메뉴 건너뛰기




Volumn 108, Issue 39, 2011, Pages 16159-16163

Dynamics and dissipation in enzyme catalysis

Author keywords

Enzyme dynamics; Hydrogen tunneling; Path integral; Ring polymer molecular dynamics

Indexed keywords

DIHYDROFOLATE REDUCTASE;

EID: 80053636473     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1106397108     Document Type: Article
Times cited : (158)

References (43)
  • 2
    • 76549109225 scopus 로고    scopus 로고
    • Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands
    • Boehr DD, McElheny D, Dyson HJ, Wright PE (2010) Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands. Proc Natl Acad Sci USA 107:1373-1378.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 1373-1378
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 4
    • 77951226274 scopus 로고    scopus 로고
    • At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
    • Kamerlin SCL, Warshel A (2010) At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins 78:1339-1375.
    • (2010) Proteins , vol.78 , pp. 1339-1375
    • Kamerlin, S.C.L.1    Warshel, A.2
  • 6
    • 0346726109 scopus 로고    scopus 로고
    • How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations
    • DOI 10.1126/science.1088172
    • Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (2004) How enzymes work: Analysis by modern rate theory and computer simulations. Science 303:186-195. (Pubitemid 38057561)
    • (2004) Science , vol.303 , Issue.5655 , pp. 186-195
    • Garcia-Viloca, M.1    Gao, J.2    Karplus, M.3    Truhlar, D.G.4
  • 7
    • 68049093016 scopus 로고    scopus 로고
    • Enzymatic transition states and dynamic motion in barrier crossing
    • Schwartz SD, Schramm VL (2009) Enzymatic transition states and dynamic motion in barrier crossing. Nat Chem Biol 5:551-559.
    • (2009) Nat Chem Biol , vol.5 , pp. 551-559
    • Schwartz, S.D.1    Schramm, V.L.2
  • 8
    • 77955165752 scopus 로고    scopus 로고
    • On the origin of the chemical barrier and tunneling in enzymes
    • Machleder SQ, Pineda JRET, Schwartz SD (2010) On the origin of the chemical barrier and tunneling in enzymes. J Phys Org Chem 23:690-695.
    • (2010) J Phys Org Chem , vol.23 , pp. 690-695
    • Machleder, S.Q.1    Pineda, J.2    Schwartz, S.D.3
  • 9
    • 33645801770 scopus 로고    scopus 로고
    • Atomic description of an enzyme reaction dominated by proton tunneling
    • Masgrau L, et al. (2006) Atomic description of an enzyme reaction dominated by proton tunneling. Science 312:237-241.
    • (2006) Science , vol.312 , pp. 237-241
    • Masgrau, L.1
  • 10
    • 68049085675 scopus 로고    scopus 로고
    • A 21st century revisionist's view at a turning point in enzymology
    • Nagel ZD, Klinman JP (2009) A 21st century revisionist's view at a turning point in enzymology. Nat Chem Biol 5:543-550.
    • (2009) Nat Chem Biol , vol.5 , pp. 543-550
    • Nagel, Z.D.1    Klinman, J.P.2
  • 12
    • 33745362450 scopus 로고    scopus 로고
    • Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions
    • DOI 10.1021/ja061585l
    • Pang JY, Pu JZ, Gao JL, Truhlar DG, Allemann RK (2006) Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions. J Am Chem Soc 128:8015-8023. (Pubitemid 43945743)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.24 , pp. 8015-8023
    • Pang, J.1    Pu, J.2    Gao, J.3    Truhlar, D.G.4    Allemann, R.K.5
  • 15
    • 32244432145 scopus 로고    scopus 로고
    • Effects of a distal mutation on active site chemistry
    • DOI 10.1021/bi0518242
    • Wang L, Tharp S, Selzer T, Benkovic SJ, Kohen A (2006) Effects of a distal mutation on active site chemistry. Biochemistry 45:1383-1392. (Pubitemid 43214803)
    • (2006) Biochemistry , vol.45 , Issue.5 , pp. 1383-1392
    • Wang, L.1    Tharp, S.2    Selzer, T.3    Benkovic, S.J.4    Kohen, A.5
  • 16
    • 79953823548 scopus 로고    scopus 로고
    • A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
    • Gira B, et al. (2011) A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332:234-238.
    • (2011) Science , vol.332 , pp. 234-238
    • Gira, B.1
  • 17
    • 33645836711 scopus 로고    scopus 로고
    • Enzyme motions inside and out
    • Benkovic SJ, Hammes-Schiffer S (2006) Enzyme motions inside and out. Science 312:208-209.
    • (2006) Science , vol.312 , pp. 208-209
    • Benkovic, S.J.1    Hammes-Schiffer, S.2
  • 18
    • 77955165990 scopus 로고    scopus 로고
    • Tunneling in enzymatic and nonenzymatic hydrogen transfer reactions
    • Truhlar DG (2010) Tunneling in enzymatic and nonenzymatic hydrogen transfer reactions. J Phys Org Chem 23:660-676.
