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Volumn 46, Issue 46, 2007, Pages 13352-13369

The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DENSITY FUNCTIONAL THEORY; ELECTRONIC STRUCTURE; FREE ENERGY; HYDROLYSIS; MOLECULAR MECHANICS; QUANTUM THEORY;

EID: 36248990205     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi700460c     Document Type: Article
Times cited : (131)

References (110)
  • 1
    • 0036273082 scopus 로고    scopus 로고
    • Bacterial detoxification of organophosphate nerve agents
    • Raushel, F. M. (2002) Bacterial detoxification of organophosphate nerve agents, Curr. Opin. Microbiol. 5, 288-295.
    • (2002) Curr. Opin. Microbiol , vol.5 , pp. 288-295
    • Raushel, F.M.1
  • 2
    • 0029923114 scopus 로고    scopus 로고
    • Molecular aspects of pesticide degradation by microorganisms
    • Kumar, S., Mukerji, K. G., and Lai, R. (1996) Molecular aspects of pesticide degradation by microorganisms, Crit. Rev. Microbiol. 22, 1-26.
    • (1996) Crit. Rev. Microbiol , vol.22 , pp. 1-26
    • Kumar, S.1    Mukerji, K.G.2    Lai, R.3
  • 4
    • 0026748791 scopus 로고
    • Characterization of the zinc binding site of bacterial phosphotriesterase
    • Omburo, G. A., Kuo, J. M., Mullins, L. S., and Raushel, F. M. (1992) Characterization of the zinc binding site of bacterial phosphotriesterase, J. Biol. Chem. 267, 13278-13283.
    • (1992) J. Biol. Chem , vol.267 , pp. 13278-13283
    • Omburo, G.A.1    Kuo, J.M.2    Mullins, L.S.3    Raushel, F.M.4
  • 5
    • 0026235932 scopus 로고
    • Detoxification of organophosphate pesticides using a nylon based immobilized phosphotriesterase from Pseudomonas diminuta
    • Caldwell, S. R., and Raushel, F. M. (1991) Detoxification of organophosphate pesticides using a nylon based immobilized phosphotriesterase from Pseudomonas diminuta, Appl. Biochem. Biotechnol. 31, 59-73.
    • (1991) Appl. Biochem. Biotechnol , vol.31 , pp. 59-73
    • Caldwell, S.R.1    Raushel, F.M.2
  • 6
    • 0026071672 scopus 로고    scopus 로고
    • Detoxification of organophosphate pesticides using an immobilized phosphotriesterase from Pseudomonas diminuta
    • Caldwell, S. R., and Raushel, F. M. (2006) Detoxification of organophosphate pesticides using an immobilized phosphotriesterase from Pseudomonas diminuta, Biotechnol. Bioeng. 37, 103-109.
    • (2006) Biotechnol. Bioeng , vol.37 , pp. 103-109
    • Caldwell, S.R.1    Raushel, F.M.2
  • 8
    • 0037068856 scopus 로고    scopus 로고
    • Coordination Geometries of Zn(II) and Cd(II) in Phosphotriesterase: Influence of Water Molecules in the Active Site
    • Krauss, M., Olsen, L., Antony, J., and Hemmingsen, L. (2002) Coordination Geometries of Zn(II) and Cd(II) in Phosphotriesterase: Influence of Water Molecules in the Active Site, J. Phys. Chem. B 106, 9446-9453.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 9446-9453
    • Krauss, M.1    Olsen, L.2    Antony, J.3    Hemmingsen, L.4
  • 9
    • 0035234441 scopus 로고    scopus 로고
    • Ab Initio Structure of the Active Site of Phosphotriesterase
    • Krauss, M. (2001) Ab Initio Structure of the Active Site of Phosphotriesterase, J. Chem. Inf. Model. 41, 8-17.
    • (2001) J. Chem. Inf. Model , vol.41 , pp. 8-17
    • Krauss, M.1
  • 10
    • 0001099193 scopus 로고    scopus 로고
    • Ab initio determination of the structure of the active site of a metalloenzyme: Metal substitution in phosphotriesterase using density functional methods
    • Kafafi, S. A., and Krauss, M. (1999) Ab initio determination of the structure of the active site of a metalloenzyme: Metal substitution in phosphotriesterase using density functional methods, Int. J. Quantum Chem. 75, 289-299.
    • (1999) Int. J. Quantum Chem , vol.75 , pp. 289-299
    • Kafafi, S.A.1    Krauss, M.2
  • 11
    • 0035819590 scopus 로고    scopus 로고
    • Koča, J., Zhan, C. G., Rittenhouse, R. C., and Ornstein, R. L. (2001) Mobility of the Active Site Bound Paraoxon and Sarin in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Quantum Chemical Calculation, J. Am. Chem. Soc. 123, 817-826.
    • Koča, J., Zhan, C. G., Rittenhouse, R. C., and Ornstein, R. L. (2001) Mobility of the Active Site Bound Paraoxon and Sarin in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Quantum Chemical Calculation, J. Am. Chem. Soc. 123, 817-826.
  • 12
    • 0037328259 scopus 로고    scopus 로고
    • Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics
    • Koča, J., Zhan, C.-G., Rittenhouse, R. C., and Ornstein, R. L. (2003) Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics, J. Comput. Chem. 24, 368-378.
    • (2003) J. Comput. Chem , vol.24 , pp. 368-378
    • Koča, J.1    Zhan, C.-G.2    Rittenhouse, R.C.3    Ornstein, R.L.4
  • 13
    • 0033581183 scopus 로고    scopus 로고
    • Zhan, C. G., de Souza, O. N., Rittenhouse, R., and Ornstein, R. L. (1999) Determination of Two Structural Forms of Catalytic Bridging Ligand in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Quantum Chemical Calculation, J. Am. Chem. Soc. 121, 7279-7282.
