메뉴 건너뛰기




Volumn 57, Issue 3, 2004, Pages 444-457

The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase

Author keywords

Catalytic rate; Conformational change; Energy barrier; Enzymes; Preorganization; Protein design

Indexed keywords

DIHYDROFOLATE REDUCTASE; ENZYME; GLYCINE; LIGAND; METHIONINE; SERINE; VALINE;

EID: 6344294816     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20219     Document Type: Article
Times cited : (47)

References (44)
  • 1
    • 0023668190 scopus 로고
    • Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli
    • Fierke CA, Johnson KA, Benkovic SJ. 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
  • 2
    • 0031015737 scopus 로고    scopus 로고
    • Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence
    • Sawaya MR, 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
  • 3
    • 0028049327 scopus 로고
    • Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis
    • Falzone CJ, Wright PE, Benkovic SJ. Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis. Biochemistry 1994;33:439-442.
    • (1994) Biochemistry , vol.33 , pp. 439-442
    • Falzone, C.J.1    Wright, P.E.2    Benkovic, S.J.3
  • 4
    • 0028438718 scopus 로고
    • 1H, 15N and 13C resonance assignments, secondary structure, and the conformation of substrate in the binary folate complex of Escherichia coli dihydrofolate reductase
    • Falzone CJ, Cavanagh J, Cowart M, Palmer AG, Matthews CR, Benkovic SJ, Wright PE. 1H, 15N and 13C resonance assignments, secondary structure, and the conformation of substrate in the binary folate complex of Escherichia coli dihydrofolate reductase. J Biomol NMR 1994;4:349-366.
    • (1994) J Biomol NMR , vol.4 , pp. 349-366
    • Falzone, C.J.1    Cavanagh, J.2    Cowart, M.3    Palmer, A.G.4    Matthews, C.R.5    Benkovic, S.J.6    Wright, P.E.7
  • 5
    • 0029102089 scopus 로고
    • Dynamics of the dihydrofolate reductase-folate complex: Catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features
    • Epstein DM, Benkovic SJ, Wright PE. Dynamics of the dihydrofolate reductase-folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features. Biochemistry 1995;34:11037-11048.
    • (1995) Biochemistry , vol.34 , pp. 11037-11048
    • Epstein, D.M.1    Benkovic, S.J.2    Wright, P.E.3
  • 6
    • 0035928796 scopus 로고    scopus 로고
    • Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism
    • Osborne MJ, Schnell J, Benkovic SJ, Dyson HJ, Wright PE. 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
  • 7
    • 0026760364 scopus 로고
    • Complementary perturbation of the kinetic mechanism and catalytic effectiveness of dihydrofolate reductase by side-chain interchange
    • Wagner CR, Thillet J, Benkovic SJ. Complementary perturbation of the kinetic mechanism and catalytic effectiveness of dihydrofolate reductase by side-chain interchange. Biochemistry 1992;31:7834-7840.
    • (1992) Biochemistry , vol.31 , pp. 7834-7840
    • Wagner, C.R.1    Thillet, J.2    Benkovic, S.J.3
  • 8
    • 0028037407 scopus 로고
    • Nonadditivity of mutational effects at the folate binding site of Escherichia coli dihydrofolate reductase
    • Wagner CR, Huang Z, Benkovic SJ. Nonadditivity of mutational effects at the folate binding site of Escherichia coli dihydrofolate reductase. Biochemistry 1994;33:11576-11585.
    • (1994) Biochemistry , vol.33 , pp. 11576-11585
    • Wagner, C.R.1    Huang, Z.2    Benkovic, S.J.3
  • 9
    • 0028828696 scopus 로고
    • Molecular basis for nonadditive mutational effects in Escherichia coli dihydrofolate reductase
    • Wagner CR, Huang Z, Singleton SF, Benkovic SJ. Molecular basis for nonadditive mutational effects in Escherichia coli dihydrofolate reductase. Biochemistry 1995;34:15671-15680.
    • (1995) Biochemistry , vol.34 , pp. 15671-15680
    • Wagner, C.R.1    Huang, Z.2    Singleton, S.F.3    Benkovic, S.J.4
  • 10
    • 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 CE, Benkovic SJ. 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
  • 11
    • 0032485627 scopus 로고    scopus 로고
    • Deletion of a highly motional residue affects formation of the Michaelis complex for Escherichia coli dihydrofolate reductase
    • Miller GP, Benkovic SJ. Deletion of a highly motional residue affects formation of the Michaelis complex for Escherichia coli dihydrofolate reductase. Biochemistry 1998;37:6327-6335.
    • (1998) Biochemistry , vol.37 , pp. 6327-6335
    • Miller, G.P.1    Benkovic, S.J.2
  • 12
    • 0037159205 scopus 로고    scopus 로고
    • Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: Mutational effects on hydride transfer rates
    • Rajagopalan PTR, Lutz S, Benkovic SJ. 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
  • 13
    • 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
  • 14
    • 0037180004 scopus 로고    scopus 로고
