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Volumn 26, Issue 3, 2007, Pages 676-690

Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase

Author keywords

Citrate synthase; Enolate intermediate; Enzyme catalysis; Low barrier hydrogen bond; Proton transfer; QM MM

Indexed keywords

CHEMICAL BONDS; DEPROTONATION; ENZYMES; HYDROLYSIS; REACTION KINETICS; SULFUR COMPOUNDS;

EID: 34848908954     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2007.04.002     Document Type: Article
Times cited : (19)

References (90)
  • 1
    • 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. How enzymes work: analysis by modern rate theory and computer simulations. Science 303 (2004) 186-195
    • (2004) Science , vol.303 , pp. 186-195
    • Garcia-Viloca, M.1    Gao, J.2    Karplus, M.3    Truhlar, D.G.4
  • 2
    • 0027506191 scopus 로고
    • Computer modelling of enzyme catalysed reaction mechanisms
    • Mulholland A.J., Grant G.H., and Richards W.G. Computer modelling of enzyme catalysed reaction mechanisms. Prot. Eng. 6 (1993) 133-147
    • (1993) Prot. Eng. , vol.6 , pp. 133-147
    • Mulholland, A.J.1    Grant, G.H.2    Richards, W.G.3
  • 3
    • 27144494583 scopus 로고    scopus 로고
    • Modelling enzyme reaction mechanisms, specificity and catalysis
    • Mulholland A.J. Modelling enzyme reaction mechanisms, specificity and catalysis. Drug Discov. Today 10 (2005) 1393-1402
    • (2005) Drug Discov. Today , vol.10 , pp. 1393-1402
    • Mulholland, A.J.1
  • 4
    • 0032568612 scopus 로고    scopus 로고
    • Computer simulations of enzyme catalysis: finding out what has been optimized by evolution
    • Warshel A., and Florián J. Computer simulations of enzyme catalysis: finding out what has been optimized by evolution. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 5950-5955
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 5950-5955
    • Warshel, A.1    Florián, J.2
  • 5
    • 1842340659 scopus 로고    scopus 로고
    • Studies on the reaction mechanism of citrate synthase
    • C3-C3
    • Mulholland A.J., and Richards W.G. Studies on the reaction mechanism of citrate synthase. FASEB J. 10 (1996) C3-C3
    • (1996) FASEB J. , vol.10
    • Mulholland, A.J.1    Richards, W.G.2
  • 6
    • 0000776297 scopus 로고    scopus 로고
    • A model of the condensation step in the citrate synthase reaction
    • Mulholland A.J., and Richards W.G. A model of the condensation step in the citrate synthase reaction. J. Mol. Struct. (Theochem.) 427 (1998) 175-184
    • (1998) J. Mol. Struct. (Theochem.) , vol.427 , pp. 175-184
    • Mulholland, A.J.1    Richards, W.G.2
  • 7
    • 0038305457 scopus 로고    scopus 로고
    • Quantum chemical studies of radical-containing enzymes
    • Himo F., and Siegbahn P.E.M. Quantum chemical studies of radical-containing enzymes. Chem. Rev. 103 (2003) 2421-2456
    • (2003) Chem. Rev. , vol.103 , pp. 2421-2456
    • Himo, F.1    Siegbahn, P.E.M.2
  • 8
    • 4143088551 scopus 로고    scopus 로고
    • An efficient linear scaling method for ab initio calculation of electron density of proteins
    • Gao A.M., Zhang D.W., Zhang J.Z.H., and Zhang Y.K. An efficient linear scaling method for ab initio calculation of electron density of proteins. Chem. Phys. Lett. 394 (2004) 293-297
    • (2004) Chem. Phys. Lett. , vol.394 , pp. 293-297
    • Gao, A.M.1    Zhang, D.W.2    Zhang, J.Z.H.3    Zhang, Y.K.4
  • 9
    • 34547237228 scopus 로고    scopus 로고
    • A fragment energy assembler method for Hartree-Fock calculations of large molecules
    • Li W., Fang T., and Li S.H. A fragment energy assembler method for Hartree-Fock calculations of large molecules. J. Chem. Phys. (2006) 124
