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Volumn 1814, Issue 11, 2011, Pages 1438-1446

Molecular dynamics simulations of the intramolecular proton transfer and carbanion stabilization in the pyridoxal 5′-phosphate dependent enzymes l-dopa decarboxylase and alanine racemase

Author keywords

Carbanion stabilization; Enzymatic decarboxylation; Internal proton transfer of PLP; QM MM simulation; Racemization

Indexed keywords

ALANINE RACEMASE; CARBON 13; LEVODOPA; PYRIDOXAL 5 PHOSPHATE; SCHIFF BASE;

EID: 80054696190     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2011.05.002     Document Type: Review
Times cited : (28)

References (72)
  • 2
    • 9744235147 scopus 로고    scopus 로고
    • Reaction specificity in pyridoxal phosphate enzymes
    • DOI 10.1016/j.abb.2004.09.037, PII S0003986104005338
    • M.D. Toney Reaction specificity in pyridoxal phosphate enzymes Arch. Biochem. Biophys. 433 2005 279 287 (Pubitemid 39586598)
    • (2005) Archives of Biochemistry and Biophysics , vol.433 , Issue.1 , pp. 279-287
    • Toney, M.D.1
  • 3
    • 0034605454 scopus 로고    scopus 로고
    • Formation and stability of organic zwitterions in aqueous solution: Enolates of the amino acid glycine and its derivatives
    • A. Rios, T.L. Amyes, and J.P. Richard Formation and stability of organic zwitterions in aqueous solution: enolates of the amino acid glycine and its derivatives J. Am. Chem. Soc. 122 2000 9373 9385
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 9373-9385
    • Rios, A.1    Amyes, T.L.2    Richard, J.P.3
  • 4
    • 33845569858 scopus 로고    scopus 로고
    • A combined quantum mechanical and molecular mechanical study of the reaction mechanism and α-amino acidity in alanine racemase
    • DOI 10.1021/ja066334r
    • D.T. Major, and J. Gao A combined quantum mechanical and molecular mechanical study of the reaction mechanism and α-amino acidity in alanine racemase J. Am. Chem. Soc. 128 2006 16345 16357 (Pubitemid 44936630)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.50 , pp. 16345-16357
    • Major, D.T.1    Gao, J.2
  • 5
    • 33745656984 scopus 로고    scopus 로고
    • Transition state stabilization and α-amino carbon acidity in alanine racemase
    • DOI 10.1021/ja062272t
    • D.T. Major, K. Nam, and J. Gao Transition state stabilization and α-amino carbon acidity in alanine racemase J. Am. Chem. Soc. 128 2006 8114 8115 (Pubitemid 43967737)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.25 , pp. 8114-8115
    • Major, D.T.1    Nam, K.2    Gao, J.3
  • 6
    • 73449108093 scopus 로고    scopus 로고
    • Internal proton transfer in the external pyridoxal 5′-phosphate Schiff base in dopa decarboxylase
    • Y.L. Lin, and J. Gao Internal proton transfer in the external pyridoxal 5′-phosphate Schiff base in dopa decarboxylase Biochemistry 49 2010 84 94
    • (2010) Biochemistry , vol.49 , pp. 84-94
    • Lin, Y.L.1    Gao, J.2
  • 7
    • 4644340182 scopus 로고    scopus 로고
    • On the importance of being zwitterionic: Enzymatic catalysis of decarboxylation and deprotonation of cationic carbon
    • DOI 10.1016/j.bioorg.2004.05.002, PII S004520680400032X, Mechanic Enzymology
    • J.P. Richard, and T.L. Amyes On the importance of being zwitterionic: enzymatic catalysis of decarboxylation and deprotonation of cationic carbon Bioorg. Chem. 32 2004 354 366 (Pubitemid 39277442)
    • (2004) Bioorganic Chemistry , vol.32 , Issue.5 , pp. 354-366
    • Richard, J.P.1    Amyes, T.L.2
  • 8
    • 33947279804 scopus 로고    scopus 로고
    • Covalent catalysis by pyridoxal: Evaluation of the effect of the cofactor on the carbon acidity of glycine
    • DOI 10.1021/ja0679228
