메뉴 건너뛰기




Volumn 39, Issue 2, 2006, Pages 93-100

Hydrogen tunneling and protein motion in enzyme reactions

Author keywords

[No Author keywords available]

Indexed keywords

DEUTERIUM; DIHYDROFOLATE REDUCTASE; HYDROGEN; LIPOXYGENASE; PROTEIN; PROTON;

EID: 33644990365     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar040199a     Document Type: Article
Times cited : (217)

References (54)
  • 1
    • 0346726109 scopus 로고    scopus 로고
    • How enzymes work: Analysis by modern rate theory and computer simulations
    • Garcia-Viloca, M.; Gao, J.; Karplus, M.; Truhlar, D. G. How enzymes work: Analysis by modern rate theory and computer simulations. Science 2004, 303, 186-195.
    • (2004) Science , vol.303 , pp. 186-195
    • Garcia-Viloca, M.1    Gao, J.2    Karplus, M.3    Truhlar, D.G.4
  • 2
    • 0041821836 scopus 로고    scopus 로고
    • A perspective on enzyme catalysis
    • Benkovic, S. J.; Hammes-Schiffer, S. A perspective on enzyme catalysis. Science 2003, 301, 1196-1202.
    • (2003) Science , vol.301 , pp. 1196-1202
    • Benkovic, S.J.1    Hammes-Schiffer, S.2
  • 4
    • 0000044605 scopus 로고
    • A quantum molecular dynamics study of proton-transfer reactions along asymmetrical H-bonds in solution
    • Azzouz, H.; Borgis, D. A quantum molecular dynamics study of proton-transfer reactions along asymmetrical H-bonds in solution. J. Chem. Phys. 1993, 98, 7361-7375.
    • (1993) J. Chem. Phys. , vol.98 , pp. 7361-7375
    • Azzouz, H.1    Borgis, D.2
  • 5
    • 36449005418 scopus 로고
    • Proton transfer in solution: Molecular dynamics with quantum transitions
    • Hammes-Schiffer, S.; Tully, J. C. Proton transfer in solution: Molecular dynamics with quantum transitions. J. Chem. Phys. 1994, 101, 4657-4667.
    • (1994) J. Chem. Phys. , vol.101 , pp. 4657-4667
    • Hammes-Schiffer, S.1    Tully, J.C.2
  • 6
    • 0037035158 scopus 로고    scopus 로고
    • Nonlinear free energy relations for adiabatic proton-transfer reactions in a polar environment. II. Inclusion of the hydrogen bond vibration
    • Kiefer, P. M.; Hynes, J. T. Nonlinear free energy relations for adiabatic proton-transfer reactions in a polar environment. II. Inclusion of the hydrogen bond vibration. J. Phys. Chem. A 2002, 106, 1850-1861.
    • (2002) J. Phys. Chem. A , vol.106 , pp. 1850-1861
    • Kiefer, P.M.1    Hynes, J.T.2
  • 7
    • 0346725553 scopus 로고
    • Dynamical theory of proton tunneling transfer rates in solution: General formulation
    • Borgis, D.; Hynes, J. T. Dynamical theory of proton tunneling transfer rates in solution: general formulation. Chem. Phys. 1993, 170, 315-346.
    • (1993) Chem. Phys. , vol.170 , pp. 315-346
    • Borgis, D.1    Hynes, J.T.2
  • 8
    • 0037104752 scopus 로고    scopus 로고
    • Promoting modes and demoting modes in enzyme-catalyzed proton-transfer reactions: A study of models and realistic systems
    • Cui, Q.; Karplus, M. Promoting modes and demoting modes in enzyme-catalyzed proton-transfer reactions: A study of models and realistic systems. J. Phys. Chem. B 2002, 106, 7927-7947.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 7927-7947
    • Cui, Q.1    Karplus, M.2
  • 10
    • 0037518552 scopus 로고    scopus 로고
    • Dynamic barriers and tunneling. New views of hydrogen transfer in enzyme reactions
    • Klinman, J. P. Dynamic barriers and tunneling. New views of hydrogen transfer in enzyme reactions. Pure Appl. Chem. 2003, 75, 601-608.
    • (2003) Pure Appl. Chem. , vol.75 , pp. 601-608
    • Klinman, J.P.1
  • 11
    • 0036305396 scopus 로고    scopus 로고
    • A new conceptual framework for enzyme catalysis
    • Sutcliffe, M. J.; Scrutton, N. S. A new conceptual framework for enzyme catalysis. Eur. J. Biochem. 2002, 269, 3096-3102.
