8 1999 1321 1328 (Pubitemid 129549140)
102. N.A. Khanjin, and J.P. Snyder Mechanism of chorismate mutase: contribution of conformational restriction to catalysis in the claisen rearrangement J. Am. Chem. Soc. 121 1999 11831
103. O. Khersonsky, and C. Roodveldt Enzyme promiscuity: evolutionary and mechanistic aspects Curr. Opin. Chem. Biol. 10 5 2006 498 508 (Pubitemid 44375065)
104. A. Kienhöfer, and P. Kast Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor J. Am. Chem. Soc. 125 11 2003 3206 3207 (Pubitemid 36512450)
105. A.V. Kimmel, and P.V. Sushko Effect of molecular and lattice structure on hydrogen transfer in molecular crystals of diamino-dinitroethylene and triamino-trinitrobenzene J. Phys. Chem. A 112 19 2008 4496 4500
106. W. Koch, and M.C. Holthausen A Chemist's Guide to Density Functional Theory 2001 Wiley Weinheim, Germany
107. P.A. Kollman, and B. Kuhn Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution Acc. Chem. Res. 34 2001 72
108. M. Kontoyianni, and L.M. McClellan Evaluation of docking performance: comparative data on docking algorithms J. Med. Chem. 47 3 2004 558 565 (Pubitemid 38129714)
109. S. Kumar, and J.M. Rosenberg THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 13 8 1992 1011 1021
110. D.E. Künzler, and S. Sasso Mechanistic insights into the isochorismate pyruvate lyase activity of the catalytically promiscuous PchB from combinatorial mutagenesis and selection J. Biol. Chem. 280 38 2005 32827 32834 (Pubitemid 41368330)
111. A. Laio, and M. Parrinello Escaping free-energy minima Proc. Natl. Acad. Sci. USA 99 20 2002 12562 12566
112. A. Laio, and J. VandeVondele D-RESP: dynamically generated electrostatic potential derived charges from quantum mechanics/molecular mechanics simulations J. Phys. Chem. B 106 29 2002 7300 7307 (Pubitemid 35383057)
113. A. Laio, and J. VandeVondele A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations J. Chem. Phys. 116 16 2002 6941 6947 (Pubitemid 34537077)
114. J.K. Lassila, and J.R. Keeffe Computationally designed variants of Escherichia coli chorismate mutase show altered catalytic activity Protein Eng. Des. Sel. 18 4 2005 161 163 (Pubitemid 40695120)
115. J.K. Lassila, and J.R. Keeffe Exhaustive Mutagenesis of six secondary active-site residues in Escherichia coli chorismate mutase shows the importance of hydrophobic side chains and a helix N-Capping position for stability and catalysis Biochemistry 46 23 2007 6883 6891 (Pubitemid 46906417)
116. A.Y. Lee, and P.A. Karplus Atomic structure of the buried catalytic pocket of Escherichia coli chorismate mutase J. Am. Chem. Soc. 117 12 1995 3627 3628
117. Y.S. Lee, and S.E. Worthington Reaction mechanism of chorismate mutase studied by the combined potentials of quantum mechanics and molecular mechanics J. Phys. Chem. B 106 46 2002 12059 12065 (Pubitemid 35433960)
118. H. Lin, and D.G. Truhlar QM/MM: what have we learned, where are we, and where do we go from here? Theor. Chem. Acc. 117 2 2007 185 199
119. A. Lodola, and M. Mor Identification of productive inhibitor binding orientation in fatty acid amide hydrolase (FAAH) by QM/MM mechanistic modelling Chem. Commun. (Camb.) 2 2008 214 216 (Pubitemid 350294105)
120. R. Lonsdale, and J.N. Harvey Comment on "A Stationary-Wave Model of Enzyme Catalysis" By Carlo Canepa J. Comput. Chem. 32 2 2011 368 369
121. R. Lonsdale, and K.E. Ranaghan Computational enzymology Chem. Commun. (Camb.) 46 14 2010 2354 2372
122. Y. Lu, and N. Yeung Design of functional metalloproteins Nature 460 7257 2009 855 862
