-
1
-
-
0035543093
-
The depth of chemical time and the power of enzymes as catalysts
-
Wolfenden R, Snider MJ (2001) The depth of chemical time and the power of enzymes as catalysts. Acc Chem Res 34:938-945.
-
(2001)
Acc Chem Res
, vol.34
, pp. 938-945
-
-
Wolfenden, R.1
Snider, M.J.2
-
2
-
-
0041821836
-
A perspective on enzyme catalysis
-
DOI 10.1126/science.1085515
-
Benkovic SJ, Hammes-Schiffer S (2003) A perspective on enzyme catalysis. Science 301:1196-1202. (Pubitemid 37052200)
-
(2003)
Science
, vol.301
, Issue.5637
, pp. 1196-1202
-
-
Benkovic, S.J.1
Hammes-Schiffer, S.2
-
3
-
-
33748633480
-
Electrostatic basis for enzyme catalysis
-
DOI 10.1021/cr0503106
-
Warshel A, et al. (2006) Electrostatic basis for enzyme catalysis. Chem Rev 106:3210-3235. (Pubitemid 44376933)
-
(2006)
Chemical Reviews
, vol.106
, Issue.8
, pp. 3210-3235
-
-
Warshel, A.1
Sharma, P.K.2
Kato, M.3
Xiang, Y.4
Liu, H.5
Olsson, M.H.M.6
-
4
-
-
70350453758
-
Enzyme millisecond conformational dynamics do not catalyze the chemical step
-
Pisliakov AV, Cao J, Kamerlin SC, Warshel A (2009) Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc Natl Acad Sci USA 106:17359-17364.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 17359-17364
-
-
Pisliakov, A.V.1
Cao, J.2
Kamerlin, S.C.3
Warshel, A.4
-
5
-
-
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
-
-
77952355806
-
The role of conformation transitions in adenylate kinase
-
Karplus M (2010) The role of conformation transitions in adenylate kinase. Proc Natl Acad Sci USA 107:E71.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
-
-
Karplus, M.1
-
7
-
-
77952340641
-
Reply to Karplus: Conformational dynamics have no role in the chemical step
-
Warshel A (2010) Reply to Karplus: Conformational dynamics have no role in the chemical step. Proc Natl Acad Sci USA 107:E72.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
-
-
Warshel, A.1
-
8
-
-
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
-
9
-
-
4143095852
-
Protein dynamics and enzymatic catalysis: Investigating the peptidyl-prolyl cis-trans isomerization activity of cyclophilin A
-
DOI 10.1021/bi0495228
-
Agarwal PK, Geist A, Gorin A (2004) Protein dynamics and enzymatic catalysis: Investigating the peptidyl-prolyl cis-trans isomerization activity of cyclophilin A. Biochemistry 43:10605-10618. (Pubitemid 39096703)
-
(2004)
Biochemistry
, vol.43
, Issue.33
, pp. 10605-10618
-
-
Agarwal, P.K.1
Geist, A.2
Gorin, A.3
-
10
-
-
80052149070
-
Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
-
Adamczyk AJ, Cao J, Kamerlin SC, Warshel A (2011) Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions. Proc Natl Acad Sci USA 108:14115-14120.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 14115-14120
-
-
Adamczyk, A.J.1
Cao, J.2
Kamerlin, S.C.3
Warshel, A.4
-
11
-
-
79953823548
-
A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
-
Bhabha G, 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
-
-
Bhabha, G.1
-
12
-
-
0037154884
-
Enzyme dynamics during catalysis
-
DOI 10.1126/science.1066176
-
Eisenmesser EZ, Bosco DA, Akke M, Kern D (2002) Enzyme dynamics during catalysis. Science 295:1520-1523. (Pubitemid 34174006)
-
(2002)
Science
, vol.295
, Issue.5559
, pp. 1520-1523
-
-
Eisenmesser, E.Z.1
Bosco, D.A.2
Akke, M.3
Kern, D.4
-
13
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
DOI 10.1038/nature04105, PII N04105
-
Eisenmesser EZ, et al. (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438:117-121. (Pubitemid 41599831)
-
(2005)
Nature
, vol.438
, Issue.7064
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.M.4
Wolf-Watz, M.5
Bosco, D.A.6
Skalicky, J.J.7
Kay, L.E.8
Kern, D.9
-
14
-
-
30944460113
-
Fluctuating enzymes: Lessons from single-molecule studies
-
Min W, et al. (2005) Fluctuating enzymes: Lessons from single-molecule studies. Acc Chem Res 38:923-931.