    • (2006) J. Chem. Phys. , pp. 124
    • Li, W.1    Fang, T.2    Li, S.H.3
  • 10
    • 22944470256 scopus 로고    scopus 로고
    • A new method for direct calculation of total energy of protein
    • He X., and Zhang J.Z.H. A new method for direct calculation of total energy of protein. J. Chem. Phys. (2005) 122
    • (2005) J. Chem. Phys. , pp. 122
    • He, X.1    Zhang, J.Z.H.2
  • 11
    • 12344294827 scopus 로고    scopus 로고
    • A quantum chemical method for rapid optimization of protein structures
    • Wada M., and Sakurai M. A quantum chemical method for rapid optimization of protein structures. J. Comp. Chem. 26 (2005) 160-168
    • (2005) J. Comp. Chem. , vol.26 , pp. 160-168
    • Wada, M.1    Sakurai, M.2
  • 12
    • 0001499720 scopus 로고    scopus 로고
    • Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method
    • Van Der Vaart A., Gogonea V., Dixon S.L., and Merz K.M. Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method. J. Comp. Chem. 21 (2000) 1494-1504
    • (2000) J. Comp. Chem. , vol.21 , pp. 1494-1504
    • Van Der Vaart, A.1    Gogonea, V.2    Dixon, S.L.3    Merz, K.M.4
  • 13
    • 0032097513 scopus 로고    scopus 로고
    • Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronic structure methods
    • York D.M., Lee T.S., and Yang W.T. Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronic structure methods. Phys. Rev. Lett. 80 (1998) 5011-5014
    • (1998) Phys. Rev. Lett. , vol.80 , pp. 5011-5014
    • York, D.M.1    Lee, T.S.2    Yang, W.T.3
  • 14
    • 84986513644 scopus 로고
    • A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations
    • Field M.J., Bash P.A., and Karplus M. A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations. J. Comp. Chem. 11 (1990) 700-733
    • (1990) J. Comp. Chem. , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 15
    • 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. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Ann. Rev. Phys. Chem. 56 (2005) 389-427
    • (2005) Ann. Rev. Phys. Chem. , vol.56 , pp. 389-427
    • Friesner, R.A.1    Guallar, V.2
  • 16
    • 33845283509 scopus 로고
    • Free-energy perturbation method for chemical-reactions in the condensed phase: a dynamical-approach based on a combined quantum and molecular mechanics potential
    • Bash P.A., Field M.J., and Karplus M. Free-energy perturbation method for chemical-reactions in the condensed phase: a dynamical-approach based on a combined quantum and molecular mechanics potential. J. Am. Chem. Soc. 109 (1987) 8092-8094
    • (1987) J. Am. Chem. Soc. , vol.109 , pp. 8092-8094
    • Bash, P.A.1    Field, M.J.2    Karplus, M.3
  • 19
    • 33750157202 scopus 로고    scopus 로고
    • Mechanisms of reaction in cytochrome P450: hydroxylation of camphor in P450cam
    • Zurek J., Foloppe N., Harvey J.N., and Mulholland A.J. Mechanisms of reaction in cytochrome P450: hydroxylation of camphor in P450cam. Org. Biomol. Chem. 4 (2006) 3931-3937
    • (2006) Org. Biomol. Chem. , vol.4 , pp. 3931-3937
    • Zurek, J.1    Foloppe, N.2    Harvey, J.N.3    Mulholland, A.J.4
  • 20
    • 0031033361 scopus 로고    scopus 로고
    • Acetyl-CoA enolization in citrate synthase: a quantum mechanical/molecular mechanical (QM/MM) study
    • Mulholland A.J., and Richards W.G. Acetyl-CoA enolization in citrate synthase: a quantum mechanical/molecular mechanical (QM/MM) study. Prot. Struct. Funct. Genet. 27 (1997) 9-25
    • (1997) Prot. Struct. Funct. Genet. , vol.27 , pp. 9-25
    • Mulholland, A.J.1    Richards, W.G.2
  • 21
    • 0026485965 scopus 로고
    • Structure and mechanism of citrate synthase
    • Remington S.J. Structure and mechanism of citrate synthase. Curr. Top. Cell. Regul. 33 (1992) 209-229
