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Volumn 32, Issue , 2003, Pages 425-443

Computer simulations of enzyme catalysis: Methods, progress, and insights

Author keywords

Catalysis; EVB; QM MM; Transition state stabilization

Indexed keywords

CATALYSIS; COMPUTER MODEL; COMPUTER SIMULATION; ELECTRICITY; ENERGY; ENTROPY; ENZYME CONFORMATION; HUMAN; HYDROGEN BOND; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; QUANTUM MECHANICS; REACTION ANALYSIS; REVIEW;

EID: 0041876227     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.32.110601.141807     Document Type: Review
Times cited : (453)

References (76)
  • 1
    • 0033577302 scopus 로고    scopus 로고
    • Quantum mechanical dynamical effects in an enzyme-catalyzed proton transfer reaction
    • Alhambra C, Gao J, Corchado JC, Villà J, Truhlar DG. 1999. Quantum mechanical dynamical effects in an enzyme-catalyzed proton transfer reaction. J. Am. Chem. Soc. 121:2253-58
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 2253-2258
    • Alhambra, C.1    Gao, J.2    Corchado, J.C.3    Villà, J.4    Truhlar, D.G.5
  • 2
    • 0029989997 scopus 로고    scopus 로고
    • Computer simulation of the triosephosphate isomerase catalyzed reaction
    • Åqvist J, Fothergill M. 1996. Computer simulation of the triosephosphate isomerase catalyzed reaction. J. Biol. Chem. 271:10010-16
    • (1996) J. Biol. Chem. , vol.271 , pp. 10010-10016
    • Åqvist, J.1    Fothergill, M.2
  • 3
    • 4243810035 scopus 로고
    • Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
    • Åqvist J, Warshel A. 1993. Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches. Chem. Rev. 93:2523-44
    • (1993) Chem. Rev. , vol.93 , pp. 2523-2544
    • Åqvist, J.1    Warshel, A.2
  • 4
    • 0345713551 scopus 로고    scopus 로고
    • Hybrid models for combined quantum mechanical and molecular approaches
    • Bakowies D, Thiel W. 1996. Hybrid models for combined quantum mechanical and molecular approaches. J. Phys. Chem. 100:10580-94
    • (1996) J. Phys. Chem. , vol.100 , pp. 10580-10594
    • Bakowies, D.1    Thiel, W.2
  • 6
    • 11644294259 scopus 로고    scopus 로고
    • Hybrid ab initio quantum mechanics/molecular mechanics calculations of free energy surfaces for enzymatic reactions: The nucleophilic attack in subtilisin
    • Bentzien J, Muller RP, Florián J, Warshel A. 1998. Hybrid ab initio quantum mechanics/molecular mechanics calculations of free energy surfaces for enzymatic reactions: the nucleophilic attack in subtilisin. J. Phys. Chem. B 102:2293-301
    • (1998) J. Phys. Chem. B , vol.102 , pp. 2293-2301
    • Bentzien, J.1    Muller, R.P.2    Florián, J.3    Warshel, A.4
  • 7
    • 0035807631 scopus 로고    scopus 로고
    • A quantum mechanical approach to the study of reaction mechanisms of redox active metalloenzymes
    • Bloomberg MRA, Siegbahn PEM. 2001. A quantum mechanical approach to the study of reaction mechanisms of redox active metalloenzymes. J. Phys. Chem. 105:9376-86
    • (2001) J. Phys. Chem. , vol.105 , pp. 9376-9386
    • Bloomberg, M.R.A.1    Siegbahn, P.E.M.2
  • 8
    • 0034656302 scopus 로고    scopus 로고
    • So do we understand how enzymes work?