    • Zhan, C. G., de Souza, O. N., Rittenhouse, R., and Ornstein, R. L. (1999) Determination of Two Structural Forms of Catalytic Bridging Ligand in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Quantum Chemical Calculation, J. Am. Chem. Soc. 121, 7279-7282.
  • 14
    • 0037165455 scopus 로고    scopus 로고
    • Theoretical Determination of Two Structural Forms of the Active Site in Cadmium-Containing Phosphotriesterases
    • Zheng, F., Zhan, C. G., and Ornstein, R. L. (2002) Theoretical Determination of Two Structural Forms of the Active Site in Cadmium-Containing Phosphotriesterases, J. Phys. Chem. B 106, 717-722.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 717-722
    • Zheng, F.1    Zhan, C.G.2    Ornstein, R.L.3
  • 15
    • 0035543503 scopus 로고    scopus 로고
    • Theoretical studies of reaction pathways and energy barriers for alkaline hydrolysis of phosphotriesterase substrates paraoxon and related toxic phosphofluoridate nerve agents
    • Zheng, F., Zhan, C.-G., and Ornstein, R. L. (2001) Theoretical studies of reaction pathways and energy barriers for alkaline hydrolysis of phosphotriesterase substrates paraoxon and related toxic phosphofluoridate nerve agents, J. Chem. Soc., Perkin Trans. 2, 2355-2363.
    • (2001) J. Chem. Soc., Perkin Trans , vol.2 , pp. 2355-2363
    • Zheng, F.1    Zhan, C.-G.2    Ornstein, R.L.3
  • 16
    • 0035889687 scopus 로고    scopus 로고
    • Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method
    • Pang, Y.-P. (2001) Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method, Proteins: Struct., Funct., Genet. 45, 183-189.
    • (2001) Proteins: Struct., Funct., Genet , vol.45 , pp. 183-189
    • Pang, Y.-P.1
  • 17
    • 27444433822 scopus 로고    scopus 로고
    • Ab Initio Molecular Orbital and Density Functional Studies on the Solvolysis of Sarin and O,S-Dimethyl Methylphosphonothiolate, a VX-like Compound
    • Šečkute, J., Menke, J. L., Emnett, R. J., Patterson, E. V., and Cramer, C. J. (2005) Ab Initio Molecular Orbital and Density Functional Studies on the Solvolysis of Sarin and O,S-Dimethyl Methylphosphonothiolate, a VX-like Compound, J. Org. Chem. 70, 8649-8660.
    • (2005) J. Org. Chem , vol.70 , pp. 8649-8660
    • Šečkute, J.1    Menke, J.L.2    Emnett, R.J.3    Patterson, E.V.4    Cramer, C.J.5
  • 18
    • 2442496666 scopus 로고    scopus 로고
    • Mechanism for the Hydrolysis of Organophosphates by the Bacterial Phosphotriesterase
    • Aubert, S. D., Li, Y., and Raushel, F. M. (2004) Mechanism for the Hydrolysis of Organophosphates by the Bacterial Phosphotriesterase, Biochemistry 43, 5707-5715.
    • (2004) Biochemistry , vol.43 , pp. 5707-5715
    • Aubert, S.D.1    Li, Y.2    Raushel, F.M.3
  • 19
    • 33748584863 scopus 로고    scopus 로고
    • Mechanisms and free energies of enzymatic reactions
    • Gao, J., Ma, S., Major, D. T., Nam, K., Pu, J., and Truhlar, D. G. (2006) Mechanisms and free energies of enzymatic reactions, Chem. Rev. 106, 3188-3209.
    • (2006) Chem. Rev , vol.106 , pp. 3188-3209
    • Gao, J.1    Ma, S.2    Major, D.T.3    Nam, K.4    Pu, J.5    Truhlar, D.G.6
  • 20
    • 84962367344 scopus 로고
    • Methods and applications of combined quantum mechanical and molecular mechanical potentials
    • Gao, J. (1995) Methods and applications of combined quantum mechanical and molecular mechanical potentials, Rev. Comput. Chem. 7, 119-185.
    • (1995) Rev. Comput. Chem , vol.7 , pp. 119-185
    • Gao, J.1
  • 21
    • 0029993512 scopus 로고    scopus 로고
    • Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with the Bound Substrate Analog Diethyl 4-Methylbenzylphosphonate
    • Vanhooke, J. L., Benning, M. M., Raushel, F. M., and Holden, H. M. (1996) Three-Dimensional Structure of the Zinc-Containing Phosphotriesterase with the Bound Substrate Analog Diethyl 4-Methylbenzylphosphonate, Biochemistry 35, 6020-6025.
    • (1996) Biochemistry , vol.35 , pp. 6020-6025
    • Vanhooke, J.L.1    Benning, M.M.2    Raushel, F.M.3    Holden, H.M.4
  • 22
    • 0034730534 scopus 로고    scopus 로고
    • The Binding of Substrate Analogs to Phosphotriesterase
    • Benning, M. M., Hong, S.-B., Raushel, F. M., and Holden, H. M. (2000) The Binding of Substrate Analogs to Phosphotriesterase, J. Biol. Chem. 275, 30556-30560.
    • (2000) J. Biol. Chem , vol.275 , pp. 30556-30560
    • Benning, M.M.1    Hong, S.-B.2    Raushel, F.M.3    Holden, H.M.4
  • 23
    • 0001431264 scopus 로고    scopus 로고
    • Binuclear metallohydrolases
    • Wilcox, D. E. (1996) Binuclear metallohydrolases, Chem. Rev. 96, 2435-2458.
    • (1996) Chem. Rev , vol.96 , pp. 2435-2458
    • Wilcox, D.E.1
  • 25
    • 0025836538 scopus 로고
    • Limits of diffusion in the hydrolysis of substrates by the phosphotriesterase from Pseudomonas diminuta
    • Caldwell, S. R., Newcomb, J. R., Schlecht, K. A., and Raushel, F. M. (1991) Limits of diffusion in the hydrolysis of substrates by the phosphotriesterase from Pseudomonas diminuta, Biochemistry 30, 7438-7444.