    • K. Toth, and J.P. Richard Covalent catalysis by pyridoxal: evaluation of the effect of the cofactor on the carbon acidity of glycine J. Am. Chem. Soc. 129 2007 3013 3021 (Pubitemid 46417979)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.10 , pp. 3013-3021
    • Toth, K.1    Richard, J.P.2
  • 9
    • 34249111417 scopus 로고    scopus 로고
    • NMR studies of coupled low- and high-barrier hydrogen bonds in pyridoxal-5′-phosphate model systems in polar solution
    • DOI 10.1021/ja070296+
    • S. Sharif, G.S. Denisov, M.D. Toney, and H.-H. Limbach NMR studies of coupled low- and high-barrier hydrogen bonds in pyridoxal-5′-phosphate model systems in polar solution J. Am. Chem. Soc. 129 2007 6313 6327 (Pubitemid 46786826)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.19 , pp. 6313-6327
    • Sharif, S.1    Denisov, G.S.2    Toney, M.D.3    Limbach, H.-H.4
  • 10
    • 34247114263 scopus 로고    scopus 로고
    • Coupling of functional hydrogen bonds in pyridoxal-5′-phosphate- enzyme model systems observed by solid-state NMR spectroscopy
    • DOI 10.1021/ja066240h
    • S. Sharif, D. Schagen, M.D. Toney, and H.-H. Limbach Coupling of functional hydrogen bonds in pyridoxal-5′-phosphate-enzyme model systems observed by solid-state NMR spectroscopy J. Am. Chem. Soc. 129 2007 4440 4455 (Pubitemid 46595460)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.14 , pp. 4440-4455
    • Sharif, S.1    Schagen, D.2    Toney, M.D.3    Limbach, H.-H.4
  • 11
    • 33644940104 scopus 로고    scopus 로고
    • NMR studies of solvent-assisted proton transfer in a biologically relevant Schiff base: Toward a distinction of geometric and equilibrium H-bond isotope effects
    • S. Sharif, G.S. Denisov, M.D. Toney, and H.-H. Limbach NMR studies of solvent-assisted proton transfer in a biologically relevant Schiff base: toward a distinction of geometric and equilibrium H-bond isotope effects J. Am. Chem. Soc. 128 2006 3375 3387
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 3375-3387
    • Sharif, S.1    Denisov, G.S.2    Toney, M.D.3    Limbach, H.-H.4
  • 12
    • 34247868777 scopus 로고    scopus 로고
    • 15N nuclear magnetic resonance studies of acid-base properties of pyridoxal-5′-phosphate aldimines in aqueous solution
    • DOI 10.1021/jp067334g
    • S. Sharif, M.C. Huot, P.M. Tolstoy, M.D. Toney, K.H.M. Jonsson, and H.-H. Limbach 15 N nuclear magnetic resonance studies of acid-base properties of pyridoxal-5′-phosphate aldimines in aqueous solution J. Phys. Chem. B 111 2007 3869 3876 (Pubitemid 46693347)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.15 , pp. 3869-3876
    • Sharif, S.1    Huot, M.C.2    Tolstoy, P.M.3    Toney, M.D.4    Jonsson, K.H.M.5    Limbach, H.-H.6
  • 13
    • 0015808679 scopus 로고
    • Comparison of the rate constants for general base catalyzed prototropy and racemization of the aldimine species formed from 3-hydroxypyridine-4- carboxaldehyde and alanine
    • J.E. Dixon, and T.C. Bruice Comparison of the rate constants for general base catalyzed prototropy and racemization of the aldimine species formed from 3-hydroxypyridine-4-carboxaldehyde and alanine Biochemistry 12 1973 4762 4766
    • (1973) Biochemistry , vol.12 , pp. 4762-4766
    • Dixon, J.E.1    Bruice, T.C.2
  • 14
    • 3943113663 scopus 로고    scopus 로고
    • Pyridoxal phosphate enzymes: Mechanistic, structural, and evolutionary considerations
    • DOI 10.1146/annurev.biochem.73.011303.074021
    • A.C. Eliot, and J.F. Kirsch Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations Ann. Rev. Biochem. 73 2004 383 415 (Pubitemid 39050374)
    • (2004) Annual Review of Biochemistry , vol.73 , pp. 383-415
    • Eliot, A.C.1    Kirsch, J.F.2
  • 16
    • 0027536853 scopus 로고