123. H. Ludwig Advances in High Pressure Bioscience and Biotechnology 1998 Springer-Verlag Berlin
124. S. Lutz, and U. Bornscheuer Protein Engineering Handbook 2009 Wiley-VCH Weinheim
125. P.D. Lyne, and A.J. Mulholland Insights into chorismate mutase catalysis from a combined QM/MM simulation of the enzyme reaction J. Am. Chem. Soc. 117 45 1995 11345 11350
126. B. Ma, and R. Nussinov Enzyme dynamics point to stepwise conformational selection in catalysis Curr. Opin. Chem. Biol. 14 5 2010 652 659
127. M.M. Mader, and P.A. Bartlett Binding energy and catalysis: the implications for transition-state analogs and catalytic antibodies Chem. Rev. 97 5 1997 1281 1302
128. A. Magistrato, and T.K. Woo Enantioselective palladium-catalyzed hydrosilylation of styrene: detailed reaction mechanism from first-principles and hybrid QM/MM molecular dynamics simulations Organometallics 23 13 2004 3218 3227
129. O. Maglio, and F. Nastri Diiron-containing metalloproteins: developing functional models C. R. Chim. 10 8 2007 703 720
130. A. Mandal, and D. Hilvert Charge Optimization Increases the Potency and Selectivity of a Chorismate Mutase Inhibitor J. Am. Chem. Soc. 125 2003 5598
131. S. Marti, and J. Andres Computational design of biological catalysts Chem. Soc. Rev. 37 12 2008 2634 2643
132. S. Martí, and J. Andrés A hybrid potential reaction path and free energy study of the chorismate mutase reaction J. Am. Chem. Soc. 123 8 2001 1709 1712 (Pubitemid 32179420)
133. S. Martí, and J. Andrés Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case Chem. Eur. J. 9 4 2003 984 991
134. S. Martí, and J. Andrés A comparative study of claisen and cope Rearrangements catalyzed by chorismate mutase. An insight into enzymatic efficiency: transition state stabilization or substrate preorganization? J. Am. Chem. Soc. 126 1 2004 311 319 (Pubitemid 38090371)
135. S. Martí, and J. Andrés Computer-aided rational design of catalytic antibodies: the 1F7 case Angew. Chem. Int. Ed. 46 1-2 2007 286 290 (Pubitemid 46071719)
136. S. Martí, and J. Andrés Predicting an improvement of secondary catalytic activity of promiscuos isochorismate pyruvate lyase by computational design J. Am. Chem. Soc. 130 10 2008 2894 2895
137. S. Martí, and J. Andrés Mechanism and plasticity of isochorismate pyruvate lyase by computational study J. Am. Chem. Soc. 131 44 2009 16156 16161
138. S. Martí, and V. Moliner QM/MM calculations on kinetic isotope effects in the chorismate mutase active site Org. Biomol. Chem. 1 2003 483
139. S. Martí, and V. Moliner Improving the QM/MM description of chemical processes: a dual level strategy to explore the potential energy surface in very large systems J. Chem. Theory Comp. 1 5 2005 1008 1016
140. S. Martí, and V. Moliner Computing kinetic isotope effects for chorismate mutase with high accuracy. A new DFT/MM Strategy J. Phys. Chem. B 109 2005 3707
141. S. Martí, and M. Roca Theoretical insights in enzyme catalysis Chem. Soc. Rev. 33 2 2004 98 107 (Pubitemid 38388008)
142. R.M. Martin Electronic Structure. Basic Theory and Practical Methods 2004 Cambridge University Press Cambridge, UK
143. M.E. Martin, and M.L. Sanchez A multiconfiguration self-consistent field/molecular dynamics study of the (n -> pi[sup *])[sup 1] transition of carbonyl compounds in liquid water J. Chem. Phys. 113 15 2000 6308 6315
144. R.A. Mata Application of high level wavefunction methods in quantum mechanics/molecular mechanics hybrid schemes Phys. Chem. Chem. Phys. 12 19 2010 5041 5052