    • (1991) Biochemistry , vol.30 , pp. 7438-7444
    • Caldwell, S.R.1    Newcomb, J.R.2    Schlecht, K.A.3    Raushel, F.M.4
  • 26
    • 33748591572 scopus 로고    scopus 로고
    • Enzymatic mechanisms of phosphate and sulfate transfer
    • Cleland, W. W., and Hengge, A. C. (2006) Enzymatic mechanisms of phosphate and sulfate transfer, Chem. Rev. 106, 3252-3278.
    • (2006) Chem. Rev , vol.106 , pp. 3252-3278
    • Cleland, W.W.1    Hengge, A.C.2
  • 27
    • 0033604866 scopus 로고    scopus 로고
    • Stereochemical Constraints on the Substrate Specificity of Phosphotriesterase
    • Hong, S. B., and Raushel, F. M. (1999) Stereochemical Constraints on the Substrate Specificity of Phosphotriesterase, Biochemistry 38, 1159-1165.
    • (1999) Biochemistry , vol.38 , pp. 1159-1165
    • Hong, S.B.1    Raushel, F.M.2
  • 28
    • 0035814818 scopus 로고    scopus 로고
    • Structural Determinants of the Substrate and Stereochemical Specificity of Phosphotriesterase
    • Chen-Goodspeed, M., Sogorb, M. A., Wu, F., Hong, S. B., and Raushel, F. M. (2001) Structural Determinants of the Substrate and Stereochemical Specificity of Phosphotriesterase, Biochemistry 40, 1325-1331.
    • (2001) Biochemistry , vol.40 , pp. 1325-1331
    • Chen-Goodspeed, M.1    Sogorb, M.A.2    Wu, F.3    Hong, S.B.4    Raushel, F.M.5
  • 29
    • 0024281297 scopus 로고
    • Mechanism and stereochemical course at phosphorus of the reaction catalyzed by a bacterial phosphotriesterase
    • Lewis, V. E., Donarski, W. J., Wild, J. R., and Raushel, F. M. (1988) Mechanism and stereochemical course at phosphorus of the reaction catalyzed by a bacterial phosphotriesterase, Biochemistry 27, 1591-1597.
    • (1988) Biochemistry , vol.27 , pp. 1591-1597
    • Lewis, V.E.1    Donarski, W.J.2    Wild, J.R.3    Raushel, F.M.4
  • 30
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic behavior
    • Becke, A. D. (1988) Density-functional exchange-energy approximation with correct asymptotic behavior, Phys. Rev. A 38, 3098.
    • (1988) Phys. Rev. A , vol.38 , pp. 3098
    • Becke, A.D.1
  • 31
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    • Lee, C., Yang, W., and Parr, R. G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B 37, 785.
    • (1988) Phys. Rev. B , vol.37 , pp. 785
    • Lee, C.1    Yang, W.2    Parr, R.G.3
  • 32
    • 33751157732 scopus 로고
    • Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force
    • Stephens, P. J., Devlin, F. J., Chabalowski, C. F., and Frisch, M. J. (1994) Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force, J. Phys. Chem. 98, 11623.
    • (1994) J. Phys. Chem , vol.98 , pp. 11623
    • Stephens, P.J.1    Devlin, F.J.2    Chabalowski, C.F.3    Frisch, M.J.4
  • 33
    • 4243810035 scopus 로고
    • Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
    • Aqvist, J., and Warshel, A. (1993) Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches, Chem. Rev. 93, 2523-2544.
    • (1993) Chem. Rev , vol.93 , pp. 2523-2544
    • Aqvist, J.1    Warshel, A.2
  • 34
    • 84986513644 scopus 로고
    • A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
    • Field, M. J., Bash, P. A., and Karplus, M. (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations, J. Comput. Chem. 11, 700-733.
    • (1990) J. Comput. Chem , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 35
    • 0027125907 scopus 로고
    • A prior evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations
    • Gao, J., and Xia, X. (1992) A prior evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations, Science 258, 631-635.
    • (1992) Science , vol.258 , pp. 631-635
    • Gao, J.1    Xia, X.2
  • 36
    • 0035786390 scopus 로고    scopus 로고
    • The QM/MM approach to enzymatic reactions
    • Mulholland, A. J. (2001) The QM/MM approach to enzymatic reactions, Theor. Comput. Chem. 9, 597-653.
    • (2001) Theor. Comput. Chem , vol.9 , pp. 597-653
    • Mulholland, A.J.1
  • 37
    • 0346726109 scopus 로고    scopus 로고
    • How enzymes work: Analysis by modern rate theory and computer simulations
    • Garcia-Viloca, M., Gao, J., Karplus, M., and Truhlar, D. G. (2004) How enzymes work: Analysis by modern rate theory and computer simulations, Science 303, 186-195.
    • (2004) Science , vol.303 , pp. 186-195
    • Garcia-Viloca, M.1    Gao, J.2    Karplus, M.3    Truhlar, D.G.4
  • 38
    • 0036025446 scopus 로고    scopus 로고
    • Quantum mechanical methods for enzyme kinetics
    • Gao, J., and Truhlar, D. G. (2002) Quantum mechanical methods for enzyme kinetics, Annu. Rev. Phys. Chem. 53, 467-505.
    • (2002) Annu. Rev. Phys. Chem , vol.53 , pp. 467-505
    • Gao, J.1    Truhlar, D.G.2
  • 39
    • 0000078321 scopus 로고
    • Potential of mean force for the isomerization of DMF in aqueous solution: A Monte Carlo QM/MM simulation study
    • Gao, J. (1993) Potential of mean force for the isomerization of DMF in aqueous solution: a Monte Carlo QM/MM simulation study, J. Am. Chem. Soc. 115, 2930-2935.