    • Rat liver aromatic L-amino acid decarboxylase: Spectroscopic and kinetic analysis of the coenzyme and reaction intermediates
    • DOI 10.1021/bi00054a011
    • H. Hayashi, H. Mizuguchi, and H. Kagamiyama Rat liver aromatic L-amino acid decarboxylase: spectroscopic and kinetic analysis of the coenzyme and reaction intermediates Biochemistry 32 1993 812 818 (Pubitemid 23059361)
    • (1993) Biochemistry , vol.32 , Issue.3 , pp. 812-818
    • Hayashi, H.1    Mizuguchi, H.2    Kagamiyama, H.3
  • 17
    • 0033598686 scopus 로고    scopus 로고
    • Acid-base chemistry of the reaction of aromatic L-amino acid decarboxylase and dopa analyzed by transient and steady-state kinetics: Preferential binding of the substrate with its amino group unprotonated
    • H. Hayashi, F. Tsukiyama, S. Ishii, H. Mizuguchi, and H. Kagamiyama Acid-base chemistry of the reaction of aromatic l-amino acid decarboxylase and dopa analyzed by transient and steady-state kinetics: preferential binding of the substrate with its amino group unprotonated Biochemistry 38 1999 15615 15622 (Pubitemid 129503604)
    • (1999) Biochemistry , vol.38 , Issue.47 , pp. 15615-15622
    • Hayashi, H.1    Tsukiyama, F.2    Ishii, S.3    Mizuguchi, H.4    Kagamiyama, H.5
  • 19
    • 0031032448 scopus 로고    scopus 로고
    • Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-Å resolution
    • DOI 10.1021/bi961856c
    • J.P. Shaw, G.A. Petsko, and D. Ringe Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-Å resolution Biochemistry 36 1997 1329 1342 (Pubitemid 27074957)
    • (1997) Biochemistry , vol.36 , Issue.6 , pp. 1329-1342
    • Shaw, J.P.1    Petsko, G.A.2    Ringe, D.3
  • 20
    • 0033574155 scopus 로고    scopus 로고
    • Structure of a Michaelis complex analog: Propionate binds in the substrate carboxylate site of alanine racemase
    • A.A. Morollo, G.A. Petsko, and D. Ringe Structure of a Michaelis complex analog: propionate binds in the substrate carboxylate site of alanine racemase Biochemistry 38 1999 3293 3301
    • (1999) Biochemistry , vol.38 , pp. 3293-3301
    • Morollo, A.A.1    Petsko, G.A.2    Ringe, D.3
  • 21
    • 0033616634 scopus 로고    scopus 로고
    • Evidence for a two-base mechanism involving tyrosine-265 from arginine-219 mutants of alanine racemase
    • S.X. Sun, and M.D. Toney Evidence for a two-base mechanism involving tyrosine-265 from arginine-219 mutants of alanine racemase Biochemistry 38 1999 4058 4065
    • (1999) Biochemistry , vol.38 , pp. 4058-4065
    • Sun, S.X.1    Toney, M.D.2
  • 22
    • 33748584863 scopus 로고    scopus 로고
    • Mechanisms and free energies of enzymatic reactions
    • DOI 10.1021/cr050293k
    • J. Gao, S. Ma, D.T. Major, K. Nam, J. Pu, and D.G. Truhlar Mechanisms and free energies of enzymatic reactions Chem. Rev. 106 2006 3188 3209 (Pubitemid 44376932)
    • (2006) Chemical Reviews , vol.106 , Issue.8 , pp. 3188-3209
    • Gao, J.1    Ma, S.2    Major, D.T.3    Nam, K.4    Pu, J.5    Truhlar, D.G.6
  • 23
    • 77955578037 scopus 로고    scopus 로고
    • A non-orthogonal block-localized effective Hamiltonian approach for chemical and enzymatic reactions
    • A. Cembran, A. Payaka, Y.L. Lin, W.S. Xie, Y.R. Mo, L.C. Song, and J.L. Gao A non-orthogonal block-localized effective Hamiltonian approach for chemical and enzymatic reactions J. Chem. Theory Comput. 6 2010 2242 2251
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 2242-2251
    • Cembran, A.1    Payaka, A.2    Lin, Y.L.3    Xie, W.S.4    Mo, Y.R.5    Song, L.C.6    Gao, J.L.7
  • 24
    • 0027125907 scopus 로고
    • A prior evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations
    • J. Gao, and X. Xia A prior evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations Science 258 1992 631 635