    • Computational methods for the study of enzymatic reaction mechanisms: I. Application to the hydride transfer step in the catalysis of dihydrofolate reductase
    • Cummins PL, Greatbanks SP, Rendell AP, Gready JE. Computational methods for the study of enzymatic reaction mechanisms: I. 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
  • 15
    • 0033955055 scopus 로고    scopus 로고
    • Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase
    • Radkiewicz JL, Brooks CL. 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
  • 16
    • 0038810233 scopus 로고    scopus 로고
    • Correlated motion and the effect of distal mutations in dihydrofolate reductase
    • Rod TH, Radkiewicz JL, Brooks CL III. Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc Natl Acad Sci USA 2003;100:6980-6985.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 6980-6985
    • Rod, T.H.1    Radkiewicz, J.L.2    Brooks III, C.L.3
  • 17
    • 0037188007 scopus 로고    scopus 로고
    • Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis
    • Agarwal PK, Billeter SR, 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
  • 18
    • 0037414270 scopus 로고    scopus 로고
    • Effect of mutation on enzyme motion in dihydrofolate reductase
    • Watney JB, Agarwal PK, 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
  • 19
    • 0346936519 scopus 로고    scopus 로고
    • Barriers to hydride transfer in wild-type and mutant dihydrolate reductase from E. coli
    • Thorpe IF, Brooks CL III. Barriers to hydride transfer in wild-type and mutant dihydrolate 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
  • 20
    • 0000500410 scopus 로고
    • Evaluation of the factors influencing reactivity and stereospecificity in Nad(P)H dependent dehydrogenase enzymes
    • Almarsson O, Bruice TC. Evaluation of the factors influencing reactivity and stereospecificity in Nad(P)H dependent dehydrogenase enzymes. J Am Chem Soc 1993;115:2125-2138.
    • (1993) J Am Chem Soc , vol.115 , pp. 2125-2138
    • Almarsson, O.1    Bruice, T.C.2
  • 21
    • 0028908071 scopus 로고
    • Transition structures of hydride transfer reactions of protonated pyridinium ion with 1,4-hihydropyridine and protonated nicotinamide with 1,4-dihydronicotinamide
    • Wu Y-D, Lai DKW, Houk KN. Transition structures of hydride transfer reactions of protonated pyridinium ion with 1,4-hihydropyridine and protonated nicotinamide with 1,4-dihydronicotinamide. J Am Chem Soc 1995;117:4100-4108.
    • (1995) J Am Chem Soc , vol.117 , pp. 4100-4108
    • Wu, Y.-D.1    Lai, D.K.W.2    Houk, K.N.3
  • 24
    • 0027393187 scopus 로고
    • Statistical clustering techniques for the analysis of long molecular dynamics trajectories: Analysis of 2.2-ns trajectories of YPGDV
    • Karpen ME, Tobias DJ, Brooks CL III. Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. Biochemistry 1993;32:412-420.
    • (1993) Biochemistry , vol.32 , pp. 412-420
    • Karpen, M.E.1    Tobias, D.J.2    Brooks III, C.L.3
  • 26
    • 0000516026 scopus 로고    scopus 로고
    • Molecular dynamics and normal mode analysis of biomolecular rigidity
    • Thorpe MF, Duxbury PM, editors. New York: Kluwer Academic/Plenum Press
    • Case DA. Molecular dynamics and normal mode analysis of biomolecular rigidity. In: Thorpe MF, Duxbury PM, editors. Rigidity theory and applications. New York: Kluwer Academic/Plenum Press; 1999.
    • (1999) Rigidity Theory and Applications
    • Case, D.A.1
  • 27
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems: I. Methodology
    • Brooks BR, Janežic DA, Karplus M. Harmonic analysis of large systems: I. Methodology. J Comput Chem 1995;16:1522-1542.
    • (1995) J Comput Chem , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janežic, D.A.2    Karplus, M.3
  • 28
    • 0035828630 scopus 로고    scopus 로고
    • On the calculation of entropy from covariance matrices of the atomic fluctuations
    • Andricioaei I, Karplus M. On the calculation of entropy from covariance matrices of the atomic fluctuations. J Chem Phys 2001;115:6289-6292.
    • (2001) J Chem Phys , vol.115 , pp. 6289-6292
    • Andricioaei, I.1    Karplus, M.2
  • 29
    • 0038016725 scopus 로고    scopus 로고
    • Influence of structural fluctuations on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies
    • Zhang Y, Kua J, McCammon JA. Influence of structural fluctuations on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies. J Phys Chem B 2003;107:4459-4463.
    • (2003) J Phys Chem B , vol.107 , pp. 4459-4463
    • Zhang, Y.1    Kua, J.2    McCammon, J.A.3
  • 30
    • 0038298137 scopus 로고    scopus 로고
    • How dihydrofolate reductase facilitates protonation of dihydrofolate
    • Rod TH, Brooks CL III. How dihydrofolate reductase facilitates protonation of dihydrofolate. J Am Chem Soc 2003;125:8718-8719.
    • (2003) J Am Chem Soc , vol.125 , pp. 8718-8719
