-
1
-
-
0037022683
-
Network of coupled promoting motions in enzyme catalysis
-
doi:10.1073/pnas. 052005999
-
Agarwal, P. K., Billeter, S. R., Ravi Rajagopalan, P. T., Benkovic, S. J. & Hammes-Schififer, S. 2002a Network of coupled promoting motions in enzyme catalysis. Proc. Natl Acad. Sci. USA 99, 2794-2799. (doi:10.1073/pnas. 052005999)
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 2794-2799
-
-
Agarwal, P.K.1
Billeter, S.R.2
Ravi Rajagopalan, P.T.3
Benkovic, S.J.4
Hammes-Schififer, S.5
-
2
-
-
0037188007
-
Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis
-
doi:10.1021/jp020190v
-
Agarwal, P. K., Billeter, S. R. & Hammes-Schiffer, S. 2002b Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis. J. Phys. Chem. B 106, 3283-3293. (doi:10.1021/jp020190v)
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 3283-3293
-
-
Agarwal, P.K.1
Billeter, S.R.2
Hammes-Schiffer, S.3
-
3
-
-
0035859446
-
Internal enzyme motions as a source of catalytic activity: Rate-promoting vibrations and hydrogen tunneling
-
doi:10.1021/jp004547b
-
Antoniou, D. & Schwartz, D. 2001 Internal enzyme motions as a source of catalytic activity: rate-promoting vibrations and hydrogen tunneling. J. Phys. Chem. B 105, 5553-5558. (doi:10.1021/jp004547b)
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 5553-5558
-
-
Antoniou, D.1
Schwartz, D.2
-
4
-
-
7044254777
-
Transition pat sampling study of classical rate-promoting vibrations
-
doi:10.1063/1.1782813
-
Antoniou, D. & Schwartz, D. 2004 Transition pat sampling study of classical rate-promoting vibrations. J. Chem. Phys. 121, 6442-6447. (doi:10.1063/1.1782813)
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 6442-6447
-
-
Antoniou, D.1
Schwartz, D.2
-
5
-
-
0036305753
-
Barrier passage and protein dynamics in enzymatically catalyzed reactions
-
doi:10.1046/j.1432-1033.2002.03021.x
-
Antoniou, D., Caratzoulas, S., Kalyanaraman, C., Mincer, J. S. & Schwartz, D. 2002 Barrier passage and protein dynamics in enzymatically catalyzed reactions. Eur. J. Biochem. 269, 3103-3112. (doi:10.1046/j.1432-1033. 2002.03021.x)
-
(2002)
Eur. J. Biochem.
, vol.269
, pp. 3103-3112
-
-
Antoniou, D.1
Caratzoulas, S.2
Kalyanaraman, C.3
Mincer, J.S.4
Schwartz, D.5
-
6
-
-
33748360193
-
-
In pressa. (ed. J. Richards). Oxford, UK: Elsevier to be published
-
Antoniou, D., Basner, J. S., Nunez, S. & Schwartz, S. D. In pressa. Advances in physical organic chemistry (ed. J. Richards). Oxford, UK: Elsevier (to be published 2006).
-
(2006)
Advances in Physical Organic Chemistry
-
-
Antoniou, D.1
Basner, J.S.2
Nunez, S.3
Schwartz, S.D.4
-
7
-
-
85020787834
-
-
In pressb. (ed. R. D. Kuchta, Vern Schramm guest editor). American Chemical Society to be published
-
Antoniou, D., Basner, J. S., Nunez, S. & Schwartz, S. D. In pressb. Chemical reviews (ed. R. D. Kuchta, Vern Schramm guest editor). American Chemical Society (to be published 2006).
-
(2006)
Chemical Reviews
-
-
Antoniou, D.1
Basner, J.S.2
Nunez, S.3
Schwartz, S.D.4
-
8
-
-
1042282260
-
Donor acceptor distance and protein promoting vibration coupling as a mechanism for kinetic control in isozymes of human lactate dehydrogenase
-
doi:10.1021/jp0364349
-
Basner, J. E. & Schwartz, D. 2004 Donor acceptor distance and protein promoting vibration coupling as a mechanism for kinetic control in isozymes of human lactate dehydrogenase. J. Phys. Chem. B. 108, 444-451. (doi:10.1021/jp0364349)
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 444-451
-
-
Basner, J.E.1
Schwartz, D.2
-
9
-
-
26444486352
-
How enzyme dynamics helps catalyze a reaction in atomic detail: A transition path sampling study
-
doi:10.1021/ja043320h
-
Basner, J. E. & Schwartz, S. D. 2005 How enzyme dynamics helps catalyze a reaction in atomic detail: a transition path sampling study. J. Am. Chem. Soc. 127, 13 822-13 831. (doi:10.1021/ja043320h)
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 13822-13831
-
-
Basner, J.E.1
Schwartz, S.D.2
-
10
-
-
2742515916
-
Sampling ensembles of deterministic transition pathways
-
doi:10.1039/a801266k
-
Bolhuis, P. G., Dellago, C. & Chandler, D. 1998 Sampling ensembles of deterministic transition pathways. Faraday Disc. 110, 421-436. (doi:10.1039/a801266k)
-
(1998)
Faraday Disc.