    • (1992) Science , vol.258 , pp. 631-635
    • Gao, J.1    Xia, X.2
  • 25
    • 0035827163 scopus 로고    scopus 로고
    • Inclusion of quantum-mechanical vibrational energy in reactive potentials of mean force
    • DOI 10.1063/1.1371497
    • M. Garcia-Viloca, C. Alhambra, D.G. Truhlar, and J. Gao Inclusion of quantum-mechanical vibrational energy in reactive potentials of mean force J. Chem. Phys. 114 2001 9953 9958 (Pubitemid 32586000)
    • (2001) Journal of Chemical Physics , vol.114 , Issue.22 , pp. 9953-9958
    • Garcia-Viloca, M.1    Alhambra, C.2    Truhlar, D.G.3    Gao, J.4
  • 26
    • 33748613208 scopus 로고    scopus 로고
    • Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions
    • DOI 10.1021/cr050308e
    • J. Pu, J. Gao, and D.G. Truhlar Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions Chem. Rev. 106 2006 3140 3169 (Pubitemid 44376930)
    • (2006) Chemical Reviews , vol.106 , Issue.8 , pp. 3140-3169
    • Pu, J.1    Gao, J.2    Truhlar, D.G.3
  • 27
    • 36148963327 scopus 로고    scopus 로고
    • An integrated path integral and free-energy perturbation-umbrella sampling method for computing kinetic isotope effects of chemical reactions in solution and in enzymes
    • D.T. Major, and J. Gao An integrated path integral and free-energy perturbation-umbrella sampling method for computing kinetic isotope effects of chemical reactions in solution and in enzymes J. Chem. Theory Comput. 3 2007 949 960
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 949-960
    • Major, D.T.1    Gao, J.2
  • 29
    • 84962367344 scopus 로고    scopus 로고
    • Methods and applications of combined quantum mechanical and molecular mechanical potentials
    • J. Gao Methods and applications of combined quantum mechanical and molecular mechanical potentials K.B. Lipkowitz, D.B. Boyd, Rev. Comput. Chem vol. 7 1995 VCH New York 119 185 (Pubitemid 126676953)
    • (1996) Reviews in Computational Chemistry , vol.7 , pp. 119-185
    • Gao, J.1
  • 30
    • 0842341771 scopus 로고
    • Development and use of quantum mechanical molecular models. 76. AM1: A new general purpose quantum mechanical molecular model
    • M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, and J.J.P. Stewart Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model J. Am. Chem. Soc. 107 1985 3902 3909
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 3902-3909
    • Dewar, M.J.S.1    Zoebisch, E.G.2    Healy, E.F.3    Stewart, J.J.P.4
  • 31
    • 5244287607 scopus 로고
    • An automated procedure for simulating chemical reactions in solution. Application to the decarboxylation of 3-carboxybenzisoxazole in water
    • J. Gao An automated procedure for simulating chemical reactions in solution. Application to the decarboxylation of 3-carboxybenzisoxazole in water J. Am. Chem. Soc. 117 1995 8600 8607
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 8600-8607
    • Gao, J.1
  • 33
    • 0037396515 scopus 로고    scopus 로고
    • Catalysis by enzyme conformational change as illustrated by orotidine 5′-monophosphate decarboxylase
    • DOI 10.1016/S0959-440X(03)00041-1
    • J. Gao Catalysis by enzyme conformational change as illustrated by orotidine 5′-monophosphate decarboxylase Curr. Opin. Struct. Biol. 13 2003 184 192 (Pubitemid 36515146)
    • (2003) Current Opinion in Structural Biology , vol.13 , Issue.2 , pp. 184-192
    • Gao, J.1
  • 34
    • 42449089815 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biotin carboxylase
    • S.O.N. Lill, J. Gao, and G.L. Waldrop Molecular dynamics simulations of biotin carboxylase J. Phys. Chem. B 112 2008 3149 3156
    • (2008) J. Phys. Chem. B , vol.112 , pp. 3149-3156