    • Blow D. 2000. So do we understand how enzymes work? Structure 8:R77-R81
    • (2000) Structure , vol.8
    • Blow, D.1
  • 9
    • 0036009145 scopus 로고    scopus 로고
    • A view at the millennium: The efficiency of enzymatic catalysis
    • Bruice TC. 2002. A view at the millennium: the efficiency of enzymatic catalysis. Acc. Chem. Res. 35:139-48
    • (2002) Acc. Chem. Res. , vol.35 , pp. 139-148
    • Bruice, T.C.1
  • 10
    • 4243606192 scopus 로고
    • Unified approach for molecular dynamics and density-functional theory
    • Car R, Parrinello M. 1985. Unified approach for molecular dynamics and density-functional theory. Phys. Rev. Lett. 55:2471-74
    • (1985) Phys. Rev. Lett. , vol.55 , pp. 2471-2474
    • Car, R.1    Parrinello, M.2
  • 11
    • 0037051671 scopus 로고    scopus 로고
    • Enzymatic GTP hydrolysis: Insights from an ab initio molecular dynamics study
    • Cavalli A, Carloni P. 2002. Enzymatic GTP hydrolysis: insights from an ab initio molecular dynamics study. J. Am Chem. Soc. 124:3763-68
    • (2002) J. Am Chem. Soc. , vol.124 , pp. 3763-3768
    • Cavalli, A.1    Carloni, P.2
  • 12
    • 0032475836 scopus 로고    scopus 로고
    • The low barrier hydrogen bond in enzymatic catalysis
    • Cleland WW, Frey PA, Gerlt JA. 1998. The low barrier hydrogen bond in enzymatic catalysis. J. Biol. Chem. 273:22529-32
    • (1998) J. Biol. Chem. , vol.273 , pp. 22529-22532
    • Cleland, W.W.1    Frey, P.A.2    Gerlt, J.A.3
  • 13
    • 34047262363 scopus 로고
    • Self-consistently determined properties of solids without band-structure calculations
    • Cortona P. 1991. Self-consistently determined properties of solids without band-structure calculations. Phys. Rev. B 44:8454-58
    • (1991) Phys. Rev. B , vol.44 , pp. 8454-8458
    • Cortona, P.1
  • 15
    • 0000928098 scopus 로고    scopus 로고
    • A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields
    • Eichinger M, Tavan P, Hutter J, Parrinello M. 1999. A hybrid method for solutes in complex solvents: density functional theory combined with empirical force fields. J. Chem. Phys. 110:10452-67
    • (1999) J. Chem. Phys. , vol.110 , pp. 10452-10467
    • Eichinger, M.1    Tavan, P.2    Hutter, J.3    Parrinello, M.4
  • 16
    • 0032657904 scopus 로고    scopus 로고
    • Implementation and testing of a frozen density matrix - Divide and conquer algorithm
    • Ermolaeva MD, van der Vaart A, Merz KM Jr. 1999. Implementation and testing of a frozen density matrix - divide and conquer algorithm. J. Phys. Chem. A 103:1868-75
    • (1999) J. Phys. Chem. A , vol.103 , pp. 1868-1875
    • Ermolaeva, M.D.1    Van Der Vaart, A.2    Merz K.M., Jr.3
  • 17
    • 0036025574 scopus 로고    scopus 로고
    • Computational modelling of enzymatic keto-enol isomerization reactions
    • Feierberg I, Åqvist J. 2002. Computational modelling of enzymatic keto-enol isomerization reactions. Theor. Chem. Acc. 108:71-84
    • (2002) Theor. Chem. Acc. , vol.108 , pp. 71-84
    • Feierberg, I.1    Åqvist, J.2
  • 18
    • 0037079574 scopus 로고    scopus 로고
    • Stimulating enzyme reactions: Challenges and perspectives
    • Field M. 2002. Stimulating enzyme reactions: challenges and perspectives. J. Comp. Chem. 23:48-58
    • (2002) J. Comp. Chem. , vol.23 , pp. 48-58
    • Field, M.1
  • 19
    • 84986513644 scopus 로고
    • A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
    • Field MJ, Bash PA, Karplus M. 1990. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comp. Chem. 11:700-33
    • (1990) J. Comp. Chem. , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 20
    • 0037118374 scopus 로고    scopus 로고
    • Comment on molecular mechanics for chemical reactions
    • Florian J. 2002. Comment on molecular mechanics for chemical reactions. J. Phys. Chem. A 106:5046-47
    • (2002) J. Phys. Chem. A , vol.106 , pp. 5046-5047
    • Florian, J.1
  • 21
    • 0037343349 scopus 로고    scopus 로고