    • (2002) Eur. J. Biochem. , vol.269 , pp. 3096-3102
    • Sutcliffe, M.J.1    Scrutton, N.S.2
  • 12
    • 0037396515 scopus 로고    scopus 로고
    • Catalysis by enzyme conformational change as illustrated by orotidine 5′-monophosphate decarboxylase
    • Gao, J. Catalysis by enzyme conformational change as illustrated by orotidine 5′-monophosphate decarboxylase. Curr. Opin. Struct. Biol. 2003, 13, 184-192.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 184-192
    • Gao, J.1
  • 13
    • 0033519723 scopus 로고    scopus 로고
    • Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase
    • Kohen, A.; Cannio, R.; Bartolucci, S.; Klinman, J. P. Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase. Nature 1999, 399, 496-499.
    • (1999) Nature , vol.399 , pp. 496-499
    • Kohen, A.1    Cannio, R.2    Bartolucci, S.3    Klinman, J.P.4
  • 14
    • 0037069410 scopus 로고    scopus 로고
    • Impact of enzyme motion on activity
    • Hammes-Schiffer, S. Impact of enzyme motion on activity. Biochemistry 2002, 41, 13335-13343.
    • (2002) Biochemistry , vol.41 , pp. 13335-13343
    • Hammes-Schiffer, S.1
  • 15
    • 0033955055 scopus 로고    scopus 로고
    • Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase
    • Radkiewicz, J. L.; Brooks, C. L. Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase. J. Am. Chem. Soc. 2000, 122, 225-231.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 225-231
    • Radkiewicz, J.L.1    Brooks, C.L.2
  • 17
    • 0037123216 scopus 로고    scopus 로고
    • Temperature-dependent isotope effects in soybean lipoxygenase-1: Correlating hydrogen tunneling with protein dynamics
    • Knapp, M. J.; Rickert, K. W.; Klinman, J. P. Temperature-dependent isotope effects in soybean lipoxygenase-1: Correlating hydrogen tunneling with protein dynamics. J. Am. Chem. Soc. 2002, 124, 3865-3874.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 3865-3874
    • Knapp, M.J.1    Rickert, K.W.2    Klinman, J.P.3
  • 18
    • 0023668190 scopus 로고
    • Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli
    • Fierke, C. A.; Johnson, K. A.; Benkovic, S. J. Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli. Biochemistry 1987, 26, 4085-4092.
    • (1987) Biochemistry , vol.26 , pp. 4085-4092
    • Fierke, C.A.1    Johnson, K.A.2    Benkovic, S.J.3
  • 19
    • 0023177955 scopus 로고
    • Leukotrienes and lipoxins: Structures, biosynthesis, and biological effects
    • Samuelsson, B.; Dahlen, S.-E.; Lindgren, J.; Rouzer, C. A.; Serhan, C. N. Leukotrienes and lipoxins: structures, biosynthesis, and biological effects. Science 1987, 237, 1171-1176.
    • (1987) Science , vol.237 , pp. 1171-1176
    • Samuelsson, B.1    Dahlen, S.-E.2    Lindgren, J.3    Rouzer, C.A.4    Serhan, C.N.5
  • 21
    • 3042780720 scopus 로고    scopus 로고
    • Proton-coupled electron transfer: A reaction chemist's view
    • Mayer, J. M. Proton-coupled electron transfer: A reaction chemist's view. Annu. Rev. Phys. Chem. 2004, 55, 363-390.
    • (2004) Annu. Rev. Phys. Chem. , vol.55 , pp. 363-390
    • Mayer, J.M.1
  • 22
    • 0037328843 scopus 로고    scopus 로고
    • Density-functional investigation on the mechanism of H-atom abstraction by lipoxygenase
    • Lehnert, N.; Solomon, E. L. Density-functional investigation on the mechanism of H-atom abstraction by lipoxygenase. J. Biol. Inorg. Chem. 2003, 8, 294-305.