    • Lill, S.O.N.1    Gao, J.2    Waldrop, G.L.3
  • 35
    • 33746911013 scopus 로고    scopus 로고
    • Path integral simulations of proton transfer reactions in aqueous solution using combined QM/MM potentials
    • D.T. Major, M. Garcia-Viloca, and J. Gao Path integral simulations of proton transfer reactions in aqueous solution using combined QM/MM potentials J. Chem. Theory Comput. 2 2006 236 245
    • (2006) J. Chem. Theory Comput. , vol.2 , pp. 236-245
    • Major, D.T.1    Garcia-Viloca, M.2    Gao, J.3
  • 36
    • 17644384320 scopus 로고    scopus 로고
    • Dependence of transition state structure on substrate: The intrinsic C-13 kinetic isotope effect is different for physiological and slow substrates of the ornithine decarboxylase reaction because of different hydrogen bonding structures
    • DOI 10.1021/ja042298p
    • D. Sicinska, D.G. Truhlar, and P. Paneth Dependence of transition state structure on substrate: the intrinsic c-13 kinetic isotope effect is different for physiological and slow substrates of the ornithine decarboxylase reaction because of different hydrogen bonding structures J. Am. Chem. Soc. 127 2005 5414 5422 (Pubitemid 40569853)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.15 , pp. 5414-5422
    • Sicinska, D.1    Truhlar, D.G.2    Paneth, P.3
  • 37
    • 0000411659 scopus 로고    scopus 로고
    • A generalized hybrid orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations
    • J. Gao, P. Amara, C. Alhambra, and M.J. Field A generalized hybrid orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations J. Phys. Chem. A 102 1998 4714 4721 (Pubitemid 128581039)
    • (1998) Journal of Physical Chemistry A , vol.102 , Issue.24 , pp. 4714-4721
    • Gao, J.1    Amara, P.2    Alhambra, C.3    Field, M.J.4
  • 38
    • 0034375393 scopus 로고    scopus 로고
    • The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: Formulation and tests of the analytical derivatives
    • P. Amara, M.J. Field, C. Alhambra, and J. Gao The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives Theor. Chem. Acc. 104 2000 336 343
    • (2000) Theor. Chem. Acc. , vol.104 , pp. 336-343
    • Amara, P.1    Field, M.J.2    Alhambra, C.3    Gao, J.4
  • 41
    • 19944369519 scopus 로고    scopus 로고
    • An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations
    • K. Nam, J. Gao, and D.M. York An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations J. Chem. Theory Comput. 1 2005 2 13
    • (2005) J. Chem. Theory Comput. , vol.1 , pp. 2-13
    • Nam, K.1    Gao, J.2    York, D.M.3
  • 42
    • 79953031248 scopus 로고    scopus 로고
    • Kinetic isotope effects of l-dopa decarboxylase
    • Y.-l. Lin, and J. Gao Kinetic isotope effects of l-dopa decarboxylase J. Am. Chem. Soc. 133 2011 4398 4403
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 4398-4403
    • Lin, Y.-L.1    Gao, J.2
  • 43
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
    • S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, and J.M. Rosenberg The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 13 1992 1011
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 44
    • 39049160691 scopus 로고    scopus 로고
    • Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water
    • DOI 10.1002/jcc.20810
    • J. Gao, K.-Y. Wong, and D.T. Major Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water J. Comput. Chem. 29 2008 514 522 (Pubitemid 351238835)
    • (2008) Journal of Computational Chemistry , vol.29 , Issue.4 , pp. 514-522
    • Gao, J.1    Wong, K.-Y.2    Major, D.T.3
  • 45
    • 0040658732 scopus 로고    scopus 로고
    • A relationship between centroid dynamics and path integral quantum transition state theory