    • Computer simulation studies of the fidelity of DNA polymerases
    • In press
    • Florian J, Goodman MF, Warshel A. 2003. Computer simulation studies of the fidelity of DNA polymerases. Biopolymers. In press
    • (2003) Biopolymers
    • Florian, J.1    Goodman, M.F.2    Warshel, A.3
  • 23
    • 0032054613 scopus 로고    scopus 로고
    • Quantum mechanical calculations on biological systems
    • Friesner R, Beachy MD. 1998. Quantum mechanical calculations on biological systems. Curr. Opin. Struct. Biol. 8:257-62
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 257-262
    • Friesner, R.1    Beachy, M.D.2
  • 24
    • 0032796313 scopus 로고    scopus 로고
    • Ab initio study of the role of lysine 16 for the molecular switching mechanism of Ras protein p21
    • Futatsugi N, Hata M, Hoshino T, Tsuda M. 1999. Ab initio study of the role of lysine 16 for the molecular switching mechanism of Ras protein p21. Biophys. J. 77:3287-92
    • (1999) Biophys. J. , vol.77 , pp. 3287-3292
    • Futatsugi, N.1    Hata, M.2    Hoshino, T.3    Tsuda, M.4
  • 25
    • 0001491955 scopus 로고    scopus 로고
    • Hybrid quantum and molecular mechanical simulations: An alternative avenue to solvent effects in organic chemistry
    • Gao J. 1996. Hybrid quantum and molecular mechanical simulations: an alternative avenue to solvent effects in organic chemistry. Acc. Chem. Res. 29:298-305
    • (1996) Acc. Chem. Res. , vol.29 , pp. 298-305
    • Gao, J.1
  • 26
    • 0035977645 scopus 로고    scopus 로고
    • A QM/MM study of the racemization of vinylglycolate catalysis by mandelate racemase enzyme
    • Garcia-Viloca M, Gonzalez-Lafont A, Lluch JM. 2001. A QM/MM study of the racemization of vinylglycolate catalysis by mandelate racemase enzyme. J. Am. Chem. Soc. 123:709-21
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 709-721
    • Garcia-Viloca, M.1    Gonzalez-Lafont, A.2    Lluch, J.M.3
  • 27
    • 0034663856 scopus 로고    scopus 로고
    • How does GAP catalyze the GTPase reaction of Ras? A computer simulation study
    • Glennon TM, Villà J, Warshel A. 2000. How does GAP catalyze the GTPase reaction of Ras? A computer simulation study. Biochemistry 39:9641-51
    • (2000) Biochemistry , vol.39 , pp. 9641-9651
    • Glennon, T.M.1    Villà, J.2    Warshel, A.3
  • 28
    • 0031575408 scopus 로고    scopus 로고
    • Energetics of nucleophile activation in a protein tyrosine phosphatase
    • Hansson T, Nordlund P, Åqvist J. 1997. Energetics of nucleophile activation in a protein tyrosine phosphatase. J. Mol. Biol. 265:118-27
    • (1997) J. Mol. Biol. , vol.265 , pp. 118-127
    • Hansson, T.1    Nordlund, P.2    Åqvist, J.3
  • 29
    • 0001325667 scopus 로고    scopus 로고
    • Constraining the electron densities in DFT method as an effective way for ab initio studies of metal catalyzed reactions
    • Hong G, Štrajbl M, Wesolowski TA, Warshel A. 2000. Constraining the electron densities in DFT method as an effective way for ab initio studies of metal catalyzed reactions. J. Comp. Chem. 21:1554-61
    • (2000) J. Comp. Chem. , vol.21 , pp. 1554-1561
    • Hong, G.1    Štrajbl, M.2    Wesolowski, T.A.3    Warshel, A.4
  • 32
    • 0037161268 scopus 로고    scopus 로고
    • Catalytic mechanism of enzymes: Preorganization, short strong hydrogen bond, and charges buffering
    • Kim K, Kim D, Lee JY, Tarakeshwar P, Oh KS. 2002. Catalytic mechanism of enzymes: preorganization, short strong hydrogen bond, and charges buffering. Biochemistry 41:5300-6
    • (2002) Biochemistry , vol.41 , pp. 5300-5306
    • Kim, K.1    Kim, D.2    Lee, J.Y.3    Tarakeshwar, P.4    Oh, K.S.5
  • 33
    • 0035948044 scopus 로고    scopus 로고
    • Prediction of electronic excited states of adsorbates on metal surfaces from first principles
    • Kluner T, Govind N, Wang YA, Carter EA. 2001. Prediction of electronic excited states of adsorbates on metal surfaces from first principles. Phys. Rev. Lett. 86:5954-57
