-
1
-
-
36849048228
-
Intrinsic motions along an enzymatic reaction trajectory
-
DOI 10.1038/nature06410, PII NATURE06410
-
Henzler-Wildman KA, et al. (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450:838-844. (Pubitemid 350231334)
-
(2007)
Nature
, vol.450
, Issue.7171
, pp. 838-844
-
-
Henzler-Wildman, K.A.1
Thai, V.2
Lei, M.3
Ott, M.4
Wolf-Watz, M.5
Fenn, T.6
Pozharski, E.7
Wilson, M.A.8
Petsko, G.A.9
Karplus, M.10
Hubner, C.G.11
Kern, D.12
-
2
-
-
76549109225
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
11
-
-
0037022683
-
Network of coupled promoting motions in enzyme catalysis
-
DOI 10.1073/pnas.052005999
-
Agarwal PK, Billeter SR, Rajagopalan PTR, Benkovic SJ, Hammes-Schiffer S (2002) Network of coupled promoting motions in enzyme catalysis. Proc Natl Acad Sci USA 99:2794-2799. (Pubitemid 34240540)
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.5
, pp. 2794-2799
-
-
Agarwal, P.K.1
Billeter, S.R.2
Rajagopalan, P.T.R.3
Benkovic, S.J.4
Hammes-Schiffer, S.5
-
12
-
-
33745362450
-
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
-
14
-
-
18744380681
-
Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase
-
DOI 10.1073/pnas.0408343102
-
Wong KF, Selzer T, Benkovic SJ, Hammes-Schiffer S (2005) Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. Proc Natl Acad Sci USA 102:6807-6812. (Pubitemid 40675397)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.19
, pp. 6807-6812
-
-
Wong, K.F.1
Selzer, T.2
Benkovic, S.J.3
Hammes-Schiffer, S.4
-
15
-
-
32244432145
-
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
-
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
-
18
-
-
77955165990
-
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
-
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
-
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
-
22
-
-
4944242943
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|