    • Erratum: 2001. 8114: 1944
    • S. Jang, and G.A. Voth A relationship between centroid dynamics and path integral quantum transition state theory J. Chem. Phys. 112 2000 8747 8757 Erratum: 2001. 8114: 1944
    • (2000) J. Chem. Phys. , vol.112 , pp. 8747-8757
    • Jang, S.1    Voth, G.A.2
  • 46
    • 0001648594 scopus 로고    scopus 로고
    • Extension of path integral quantum transition state theory to the case of nonadiabatic activated dynamics
    • C.D. Schwieters, and G.A. Voth Extension of path integral quantum transition state theory to the case of nonadiabatic activated dynamics J. Chem. Phys. 111 1999 2869 2877
    • (1999) J. Chem. Phys. , vol.111 , pp. 2869-2877
    • Schwieters, C.D.1    Voth, G.A.2
  • 47
    • 0000720458 scopus 로고
    • Staging: A sampling technique for the Monte Carlo evaluation of path integrals
    • M. Sprik, M.L. Klein, and D. Chandler Staging: a sampling technique for the Monte Carlo evaluation of path integrals Phys. Rev. B 31 1985 4234 4244
    • (1985) Phys. Rev. B , vol.31 , pp. 4234-4244
    • Sprik, M.1    Klein, M.L.2    Chandler, D.3
  • 48
    • 33751386561 scopus 로고
    • A quantized classical path approach for calculations of quantum mechanical rate constants
    • J.K. Hwang, and A. Warshel A quantized classical path approach for calculations of quantum mechanical rate constants J. Phys. Chem. 97 1993 10053 10058
    • (1993) J. Phys. Chem. , vol.97 , pp. 10053-10058
    • Hwang, J.K.1    Warshel, A.2
  • 49
    • 73949083862 scopus 로고    scopus 로고
    • Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction
    • D.T. Major, A. Heroux, A.M. Orville, M.P. Valley, P.F. Fitzpatrick, and J. Gao Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction Proc. Natl Acad. Sci. 106 2009 20734 20739
    • (2009) Proc. Natl Acad. Sci. , vol.106 , pp. 20734-20739
    • Major, D.T.1    Heroux, A.2    Orville, A.M.3    Valley, M.P.4    Fitzpatrick, P.F.5    Gao, J.6
  • 50
    • 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
    • S. Marti, V. Moliner, and I. Tunon 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 2005 1008 1016
    • (2005) J. Chem. Theory Comput. , vol.1 , pp. 1008-1016
    • Marti, S.1    Moliner, V.2    Tunon, I.3
  • 51
    • 36248990205 scopus 로고    scopus 로고
    • The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations
    • DOI 10.1021/bi700460c
    • K.-Y. Wong, and J. Gao The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations Biochemistry 46 2007 13352 13369 (Pubitemid 350136375)
    • (2007) Biochemistry , vol.46 , Issue.46 , pp. 13352-13369
    • Wong, K.-Y.1    Gao, J.2
  • 52
    • 0034703733 scopus 로고    scopus 로고
    • The rate of spontaneous decarboxylation of amino acids
    • M.J. Snider, and R. Wolfenden The rate of spontaneous decarboxylation of amino acids J. Am. Chem. Soc. 122 2000 11507 11508
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 11507-11508
    • Snider, M.J.1    Wolfenden, R.2
  • 55
    • 0021769545 scopus 로고
    • Inactivation of the Pseudomonas striata broad specificity amino acid racemase by D and L isomers of beta-substituted alanines: Kinetics, stoichiometry, active site peptide, and mechanistic studies
    • D. Roise, K. Soda, T. Yagi, and C.T. Walsh Inactivation of the Pseudomonas striata broad specificity amino acid racemase by D and L isomers of beta-substituted alanines: kinetics, stoichiometry, active site peptide, and mechanistic studies Biochemistry 23 1984 5195 5201
    • (1984) Biochemistry , vol.23 , pp. 5195-5201
    • Roise, D.1    Soda, K.2    Yagi, T.3    Walsh, C.T.4
  • 56
    • 0037166337 scopus 로고    scopus 로고
    • Reaction mechanism of alanine racemase from Bacillus stearothermophilus: X-ray crystallographic studies of the enzyme bound with N-(5′- phosphopyridoxyl)alanine