    • (1992) Curr. Top. Cell. Regul. , vol.33 , pp. 209-229
    • Remington, S.J.1
  • 22
    • 0016647269 scopus 로고
    • Enzymology of formation and breakdown of citrate
    • Srere P.A. Enzymology of formation and breakdown of citrate. Adv. Enzymol. RAMB 43 (1975) 57-101
    • (1975) Adv. Enzymol. RAMB , vol.43 , pp. 57-101
    • Srere, P.A.1
  • 23
    • 0024584420 scopus 로고
    • Citrate synthase stabilizes the enethiolate of acetyldithio coenzyme-A
    • Wlassics I.D., and Anderson V.E. Citrate synthase stabilizes the enethiolate of acetyldithio coenzyme-A. Biochemistry 28 (1989) 1627-1633
    • (1989) Biochemistry , vol.28 , pp. 1627-1633
    • Wlassics, I.D.1    Anderson, V.E.2
  • 24
    • 0023727337 scopus 로고
    • Malate synthase: proof of a stepwise claisen condensation using the double-isotope fractionation test
    • Clark J.D., O'Keefe S.J., and Knowles J.R. Malate synthase: proof of a stepwise claisen condensation using the double-isotope fractionation test. Biochemistry 27 (1988) 5961-5971
    • (1988) Biochemistry , vol.27 , pp. 5961-5971
    • Clark, J.D.1    O'Keefe, S.J.2    Knowles, J.R.3
  • 25
    • 0022425329 scopus 로고
    • Evidence from C-13 NMR for polarization of the carbonyl of oxaloacetate in the active-site of citrate synthase
    • Kurz L.C., Ackerman J.J.H., and Drysdale G.R. Evidence from C-13 NMR for polarization of the carbonyl of oxaloacetate in the active-site of citrate synthase. Biochemistry 24 (1985) 452-457
    • (1985) Biochemistry , vol.24 , pp. 452-457
    • Kurz, L.C.1    Ackerman, J.J.H.2    Drysdale, G.R.3
  • 26
    • 0023248839 scopus 로고
    • Evidence from Fourier-transform infrared-spectroscopy for polarization of the carbonyl of oxaloacetate in the active-site of citrate synthase
    • Kurz L.C., and Drysdale G.R. Evidence from Fourier-transform infrared-spectroscopy for polarization of the carbonyl of oxaloacetate in the active-site of citrate synthase. Biochemistry 26 (1987) 2623-2627
    • (1987) Biochemistry , vol.26 , pp. 2623-2627
    • Kurz, L.C.1    Drysdale, G.R.2
  • 28
    • 0025214122 scopus 로고
    • Proposed mechanism for the condensation reaction of citrate synthase: 1.9 Å structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme-A
    • Karpusas M., Branchaud B., and Remington S.J. Proposed mechanism for the condensation reaction of citrate synthase: 1.9 Å structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme-A. Biochemistry 29 (1990) 2213-2219
    • (1990) Biochemistry , vol.29 , pp. 2213-2219
    • Karpusas, M.1    Branchaud, B.2    Remington, S.J.3
  • 29
    • 0025923565 scopus 로고
    • 1.9 Å structures of ternary complexes of citrate synthase with d-malate and l-malate: mechanistic implications
    • Karpusas M., Holland D., and Remington S.J. 1.9 Å structures of ternary complexes of citrate synthase with d-malate and l-malate: mechanistic implications. Biochemistry 30 (1991) 6024-6031
    • (1991) Biochemistry , vol.30 , pp. 6024-6031
    • Karpusas, M.1    Holland, D.2    Remington, S.J.3
  • 30
    • 0029782417 scopus 로고    scopus 로고
    • Active site mutants of pig citrate synthase: effects of mutations on the enzyme catalytic and structural properties
    • Evans C.T., Kurz L.C., Remington S.J., and Srere P.A. Active site mutants of pig citrate synthase: effects of mutations on the enzyme catalytic and structural properties. Biochemistry 35 (1996) 10661-10672
    • (1996) Biochemistry , vol.35 , pp. 10661-10672
    • Evans, C.T.1    Kurz, L.C.2    Remington, S.J.3    Srere, P.A.4
  • 31
    • 0025636490 scopus 로고
    • Citrate synthase from the thermophilic archaebacterium Thermoplasma acidophilum: cloning and sequencing of the gene