-
(2005)
Acc Chem Res
, vol.38
, pp. 923-931
-
-
Min, W.1
-
16
-
-
37249032102
-
Dynamic personalities of proteins
-
DOI 10.1038/nature06522, PII NATURE06522
-
Henzler-Wildman K, Kern D (2007) Dynamic personalities of proteins. Nature 450:964-972. (Pubitemid 350273626)
-
(2007)
Nature
, vol.450
, Issue.7172
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
17
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins. Science 254:1598-1603. (Pubitemid 21917496)
-
(1991)
Science
, vol.254
, Issue.5038
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
18
-
-
0042797442
-
-
Cambridge Univ Press, Cambridge, UK
-
Wales DJ (2003) Energy Landscapes (Cambridge Univ Press, Cambridge, UK).
-
(2003)
Energy Landscapes
-
-
Wales, D.J.1
-
19
-
-
65249122552
-
A unified model of protein dynamics
-
Frauenfelder H, et al. (2009) A unified model of protein dynamics. Proc Natl Acad Sci USA 106:5129-5134.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 5129-5134
-
-
Frauenfelder, H.1
-
20
-
-
3142716857
-
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
-
Hamelberg D, Mongan J, McCammon JA (2004) Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. J Chem Phys 120:11919-11929.
-
(2004)
J Chem Phys
, vol.120
, pp. 11919-11929
-
-
Hamelberg, D.1
Mongan, J.2
McCammon, J.A.3
-
21
-
-
84985715908
-
NMR studies of the rates of Proline Cis-Trans Isomerization in Oligopeptides
-
Grathwohl C, Wuthrich K (1981) NMR studies of the rates of Proline Cis-Trans Isomerization in Oligopeptides. Biopolymers 20:2623-2633.
-
(1981)
Biopolymers
, vol.20
, pp. 2623-2633
-
-
Grathwohl, C.1
Wuthrich, K.2
-
22
-
-
0030461902
-
Steric effects on the amide isomer equilibrium of prolyl peptides. Synthesis and conformational analysis of N-acetyl-5-tert-butylproline N′-methylamides
-
Beausoleil E, Lubell WD (1996) Steric effects on the amide isomer equilibrium of prolyl peptides. Synthesis and conformational analysis of N-acetyl-5-tert-butylproline N′-methylamides. J Am Chem Soc 118:12902-12908.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 12902-12908
-
-
Beausoleil, E.1
Lubell, W.D.2
-
23
-
-
0028877264
-
Kinetic analysis of cyclophilin-catalyzed prolyl cis/trans isomerization by dynamic NMR spectroscopy
-
Kern D, Kern G, Scherer G, Fischer G, Drakenberg T (1995) Kinetic analysis of cyclophilin-catalyzed prolyl cis/trans isomerization by dynamic NMR spectroscopy. Biochemistry 34:13594-13602.
-
(1995)
Biochemistry
, vol.34
, pp. 13594-13602
-
-
Kern, D.1
Kern, G.2
Scherer, G.3
Fischer, G.4
Drakenberg, T.5
-
24
-
-
11944257991
-
Mechanistic studies of enzymic and nonenzymic prolyl cis-trans isomerization
-
Harrison RK, Stein RL (1992) Mechanistic studies of enzymic and nonenzymic prolyl cis-trans isomerization. J Am Chem Soc 114:3464-3471.
-
(1992)
J Am Chem Soc
, vol.114
, pp. 3464-3471
-
-
Harrison, R.K.1
Stein, R.L.2
-
25
-
-
79952577508
-
Extracting realistic kinetics of rare activated processes from accelerated molecular dynamics using Kramers' theory
-
Doshi U, Hamelberg D (2011) Extracting realistic kinetics of rare activated processes from accelerated molecular dynamics using Kramers' theory. J Chem Theo Comp 7:575-581.
-
(2011)
J Chem Theo Comp
, vol.7
, pp. 575-581
-
-
Doshi, U.1
Hamelberg, D.2
-
26
-
-
34247500337
-
Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy
-
DOI 10.1021/ja0687668
-
Markwick PR, Bouvignies G, Blackledge M (2007) Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. J Am Chem Soc 129:4724-4730. (Pubitemid 46648771)
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.15
, pp. 4724-4730
-
-
Markwick, P.R.L.1
Bouvignies, G.2
Blackledge, M.3
-
27
-
-
70450237199
-
Toward a unified representation of protein structural dynamics in solution
-
Markwick PR, et al. (2009) Toward a unified representation of protein structural dynamics in solution. J Am Chem Soc 131:16968-16975.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 16968-16975
-
-
Markwick, P.R.1
-
28
-
-
77950378122
-
Enhanced conformational space sampling improves the prediction of chemical shifts in proteins
-
Markwick PR, et al. (2010) Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc 132:1220-1221.