, vol.110
, pp. 421-436
-
-
Bolhuis, P.G.1
Dellago, C.2
Chandler, D.3
-
11
-
-
0034705109
-
Reaction coordinates of biomolecular isomerization
-
doi:10.1073/pnas.100127697
-
Bolhuis, P. G , Dellago, C. & Chandler, D. 2000 Reaction coordinates of biomolecular isomerization. Proc. Natl Acad. Sci. USA 97, 5877-5882. (doi:10.1073/pnas.100127697)
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 5877-5882
-
-
Bolhuis, P.G.1
Dellago, C.2
Chandler, D.3
-
12
-
-
0040362704
-
Chemical basis for enzyme catalysis
-
doi:10. 1021/bi0003689
-
Bruice, T. C. & Benkovic, S. J. 2000 Chemical basis for enzyme catalysis. Biochemistry 39, 6267-6274. (doi:10. 1021/bi0003689)
-
(2000)
Biochemistry
, vol.39
, pp. 6267-6274
-
-
Bruice, T.C.1
Benkovic, S.J.2
-
13
-
-
0035249366
-
A computational method to discover the existence of promoting vibrations for chemical reactions in condensed phases
-
doi:10.1063/1.1342817
-
Caratzoulas, S. & Schwartz, D. 2001 A computational method to discover the existence of promoting vibrations for chemical reactions in condensed phases. J. Chem. Phys. 114, 2910-2918. (doi:10.1063/1.1342817)
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 2910-2918
-
-
Caratzoulas, S.1
Schwartz, D.2
-
14
-
-
0037012441
-
Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcoholdehydrogenase
-
doi:10.1021/ja017146y
-
Caratzoulas, S., Mincer, J. S. & Schwartz, S. D. 2002 Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcoholdehydrogenase. J. Am. Chem. Soc. 124, 3270-3276. (doi:10.1021/ja017146y)
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 3270-3276
-
-
Caratzoulas, S.1
Mincer, J.S.2
Schwartz, S.D.3
-
17
-
-
0000801009
-
Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements
-
doi:10.1063/1.476378
-
Dellago, C., Bolhuis, P. G. & Chandler, D. 1998 Efficient transition path sampling: application to Lennard-Jones cluster rearrangements. J. Chem. Phys. 108, 9236-9245. (doi:10.1063/1.476378)
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 9236-9245
-
-
Dellago, C.1
Bolhuis, P.G.2
Chandler, D.3
-
19
-
-
0344391945
-
Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase
-
doi:10.1021/bi034824f
-
Garcia-Viloca, M., Truhlar, D. G. & Gao, J. 2003 Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase. Biochemistry 42, 13 558-13 575. (doi:10.1021/bi034824f)
-
(2003)
Biochemistry
, vol.42
, pp. 13558-13575
-
-
Garcia-Viloca, M.1
Truhlar, D.G.2
Gao, J.3
-
20
-
-
0016624901
-
Binding energy, specificity, and enzymic catalysis: The Circe effect
-
Jencks, W. P. 1975 Binding energy, specificity, and enzymic catalysis: the Circe effect. Adv. Enzymol. 43, 219-310.
-
(1975)
Adv. Enzymol.
, vol.43
, pp. 219-310
-
-
Jencks, W.P.1
-
22
-
-
0032501378
-
Importance of correlated motions in forming highly reactive near attack conformations in catechol-O-methyltransferase
-
Lau, E. & Bruice, C. 1998 Importance of correlated motions in forming highly reactive near attack conformations in catechol-O-methyltransferase. J. Mol. Biol. 120, 12387-12394.