145. F. Meersman, and C.M. Dobson Protein unfolding, amyloid fibril formation and configurational energy landscapes under high pressure conditions Chem. Soc. Rev. 35 10 2006 908 917 (Pubitemid 44465576)
146. R. Mishra, and R. Winter Cold- and pressure-induced dissociation of protein aggregates and amyloid fibrils Angew. Chem. Int. Ed. 47 35 2008 6518 6521
147. V. Moliner, and A.J. Turner Transition-state structural refinement with GRACE and CHARMM: realistic modelling of lactate dehydrogenase using a combined quantum/classical method J. Chem. Soc. Chem. Commun. 1997 1271
148. G. Monard, and K.M. Merz Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems Acc. Chem. Res. 32 10 1999 904 911
149. G. Monard, and X. Prat-Resina Determination of enzymatic reaction pathways using qm/mm methods Int. J. Quantum. Chem. 93 2003 229 244
150. K.L. Morley, and R.J. Kazlauskas Improving enzyme properties: when are closer mutations better? Trends Biotechnol. 23 5 2005 231 237 (Pubitemid 40615535)
151. D.J. Mowbray, and J.I. Marti nez Trends in metal oxide stability for nanorods, nanotubes, and surfaces J. Phys. Chem. C 115 5 2010 2244 2252
152. A.J. Mulholland Modelling enzyme reaction mechanisms, specificity and catalysis Drug Discov. Today 10 20 2005 1393 1402 (Pubitemid 41501794)
153. E.C. Mundorff, and M.A. Hanson Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement Biochemistry 39 4 2000 627 632 (Pubitemid 30065030)
154. P.M. Murphy, and J.M. Bolduc Alteration of enzyme specificity by computational loop remodeling and design Proc. Natl. Acad. Sci. USA 106 23 2009 9215 9220
155. A.S. Mysovsky, and P.V. Sushko Calibration of embedded-cluster method for defect studies in amorphous silica Phys. Rev. B 69 8 2004 085202
156. V. Nanda, and R.L. Koder Designing artificial enzymes by intuition and computation Nat. Chem. 2 1 2010 15 24
157. F. Neese A critical evaluation of DFT, including time-dependent DFT, applied to bioinorganic chemistry J. Biol. Inorg. Chem. 11 6 2006 702 711 (Pubitemid 44100465)
158. K.E. Neet Enzyme catalytic power minireview series J. Biol. Chem. 273 40 1998 25527 25528 (Pubitemid 28475765)
159. K.A. Nguyen, and I. Rossi A dual-level Shepard interpolation method for generating potential energy surfaces for dynamics calculations J. Chem. Phys. 103 1995 5522 5531
160. I. Nobeli, and A.D. Favia Protein promiscuity and its implications for biotechnology Nat. Biotechnol. 27 2 2009 157 167
161. J.K. Norskov, and T. Bligaard Towards the computational design of solid catalysts Nat. Chem. 1 1 2009 37 46
162. P.J. O'Brien, and D. Herschlag Catalytic promiscuity and the evolution of new enzymatic activities Chem. Biol. 6 4 1999 R91 R105
163. R.G. Parr, and W. Yang Density Functional Theory of Atoms and Molecules 1989 Oxford University Press New York
164. S. Paul, and M.B. Nardelli Rational computational design of optimal catalytic surfaces Appl. Phys. Lett. 97 23 2010 233108
165. L. Pauling Molecular architecture and biological reactions Chem. Eng. News 24 1946 1375 1377
166. L. Pauling Molecular architecture and the processes of life Am. Sci. 36 1948 51
167. L. Pauling Nature of forces between large molecules of biological in terest Nature 161 1948 707 709
168. L. Pauling The Nature of Chemical Bond 1960 Cornell University Press Ithaca, NY
169. F. Petersen, and H. Bohr The mechanisms of excited states in enzymes Theor. Chem. Acc. Theory Comput. Model. (Theor. Chim. Acta) 125 3 2010 345 352
170. S. Piana, and D. Bucher Reaction mechanism of HIV-1 protease by hybrid carparrinello/classical MD simulations J. Phys. Chem. B 108 30 2004 11139 11149