    • (2003) J. Biol. Inorg. Chem. , vol.8 , pp. 294-305
    • Lehnert, N.1    Solomon, E.L.2
  • 23
    • 2442548491 scopus 로고    scopus 로고
    • Proton-coupled electron transfer in soybean lipoxygenase
    • Hatcher, E.; Soudackov, A. V.; Hammes-Schiffer, S. Proton-coupled electron transfer in soybean lipoxygenase. J. Am. Chem. Soc. 2004, 126, 5763-5775.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 5763-5775
    • Hatcher, E.1    Soudackov, A.V.2    Hammes-Schiffer, S.3
  • 24
    • 1542317813 scopus 로고    scopus 로고
    • Simulations of the Large Kinetic Isotope Effect and the Temperature Dependence of the Hydrogen Atom Transfer in Lipoxygenase
    • Olsson, M. H. M.; Siegbahn, P. E. M.; Warshel, A. Simulations of the Large Kinetic Isotope Effect and the Temperature Dependence of the Hydrogen Atom Transfer in Lipoxygenase. J. Am. Chem. Soc. 2004, 126, 2820-2828.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 2820-2828
    • Olsson, M.H.M.1    Siegbahn, P.E.M.2    Warshel, A.3
  • 25
    • 1842763785 scopus 로고    scopus 로고
    • Temperature dependence of kinetic isotope effects for enzymatic carbon-hydrogen bond cleavage
    • Siebrand, W.; Smedarchina, Z. Temperature dependence of kinetic isotope effects for enzymatic carbon-hydrogen bond cleavage. J. Phys. Chem. B 2004, 108, 4185-4195.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 4185-4195
    • Siebrand, W.1    Smedarchina, Z.2
  • 26
    • 0000201328 scopus 로고    scopus 로고
    • Multistate continuum theory for multiple charge transfer reactions in solution
    • Soudackov, A.; Hammes-Schiffer, S. Multistate continuum theory for multiple charge transfer reactions in solution. J. Chem. Phys. 1999, 111, 4672-4687.
    • (1999) J. Chem. Phys. , vol.111 , pp. 4672-4687
    • Soudackov, A.1    Hammes-Schiffer, S.2
  • 27
    • 0034248772 scopus 로고    scopus 로고
    • Derivation of rate expressions for nonadiabatic proton-coupled electron transfer reactions in solution
    • Soudackov, A.; Hammes-Schiffer, S. Derivation of rate expressions for nonadiabatic proton-coupled electron transfer reactions in solution. J. Chem. Phys. 2000, 113, 2385-2396.
    • (2000) J. Chem. Phys. , vol.113 , pp. 2385-2396
    • Soudackov, A.1    Hammes-Schiffer, S.2
  • 28
    • 1942504864 scopus 로고    scopus 로고
    • Theoretical studies of proton-coupled electron transfer reactions
    • Hammes-Schiffer, S.; Iordanova, N. Theoretical studies of proton-coupled electron transfer reactions. Biochim. Biophys. Acta-Bioenerg. 2004, 1655, 29-36.
    • (2004) Biochim. Biophys. Acta-Bioenerg. , vol.1655 , pp. 29-36
    • Hammes-Schiffer, S.1    Iordanova, N.2
  • 29
    • 22944452805 scopus 로고    scopus 로고
    • Quantum and dynamical effects of proton donor-acceptor vibrational motion in nonadiabatic proton-coupled electron transfer reactions
    • No. 014505
    • Soudackov, A.; Hatcher, E.; Hammes-Schiffer, S. Quantum and dynamical effects of proton donor-acceptor vibrational motion in nonadiabatic proton-coupled electron transfer reactions. J. Chem. Phys. 2005, 122, No. 014505.
    • (2005) J. Chem. Phys. , vol.122
    • Soudackov, A.1    Hatcher, E.2    Hammes-Schiffer, S.3
  • 30
    • 28644433594 scopus 로고    scopus 로고
    • Comparison of dynamical aspects of electron, proton, and proton-coupled electron transfer reactions
    • in press
    • Hatcher, E.; Soudackov, A.; Hammes-Schiffer, S. Comparison of dynamical aspects of electron, proton, and proton-coupled electron transfer reactions. Chem. Phys., in press.
    • Chem. Phys.
    • Hatcher, E.1    Soudackov, A.2    Hammes-Schiffer, S.3
  • 31
    • 0031808658 scopus 로고    scopus 로고
    • Stretching exercises - Flexibility in dihydrofolate reductase catalysis
    • Miller, G. P.; Benkovic, S. J. Stretching exercises - flexibility in dihydrofolate reductase catalysis. Chem. Biol. 1998, 5, R105-R113.