    • Sutherland K.J., Henneke C.M., Towner P., Hough D.W., and Danson M.J. Citrate synthase from the thermophilic archaebacterium Thermoplasma acidophilum: cloning and sequencing of the gene. Eur. J. Biochem. 194 (1990) 839-844
    • (1990) Eur. J. Biochem. , vol.194 , pp. 839-844
    • Sutherland, K.J.1    Henneke, C.M.2    Towner, P.3    Hough, D.W.4    Danson, M.J.5
  • 32
    • 0030741375 scopus 로고    scopus 로고
    • The crystal structure of citrate synthase from the hyperthermophilic archaeon Pyrococcus furiosus at 1.9 Ångstrom resolution
    • Russell R.J.M., Ferguson J.M.C., Hough D.W., Danson M.J., and Taylor G.L. The crystal structure of citrate synthase from the hyperthermophilic archaeon Pyrococcus furiosus at 1.9 Ångstrom resolution. Biochemistry 36 (1997) 9983-9994
    • (1997) Biochemistry , vol.36 , pp. 9983-9994
    • Russell, R.J.M.1    Ferguson, J.M.C.2    Hough, D.W.3    Danson, M.J.4    Taylor, G.L.5
  • 33
    • 0000841544 scopus 로고
    • Mechanisms of citrate synthase and related enzymes (triose phosphate isomerase and mandelate racemase)
    • Remington S.J. Mechanisms of citrate synthase and related enzymes (triose phosphate isomerase and mandelate racemase). Curr. Opin. Struct. Biol. 2 (1992) 730-735
    • (1992) Curr. Opin. Struct. Biol. , vol.2 , pp. 730-735
    • Remington, S.J.1
  • 34
    • 0031127432 scopus 로고    scopus 로고
    • Understanding enzymic catalysis: the importance of short, strong hydrogen bonds
    • Gerlt J.A., Kreevoy M.M., Cleland W.W., and Frey P.A. Understanding enzymic catalysis: the importance of short, strong hydrogen bonds. Chem. Biol. 4 (1997) 259-267
    • (1997) Chem. Biol. , vol.4 , pp. 259-267
    • Gerlt, J.A.1    Kreevoy, M.M.2    Cleland, W.W.3    Frey, P.A.4
  • 35
    • 0028030684 scopus 로고
    • Low-barrier hydrogen-bonds and enzymatic catalysis
    • Cleland W.W., and Kreevoy M.M. Low-barrier hydrogen-bonds and enzymatic catalysis. Science 264 (1994) 1887-1890
    • (1994) Science , vol.264 , pp. 1887-1890
    • Cleland, W.W.1    Kreevoy, M.M.2
  • 36
    • 0000397708 scopus 로고
    • Unstable carbanions: general acid catalysis of the cleavage of 1-phenylcyclopropanol and 1-phenyl-2-arylcyclopropanol anions
    • Thibblin A., and Jencks W.P. Unstable carbanions: general acid catalysis of the cleavage of 1-phenylcyclopropanol and 1-phenyl-2-arylcyclopropanol anions. J. Am. Chem. Soc. 101 (1979) 4963-4973
    • (1979) J. Am. Chem. Soc. , vol.101 , pp. 4963-4973
    • Thibblin, A.1    Jencks, W.P.2
  • 37
    • 0027133903 scopus 로고
    • An explanation for rapid enzyme-catalyzed proton abstraction from carbon acids: importance of late transition-states in concerted mechanisms
    • Gerlt J.A., and Gassman P.G. An explanation for rapid enzyme-catalyzed proton abstraction from carbon acids: importance of late transition-states in concerted mechanisms. J. Am. Chem. Soc. 115 (1993) 11552-11568
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 11552-11568
    • Gerlt, J.A.1    Gassman, P.G.2
  • 38
    • 0028817050 scopus 로고
    • Do enzymes stabilize transition-states by electrostatic interactions or pK(a) balance: the case of triose phosphate isomerase (TIM)
    • Alagona G., Ghio C., and Kollman P.A. Do enzymes stabilize transition-states by electrostatic interactions or pK(a) balance: the case of triose phosphate isomerase (TIM). J. Am. Chem. Soc. 117 (1995) 9855-9862
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 9855-9862
    • Alagona, G.1    Ghio, C.2    Kollman, P.A.3
  • 39
    • 0030090490 scopus 로고    scopus 로고
    • Short strong hydrogen bonds: can they explain enzymic catalysis?