171. X. Prat-Resina, and J.M. Bofill Geometry optimization and transition state search in enzymes: different options in the micro-iterative method Int. J. Quantum. Chem. 98 2004 367 377
172. X. Prat-Resina, and A. González-Lafont How important is the refinement of transition state structures in enzymatic reactions? J. Mol. Struct. Theochem 632 2003 297
173. F. Proust-De Martín, and R. Dumas A hybrid-potential free-energy study of the isomerization step of the acetohydroxy acid isomeroreductase reaction J. Am. Chem. Soc. 122 2000 7688
174. V. Raso, and B.D. Stollar Antibody-enzyme analogy. Characterization of antibodies to phosphopyridoxyltyrosine derivatives Biochemistry 14 3 1975 584 591
175. R. Renka ALGORITHM 716. TSPACK: tension spline curve fitting package J. ACM Trans. Math. Software 19 1993 81 94 (Pubitemid 23622225)
176. D. Riccardi, and P. Schaefer Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes J. Phys. Chem. B 110 13 2006 6458 6469 (Pubitemid 43672110)
177. J.L. Rivail, and D. Rinaldi Theoretical and Computational Models for Organic Chemistry 1991 Kluwer Dodrecht
178. V.M. Robles, and E. Ortega-Carrasco What can molecular modelling bring to the design of artificial inorganic cofactors? Faraday Discuss. 148 2011 137 159
179. U.F. Rohrig, and I. Frank QM/MM Car-Parrinello molecular dynamics study of the solvent effects on the ground state and on the first excited singlet state of acetone in water Chemphyschem 4 11 2003 1177 1182
180. G. Roos, and P. Geerlings Enzymatic catalysis: the emerging role of conceptual density functional theory J. Phys. Chem. B 113 41 2009 13465 13475
181. G. Rothenberg Catalysis: Concepts and Green Applications 2008 Wiley-VCH Weinheim
182. D. Rothlisberger, and O. Khersonsky Kemp elimination catalysts by computational enzyme design Nature 453 7192 2008 190 195 (Pubitemid 351667979)
183. B. Roux The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 91 1995 275
184. J.J. Ruiz-Pernia, and E. Silla Hybrid QM/MM potentials of mean force with interpolated corrections J. Phys. Chem. B 108 24 2004 8427 8433
185. J.J. Ruiz-Pernia, and E. Silla Hybrid quantum mechanics/molecular mechanics simulations with two-dimensional interpolated corrections: application to enzymatic processes J. Phys. Chem. B 110 35 2006 17663 17670 (Pubitemid 44412517)
186. V. Schettino, and R. Bini Chemical Reactions at Very High Pressure 2005 John Wiley & Sons, Inc. Hoboken, NJ, USA
187. V.L. Schramm Enzymatic transition state poise and transition state analogues Acc. Chem. Res. 36 8 2003 588 596
188. P.G. Schultz, and R.A. Lerner Antibody catalysis of difficult chemical transformations Acc. Chem. Res. 26 8 1993 391 395
189. P. Schultz, and R. Lerner From molecular diversity to catalysis: lessons from the immune system Science 269 5232 1995 1835 1842
190. D. Sebastiani, and U. Rothlisberger Nuclear magnetic resonance chemical shifts from hybrid DFT QM/MM calculations J. Phys. Chem. B 108 9 2004 2807 2815
191. H. Senn, and W. Thiel QM/MM methods for biological systems M. Reiher, Atomistic Approaches in Modern Biology 268 2007 Springer Berlin 173 290
192. H.M. Senn, and W. Thiel QM/MM studies of enzymes Curr. Opin. Chem. Biol. 11 2 2007 182 187 (Pubitemid 46528365)
193. H.M. Senn, and W. Thiel QM/MM methods for biomolecular systems Angew. Chem. Int. Ed Engl. 48 7 2009 1198 1229
194. P. Sherwood QM/MM approaches for metal oxide, zeolite, and enzyme systems J. Mol. Graph. Model. 16 4-6 1998 275 284