    • (1998) Chem. Biol. , vol.5
    • Miller, G.P.1    Benkovic, S.J.2
  • 33
    • 0037188007 scopus 로고    scopus 로고
    • Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis
    • Agarwal, P. K.; Billeter, S. R.; Hammes-Schiffer, S. Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis. J. Phys. Chem. B 2002, 106, 3283-3293.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 3283-3293
    • Agarwal, P.K.1    Billeter, S.R.2    Hammes-Schiffer, S.3
  • 34
    • 4344669913 scopus 로고    scopus 로고
    • Analysis of electrostatics and correlated motions for hydride transfer in dihydrofolate reductase
    • Wong, K. F.; Watney, J. B.; Hammes-Schiffer, S. Analysis of electrostatics and correlated motions for hydride transfer in dihydrofolate reductase. J. Phys. Chem. B 2004, 108, 12231-12241.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 12231-12241
    • Wong, K.F.1    Watney, J.B.2    Hammes-Schiffer, S.3
  • 35
    • 0037414270 scopus 로고    scopus 로고
    • Effect of mutation on enzyme motion in dihydrofolate reductase
    • Watney, J. B.; Agarwal, P. K.; Hammes-Schiffer, S. Effect of mutation on enzyme motion in dihydrofolate reductase. J. Am. Chem. Soc. 2003, 125, 3745-3750.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 3745-3750
    • Watney, J.B.1    Agarwal, P.K.2    Hammes-Schiffer, S.3
  • 36
    • 18744380681 scopus 로고    scopus 로고
    • Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase
    • Wong, K. F.; Selzer, T.; Benkovic, S. J.; Hammes-Schiffer, S. Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. Proc. Nat. Acad. Sci. U.S.A. 2005, 102, 6807-6812.
    • (2005) Proc. Nat. Acad. Sci. U.S.A. , vol.102 , pp. 6807-6812
    • Wong, K.F.1    Selzer, T.2    Benkovic, S.J.3    Hammes-Schiffer, S.4
  • 38
    • 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.; Gao, J. Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase. Biochemistry 2003, 42, 13558-13575.
    • (2003) Biochemistry , vol.42 , pp. 13558-13575
    • Garcia-Viloca, M.1    Truhlar, D.G.2    Gao, J.3
  • 39
    • 0346936519 scopus 로고    scopus 로고
    • Barriers to hydride transfer in wild type and mutant dihydrofolate reductase from E. coli
    • Thorpe, I. F.; Brooks, C. L., III Barriers to hydride transfer in wild type and mutant dihydrofolate reductase from E. coli. J. Phys. Chem. B 2003, 107, 14042-14051.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 14042-14051
    • Thorpe, I.F.1    Brooks III, C.L.2
  • 40
    • 6344294816 scopus 로고    scopus 로고
    • The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase
    • Thorpe, I. F.; Brooks, C. L, III The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins: Struct., Funct,, Bioinformatics 2004, 57, 444-457.
    • (2004) Proteins: Struct., Funct., Bioinformatics , vol.57 , pp. 444-457
    • Thorpe, I.F.1    Brooks III, C.L.2
  • 41
    • 0033616094 scopus 로고    scopus 로고
    • Catalytic mechanism of dihydrofolate reductase enzyme: A combined quantum-mechanical/molecular mechanical characterization of transition state structure for the hydride transfer step
    • Castillo, R.; Andres, J.; Moliner, V. Catalytic mechanism of dihydrofolate reductase enzyme: A combined quantum-mechanical/molecular mechanical characterization of transition state structure for the hydride transfer step. J. Am. Chem. Soc. 1999, 121, 12140-12147.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 12140-12147
    • Castillo, R.1    Andres, J.2    Moliner, V.3
  • 42
    • 0037180004 scopus 로고    scopus 로고
    • Computational methods for the study of enzymic reaction mechanisms 1. Application to the hydride transfer step in the catalysis of dihydrofolate reductase
    • Cummins, P. L.; Greatbanks, S. P.; Rendell, A. P.; Gready, J. E. Computational methods for the study of enzymic reaction mechanisms 1. Application to the hydride transfer step in the catalysis of dihydrofolate reductase. J. Phys. Chem. B 2002, 106, 9934-9944.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 9934-9944
    • Cummins, P.L.1    Greatbanks, S.P.2    Rendell, A.P.3    Gready, J.E.4
  • 43
    • 0035870566 scopus 로고    scopus 로고
    • Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics simulations of hydrogen transfer reactions in enzymes
    • Billeter, S. R.; Webb, S. P.; Iordanov, T.; Agarwal, P. K.; Hammes-Schiffer, S. Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics simulations of hydrogen transfer reactions in enzymes. J. Chem. Phys. 2001, 114, 6925-6936.