    • Guthrie J.P. Short strong hydrogen bonds: can they explain enzymic catalysis?. Chem. Biol. 3 (1996) 163-170
    • (1996) Chem. Biol. , vol.3 , pp. 163-170
    • Guthrie, J.P.1
  • 40
    • 0029040169 scopus 로고
    • On low-barrier hydrogen-bonds and enzyme catalysis
    • Warshel A., Papazyan A., and Kollman P.A. On low-barrier hydrogen-bonds and enzyme catalysis. Science 269 (1995) 102-104
    • (1995) Science , vol.269 , pp. 102-104
    • Warshel, A.1    Papazyan, A.2    Kollman, P.A.3
  • 41
    • 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., and Papazyan A. Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 13665-13670
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 13665-13670
    • Warshel, A.1    Papazyan, A.2
  • 42
    • 0028854341 scopus 로고
    • The non-existence of specially stabilized hydrogen-bonds in enzymes
    • Scheiner S., and Kar T. The non-existence of specially stabilized hydrogen-bonds in enzymes. J. Am. Chem. Soc. 117 (1995) 6970-6975
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 6970-6975
    • Scheiner, S.1    Kar, T.2
  • 43
    • 0001020921 scopus 로고    scopus 로고
    • Modeling enzyme reaction intermediates and transition states: citrate synthase
    • Mulholland A.J., and Richards W.G. Modeling enzyme reaction intermediates and transition states: citrate synthase. J. Phys. Chem. B 102 (1998) 6635-6646
    • (1998) J. Phys. Chem. B , vol.102 , pp. 6635-6646
    • Mulholland, A.J.1    Richards, W.G.2
  • 44
    • 0344138003 scopus 로고    scopus 로고
    • Molecular Simulations Inc., San Diego, CA
    • Quanta96 (1996), Molecular Simulations Inc., San Diego, CA
    • (1996) Quanta96
  • 47
    • 0000218385 scopus 로고    scopus 로고
    • A hybrid QM-MM potential employing Hartree-Fock or density functional methods in the quantum region
    • Lyne P.D., Hodoscek M., and Karplus M. A hybrid QM-MM potential employing Hartree-Fock or density functional methods in the quantum region. J. Phys. Chem. A 103 (1999) 3462-3471
    • (1999) J. Phys. Chem. A , vol.103 , pp. 3462-3471
    • Lyne, P.D.1    Hodoscek, M.2    Karplus, M.3
  • 48
    • 0034716340 scopus 로고    scopus 로고
    • Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved
    • Mulholland A.J., Lyne P.D., and Karplus M. Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved. J. Am. Chem. Soc. 122 (2000) 534-535
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 534-535
    • Mulholland, A.J.1    Lyne, P.D.2    Karplus, M.3
  • 49
    • 0004133516 scopus 로고
    • Gaussian Inc., Pittsburgh, PA
    • Gaussian94 (1995), Gaussian Inc., Pittsburgh, PA
    • (1995) Gaussian94
  • 50
    • 33644930396 scopus 로고
    • Ab initio studies of hydrogen-bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers
    • Guo H., and Karplus M. Ab initio studies of hydrogen-bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers. J. Phys. Chem. 96 (1992) 7273-7287
    • (1992) J. Phys. Chem. , vol.96 , pp. 7273-7287
    • Guo, H.1    Karplus, M.2
  • 51
    • 0031559456 scopus 로고    scopus 로고
    • Proton transfer and correlations between the C-O, O-H, N-H and O⋯N bond lengths in amine phenolates
    • Majerz I., Malarski Z., and Sobczyk L. Proton transfer and correlations between the C-O, O-H, N-H and O⋯N bond lengths in amine phenolates. Chem. Phys. Lett. 274 (1997) 361-364
    • (1997) Chem. Phys. Lett. , vol.274 , pp. 361-364
    • Majerz, I.1    Malarski, Z.2    Sobczyk, L.3
  • 52
    • 0000167881 scopus 로고
    • Insights into chorismate mutase catalysis from a combined QM/MM simulation of the enzyme reaction
    • Lyne P.D., Mulholland A.J., and Richards W.G. Insights into chorismate mutase catalysis from a combined QM/MM simulation of the enzyme reaction. J. Am. Chem. Soc. 117 (1995) 11345-11350
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 11345-11350
    • Lyne, P.D.1    Mulholland, A.J.2    Richards, W.G.3
  • 53
    • 0027023534 scopus 로고
    • Simulation analysis of triose phosphate isomerase: conformational transition and catalysis
    • Karplus M., Evanseck J.D., Joseph D., Bash P.A., and Field M.J. Simulation analysis of triose phosphate isomerase: conformational transition and catalysis. Farad. Discuss. 93 (1992) 239-248
    • (1992) Farad. Discuss. , vol.93 , pp. 239-248
    • Karplus, M.1    Evanseck, J.D.2    Joseph, D.3    Bash, P.A.4    Field, M.J.5
  • 54
    • 0025743628 scopus 로고