195. P. Sherwood, and A.H. de Vries QUASI: a general purpose implementation of the QM/MM approach and its application to problems in catalysis J. Mol. Struct. Theochem 632 2003 1 28
196. P.E. Siegbahn, and F. Himo Recent developments of the quantum chemical cluster approach for modeling enzyme reactions J. Biol. Inorg. Chem. 14 5 2009 643 651
197. P.E.M. Siegbahn, and J.W. Tye Computational studies of [NiFe] and [FeFe] hydrogenases Chem. Rev. 107 10 2007 4414 4435 (Pubitemid 350041749)
198. J.B. Siegel, and A. Zanghellini Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction Science 329 5989 2010 309 313
199. J.L. Silva, and D. Foguel Pressure provides new insights into protein folding, dynamics and structure Trends Biochem. Sci. 26 10 2001 612 618 (Pubitemid 32925191)
200. A.A. Sokol, and S.T. Bromley Hybrid QM/MM embedding approach for the treatment of localized surface states in ionic materials Int. J. Quantum Chem. 99 5 2004 695 712
201. S.F. Sousa, and M.J. Ramos M.J. Ramos, Computational Proteomics 2008 Transworld Research Network India, Kerala 101
202. E.V. Stefanovich, and T.N. Truong Theoretical approach for modeling reactivity at solid-liquid interfaces J. Chem. Phys. 106 18 1997 7700 7705
203. A.H. Steindal, and K. Ruud Excitation energies in solution: the fully polarizable QM/MM/PCM method J. Phys. Chem. B 115 12 2011 3027 3037
204. M. Strajbl, and A. Shurki Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization J. Am. Chem. Soc. 125 34 2003 10228 10237 (Pubitemid 37022233)
205. V.B. Sulimov, and P.V. Sushko Asymmetry and long-range character of lattice deformation by neutral oxygen vacancy in alpha-quartz Phys. Rev. B 66 2 2002 024108
206. C.M. Summa, and M.M. Rosenblatt Computational de novo design, and characterization of an A(2)B(2) diiron protein J. Mol. Biol. 321 5 2002 923 938
207. P.V. Sushko, and A.L. Shluger Relative energies of surface and defect states: ab initio calculations for the MgO(001) surface Surf. Sci. 450 3 2000 153 170 (Pubitemid 30585350)
208. M.L. Sushko, and P.V. Sushko QM/MM method for metal-organic interfaces J. Comput. Chem. 31 16 2010 2955 2966
209. A. Szabo, and N.S. Ostlund Modern Quantum Chemistry 1996 Dover publications, Inc. Mineola, New York
210. B. Szefczyk, and A.J. Mulholland Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field J. Am. Chem. Soc. 126 49 2004 16148 16159 (Pubitemid 39627626)
211. D.S. Tawfik, and O. Khersonsky Enzyme promiscuity: a mechanistic and evolutionary perspective Annu. Rev. Biochem. 79 1 2010 471 505
212. S.V. Taylor, and P. Kast Investigating and engineering enzymes by genetic selection Angew. Chem. Int. Ed. 40 18 2001 3310 3335 (Pubitemid 32916593)
213. W. Thiel Perspectives on Semiempirical Molecular Orbital Theory 2007 John Wiley & Sons, Inc. Hoboken, NJ
214. G. Thomas Medicinal Chemistry 2007 Wiley Chichester pp. 127-129
215. M.A. Thompson QM/MMpol: a consistent model for solute/solvent polarization. Application to the aqueous solvation and spectroscopy of formaldehyde, acetaldehyde, and acetone J. Phys. Chem. 100 34 1996 14492 14507 (Pubitemid 126796547)
216. J. Tomasi, and M. Persico Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent Chem. Rev. 94 1994 2027
217. G.M. Torrie, and J.P. Valleau Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid Chem. Phys. Lett. 28 4 1974 578 581
218. M.D. Toscano, and K.J. Woycechowsky Minimalist active-site redesign: teaching old enzymes new tricks Angew. Chem. Int. Ed. 46 18 2007 3212 3236 (Pubitemid 46973466)