    • (2001) Phys. Rev. Lett. , vol.86 , pp. 5954-5957
    • Kluner, T.1    Govind, N.2    Wang, Y.A.3    Carter, E.A.4
  • 34
    • 0019330479 scopus 로고
    • Catalytic acceleration of reactions by enzymes. Effect of screening of apolar medium by a protein globule
    • Krishtalik LI. 1980. Catalytic acceleration of reactions by enzymes. Effect of screening of apolar medium by a protein globule. J. Theor. Biol. 86:757-71
    • (1980) J. Theor. Biol. , vol.86 , pp. 757-771
    • Krishtalik, L.I.1
  • 35
    • 0001173909 scopus 로고
    • Transition-state stabilization in the mechanism of tyrosyl-trna synthetase revealed by protein engineering
    • Leatherbarrow RJ, Fersht AR, Winter G. 1985. Transition-state stabilization in the mechanism of tyrosyl-trna synthetase revealed by protein engineering. Proc. Natl. Acad. Sci. USA 82:7840-44
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 7840-7844
    • Leatherbarrow, R.J.1    Fersht, A.R.2    Winter, G.3
  • 36
    • 0026596911 scopus 로고
    • Calculations of antibody-antigen interactions: Microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to mcpc603
    • Lee FS, Chu ZT, Bolger MB, Warshel A. 1992. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to mcpc603. Protein Eng. 5:215-28
    • (1992) Protein Eng. , vol.5 , pp. 215-228
    • Lee, F.S.1    Chu, Z.T.2    Bolger, M.B.3    Warshel, A.4
  • 37
    • 0030912339 scopus 로고    scopus 로고
    • A proficient enzyme revisited: The predicted mechanism for orotidine monophosphate decarboxylase
    • Lee JK, Houk KN. 1997. A proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase. Science 276:942-45
    • (1997) Science , vol.276 , pp. 942-945
    • Lee, J.K.1    Houk, K.N.2
  • 38
    • 0042387289 scopus 로고    scopus 로고
    • Frozen density matrix approach for electronic structure calculations
    • Lee TS, Yang W. 1998. Frozen density matrix approach for electronic structure calculations. Int. J. Quant. Chem. 69:397-404
    • (1998) Int. J. Quant. Chem. , vol.69 , pp. 397-404
    • Lee, T.S.1    Yang, W.2
  • 39
    • 0000167881 scopus 로고
    • Insights into chorismate mutase catalysis from a combined QM/MM simulation of the enzyme reaction
    • Lyne PD, Mulholland AJ, Richards WG. 1995. Insights into chorismate mutase catalysis from a combined QM/MM simulation of the enzyme reaction. J. Am. Chem. Soc. 117:11345-50
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 11345-11350
    • Lyne, P.D.1    Mulholland, A.J.2    Richards, W.G.3
  • 40
    • 0010884753 scopus 로고
    • On the theory of oxidation-reduction reactions involving electron transfer
    • Marcus RA. 1956. On the theory of oxidation-reduction reactions involving electron transfer. J. Chem. Phys. 24:966-78
    • (1956) J. Chem. Phys. , vol.24 , pp. 966-978
    • Marcus, R.A.1
  • 41
    • 0035605891 scopus 로고    scopus 로고
    • Transition structure selectivity in enzyme catalysis: A QM/MM study of chorismate mutase
    • Marti S, Andres J, Moliner V, Silla E, Tunon I, Bertran J. 2001. Transition structure selectivity in enzyme catalysis: a QM/MM study of chorismate mutase. Theor. Chem. Acc. 105:207-12
    • (2001) Theor. Chem. Acc. , vol.105 , pp. 207-212
    • Marti, S.1    Andres, J.2    Moliner, V.3    Silla, E.4    Tunon, I.5    Bertran, J.6
  • 42
    • 0035997393 scopus 로고    scopus 로고
    • Catalytic proficiency: The unusual case of Omp decarboxylase
    • Miller B, Wolfenden R. 2002. Catalytic proficiency: the unusual case of Omp decarboxylase. Annu. Rev. Biochem. 71:847-85
    • (2002) Annu. Rev. Biochem. , vol.71 , pp. 847-885
    • Miller, B.1    Wolfenden, R.2
  • 43
    • 0038613083 scopus 로고    scopus 로고
    • NMR chemical shifts in the low-pH form of a-chymotrypsin. A QM/MM and ONIOM-NMR study
    • In press
    • Molina PA, Sikorski RS, Jensen JH. 2003. NMR chemical shifts in the low-pH form of a-chymotrypsin. A QM/MM and ONIOM-NMR study. Theor. Chem. Acc. In press
    • (2003) Theor. Chem. Acc.