    • Computer-simulation and analysis of the reaction pathway of triosephosphate isomerase
    • Bash P.A., Field M.J., Davenport R.C., Petsko G.A., Ringe D., and Karplus M. Computer-simulation and analysis of the reaction pathway of triosephosphate isomerase. Biochemistry 30 (1991) 5826-5832
    • (1991) Biochemistry , vol.30 , pp. 5826-5832
    • Bash, P.A.1    Field, M.J.2    Davenport, R.C.3    Petsko, G.A.4    Ringe, D.5    Karplus, M.6
  • 55
    • 84962339874 scopus 로고
    • Hydrated proton clusters and solvent effects on the proton-transfer barrier: a density-functional study
    • Wei D.Q., and Salahub D.R. Hydrated proton clusters and solvent effects on the proton-transfer barrier: a density-functional study. J. Chem. Phys. 101 (1994) 7633-7642
    • (1994) J. Chem. Phys. , vol.101 , pp. 7633-7642
    • Wei, D.Q.1    Salahub, D.R.2
  • 57
    • 0000263008 scopus 로고
    • Study of hydrogen bonding interactions relevant to biomolecular structure and function
    • Zheng Y.-J., and Merz Jr. K.M. Study of hydrogen bonding interactions relevant to biomolecular structure and function. J. Comp. Chem. 13 (1992) 1151-1169
    • (1992) J. Comp. Chem. , vol.13 , pp. 1151-1169
    • Zheng, Y.-J.1    Merz Jr., K.M.2
  • 58
    • 0029905014 scopus 로고    scopus 로고
    • The change in hydrogen bond strength accompanying charge rearrangement: implications for enzymatic catalysis
    • Shan S.O., and Herschlag D. The change in hydrogen bond strength accompanying charge rearrangement: implications for enzymatic catalysis. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 14474-14479
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 14474-14479
    • Shan, S.O.1    Herschlag, D.2
  • 59
    • 10344265555 scopus 로고    scopus 로고
    • Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field
    • Szefczyk B., Mulholland A.J., Ranaghan K.E., and Sokalski W.A. 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 (2004) 16148-16159
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 16148-16159
    • Szefczyk, B.1    Mulholland, A.J.2    Ranaghan, K.E.3    Sokalski, W.A.4
  • 60
    • 0017058392 scopus 로고
    • Evolution of enzyme function and development of catalytic efficiency
    • Albery W.J., and Knowles J.R. Evolution of enzyme function and development of catalytic efficiency. Biochemistry 15 (1976) 5631-5640
    • (1976) Biochemistry , vol.15 , pp. 5631-5640
    • Albery, W.J.1    Knowles, J.R.2
  • 63
    • 0000047442 scopus 로고
    • Generation and stability of a simple thiol ester enolate in aqueous-solution
    • Amyes T.L., and Richard J.P. Generation and stability of a simple thiol ester enolate in aqueous-solution. J. Am. Chem. Soc. 114 (1992) 10297-10302
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 10297-10302
    • Amyes, T.L.1    Richard, J.P.2
  • 64
    • 0041111670 scopus 로고
    • Kinetic studies on citrate-condensing enzyme
    • Kosicki G.W., and Srere P.A. Kinetic studies on citrate-condensing enzyme. J. Biol. Chem. 236 (1961) 2560-2565
    • (1961) J. Biol. Chem. , vol.236 , pp. 2560-2565
    • Kosicki, G.W.1    Srere, P.A.2
  • 65
    • 0025871717 scopus 로고
    • Neutral imidazole is the electrophile in the reaction catalyzed by triosephosphate isomerase: structural origins and catalytic implications
    • Lodi P.J., and Knowles J.R. Neutral imidazole is the electrophile in the reaction catalyzed by triosephosphate isomerase: structural origins and catalytic implications. Biochemistry 30 (1991) 6948-6956
    • (1991) Biochemistry , vol.30 , pp. 6948-6956
    • Lodi, P.J.1    Knowles, J.R.2
  • 66
    • 33646371941 scopus 로고    scopus 로고
    • Low-barrier hydrogen bond hypothesis in the catalytic triad residue of serine proteases: correlation between structural rearrangement and chemical shifts in the acylation process
    • Ishida T. Low-barrier hydrogen bond hypothesis in the catalytic triad residue of serine proteases: correlation between structural rearrangement and chemical shifts in the acylation process. Biochemistry 45 (2006) 5413-5420
    • (2006) Biochemistry , vol.45 , pp. 5413-5420
    • Ishida, T.1
  • 67
    • 2442606719 scopus 로고    scopus 로고
    • The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp...His pair in serine proteases
    • Schutz C.N., and Warshel A. The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp...His pair in serine proteases. Prot. Struct. Funct. Bioinf. 55 (2004) 711-723