    • Rod, T.H.1    Brooks III, C.L.2
  • 31
    • 0026757079 scopus 로고
    • Functional role of a mobile loop of Escherichia coli dihydrofolate reductase in transition-state stabilization
    • Li L, Falzone CJ, Wright PE, Benkovic SJ. Functional role of a mobile loop of Escherichia coli dihydrofolate reductase in transition-state stabilization. Biochemistry 1992;31:7826-7833.
    • (1992) Biochemistry , vol.31 , pp. 7826-7833
    • Li, L.1    Falzone, C.J.2    Wright, P.E.3    Benkovic, S.J.4
  • 32
    • 0032485865 scopus 로고    scopus 로고
    • Strength of an interloop hydrogen bond determines the kinetic pathway in catalysis by Escherichia coli dihydrofolate reductase
    • Miller GP, Benkovic SJ. Strength of an interloop hydrogen bond determines the kinetic pathway in catalysis by Escherichia coli dihydrofolate reductase. Biochemistry 1998;37:6336-6342.
    • (1998) Biochemistry , vol.37 , pp. 6336-6342
    • Miller, G.P.1    Benkovic, S.J.2
  • 33
    • 0035969953 scopus 로고    scopus 로고
    • Interloop contacts modulate ligand cycling during catalysis by Escherichia coli dihydrofolate reductase
    • Miller GP, Wahnon DC, Benkovic SJ. Interloop contacts modulate ligand cycling during catalysis by Escherichia coli dihydrofolate reductase. Biochemistry 2001;40:867-875.
    • (2001) Biochemistry , vol.40 , pp. 867-875
    • Miller, G.P.1    Wahnon, D.C.2    Benkovic, S.J.3
  • 34
    • 0344391945 scopus 로고    scopus 로고
    • Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase
    • Garcia-Viloca M, Truhlar DG, 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
  • 35
    • 0345832242 scopus 로고    scopus 로고
    • Effect of cofactor binding and loop conformation on side chain methyl dynamics in dihydrofolate reductase
    • Schnell JR, Dyson HJ, Wright PE. Effect of cofactor binding and loop conformation on side chain methyl dynamics in dihydrofolate reductase. Biochemistry 2004;43:374-383.
    • (2004) Biochemistry , vol.43 , pp. 374-383
    • Schnell, J.R.1    Dyson, H.J.2    Wright, P.E.3
  • 36
    • 0346726109 scopus 로고    scopus 로고
    • How enzymes work: Analysis by modern rate theory and computer simulations
    • Garcia-Viloca M, Gao J, Karplus M, Truhlar DG. 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
  • 37
    • 0040362704 scopus 로고    scopus 로고
    • Chemical basis for enzyme catalysis
    • Benkovic SJ, Bruice T. Chemical basis for enzyme catalysis. Biochemistry 2000;39:6267-6274.
    • (2000) Biochemistry , vol.39 , pp. 6267-6274
    • Benkovic, S.J.1    Bruice, T.2
  • 38
    • 0142091405 scopus 로고    scopus 로고
    • The near attack conformation approach to the study of the chorismate to prephenate reaction
    • Hur S, Bruice TC. The near attack conformation approach to the study of the chorismate to prephenate reaction. Proc Natl Acad Sci USA 2003;100:12015-12020.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12015-12020
    • Hur, S.1    Bruice, T.C.2
  • 39
    • 0029147823 scopus 로고
    • Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures
    • Swindells MB, MacArthur MW, Thornton JM. Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures. Nat Struct Biol 1995;2:596-603.
    • (1995) Nat Struct Biol , vol.2 , pp. 596-603
    • Swindells, M.B.1    MacArthur, M.W.2    Thornton, J.M.3
  • 40
    • 1042282260 scopus 로고    scopus 로고
    • Donor-acceptor distance and protein promoting vibration coupling to hydride transfer: A possible mechanism for kinetic control in isozymes of human lactate dehydrogenase
    • Basner JE, Schwartz SD. Donor-acceptor distance and protein promoting vibration coupling to hydride transfer: a possible mechanism for kinetic control in isozymes of human lactate dehydrogenase. J Phys Chem B 2004;108:444-451.
    • (2004) J Phys Chem B , vol.108 , pp. 444-451
    • Basner, J.E.1    Schwartz, S.D.2
  • 41
    • 0035122917 scopus 로고    scopus 로고
    • Predicting the emergence of antibiotic resistance by directed evolution and structural analysis
    • Orencia MC, Yoon JS, Ness JE, Stemmer WP, Stevens RC. Predicting the emergence of antibiotic resistance by directed evolution and structural analysis. Nat Struct Biol 2001;8:238-242.
    • (2001) Nat Struct Biol , vol.8 , pp. 238-242
    • Orencia, M.C.1    Yoon, J.S.2    Ness, J.E.3    Stemmer, W.P.4    Stevens, R.C.5
  • 42
    • 0034710950 scopus 로고    scopus 로고
    • Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble
    • Pan H, Lee JC, Hilser VJ. Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble. Proc Natl Acad Sci USA 2000;97:12020-12025.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 12020-12025
    • Pan, H.1    Lee, J.C.2    Hilser, V.J.3
  • 44
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;22:946-950.
    • (1991) J Appl Crystallogr , vol.22 , pp. 946-950
    • Kraulis, P.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.