    • (1993) J. Am. Chem. Soc , vol.115 , pp. 2930-2935
    • Gao, J.1
  • 40
    • 0028408529 scopus 로고
    • Origin of the solvent effects on the barrier to amide isomerization from combined QM/MM Monte Carlo simulations
    • Gao, J. (1994) Origin of the solvent effects on the barrier to amide isomerization from combined QM/MM Monte Carlo simulations, Proc. - Indian Acad. Sci., Chem. Sci. 106, 507-519.
    • (1994) Proc. - Indian Acad. Sci., Chem. Sci , vol.106 , pp. 507-519
    • Gao, J.1
  • 41
    • 0034798239 scopus 로고    scopus 로고
    • New Insight on the Origin of the Unusual Acidity of Meldrum's Acid from ab Initio and Combined QM/MM Simulation Study
    • Byun, K., Mo, Y., and Gao, J. (2001) New Insight on the Origin of the Unusual Acidity of Meldrum's Acid from ab Initio and Combined QM/MM Simulation Study, J. Am. Chem. Soc. 123, 3974-3979.
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 3974-3979
    • Byun, K.1    Mo, Y.2    Gao, J.3
  • 44
    • 0011123246 scopus 로고
    • AM1 parameters for phosphorus
    • Dewar, M. J. S., and Jie, C. (1989) AM1 parameters for phosphorus, THEOCHEM 187, 1-13.
    • (1989) THEOCHEM 187 , pp. 1-13
    • Dewar, M.J.S.1    Jie, C.2
  • 45
    • 0000411659 scopus 로고    scopus 로고
    • A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations
    • Gao, J., Amara, P., Alhambra, C., and Field, M. J. (1998) A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations, J. Phys. Chem. A 102, 4714-4721.
    • (1998) J. Phys. Chem. A , vol.102 , pp. 4714-4721
    • Gao, J.1    Amara, P.2    Alhambra, C.3    Field, M.J.4
  • 46
    • 0034375393 scopus 로고    scopus 로고
    • The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: Formulation and tests of the analytical derivatives
    • Amara, P., Field, M. J., Alhambra, C., and Gao, J. (2000) The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives, Theor. Chem. Acc. 104, 336-343.
    • (2000) Theor. Chem. Acc , vol.104 , pp. 336-343
    • Amara, P.1    Field, M.J.2    Alhambra, C.3    Gao, J.4
  • 47
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B 102, 3586-3616.
    • MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B 102, 3586-3616.
  • 51
    • 21244497608 scopus 로고    scopus 로고
    • Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
    • Friesner, R. A., and Guallar, V. (2005) Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis, Annu. Rev. Phys. Chem. 56, 389-427.
    • (2005) Annu. Rev. Phys. Chem , vol.56 , pp. 389-427
    • Friesner, R.A.1    Guallar, V.2
  • 52
    • 0035785737 scopus 로고    scopus 로고
    • Simulations of enzymatic systems: Perspectives from Car-Parrinello molecular dynamics simulations
    • Carloni, P., and Rothlisberger, U. (2001) Simulations of enzymatic systems: Perspectives from Car-Parrinello molecular dynamics simulations, Theor. Comput. Chem. 9, 215-251.
    • (2001) Theor. Comput. Chem , vol.9 , pp. 215-251
    • Carloni, P.1    Rothlisberger, U.2
  • 53
    • 0025390935 scopus 로고
    • MOPAC: A semiempirical molecular orbital program
    • Stewart, J. J. P. (1990) MOPAC: a semiempirical molecular orbital program, J. Comput.-Aided Mol. Des. 4, 1-105.
    • (1990) J. Comput.-Aided Mol. Des , vol.4 , pp. 1-105
    • Stewart, J.J.P.1
  • 55
    • 29244444539 scopus 로고    scopus 로고
    • Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium-Chain Acyl-CoA Dehydrogenase: Effect of Mutations on Enzyme Catalysis
    • Bhattacharyya, S., Ma, S., Stankovich, M. T., Truhlar, D. G., and Gao, J. (2005) Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium-Chain Acyl-CoA Dehydrogenase: Effect of Mutations on Enzyme Catalysis, Biochemistry 44, 16549-16562.
    • (2005) Biochemistry , vol.44 , pp. 16549-16562
    • Bhattacharyya, S.1    Ma, S.2    Stankovich, M.T.3    Truhlar, D.G.4    Gao, J.5
  • 56
    • 5444222194 scopus 로고    scopus 로고
    • PM3-compatible zinc parameters optimized for metalloenzyme active sites
    • Brothers, E. N., Suarez, D., Deerfield, D. W., II, and Merz, K. M., Jr. (2004) PM3-compatible zinc parameters optimized for metalloenzyme active sites, J. Comput. Chem. 25, 1677-1692.
    • (2004) J. Comput. Chem , vol.25 , pp. 1677-1692
    • Brothers, E.N.1    Suarez, D.2    Deerfield II, D.W.3    Merz Jr., K.M.4
  • 57
    • 34547625687 scopus 로고    scopus 로고
    • A specific reaction parameterization of the AM1/d Hamiltonian for phosphoryl transfer reactions
    • (a) Nam, K., Cui, Q., Gao, J., and York, D. M. (2007) A specific reaction parameterization of the AM1/d Hamiltonian for phosphoryl transfer reactions, J. Chem. Theory Comput. 3, 486-504.
    • (2007) J. Chem. Theory Comput , vol.3 , pp. 486-504
    • Nam, K.1    Cui, Q.2    Gao, J.3    York, D.M.4
  • 58
    • 0037718593 scopus 로고    scopus 로고
    • Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus
    • (b) Lopez, X., and York, D. M. (2003) Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus, Theor. Chem. Acc. 109, 149-159.