    • (2010) J Phys Org Chem , vol.23 , pp. 660-676
    • Truhlar, D.G.1
  • 19
    • 72249089538 scopus 로고    scopus 로고
    • Evidence to support the hypothesis that promoting vibrations enhance the rate of an enzyme catalyzed H-tunneling reaction
    • Pudney CR, et al. (2009) Evidence to support the hypothesis that promoting vibrations enhance the rate of an enzyme catalyzed H-tunneling reaction. J Am Chem Soc 131:17072-17073.
    • (2009) J Am Chem Soc , vol.131 , pp. 17072-17073
    • Pudney, C.R.1
  • 20
    • 76149110500 scopus 로고    scopus 로고
    • Solvent effects on catalysis by Escherichia coli dihydrofolate reductase
    • Loveridge EJ, Tey LH, Allemann RK (2010) Solvent effects on catalysis by Escherichia coli dihydrofolate reductase. J Am Chem Soc 132:1137-1143.
    • (2010) J Am Chem Soc , vol.132 , pp. 1137-1143
    • Loveridge, E.J.1    Tey, L.H.2    Allemann, R.K.3
  • 21
    • 55949096608 scopus 로고    scopus 로고
    • Atomic detail of chemical transformation at the transition state of an enzymatic reaction
    • Saen-Oon S, Quaytman-Machleder S, Schramm VL, Schwartz SD (2008) Atomic detail of chemical transformation at the transition state of an enzymatic reaction. Proc Natl Acad Sci USA 105:16543-16548.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 16543-16548
    • Saen-Oon, S.1    Quaytman-Machleder, S.2    Schramm, V.L.3    Schwartz, S.D.4
  • 22
    • 4944242943 scopus 로고    scopus 로고
    • By chance, or by design?
    • Ball P (2004) By chance, or by design? Nature 431:396-397.
    • (2004) Nature , vol.431 , pp. 396-397
    • Ball, P.1
  • 23
    • 4444241584 scopus 로고    scopus 로고
    • Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics
    • Craig IR, Manolopoulos DE (2004) Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics. J Chem Phys 121:3368-3373.
    • (2004) J Chem Phys , vol.121 , pp. 3368-3373
    • Craig, I.R.1    Manolopoulos, D.E.2
  • 24
    • 23744437908 scopus 로고    scopus 로고
    • A refined ring polymer molecular dynamics theory of chemical reaction rates
    • Craig IR, Manolopoulos DE (2005) A refined ring polymer molecular dynamics theory of chemical reaction rates. J Chem Phys 123:034102.
    • (2005) J Chem Phys , vol.123 , pp. 034102
    • Craig, I.R.1    Manolopoulos, D.E.2
  • 25
    • 0043141259 scopus 로고
    • An empirical valence bond approach for comparing reactions in solutions and in enzymes
    • Warshel A, Weiss RM (1980) An empirical valence bond approach for comparing reactions in solutions and in enzymes. J Am Chem Soc 102:6218-6226.
    • (1980) J Am Chem Soc , vol.102 , pp. 6218-6226
    • Warshel, A.1    Weiss, R.M.2
  • 26
    • 34547456661 scopus 로고    scopus 로고
    • Origin of the temperature dependence of isotope effects in enzymatic reactions: The case of dihydrofolate reductase
    • Liu HB, Warshel A (2007) Origin of the temperature dependence of isotope effects in enzymatic reactions: The case of dihydrofolate reductase. J Phys Chem B 111:7852-7861.
    • (2007) J Phys Chem B , vol.111 , pp. 7852-7861
    • Liu, H.B.1    Warshel, A.2
  • 27
    • 0842311640 scopus 로고    scopus 로고
    • From transition paths to transition states and rate coefficients
    • Hummer G (2004) From transition paths to transition states and rate coefficients. J Chem Phys 120:516-523.
    • (2004) J Chem Phys , vol.120 , pp. 516-523
    • Hummer, G.1
  • 28
    • 0036424048 scopus 로고    scopus 로고
    • Transition path sampling: Throwing ropes over rough mountain passes, in the dark
    • Bolhuis PG, Chandler D, Dellago C, Geissler PL (2002) Transition path sampling: Throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem 53:291-318.
    • (2002) Annu Rev Phys Chem , vol.53 , pp. 291-318
    • Bolhuis, P.G.1    Chandler, D.2    Dellago, C.3    Geissler, P.L.4
  • 29
    • 0037188007 scopus 로고    scopus 로고
    • Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis
    • DOI 10.1021/jp020190v
    • Agarwal PK, Billeter SR, Hammes-Schiffer S (2002) Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis. J Phys Chem B 106:3283-3293. (Pubitemid 35290281)
    • (2002) Journal of Physical Chemistry B , vol.106 , Issue.12 , pp. 3283-3293
    • Agarwal, P.K.1    Billeter, S.R.2    Hammes-Schiffer, S.3
  • 30
    • 0344391945 scopus 로고    scopus 로고
    • Reaction-Path Energetics and Kinetics of the Hydride Transfer Reaction Catalyzed by Dihydrofolate Reductase
    • DOI 10.1021/bi034824f
    • Garcia-Viloca M, Truhlar DG, Gao JL (2003) Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase. Biochemistry 42:13558-13575. (Pubitemid 37444907)