    • DOI 10.1074/jbc.M201615200
    • A. Watanabe, T. Yoshimura, B. Mikami, H. Hayashi, H. Kagamiyama, and N. Esaki Reaction mechanism of alanine racemase from Bacillus stearothermophilus X-ray crystallographic studies of the enzyme with bound N-(5′- phosphopyridoxyl) alanine J. Biol. Chem. 277 2002 19166 19172 (Pubitemid 34952483)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.21 , pp. 19166-19172
    • Watanabe, A.1    Yoshimura, T.2    Mikami, B.3    Hayashi, H.4    Kagamiyama, H.5    Esaki, N.6
  • 58
    • 0032757833 scopus 로고    scopus 로고
    • Tyrosine 265 of alanine racemase serves as a base abstracting {alpha}-hydrogen from L-alanine: The counterpart residue to lysine 39 specific to d-alanine
    • A. Watanabe, T. Yoshimura, B. Mikami, and N. Esaki Tyrosine 265 of alanine racemase serves as a base abstracting {alpha}-hydrogen from L-alanine: the counterpart residue to lysine 39 specific to d-alanine J. Biochem. 126 1999 781
    • (1999) J. Biochem. , vol.126 , pp. 781
    • Watanabe, A.1    Yoshimura, T.2    Mikami, B.3    Esaki, N.4
  • 59
    • 0033548158 scopus 로고    scopus 로고
    • Role of lysine 39 of alanine racemase from Bacillus stearothermophilus that binds pyridoxal 5′-phosphate. Chemical rescue studies of Lys39->Ala mutant
    • A. Watanabe, Y. Kurokawa, T. Yoshimura, T. Kurihara, K. Soda, and N. Esaki Role of lysine 39 of alanine racemase from Bacillus stearothermophilus that binds pyridoxal 5′-phosphate. Chemical rescue studies of Lys39->Ala mutant J. Biol. Chem. 274 1999 4189 4194
    • (1999) J. Biol. Chem. , vol.274 , pp. 4189-4194
    • Watanabe, A.1    Kurokawa, Y.2    Yoshimura, T.3    Kurihara, T.4    Soda, K.5    Esaki, N.6
  • 60
    • 0037657606 scopus 로고    scopus 로고
    • Multiple hydrogen kinetic isotope effects for enzymes catalyzing exchange with solvent: Application to alanine racemase
    • DOI 10.1021/bi0274064
    • M.A. Spies, and M.D. Toney Multiple hydrogen kinetic isotope effects for enzymes catalyzing exchange with solvent: application to alanine racemase Biochemistry 42 2003 5099 5107 (Pubitemid 36532064)
    • (2003) Biochemistry , vol.42 , Issue.17 , pp. 5099-5107
    • Spies, M.A.1    Toney, M.D.2
  • 62
    • 34848833283 scopus 로고    scopus 로고
    • Intrinsic primary and secondary hydrogen kinetic isotope effects for alanine racemase from global analysis of progress curves
    • DOI 10.1021/ja067643k
    • M.A. Spies, and M.D. Toney Intrinsic primary and secondary hydrogen kinetic isotope effects for alanine racemase from global analysis of progress curves J. Am. Chem. Soc. 129 2007 10678 10685 (Pubitemid 350067476)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.35 , pp. 10678-10685
    • Spies, M.A.1    Toney, M.D.2
  • 63
    • 0034813704 scopus 로고    scopus 로고
    • Glycine enolates: The large effect of iminium ion formation on α-amino carbon acidity
    • DOI 10.1021/ja016250c
    • A. Rios, J. Crugeiras, T.L. Amyes, and J.P. Richard Glycine enolates: the large effect of iminium ion formation on α-amino carbon acidity J. Am. Chem. Soc. 123 2001 7949 7950 (Pubitemid 32899377)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.32 , pp. 7949-7950
    • Rios, A.1    Crugeiras, J.2    Amyes, T.L.3    Richard, J.P.4
  • 64
    • 0015808679 scopus 로고
    • Comparison of the rate constants for general base catalyzed prototropy and racemization of the aldimine species formed from 3-hydroxypyridine-4- carboxaldehyde and alanine
    • J.E. Dixon, and T.C. Bruice Comparison of the rate constants for general base catalyzed prototropy and racemization of the aldimine species formed from 3-hydroxypyridine-4-carboxaldehyde and alanine Biochemistry 12 1973 4762 4766