    • (2003) Theor. Chem. Acc , vol.109 , pp. 149-159
    • Lopez, X.1    York, D.M.2
  • 59
    • 0347174862 scopus 로고    scopus 로고
    • Dual-level methods for electronic structure calculations of potential energy functions that use quantum mechanics as the lower level
    • Gao, J, and Thompson, M. A, Eds, pp, American Chemical Society, Wahsington, DC
    • Corchado, J. C., and Truhlar, D. G. (1998) Dual-level methods for electronic structure calculations of potential energy functions that use quantum mechanics as the lower level, in Combined Quantum Mechanical and Molecular Mechanical Methods (Gao, J., and Thompson, M. A., Eds.) pp 106-127, American Chemical Society, Wahsington, DC.
    • (1998) Combined Quantum Mechanical and Molecular Mechanical Methods , pp. 106-127
    • Corchado, J.C.1    Truhlar, D.G.2
  • 60
    • 0000556829 scopus 로고    scopus 로고
    • A Hybrid-Potential Free-Energy Study of the Isomerization Step of the Acetohydroxy Acid Isomeroreductase Reaction
    • Proust-De Martin, F., Dumas, R., and Field, M. J. (2000) A Hybrid-Potential Free-Energy Study of the Isomerization Step of the Acetohydroxy Acid Isomeroreductase Reaction, J. Am. Chem. Soc. 122, 7688-7697.
    • (2000) J. Am. Chem. Soc , vol.122 , pp. 7688-7697
    • Proust-De Martin, F.1    Dumas, R.2    Field, M.J.3
  • 61
    • 15544388511 scopus 로고    scopus 로고
    • Computing Kinetic Isotope Effects for Chorismate Mutase with High Accuracy. A New DFT/MM Strategy
    • Marti, S., Moliner, V., Tunon, I., and Williams, I. H. (2005) Computing Kinetic Isotope Effects for Chorismate Mutase with High Accuracy. A New DFT/MM Strategy, J. Phys. Chem. B 109, 3707-3710.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 3707-3710
    • Marti, S.1    Moliner, V.2    Tunon, I.3    Williams, I.H.4
  • 62
    • 33845926809 scopus 로고    scopus 로고
    • Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems
    • Marti, S., Moliner, V., and Tunon, I. (2005) 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 Comput. 1, 1008-1016.
    • (2005) J. Chem. Theory Comput , vol.1 , pp. 1008-1016
    • Marti, S.1    Moliner, V.2    Tunon, I.3
  • 63
    • 29644433206 scopus 로고    scopus 로고
    • A QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical Descriptions
    • Ferrer, S., Ruiz-Pernia, J. J., Tunon, I., Moliner, V., Garcia-Viloca, M., Gonzalez-Lafont, A., and Lluch, J. M. (2005) A QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical Descriptions, J. Chem. Theory Comput. 1, 750-761.
    • (2005) J. Chem. Theory Comput , vol.1 , pp. 750-761
    • Ferrer, S.1    Ruiz-Pernia, J.J.2    Tunon, I.3    Moliner, V.4    Garcia-Viloca, M.5    Gonzalez-Lafont, A.6    Lluch, J.M.7
  • 64
    • 33646508010 scopus 로고    scopus 로고
    • Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase
    • Rod, T. H., and Ryde, U. (2005) Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase, J. Chem. Theory Comput. 1, 1240-1251.
    • (2005) J. Chem. Theory Comput , vol.1 , pp. 1240-1251
    • Rod, T.H.1    Ryde, U.2
  • 65
    • 31144441067 scopus 로고    scopus 로고
    • ONIOM: A Multi-Layered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels-Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition
    • Svensson, M., Humbel, S., Froese, R. D. J., Matsubara, T., Sieber, S., and Morokuma, K. (1996) ONIOM: A Multi-Layered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels-Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition, J. Phys. Chem. 100, 19357-19363.
    • (1996) J. Phys. Chem , vol.100 , pp. 19357-19363
    • Svensson, M.1    Humbel, S.2    Froese, R.D.J.3    Matsubara, T.4    Sieber, S.5    Morokuma, K.6
  • 66
    • 0345713551 scopus 로고    scopus 로고
    • Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches
    • Bakowies, D., and Thiel, W. (1996) Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches, J. Phys. Chem. 100, 10580-10594.
    • (1996) J. Phys. Chem , vol.100 , pp. 10580-10594
    • Bakowies, D.1    Thiel, W.2
  • 67
    • 0037459224 scopus 로고    scopus 로고
    • Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase
    • Garcia-Viloca, M., Truhlar Donald, G., and Gao, J. (2003) Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase, J. Mol. Biol. 327, 549-560.
    • (2003) J. Mol. Biol , vol.327 , pp. 549-560
    • Garcia-Viloca, M.1    Truhlar Donald, G.2    Gao, J.3
  • 68
    • 84962407457 scopus 로고    scopus 로고
    • Orozco, M., Luque, F. J., Habibollahzadeh, D., and Gao, J. (1995) The polarization contribution to the free energy of hydration, J. Chem. Phys. 102, 6145-6152. Erratum, J. Chem. Phys. 103, 9112.
    • Orozco, M., Luque, F. J., Habibollahzadeh, D., and Gao, J. (1995) The polarization contribution to the free energy of hydration, J. Chem. Phys. 102, 6145-6152. Erratum, J. Chem. Phys. 103, 9112.
  • 69
    • 0001491955 scopus 로고    scopus 로고
    • Hybrid Quantum Mechanical/Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry
    • Gao, J. (1996) Hybrid Quantum Mechanical/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
  • 70
    • 5244287607 scopus 로고
    • An Automated Procedure for Simulating Chemical Reactions in Solution. Application to the Decarboxylation of 3-Carboxybenzisoxazole in Water
    • Gao, J. (1995) An Automated Procedure for Simulating Chemical Reactions in Solution. Application to the Decarboxylation of 3-Carboxybenzisoxazole in Water, J. Am. Chem. Soc. 117, 8600-8607.