    • (2003) Biochemistry , vol.42 , Issue.46 , pp. 13558-13575
    • Garcia-Viloca, M.1    Truhlar, D.G.2    Gao, J.3
  • 31
    • 0037159205 scopus 로고    scopus 로고
    • Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: Mutational effects on hydride transfer rates
    • DOI 10.1021/bi026369d
    • Rajagopalan PTR, Lutz S, Benkovic SJ (2002) Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: Mutational effects on hydride transfer rates. Biochemistry 41:12618-12628. (Pubitemid 35192491)
    • (2002) Biochemistry , vol.41 , Issue.42 , pp. 12618-12628
    • Ravi, R.P.T.1    Lutz, S.2    Benkovic, S.J.3
  • 32
    • 0031567076 scopus 로고    scopus 로고
    • Molecular dynamics of an enzyme reaction: Proton transfer in TIM
    • PII S0009261497000687
    • Neria E, Karplus M (1997) Molecular dynamics of an enzyme reaction: Proton transfer in TIM. Chem Phys Lett 267:23-30. (Pubitemid 127162249)
    • (1997) Chemical Physics Letters , vol.267 , Issue.1-2 , pp. 23-30
    • Neria, E.1    Karplus, M.2
  • 33
    • 19944416878 scopus 로고    scopus 로고
    • Small temperature dependence of the kinetic isotope effect for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase
    • Pu JZ, Ma SH, Gao JL, Truhlar DG (2005) Small temperature dependence of the kinetic isotope effect for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase. J Phys Chem B 109:8551-8556.
    • (2005) J Phys Chem B , vol.109 , pp. 8551-8556
    • Pu, J.Z.1    Ma, S.H.2    Gao, J.L.3    Truhlar, D.G.4
  • 34
    • 33748613208 scopus 로고    scopus 로고
    • Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions
    • Pu JZ, Gao JL, Truhlar DG (2006) Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. Chem Rev 106:3140-3169.
    • (2006) Chem Rev , vol.106 , pp. 3140-3169
    • Pu, J.Z.1    Gao, J.L.2    Truhlar, D.G.3
  • 35
    • 0037181354 scopus 로고    scopus 로고
    • Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: Effect of geometry and tunneling on proton-transfer rate constants
    • DOI 10.1021/ja0118439
    • Cui Q, Karplus M (2002) Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: Effect of geometry and tunneling on proton-transfer rate constants. J Am Chem Soc 124:3093-3124. (Pubitemid 34249983)
    • (2002) Journal of the American Chemical Society , vol.124 , Issue.12 , pp. 3093-3124
    • Cui, Q.1    Karplus, M.2
  • 37
    • 33751123245 scopus 로고    scopus 로고
    • Curve crossing formulation for proton transfer reactions in solution
    • Borgis D, Hynes JT (1996) Curve crossing formulation for proton transfer reactions in solution. J Phys Chem 100:1118-1128. (Pubitemid 126835004)
    • (1996) Journal of Physical Chemistry , vol.100 , Issue.4 , pp. 1118-1128
    • Borgis, D.1    Hynes, J.T.2
  • 38
    • 0036301901 scopus 로고    scopus 로고
    • Environmentally coupled hydrogen tunneling: Linking catalysis to dynamics
    • DOI 10.1046/j.1432-1033.2002.03022.x
    • Knapp MJ, Klinman JP (2002) Environmentally coupled hydrogen tunneling: Linking catalysis to dynamics. Eur J Biochem 269:3113-3121. (Pubitemid 34748097)
    • (2002) European Journal of Biochemistry , vol.269 , Issue.13 , pp. 3113-3121
    • Knapp, M.J.1    Klinman, J.P.2
  • 39
    • 33845287671 scopus 로고    scopus 로고
    • Enzymatic catalysis and transfers in solution. i. Theory and computations, a unified view
    • Marcus RA (2006) Enzymatic catalysis and transfers in solution. i. theory and computations, a unified view. J Chem Phys 125:194504.
    • (2006) J Chem Phys , vol.125 , pp. 194504
    • Marcus, R.A.1
  • 40
    • 0033305793 scopus 로고    scopus 로고
    • Proton and hydrogen atom tunnelling in hydrolytic and redox enzyme catalysis
    • Kuznetsov AM, Ulstrup J (1999) Proton and hydrogen atom tunnelling in hydrolytic and redox enzyme catalysis. Can J Chem 77:1085-1096. (Pubitemid 129658853)
    • (1999) Canadian Journal of Chemistry , vol.77 , Issue.5-6 , pp. 1085-1096
    • Kuznetsov, A.M.1    Ulstrup, J.2
  • 42
    • 46249092554 scopus 로고    scopus 로고
    • Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435-447.
    • (2008) J Chem Theory Comput , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 43
    • 33747589472 scopus 로고    scopus 로고
    • Towards a theory of transition paths
    • E W, Vanden-Eijnden E (2006) Towards a theory of transition paths. J Stat Phys 123:503-523.
    • (2006) J Stat Phys , vol.123 , pp. 503-523
    • Vanden-Eijnden, E.E.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.