    • Molina, P.A.1    Sikorski, R.S.2    Jensen, J.H.3
  • 44
    • 0032711930 scopus 로고    scopus 로고
    • Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems
    • Monard G, Merz KM. 1999. Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Acc. Chem. Res. 32:904-11
    • (1999) Acc. Chem. Res. , vol.32 , pp. 904-911
    • Monard, G.1    Merz, K.M.2
  • 45
    • 0034716340 scopus 로고    scopus 로고
    • Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved
    • Mulholland AJ, Lyne PD, Karplus M. 2000. Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved. J. Am Chem. Soc. 122:534-35
    • (2000) J. Am Chem. Soc. , vol.122 , pp. 534-535
    • Mulholland, A.J.1    Lyne, P.D.2    Karplus, M.3
  • 46
    • 84962477135 scopus 로고    scopus 로고
    • Characterization of low-barrier hydrogen bonds. 6. Cavity polarity effects on the formic acid-formate anion model system. An ab initio and DFT investigation
    • Pan Y, McAllister MA. 1998. Characterization of low-barrier hydrogen bonds. 6. Cavity polarity effects on the formic acid-formate anion model system. An ab initio and DFT investigation. J. Am. Chem. Soc. 120:166-69
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 166-169
    • Pan, Y.1    McAllister, M.A.2
  • 47
    • 33947547892 scopus 로고
    • Molecular architecture and biological reactions
    • Pauling L. 1946. Molecular architecture and biological reactions. Chem. Eng. News. 24:1375-77
    • (1946) Chem. Eng. News. , vol.24 , pp. 1375-1377
    • Pauling, L.1
  • 48
    • 0000211313 scopus 로고
    • Überadsorptionskatalyse Z
    • Polanyi M. 1921. Überadsorptionskatalyse Z. Elektrochem. 27:143-52
    • (1921) Elektrochem , vol.27 , pp. 143-152
    • Polanyi, M.1
  • 49
    • 2042457193 scopus 로고    scopus 로고
    • The buzz about a remarkable enzyme
    • Rouhi AM. 2000. The buzz about a remarkable enzyme. Chem. Eng. News. 78:42-46
    • (2000) Chem. Eng. News. , vol.78 , pp. 42-46
    • Rouhi, A.M.1
  • 50
    • 84962450020 scopus 로고    scopus 로고
    • How much do enzymes really gain by restraining their reacting fragments?
    • Shurki A, Štrajbl M, Villà J, Warshel A. 2002. How much do enzymes really gain by restraining their reacting fragments? J. Am. Chem. Soc. 124:4097-107
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 4097-4107
    • Shurki, A.1    Štrajbl, M.2    Villà, J.3    Warshel, A.4
  • 51
    • 2642622572 scopus 로고    scopus 로고
    • Combined ab initio and free energy calculations to study reactions in enzymes and solution: Amide hydrolysis in trypsin and aqueous solution
    • Stanton RV, Peräkylä M, Bakowies D, Kollman PA. 1998. Combined ab initio and free energy calculations to study reactions in enzymes and solution: amide hydrolysis in trypsin and aqueous solution. J. Am. Chem. Soc. 120:3448-57
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 3448-3457
    • Stanton, R.V.1    Peräkylä, M.2    Bakowies, D.3    Kollman, P.A.4
  • 52
    • 0037180863 scopus 로고    scopus 로고
    • Abinition QM/MM simulation with proper sampling: "fst principle" calculations of the free energy of the auto-dissociation of water in aqueous solution
    • Štrajbl M, Hong G, Warshel A. 2002. Abinition QM/MM simulation with proper sampling: "first principle" calculations of the free energy of the auto-dissociation of water in aqueous solution. J. Phys. Chem. B. 106:13333-43
    • (2002) J. Phys. Chem. B , vol.106 , pp. 13333-13343
    • Štrajbl, M.1    Hong, G.2    Warshel, A.3
  • 53
    • 0001214684 scopus 로고
    • Enzyme catalysis and transition structures in vacuo. Transition structures for the enolization, carboxylation and oxygenation reactions in ribulose-1,5-bisphosphate carboxylase/oxygenase enzyme (rubisco)
    • Tapia OA, Andrês J, Safront VS. 1994. Enzyme catalysis and transition structures in vacuo. Transition structures for the enolization, carboxylation and oxygenation reactions in ribulose-1,5-bisphosphate carboxylase/oxygenase enzyme (rubisco). J. Chem. Soc. Faraday Trans. 90:2365-74