    • (1995) J. Am. Chem. Soc , vol.117 , pp. 8600-8607
    • Gao, J.1
  • 71
    • 0000342940 scopus 로고    scopus 로고
    • Ab initio QM/MM simulations with a molecular orbital-valence bond (MOVB) method: Application to an SN2 reaction in water
    • Mo, Y., and Gao, J. (2000) Ab initio QM/MM simulations with a molecular orbital-valence bond (MOVB) method: application to an SN2 reaction in water, J. Comput. Chem. 21, 1458-1469.
    • (2000) J. Comput. Chem , vol.21 , pp. 1458-1469
    • Mo, Y.1    Gao, J.2
  • 72
    • 0031490976 scopus 로고    scopus 로고
    • Solvent effects on the n → π* transition of pyrimidine in aqueous solution
    • Gao, J., and Byun, K. (1997) Solvent effects on the n → π* transition of pyrimidine in aqueous solution, Theor. Chem. Acc. 96, 151-156.
    • (1997) Theor. Chem. Acc , vol.96 , pp. 151-156
    • Gao, J.1    Byun, K.2
  • 73
    • 0000188281 scopus 로고    scopus 로고
    • The MIDI! basis set for quantum mechanical calculations of molecular geometries and partial charges
    • Easton, R. E., Giesen, D. J., Welch, A., Cramer, C. J., and Truhlar, D. G. (1996) The MIDI! basis set for quantum mechanical calculations of molecular geometries and partial charges, Theor. Chim. Acta 93, 281-301.
    • (1996) Theor. Chim. Acta , vol.93 , pp. 281-301
    • Easton, R.E.1    Giesen, D.J.2    Welch, A.3    Cramer, C.J.4    Truhlar, D.G.5
  • 74
    • 36249029970 scopus 로고    scopus 로고
    • Frisch, M. J, Trucks, G. W, Schlegel, H. B, Scuseria, G. E, Robb, M. A, Cheeseman, J. R, Montgomery, J. A, Jr, Vreven, T, Kudin, K. N, Burant, J. C, Millam, J. M, Iyengar, S. S, Tomasi, J, Barone, V, Mennucci, B, Cossi, M, Scalmani, G, Rega, N, Petersson, G. A, Nakatsuji, H, Hada, M, Ehara, M, Toyota, K, Fukuda, R, Hasegawa, J, Ishida, M, Nakajima, T, Honda, Y, Kitao, O, Nakai, H, Klene, M, Li, X, Knox, J. E, Hratchian, H. P, Cross, J. B, Bakken, V, Adamo, C, Jaramillo, J, Gomperts, R, Stratmann, R. E, Yazyev, O, Austin, A. J, Cammi, R, Pomelli, C, Ochterski, J. W, Ayala, P. Y, Morokuma, K, Voth, G. A, Salvador, P, Dannenberg, J. J, Zakrzewski, V. G, Dapprich, S, Daniels, A. D, Strain, M. C, Farkas, O, Malick, D. K, Rabuck, A. D, Raghavachari, K, Foresman, J. B, Ortiz, J. V, Cui, Q, Baboul, A. G, Clifford, S, Cioslowski, J, Stefanov, B. B, Liu, G, Liashenko, A, Piskorz, P, Komaromi, I, Martin, R. L, Fox, D. J, Keit
    • Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Jr., Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., and Pople, J. A. (2004) Gaussian 03, revision C.02, Gaussian, Inc., Wallingford, CT.
  • 77
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood, J. G. (1935) Statistical mechanics of fluid mixtures, J. Chem. Phys. 3, 300-313.
    • (1935) J. Chem. Phys , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 78
    • 0035940264 scopus 로고    scopus 로고
    • Energetics and dynamics of enzymatic reactions
    • Villa, J., and Warshel, A. (2001) Energetics and dynamics of enzymatic reactions, J. Phys. Chem. B 105, 7887-7907.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 7887-7907
    • Villa, J.1    Warshel, A.2
  • 79
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
    • Torrie, G. M., and Valleau, J. P. (1977) Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling, J. Comput. Phys. 23, 187-199.
    • (1977) J. Comput. Phys , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 80
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
    • Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A., and Rosenberg, J. M. (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method, J. Comput. Chem. 13, 1011-1021.
    • (1992) J. Comput. Chem , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 81
    • 0035892157 scopus 로고    scopus 로고
    • Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase
    • Alhambra, C., Corchado, J., Sanchez, M. L., Garcia-Viloca, M., Gao, J., and Truhlar, D. G. (2001) Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase, J. Phys. Chem. B 105, 11326-11340.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 11326-11340
    • Alhambra, C.1    Corchado, J.2    Sanchez, M.L.3    Garcia-Viloca, M.4    Gao, J.5    Truhlar, D.G.6
  • 82
    • 0022068152 scopus 로고
    • Active site dynamics in protein molecules: A stochastic boundary molecular-dynamics approach
    • Brooks, C. L., III, Brunger, A., and Karplus, M. (1985) Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach, Biopolymers 24, 843-865.
    • (1985) Biopolymers , vol.24 , pp. 843-865
    • Brooks III, C.L.1    Brunger, A.2    Karplus, M.3
  • 83
    • 0024354001 scopus 로고
    • Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme
    • Brooks, C. L., III., and Karplus, M. (1989) Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme, J. Mol. Biol. 208, 159-181.
    • (1989) J. Mol. Biol , vol.208 , pp. 159-181
    • Brooks III, C.L.1    Karplus, M.2
  • 84
    • 36749119973 scopus 로고
    • Deformable stochastic boundaries in molecular dynamics
    • Brooks, C. L., III, and Karplus, M. (1983) Deformable stochastic boundaries in molecular dynamics, J. Chem. Phys. 79, 6312-6325.