-
(1998)
J. Mol. Biol.
, vol.120
, pp. 12387-12394
-
-
Lau, E.1
Bruice, C.2
-
23
-
-
0023430366
-
Monte-carlo-minimization approach to the multiple-minima problem in protein folding
-
doi:10.1073/pnas.84.19.6611
-
Li, Z. & Scheraga, A. 1987 Monte-carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl Acad. Sci. USA 84, 6611-6615. (doi:10.1073/pnas.84.19.6611)
-
(1987)
Proc. Natl Acad. Sci. USA
, vol.84
, pp. 6611-6615
-
-
Li, Z.1
Scheraga, A.2
-
24
-
-
36749114243
-
-
doi:10. 1063/1.430676
-
Miller, Wm. H. 1974 J. Chem. Phys. 62, 1899-1906. (doi:10. 1063/1.430676)
-
(1974)
J. Chem. Phys.
, vol.62
, pp. 1899-1906
-
-
Miller, Wm.H.1
-
25
-
-
10044273966
-
-
Nunez, S., Antoniou, D., Schramm, V. L. & Schwartz, S. D. 2004 J. Am. Chem. Soc. 126, 15 720-15 729.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 15720-15729
-
-
Nunez, S.1
Antoniou, D.2
Schramm, V.L.3
Schwartz, S.D.4
-
26
-
-
0000421878
-
The nature of forces between large molecules of biological interest
-
Pauling, L. 1948 The nature of forces between large molecules of biological interest. Nature 161, 707-709.
-
(1948)
Nature
, vol.161
, pp. 707-709
-
-
Pauling, L.1
-
27
-
-
36749104593
-
Classical transition state theory is exact if the transition state is unique
-
doi:10.1063/1.438575
-
Pechukas, P. & Pollak, E. 1979 Classical transition state theory is exact if the transition state is unique. J. Chem. Phys. 71, 2062-2068. (doi:10.1063/1.438575)
-
(1979)
J. Chem. Phys.
, vol.71
, pp. 2062-2068
-
-
Pechukas, P.1
Pollak, E.2
-
28
-
-
0038810233
-
Correlated motion and the effect of distal mutations in dihydrofolate reductase
-
doi:10.1073/pnas.1230801100
-
Rod, T. H., Radkiewicz, J. L. & Brooks III, L. 2003 Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc. Natl Acad. Sci. USA 100, 6980-6985. (doi:10.1073/pnas.1230801100)
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 6980-6985
-
-
Rod, T.H.1
Radkiewicz, J.L.2
Brooks III, L.3
-
32
-
-
0346936519
-
Barriers to hydride transfer in wild type and mutant dihydrofolate reductase from E. coli
-
doi:10. 1021/jp035734n
-
Thorpe, I. F. & Brooks III, L. 2003 Barriers to hydride transfer in wild type and mutant dihydrofolate reductase from E. coli. J. Phys. Chem. B 107, 14 042-14 051. (doi:10. 1021/jp035734n)
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 14042-14051
-
-
Thorpe, I.F.1
Brooks III, L.2
-
33
-
-
6344294816
-
The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase
-
doi:10.1002/prot.20219
-
Thorpe, I. F. & Brooks III, L. 2004 The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins 57, 444-457. (doi:10.1002/prot.20219)
-
(2004)
Proteins
, vol.57
, pp. 444-457
-
-
Thorpe, I.F.1
Brooks III, L.2
-
34
-
-
0033568337
-
+ in the active site of formate dehydrogenase
-
doi:10.1021/ja9912731
-
+ in the active site of formate dehydrogenase. J. Am. Chem. Soc. 121, 8164-8173. (doi:10.1021/ja9912731)
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 8164-8173
-
-
Torres, R.A.1
Schiott, B.S.2
Bruice, C.3
-
35
-
-
27644558553
-
Transitional state theory: Variational formulation, dynamical corrections, and error estimates
-
doi:10.1063/1. 2102898
-
Vanden-Eijnden, E. & Tal, A. 2005 Transitional state theory: variational formulation, dynamical corrections, and error estimates. J. Chem. Phys. 123, 184103. (doi:10.1063/1. 2102898)
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 184103
-
-
Vanden-Eijnden, E.1
Tal, A.2
-
36
-
-
18744380681
-
-
doi:10. 1073/pnas.0408343102
-
Wong, K. F., Selzer, T., Benkovic, S. J. & Hammes-Schiffer, S. 2005 Proc. Natl Acad. Sci. USA 102, 6807-6812. (doi:10. 1073/pnas.0408343102)
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 6807-6812
-
-
Wong, K.F.1
Selzer, T.2
Benkovic, S.J.3
Hammes-Schiffer, S.4
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