    • (1994) J. Chem. Soc. Faraday Trans. , vol.90 , pp. 2365-2374
    • Tapia, O.A.1    Andrês, J.2    Safront, V.S.3
  • 54
    • 84986492373 scopus 로고
    • Quantum mechanical computations on very large molecular systems: The local self-consistent field method
    • Théry V, Rinaldi D, Rivail J-L, Maigret B, Ferenczy GG. 1994. Quantum mechanical computations on very large molecular systems: the local self-consistent field method. J. Comp. Chem. 15:269-82
    • (1994) J. Comp. Chem. , vol.15 , pp. 269-282
    • Théry, V.1    Rinaldi, D.2    Rivail, J.-L.3    Maigret, B.4    Ferenczy, G.G.5
  • 55
    • 0037118377 scopus 로고    scopus 로고
    • Reply to comment on molecular mechanics for chemical reactions
    • Truhlar DG. 2003. Reply to comment on molecular mechanics for chemical reactions. J. Phys. Chem. A 106(19):5048-50
    • (2003) J. Phys. Chem. A , vol.106 , Issue.19 , pp. 5048-5050
    • Truhlar, D.G.1
  • 56
    • 0031034836 scopus 로고    scopus 로고
    • On the quantum nature of the shared proton in hydrogen bonds
    • Tuckerman M, Marx D, Klein ML, Parrinello M. 1997. On the quantum nature of the shared proton in hydrogen bonds. Science 275:817-20
    • (1997) Science , vol.275 , pp. 817-820
    • Tuckerman, M.1    Marx, D.2    Klein, M.L.3    Parrinello, M.4
  • 58
    • 0035940264 scopus 로고    scopus 로고
    • Energetics and dynamics of enzymatic reactions
    • Villà J, Warshel A. 2001. Energetics and dynamics of enzymatic reactions. J. Phys. Chem. B 33:7887-907
    • (2001) J. Phys. Chem. B , vol.33 , pp. 7887-7907
    • Villà, J.1    Warshel, A.2
  • 59
    • 0034702677 scopus 로고    scopus 로고
    • The oniom (our own n-layered integrated molecular orbital + molecular mechanics) method for the first singlet excited (s1) state photoisomerization path of a retinal protonated Schiff base
    • Vreven T, Morokuma K. 2000. The oniom (our own n-layered integrated molecular orbital + molecular mechanics) method for the first singlet excited (s1) state photoisomerization path of a retinal protonated Schiff base. J. Chem. Phys. 113:2969-75
    • (2000) J. Chem. Phys. , vol.113 , pp. 2969-2975
    • Vreven, T.1    Morokuma, K.2
  • 60
    • 0000230329 scopus 로고
    • Energetics of enzyme catalysis
    • Warshel A. 1978. Energetics of enzyme catalysis. Proc. Natl. Acad. Sci. USA 75:5250-54
    • (1978) Proc. Natl. Acad. Sci. USA , vol.75 , pp. 5250-5254
    • Warshel, A.1
  • 62
    • 0032538627 scopus 로고    scopus 로고
    • Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites
    • Warshel A. 1998. Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites. J. Biol. Chem. 273:27035-38
    • (1998) J. Biol. Chem. , vol.273 , pp. 27035-27038
    • Warshel, A.1
  • 63
    • 0032568612 scopus 로고    scopus 로고
    • Computer simulations of enzyme catalysis: Finding out what has been optimized by evolution
    • Warshel A, Florian J. 1998. Computer simulations of enzyme catalysis: finding out what has been optimized by evolution. Proc. Natl. Acad. Sci. USA 95:5950-55
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5950-5955
    • Warshel, A.1    Florian, J.2
  • 64
    • 0017100947 scopus 로고
    • Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
    • Warshel A, Levitt M. 1976. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103:227-49
    • (1976) J. Mol. Biol. , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 66
    • 0030462453 scopus 로고    scopus 로고
    • Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds
    • Warshel A, Papazyan A. 1996. Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds. Proc. Natl. Acad. Sci. USA 93:13665-70
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 13665-13670
    • Warshel, A.1    Papazyan, A.2
  • 67
    • 0035707451 scopus 로고    scopus 로고
    • Dynamics of biochemical and biophysical reactions: Insight from computer simluations