    • (1983) J. Chem. Phys , vol.79 , pp. 6312-6325
    • Brooks III, C.L.1    Karplus, M.2
  • 85
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J. Comput. Phys. 23, 327-341.
    • (1977) J. Comput. Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 86
    • 22944467757 scopus 로고
    • Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
    • Verlet, L. (1967) Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules, Phys. Rev. 159, 98-103.
    • (1967) Phys. Rev , vol.159 , pp. 98-103
    • Verlet, L.1
  • 87
    • 0000846380 scopus 로고    scopus 로고
    • Hydrogen-bonding interactions in the active site of a low molecular weight protein-tyrosine phosphatase
    • Alhambra, C., and Gao, J. (2000) Hydrogen-bonding interactions in the active site of a low molecular weight protein-tyrosine phosphatase, J. Comput. Chem. 21, 1192-1203.
    • (2000) J. Comput. Chem , vol.21 , pp. 1192-1203
    • Alhambra, C.1    Gao, J.2
  • 89
    • 0037472678 scopus 로고    scopus 로고
    • Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects
    • Garcia-Viloca, M., Alhambra, C., Truhlar Donald, G., and Gao, J. (2003) Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects, J. Comput. Chem. 24, 177-190.
    • (2003) J. Comput. Chem , vol.24 , pp. 177-190
    • Garcia-Viloca, M.1    Alhambra, C.2    Truhlar Donald, G.3    Gao, J.4
  • 91
    • 36248976080 scopus 로고    scopus 로고
    • Dennington, R, II, Keith, T, Millam, J, Eppinnett, K, Hovell, W. L, and Gilliland, R, 2003 GaussView, version 3.07, Semichem, Inc, Shawnee Mission, KS
    • Dennington, R., II, Keith, T., Millam, J., Eppinnett, K., Hovell, W. L., and Gilliland, R. (2003) GaussView, version 3.07, Semichem, Inc., Shawnee Mission, KS.
  • 92
    • 5244245983 scopus 로고
    • A correlation of reaction rates
    • Hammond, G. S. (1955) A correlation of reaction rates, J. Am. Chem. Soc. 77, 334-338.
    • (1955) J. Am. Chem. Soc , vol.77 , pp. 334-338
    • Hammond, G.S.1
  • 93
    • 0012154673 scopus 로고    scopus 로고
    • Gaussian-3 (G3) theory for molecules containing first and second-row atoms
    • Curtiss, L. A., Raghavachari, K., Redfern, P. C., Rassolov, V., and Pople, J. A. (1998) Gaussian-3 (G3) theory for molecules containing first and second-row atoms, J. Chem. Phys. 109, 7764-7776.
    • (1998) J. Chem. Phys , vol.109 , pp. 7764-7776
    • Curtiss, L.A.1    Raghavachari, K.2    Redfern, P.C.3    Rassolov, V.4    Pople, J.A.5
  • 94
    • 36449005292 scopus 로고
    • A study of some organic reactions using density functional theory
    • Baker, J., Muir, M., and Andzelm, J. (1995) A study of some organic reactions using density functional theory, J. Chem. Phys. 102, 2063-2079.
    • (1995) J. Chem. Phys , vol.102 , pp. 2063-2079
    • Baker, J.1    Muir, M.2    Andzelm, J.3
  • 95
    • 0035810443 scopus 로고    scopus 로고
    • How Well Can Hybrid Density Functional Methods Predict Transition State Geometries and Barrier Heights?
    • Lynch, B. J., and Truhlar, D. G. (2001) How Well Can Hybrid Density Functional Methods Predict Transition State Geometries and Barrier Heights?, J. Phys. Chem. A 105, 2936-2941.
    • (2001) J. Phys. Chem. A , vol.105 , pp. 2936-2941
    • Lynch, B.J.1    Truhlar, D.G.2
  • 96
    • 0035912842 scopus 로고    scopus 로고
    • Molecular structure of dihydroorotase: A paradigm for catalysis through the use of a binuclear metal center
    • Thoden, J. B., Phillips, G. N., Jr., Neal, T. M., Raushel, F. M., and Holden, H. M. (2001) Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center, Biochemistry 40, 6989-6997.
    • (2001) Biochemistry , vol.40 , pp. 6989-6997
    • Thoden, J.B.1    Phillips Jr., G.N.2    Neal, T.M.3    Raushel, F.M.4    Holden, H.M.5
  • 97
    • 0028225131 scopus 로고
    • X-ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence for Metal Movement during Catalysis
    • Lavie, A., Allen, K. N., Petsko, G. A., and Ringe, D. (1994) X-ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence for Metal Movement during Catalysis, Biochemistry 33, 5469-5480.
    • (1994) Biochemistry , vol.33 , pp. 5469-5480
    • Lavie, A.1    Allen, K.N.2    Petsko, G.A.3    Ringe, D.4
  • 98
    • 0028953745 scopus 로고
    • Design, Synthesis, and Characterization of a Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-ray Crystallographic Structure of the Enzyme-Inhibitor Complex
    • Allen, K. N., Lavie, A., Petsko, G. A., and Ringe, D. (1995) Design, Synthesis, and Characterization of a Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-ray Crystallographic Structure of the Enzyme-Inhibitor Complex, Biochemistry 34, 3742-3749.
    • (1995) Biochemistry , vol.34 , pp. 3742-3749
    • Allen, K.N.1    Lavie, A.2    Petsko, G.A.3    Ringe, D.4
  • 99
    • 33847410577 scopus 로고    scopus 로고
    • Theoretical Study of the Phosphotriesterase Reaction Mechanism
    • Chen, S.-L., Fang, W.-H., Himo, F. (2007) Theoretical Study of the Phosphotriesterase Reaction Mechanism, J. Phys. Chem. B 111, 1253.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 1253
    • Chen, S.-L.1    Fang, W.-H.2    Himo, F.3
  • 100
    • 0344391945 scopus 로고    scopus 로고
    • Reaction-Path Energetics and Kinetics of the Hydride Transfer Reaction Catalyzed by Dihydrofolate Reductase
    • Garcia-Viloca, M., Truhlar, D. G., and Gao, J. (2003) Reaction-Path Energetics and Kinetics of the Hydride Transfer Reaction Catalyzed by Dihydrofolate Reductase, Biochemistry 42, 13558-13575.