    • (2001) J. Chem. Phys. , vol.114 , pp. 6925-6936
    • Billeter, S.R.1    Webb, S.P.2    Iordanov, T.3    Agarwal, P.K.4    Hammes-Schiffer, S.5
  • 44
    • 0034300544 scopus 로고    scopus 로고
    • Fourier grid Hamiltonian multiconfigurational self-consistent field: A method to calculate multidimensional hydrogen vibrational wave functions
    • Webb, S. P.; Hammes-Schiffer, S. Fourier grid Hamiltonian multiconfigurational self-consistent field: A method to calculate multidimensional hydrogen vibrational wave functions. J. Chem. Phys. 2000, 113, 5214-5227.
    • (2000) J. Chem. Phys. , vol.113 , pp. 5214-5227
    • Webb, S.P.1    Hammes-Schiffer, S.2
  • 47
    • 0000843443 scopus 로고    scopus 로고
    • A position dependent friction model for solution reactions in the high friction regime: Proton transfer in triosephosphate isomerase (TIM)
    • Neria, E.; Karplus, M. A position dependent friction model for solution reactions in the high friction regime: Proton transfer in triosephosphate isomerase (TIM). J. Chem. Phys. 1996, 105, 10812-10818.
    • (1996) J. Chem. Phys. , vol.105 , pp. 10812-10818
    • Neria, E.1    Karplus, M.2
  • 48
    • 13044304431 scopus 로고
    • Molecular dynamics with electronic transitions
    • Tully, J. C. Molecular dynamics with electronic transitions. J. Chem. Phys. 1990, 93, 1061-1071.
    • (1990) J. Chem. Phys. , vol.93 , pp. 1061-1071
    • Tully, J.C.1
  • 49
    • 0031015737 scopus 로고    scopus 로고
    • Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence
    • Sawaya, M. R.; Kraut, J. Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence. Biochemistry 1997, 36, 586-603.
    • (1997) Biochemistry , vol.36 , pp. 586-603
    • Sawaya, M.R.1    Kraut, J.2
  • 50
    • 0035928796 scopus 로고    scopus 로고
    • Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism
    • Osborne, M. J.; Schnell, J.; Benkovic, S. J.; Dyson, H. J.; Wright, P. E. Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism. Biochemistry 2001, 40, 9846-9859.
    • (2001) Biochemistry , vol.40 , pp. 9846-9859
    • Osborne, M.J.1    Schnell, J.2    Benkovic, S.J.3    Dyson, H.J.4    Wright, P.E.5
  • 51
    • 0037159205 scopus 로고    scopus 로고
    • Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: Mutational effects on hydride transfer rates
    • Rajagopalan, P. T. R.; Lutz, S.; Benkovic, S. J. Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: Mutational effects on hydride transfer rates. Biochemistry 2002, 41, 12618-12628.
    • (2002) Biochemistry , vol.41 , pp. 12618-12628
    • Rajagopalan, P.T.R.1    Lutz, S.2    Benkovic, S.J.3
  • 53
    • 0031443372 scopus 로고    scopus 로고
    • Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant
    • Cameron, C. E.; Benkovic, S. J. Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant. Biochemistry 1997, 36, 15792-15800.
    • (1997) Biochemistry , vol.36 , pp. 15792-15800
    • Cameron, C.E.1    Benkovic, S.J.2
  • 54
    • 1842531419 scopus 로고    scopus 로고
    • Pivotal role of Gly 121 in dihydrofolate reductase from Escherichia coli: The altered structure of a mutant enzyme may form the basis of its diminished catalytic performance
    • Swanwick, R. S.; Shrimpton, P. J.; Allemann, R. K. Pivotal role of Gly 121 in dihydrofolate reductase from Escherichia coli: The altered structure of a mutant enzyme may form the basis of its diminished catalytic performance. Biochemistry 2004, 43, 4119-4127.
    • (2004) Biochemistry , vol.43 , pp. 4119-4127
    • Swanwick, R.S.1    Shrimpton, P.J.2    Allemann, R.K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.