    • (2004) Prot. Struct. Funct. Bioinf. , vol.55 , pp. 711-723
    • Schutz, C.N.1    Warshel, A.2
  • 68
    • 0038613083 scopus 로고    scopus 로고
    • NMR chemical shifts in the low-pH form of alpha-chymotrypsin. A QM/MM and ONIOM-NMR study
    • Molina P.A., Sikorski R.S., and Jensen J.H. NMR chemical shifts in the low-pH form of alpha-chymotrypsin. A QM/MM and ONIOM-NMR study. Theor. Chem. Accounts 109 (2003) 100-107
    • (2003) Theor. Chem. Accounts , vol.109 , pp. 100-107
    • Molina, P.A.1    Sikorski, R.S.2    Jensen, J.H.3
  • 69
    • 0037899651 scopus 로고    scopus 로고
    • Computational study of the citrate synthase catalyzed deprotonation of acetyl-coenzyme A and fluoroacetyl-coenzyme A: demonstration of a layered quantum mechanical approach
    • Yang W., and Drueckhammer D.G. Computational study of the citrate synthase catalyzed deprotonation of acetyl-coenzyme A and fluoroacetyl-coenzyme A: demonstration of a layered quantum mechanical approach. J. Phys. Chem. B 107 (2003) 5986-5994
    • (2003) J. Phys. Chem. B , vol.107 , pp. 5986-5994
    • Yang, W.1    Drueckhammer, D.G.2
  • 70
    • 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. 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 (1996) 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
  • 71
    • 0038617502 scopus 로고    scopus 로고
    • Improved second-order Møller-Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies
    • Grimme S. Improved second-order Møller-Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies. J. Chem. Phys. 118 (2003) 9095-9102
    • (2003) J. Chem. Phys. , vol.118 , pp. 9095-9102
    • Grimme, S.1
  • 74
    • 0010114887 scopus 로고
    • Deuterium isotope rate effects with citrate-condensing enzyme
    • Kosicki G., and Srere Pa. Deuterium isotope rate effects with citrate-condensing enzyme. J. Biol. Chem. 236 (1961) 2566
    • (1961) J. Biol. Chem. , vol.236 , pp. 2566
    • Kosicki, G.1    Srere, Pa.2
  • 75
    • 1442277682 scopus 로고    scopus 로고
    • Computational modeling of the catalytic reaction in triosephosphate isomerase
    • Guallar V., Jacobson M., Mcdermott A., and Friesner R.A. Computational modeling of the catalytic reaction in triosephosphate isomerase. J. Mol. Biol. 337 (2004) 227-239
    • (2004) J. Mol. Biol. , vol.337 , pp. 227-239
    • Guallar, V.1    Jacobson, M.2    Mcdermott, A.3    Friesner, R.A.4
  • 76
    • 0028241778 scopus 로고
    • A very short hydrogen bond provides only moderate stabilization of an enzyme-inhibitor complex of citrate synthase
    • Usher K.C., Remington S.J., Martin D.P., and Drueckhammer D.G. A very short hydrogen bond provides only moderate stabilization of an enzyme-inhibitor complex of citrate synthase. Biochemistry 33 (1994) 7753-7759
    • (1994) Biochemistry , vol.33 , pp. 7753-7759
    • Usher, K.C.1    Remington, S.J.2    Martin, D.P.3    Drueckhammer, D.G.4
  • 77
    • 0031179495 scopus 로고    scopus 로고
    • A low energy short hydrogen bond in very high resolution structures of protein receptor phosphate complexes
    • Wang Z.M., Luecke H., Yao N.H., and Quiocho F.A. A low energy short hydrogen bond in very high resolution structures of protein receptor phosphate complexes. Nat. Struct. Biol. 4 (1997) 519-522
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 519-522
    • Wang, Z.M.1    Luecke, H.2    Yao, N.H.3    Quiocho, F.A.4
  • 78
    • 0000756814 scopus 로고
    • The ionic hydrogen-bond and ion solvation. 5. OH...O-bonds: gas-phase solvation and clustering of alkoxide and carboxylate anions
    • Meot-Ner M., and Sieck L.W. The ionic hydrogen-bond and ion solvation. 5. OH...O-bonds: gas-phase solvation and clustering of alkoxide and carboxylate anions. J. Am. Chem. Soc. 108 (1986) 7525-7529
    • (1986) J. Am. Chem. Soc. , vol.108 , pp. 7525-7529
    • Meot-Ner, M.1    Sieck, L.W.2
  • 79
    • 0029926948 scopus 로고    scopus 로고
    • The energetics of hydrogen bonds in model systems: implications for enzymatic catalysis
    • Shan S.O., Loh S., and Herschlag D. The energetics of hydrogen bonds in model systems: implications for enzymatic catalysis. Science 272 (1996) 97-101
    • (1996) Science , vol.272 , pp. 97-101
    • Shan, S.O.1    Loh, S.2    Herschlag, D.3
  • 80
    • 4243810035 scopus 로고
    • Simulation of enzyme-reactions using valence-bond force-fields and other hybrid quantum-classical approaches