    • (2003) Biochemistry , vol.42 , pp. 13558-13575
    • Garcia-Viloca, M.1    Truhlar, D.G.2    Gao, J.3
  • 101
    • 33845377773 scopus 로고
    • Energy profile for a nonconcerted SN2 reaction in solution
    • Chandrasekhar, J., and Jorgensen, W. L. (1985) Energy profile for a nonconcerted SN2 reaction in solution, J. Am. Chem. Soc. 107, 2974-2975.
    • (1985) J. Am. Chem. Soc , vol.107 , pp. 2974-2975
    • Chandrasekhar, J.1    Jorgensen, W.L.2
  • 102
    • 33747503207 scopus 로고    scopus 로고
    • Transesterification Thio Effects of Phosphate Diesters: Free Energy Barriers and Kinetic and Equilibrium Isotope Effects from Density-Functional Theory
    • Liu, Y., Gregersen, B. A., Hengge, A., and York, D. M. (2006) Transesterification Thio Effects of Phosphate Diesters: Free Energy Barriers and Kinetic and Equilibrium Isotope Effects from Density-Functional Theory, Biochemistry 45, 10043-10053.
    • (2006) Biochemistry , vol.45 , pp. 10043-10053
    • Liu, Y.1    Gregersen, B.A.2    Hengge, A.3    York, D.M.4
  • 104
    • 23944485399 scopus 로고    scopus 로고
    • The Structure of an Enzyme-Product Complex Reveals the Critical Role of a Terminal Hydroxide Nucleophile in the Bacterial Phosphotriesterase Mechanism
    • Jackson, C., Kim, H. K., Carr, P. D., Liu, J. W., and Ollis, D. L. (2005) The Structure of an Enzyme-Product Complex Reveals the Critical Role of a Terminal Hydroxide Nucleophile in the Bacterial Phosphotriesterase Mechanism, Biochim. Biophys. Acta 1752, 56.
    • (2005) Biochim. Biophys. Acta , vol.1752 , pp. 56
    • Jackson, C.1    Kim, H.K.2    Carr, P.D.3    Liu, J.W.4    Ollis, D.L.5
  • 105
    • 0033081891 scopus 로고    scopus 로고
    • A New Proposal for Urease Mechanism Based on the Crystal Structures of the Native and Inhibited Enzyme From Bacillus Pasteurii: Why Urea hydrolysis Costs two Nickels
    • Benini, S., Rypniewski, W. R., Wilson, K. S., Ciurli, S., and Mangani, S. (1999) A New Proposal for Urease Mechanism Based on the Crystal Structures of the Native and Inhibited Enzyme From Bacillus Pasteurii: Why Urea hydrolysis Costs two Nickels, Struct. Fold. Des. 7, 205.
    • (1999) Struct. Fold. Des , vol.7 , pp. 205
    • Benini, S.1    Rypniewski, W.R.2    Wilson, K.S.3    Ciurli, S.4    Mangani, S.5
  • 106
    • 0038671973 scopus 로고    scopus 로고
    • High Resolution X-ray Structure of Isoaspartyl Dipeptidase from Escherichia Coli
    • Thoden, J. B., Marti-Arbona, R., Raushel, F. M., and Holden, H. M. (2003) High Resolution X-ray Structure of Isoaspartyl Dipeptidase from Escherichia Coli, Biochemistry 42, 4874.
    • (2003) Biochemistry , vol.42 , pp. 4874
    • Thoden, J.B.1    Marti-Arbona, R.2    Raushel, F.M.3    Holden, H.M.4
  • 107
    • 0025974544 scopus 로고
    • A Metal-Mediated Hydride Shift Mechanism for Xylose Isomerase based on the 1.6 A Streptomyces Rubiginosus Structure with Xylitol and D-Xylose
    • Whiltlow, M., Howard, A. J., Finzel, B. C., Poulos, T. L., Winborne, E., and Gilliland, G. L. (1991) A Metal-Mediated Hydride Shift Mechanism for Xylose Isomerase based on the 1.6 A Streptomyces Rubiginosus Structure with Xylitol and D-Xylose, Proteins: Struct., Funct., Genet. 9, 153-173.
    • (1991) Proteins: Struct., Funct., Genet , vol.9 , pp. 153-173
    • Whiltlow, M.1    Howard, A.J.2    Finzel, B.C.3    Poulos, T.L.4    Winborne, E.5    Gilliland, G.L.6
  • 108
    • 24644514643 scopus 로고    scopus 로고
    • Catalysis by Enzyme Conformational Change
    • Gao, J., Byun, K. L., and Kluger, R. (2004) Catalysis by Enzyme Conformational Change, Top. Curr. Chem. 238, 113-136.
    • (2004) Top. Curr. Chem , vol.238 , pp. 113-136
    • Gao, J.1    Byun, K.L.2    Kluger, R.3
  • 109
    • 4344567022 scopus 로고    scopus 로고
    • Sensitivity of Molecular Dynamics Simulations to the Choice of the X-Ray Structure used to Model an Enzymatic Reaction
    • Garcia-Viloca, M., Poulsen, T. D., Truhlar, D. G., and Gao, J. (2004) Sensitivity of Molecular Dynamics Simulations to the Choice of the X-Ray Structure used to Model an Enzymatic Reaction, Protein Sci. 13, 2341-2354.
    • (2004) Protein Sci , vol.13 , pp. 2341-2354
    • Garcia-Viloca, M.1    Poulsen, T.D.2    Truhlar, D.G.3    Gao, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.