    • (1973) Biochemistry , vol.12 , pp. 4762-4766
    • Dixon, J.E.1    Bruice, T.C.2
  • 65
    • 67650545663 scopus 로고    scopus 로고
    • Catalyzing racemizations in the absence of a cofactor: The reaction mechanism in proline racemase
    • A. Rubinstein, and D.T. Major Catalyzing racemizations in the absence of a cofactor: the reaction mechanism in proline racemase J. Am. Chem. Soc. 131 2009 8513 8521
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 8513-8521
    • Rubinstein, A.1    Major, D.T.2
  • 66
    • 77951923612 scopus 로고    scopus 로고
    • Understanding catalytic specificity in alanine racemase from quantum mechanical and molecular mechanical simulations of the arginine 219 mutant
    • A. Rubinstein, and D.T. Major Understanding catalytic specificity in alanine racemase from quantum mechanical and molecular mechanical simulations of the arginine 219 mutant Biochemistry 49 2010 3957 3964
    • (2010) Biochemistry , vol.49 , pp. 3957-3964
    • Rubinstein, A.1    Major, D.T.2
  • 67
    • 0041431075 scopus 로고    scopus 로고
    • Conversion of the catalytic specificity of alanine racemase to a D-amino acid aminotransferase activity by a double active-site mutation
    • DOI 10.1016/S1381-1177(03)00094-8
    • G.Y. Yow, A. Watanabe, T. Yoshimura, and N. Esaki Conversion of the catalytic specificity of alanine racemase to a d-amino acid aminotransferase activity by a double active-site mutation J. Mol. Cat. B 23 2003 311 319 (Pubitemid 37011206)
    • (2003) Journal of Molecular Catalysis B: Enzymatic , vol.23 , Issue.2-6 , pp. 311-319
    • Yow, G.-Y.1    Watanabe, A.2    Yoshimura, T.3    Esaki, N.4
  • 68
    • 0037952855 scopus 로고    scopus 로고
    • A side reaction of alanine racemase: Transamination of cycloserine
    • DOI 10.1021/bi027022d
    • T.D. Fenn, G.F. Stamper, A.A. Morollo, and D. Ringe A side reaction of alanine racemase: transamination of cycloserine Biochemistry 42 2003 5775 5783 (Pubitemid 36582869)
    • (2003) Biochemistry , vol.42 , Issue.19 , pp. 5775-5783
    • Fenn, T.D.1    Stamper, G.F.2    Morollo, A.A.3    Ringe, D.4
  • 69
    • 16844378698 scopus 로고    scopus 로고
    • Effect of a Y265F mutant on the transamination-based cycloserine inactivation of alanine racemase
    • DOI 10.1021/bi047842l
    • T.D. Fenn, T. Holyoak, G.F. Stamper, and D. Ringe Effect of a Y265F mutant on the transamination-based cycloserine inactivation of alanine racemase Biochemistry 44 2005 5317 5327 (Pubitemid 40489971)
    • (2005) Biochemistry , vol.44 , Issue.14 , pp. 5317-5327
    • Fenn, T.D.1    Holyoak, T.2    Stamper, G.F.3    Ringe, D.4
  • 70
    • 0041429626 scopus 로고    scopus 로고
    • Conversion of a PLP-dependent racemase into an aldolase by a single active site mutation
    • DOI 10.1021/ja036707d
    • F.P. Seebeck, and D. Hilvert Conversion of a PLP-dependent racemase into an aldolase by a single active site mutation J. Am. Chem. Soc. 125 2003 10158 10159 (Pubitemid 37022211)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.34 , pp. 10158-10159
    • Seebeck, F.P.1    Hilvert, D.2
  • 72
    • 0033604832 scopus 로고    scopus 로고
    • Effects of the E177K mutation in d-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity
    • P.W. van Ophem, D. Peisach, S.D. Erickson, K. Soda, D. Ringe, and J.M. Manning Effects of the E177K mutation in d-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity Biochemistry 38 1999 1323 1331
    • (1999) Biochemistry , vol.38 , pp. 1323-1331
    • Van Ophem, P.W.1    Peisach, D.2    Erickson, S.D.3    Soda, K.4    Ringe, D.5    Manning, J.M.6


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