    • Åqvist J., and Warshel A. Simulation of enzyme-reactions using valence-bond force-fields and other hybrid quantum-classical approaches. Chem. Rev. 93 (1993) 2523-2544
    • (1993) Chem. Rev. , vol.93 , pp. 2523-2544
    • Åqvist, J.1    Warshel, A.2
  • 81
    • 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 V., Peräkylä P., Bakowies D., and Kollman P.A. 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 (1998) 3448-3457
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 3448-3457
    • Stanton, V.1    Peräkylä, P.2    Bakowies, D.3    Kollman, P.A.4
  • 82
    • 0035155864 scopus 로고    scopus 로고
    • 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
    • Kollman P.A., Kuhn B., Donini O., Perakyla M., Stanton R., and Bakowies D. 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) 72-79
    • (2001) Acc. Chem. Res. , vol.34 , pp. 72-79
    • Kollman, P.A.1    Kuhn, B.2    Donini, O.3    Perakyla, M.4    Stanton, R.5    Bakowies, D.6
  • 83
    • 0034645570 scopus 로고    scopus 로고
    • QM-FE calculations of aliphatic hydrogen abstraction in citrate synthase and in solution: reproduction of the effect of enzyme catalysis and demonstration that an enolate rather than an enol is formed
    • Donini O., Darden T., and Kollman P.A. QM-FE calculations of aliphatic hydrogen abstraction in citrate synthase and in solution: reproduction of the effect of enzyme catalysis and demonstration that an enolate rather than an enol is formed. J. Am. Chem. Soc. 122 (2000) 12270-12280
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 12270-12280
    • Donini, O.1    Darden, T.2    Kollman, P.A.3
  • 84
    • 0020483375 scopus 로고
    • Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1. 7 Å resolution
    • Remington S., Wiegand G., and Huber R. Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1. 7 Å resolution. J. Mol. Biol. 158 (1982) 111-152
    • (1982) J. Mol. Biol. , vol.158 , pp. 111-152
    • Remington, S.1    Wiegand, G.2    Huber, R.3
  • 85
    • 33747151589 scopus 로고    scopus 로고
    • QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase
    • Harvey J.N., Bathelt C.M., and Mulholland A.J. QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase. J. Comp. Chem. 27 (2006) 1352-1362
    • (2006) J. Comp. Chem. , vol.27 , pp. 1352-1362
    • Harvey, J.N.1    Bathelt, C.M.2    Mulholland, A.J.3
  • 86
    • 3042691605 scopus 로고    scopus 로고
    • Hybrid QM/MM potentials of mean force with interpolated corrections
    • Ruiz-Pernia J.J., Silla E., Tunon I., Marti S., and Moliner V. Hybrid QM/MM potentials of mean force with interpolated corrections. J. Phys. Chem. B 108 (2004) 8427-8433
    • (2004) J. Phys. Chem. B , vol.108 , pp. 8427-8433
    • Ruiz-Pernia, J.J.1    Silla, E.2    Tunon, I.3    Marti, S.4    Moliner, V.5
  • 87
    • 0037151638 scopus 로고    scopus 로고
    • Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9.10-oxide
    • Ridder L.O., Rietjens I.M.C.M., Vervoort J., and Mulholland A.J. Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9.10-oxide. J. Am. Chem. Soc. 124 (2002) 9926-9936
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 9926-9936
    • Ridder, L.O.1    Rietjens, I.M.C.M.2    Vervoort, J.3    Mulholland, A.J.4
  • 88
    • 0035138648 scopus 로고    scopus 로고
    • A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method
    • Cui Q., Elstner M., Kaxiras E., Frauenheim T., and Karplus M. A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. J. Phys. Chem. B 105 (2001) 569-585
    • (2001) J. Phys. Chem. B , vol.105 , pp. 569-585
    • Cui, Q.1    Elstner, M.2    Kaxiras, E.3    Frauenheim, T.4    Karplus, M.5
  • 89
    • 84961974890 scopus 로고    scopus 로고
    • Hybrid ab initio QM/MM simulation of N-methylacetamide in aqueous solution
    • Gao J.L., and Freindorf M. Hybrid ab initio QM/MM simulation of N-methylacetamide in aqueous solution. J. Phys. Chem. A 101 (1997) 3182-3188
    • (1997) J. Phys. Chem. A , vol.101 , pp. 3182-3188
    • Gao, J.L.1    Freindorf, M.2
  • 90
    • 2642585833 scopus 로고    scopus 로고
    • Importance of Van der Waals interactions in QM/MM simulations
    • Riccardi D., Li G.H., and Cui Q. Importance of Van der Waals interactions in QM/MM simulations. J. Phys. Chem. B 108 (2004) 6467-6478
    • (2004) J. Phys. Chem. B , vol.108 , pp. 6467-6478
    • Riccardi, D.1    Li, G.H.2    Cui, Q.3


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