    • Warshel A, Parson WW. 2001. Dynamics of biochemical and biophysical reactions: insight from computer simluations. Q. Rev. Biophys. 34:563-679
    • (2001) Q. Rev. Biophys. , vol.34 , pp. 563-679
    • Warshel, A.1    Parson, W.W.2
  • 68
    • 0034610398 scopus 로고    scopus 로고
    • Remarkable rate enhancement of orotidine 5′-monophosphate decarboxylase is due to transition state stabilization rather than ground state destabilization
    • Warshel A, Villà J, Štrajbl M, Florián J. 2000. Remarkable rate enhancement of orotidine 5′-monophosphate decarboxylase is due to transition state stabilization rather than ground state destabilization. Biochemistry 39:14728-38
    • (2000) Biochemistry , vol.39 , pp. 14728-14738
    • Warshel, A.1    Villà, J.2    Štrajbl, M.3    Florián, J.4
  • 69
    • 85038278888 scopus 로고    scopus 로고
    • Comment on "prediction of electronic excited states of adsorbates on metal surfaces from first principles." Phys
    • Wesolowski T. 2002. Comment on "prediction of electronic excited states of adsorbates on metal surfaces from first principles." Phys. Rev. Lett. 88:209701-1
    • (2002) Rev. Lett. , vol.88 , pp. 209701-209701
    • Wesolowski, T.1
  • 70
    • 33750447832 scopus 로고
    • Frozen density functional approach for ab initio calculations of solvated molecules
    • Wesolowski TA, Warshel A. 1993. Frozen density functional approach for ab initio calculations of solvated molecules. J. Phys. Chem. 97:8050-53
    • (1993) J. Phys. Chem. , vol.97 , pp. 8050-8053
    • Wesolowski, T.A.1    Warshel, A.2
  • 71
    • 0035543093 scopus 로고    scopus 로고
    • The depth of chemical time and the power of enzymes as catalysts
    • Wolfenden R, Snider MJ. 2001. The depth of chemical time and the power of enzymes as catalysts. Acc. Chem. Res. 34:938-45
    • (2001) Acc. Chem. Res. , vol.34 , pp. 938-945
    • Wolfenden, R.1    Snider, M.J.2
  • 72
    • 0031549622 scopus 로고    scopus 로고
    • A combined Car-Parrinello QM/MM implementation for ab initio molecular dynamics simulations of extended systems: Application to the transition metal catalysis
    • Woo TK, Margl PM, Blochl PE, Ziegler T. 1997. A combined Car-Parrinello QM/MM implementation for ab initio molecular dynamics simulations of extended systems: application to the transition metal catalysis. J. Phys. Chem. B 101:7877-80
    • (1997) J. Phys. Chem. B , vol.101 , pp. 7877-7880
    • Woo, T.K.1    Margl, P.M.2    Blochl, P.E.3    Ziegler, T.4
  • 73
    • 0034102419 scopus 로고    scopus 로고
    • Electrostatic stress in catalysis: Structure and mechanism of the enzyme orotidine monophosphate decarboxylase
    • Wu N, Mo Y, Gao J, Pai EF. 2000. Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. Proc. Natl. Acad. Sci. USA 97:2017-22
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 2017-2022
    • Wu, N.1    Mo, Y.2    Gao, J.3    Pai, E.F.4
  • 74
    • 0000561390 scopus 로고
    • Role of solvent reorganization energies in the catalytic activity of enzymes
    • Yadav A, Jackson RM, Holbrook JJ, Warshel A. 1991. Role of solvent reorganization energies in the catalytic activity of enzymes. J. Am. Chem. Soc. 113:4800-5
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 4800-4805
    • Yadav, A.1    Jackson, R.M.2    Holbrook, J.J.3    Warshel, A.4
  • 75
    • 0011621942 scopus 로고
    • Direct calculation of electron density in density-functional theory
    • Yang W. 1991. Direct calculation of electron density in density-functional theory. Phys. Rev. Lett. 66:1438-41
    • (1991) Phys. Rev. Lett. , vol.66 , pp. 1438-1441
    • Yang, W.1
  • 76
    • 0000145441 scopus 로고    scopus 로고
    • Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface
    • Zhang Y, Liu H, Yang W. 2000. Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface. J. Chem. Phys. 112:3483-92
    • (2000) J. Chem. Phys. , vol.112 , pp. 3483-3492
    • Zhang, Y.1    Liu, H.2    Yang, W.3


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