219. D.G. Truhlar Molecular modeling of complex chemical systems J. Am. Chem. Soc. 130 50 2008 16824 16827
220. A.J. Turner, and V. Moliner Transition-state structural refinement with GRACE and CHARMM: flexible QM/MM modelling for lactate dehydrogenase J. Phys. Chem. Chem. Phys. 1 1999 1323
221. H.D. Ulrich, and E. Mundorff The interplay between binding energy and catalysis in the evolution of a catalytic antibody Nature 389 6648 1997 271 275 (Pubitemid 27406637)
222. J. VandeVondele, and M.C. Colombo QM/MM study of the copper binding site of prion protein Biophys. J. 82 1 2002 2377
223. J. Vill, and A. Warshel Energetics and dynamics of enzymatic reactions J. Phys. Chem. B 105 2001 7887
224. T. Vreven, and K. Morokuma Chapter 3 hybrid methods: ONIOM(QM:MM) and QM/MM C.S. David, Annual Reports in Computational Chemistry Vol. 2 2006 Elsevier USA 35 51
225. T. Vreven, and K. Morokuma Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints J. Comput. Chem. 24 2003 760
226. A. Warshel Computer Modeling of Chemical Reactions in Enzymes and Solutions 1991 Wiley New York
227. A. Warshel Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites J. Biol. Chem. 273 42 1998 27035 27038 (Pubitemid 28500403)
228. A. Warshel Computer simulations of enzyme catalysis: methods, progress, and insights Annu. Rev. Biophys. Biomol. Struct. 32 2003 425 443 (Pubitemid 37056236)
229. A. Warshel, and M. Levitt Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme J. Mol. Biol. 103 2 1976 227 249
230. A. Warshel, and P.K. Sharma Electrostatic basis for enzyme catalysis Chem. Rev. 106 8 2006 3210 3235 (Pubitemid 44376933)
231. I.H. Williams Catalysis: transition-state molecular recognition? Beilstein J. Org. Chem. 6 2010 1026 1034
232. R. Winter, and D. Lopes Towards an understanding of the temperature/pressure configurational and free-energy landscape of biomolecules J. Non-Equilib. Thermodyn. 32 1 2007 41 97 (Pubitemid 46326288)
233. R. Wolfenden Analog approaches to the structure of the transition state in enzyme reactions Acc. Chem. Res. 5 1 1972 10 18
234. Q. Wu, and B.K. Liu Enzymatic promiscuity for organic synthesis and cascade process Curr. Org. Chem. 14 2010 1966 1988
235. F.M. Ytreberg, and R.H. Swendsen Comparison of free energy methods for molecular systems J. Chem. Phys. 125 18 2006 184114
236. F. Zaera The new materials science of catalysis: toward controlling selectivity by designing the structure of the active site J. Phys. Chem. Lett. 1 3 2010 621 627
237. J.G. Zalatan, and D. Herschlag The far reaches of enzymology Nat. Chem. Biol. 5 8 2009 516 520
238. A. Zanghellini, and L. Jiang New algorithms and an in silico benchmark for computational enzyme design Protein Sci. 15 12 2006 2785 2794 (Pubitemid 44833759)
239. Y. Zhang Pseudobond ab initio QM/MM approach and its applications to enzyme reactions Theor. Chem. Acc. Theory Comput. Model. (Theor. Chim. Acta) 116 1 2006 43 50 (Pubitemid 44318414)
240. Y. Zhang, and H. Lin Self-consistent polarization of the boundary in the redistributed charge and dipole scheme for combined quantum-mechanical and molecular-mechanical calculations J. Chem. Theory Comput. 3 4 2007 1378 1398
241. Y. Zhou, and S. Wang Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations J. Phys. Chem. B 114 26 2010 8817 8825
242. K.T. Ziebart, and M.D. Toney Nucleophile specificity in anthranilate synthase, aminodeoxychorismate synthase, isochorismate synthase, and salicylate synthase Biochemistry 49 13 2010 2851 2859
243. K. Sanderson Chemistry: enzyme expertise Nature 471 2011 397