-
(2010)
J Am Chem Soc
, vol.132
, pp. 1220-1221
-
-
Markwick, P.R.1
-
29
-
-
77953599895
-
Examining the limits of time reweighting and Kramers' rate theory to obtain correct kinetics from accelerated molecular dynamics
-
Xin Y, Doshi U, Hamelberg D (2010) Examining the limits of time reweighting and Kramers' rate theory to obtain correct kinetics from accelerated molecular dynamics. J Chem Phys 132:224101.
-
(2010)
J Chem Phys
, vol.132
, pp. 224101
-
-
Xin, Y.1
Doshi, U.2
Hamelberg, D.3
-
31
-
-
38749105098
-
Two-dimensional reaction free energy surfaces of catalytic reaction: Effects of protein conformational dynamics on enzyme catalysis
-
DOI 10.1021/jp076533c
-
Min W, Xie XS, Bagchi B (2008) Two-dimensional reaction free energy surfaces of catalytic reaction: Effects of protein conformational dynamics on enzyme catalysis. J Phys Chem B 112:454-466. (Pubitemid 351184620)
-
(2008)
Journal of Physical Chemistry B
, vol.112
, Issue.2
, pp. 454-466
-
-
Min, W.1
Xie, X.S.2
Bagchi, B.3
-
32
-
-
34547275473
-
Brownnian motion in a field of force and diffusion model of chemical reactions
-
Kramers HA (1940) Brownnian motion in a field of force and diffusion model of chemical reactions. Physica (Utrecht) 7:284-304.
-
(1940)
Physica (Utrecht)
, vol.7
, pp. 284-304
-
-
Kramers, H.A.1
-
33
-
-
0347193736
-
Reaction-rate theory: Fifty years after Kramers
-
Hanggi P, Talkner P, Borkovec M (1990) Reaction-rate theory: Fifty years after Kramers. Rev Mod Phys 62:251-342.
-
(1990)
Rev Mod Phys
, vol.62
, pp. 251-342
-
-
Hanggi, P.1
Talkner, P.2
Borkovec, M.3
-
34
-
-
77956587811
-
Water's contribution to the energetic roughness from peptide dynamics
-
Johnson Q, Doshi U, Shen T, Hamelberg D (2010) Water's contribution to the energetic roughness from peptide dynamics. J Chem Theo Comp 6:2591-2597.
-
(2010)
J Chem Theo Comp
, vol.6
, pp. 2591-2597
-
-
Johnson, Q.1
Doshi, U.2
Shen, T.3
Hamelberg, D.4
-
35
-
-
73349094393
-
Re-optimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics
-
Doshi U, Hamelberg D (2009) Re-optimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics. J Phys Chem B 113:16590-16595.
-
(2009)
J Phys Chem B
, vol.113
, pp. 16590-16595
-
-
Doshi, U.1
Hamelberg, D.2
-
36
-
-
71449103005
-
Hidden alternative structures of proline isomerase essential for catalysis
-
Fraser JS, et al. (2009) Hidden alternative structures of proline isomerase essential for catalysis. Nature 462:669-673.
-
(2009)
Nature
, vol.462
, pp. 669-673
-
-
Fraser, J.S.1
-
37
-
-
0345529841
-
What Is so Special about Arg 55 in the Catalysis of Cyclophilin A? Insights from Hybrid QM/MM Simulations
-
DOI 10.1021/ja0367851
-
Cui Q, Li G (2003) What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations. J Am Chem Soc 125:15028-15038. (Pubitemid 37509666)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.49
, pp. 15028-15038
-
-
Li, G.1
Cui, Q.2
-
38
-
-
62649138297
-
Mechanistic insight into the role of transitionstate stabilization in cyclophilin A
-
Hamelberg D, McCammon JA (2009) Mechanistic insight into the role of transitionstate stabilization in cyclophilin A. J Am Chem Soc 131:147-152.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 147-152
-
-
Hamelberg, D.1
McCammon, J.A.2
-
39
-
-
77957754309
-
Enzyme dynamics point to stepwise conformational selection in catalysis
-
Ma B, Nussinov R (2010) Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol 14:652-659.
-
(2010)
Curr Opin Chem Biol
, vol.14
, pp. 652-659
-
-
Ma, B.1
Nussinov, R.2
-
40
-
-
8644261670
-
Kinetics of alpha-helix formation as diffusion on a onedimensional free energy surface
-
Doshi U, Munoz V (2004) Kinetics of alpha-helix formation as diffusion on a onedimensional free energy surface. Chem Phys 307:129-136.
-
(2004)
Chem Phys
, vol.307
, pp. 129-136
-
-
Doshi, U.1
Munoz, V.2
-
41
-
-
34247880253
-
Protein folding kinetics: Barrier effects in chemical and thermal denaturation experiments
-
DOI 10.1021/ja0689740
-
Naganathan AN, Doshi U, Munoz V (2007) Protein folding kinetics: Barrier effects in chemical and thermal denaturation experiments. J Am Chem Soc 129:5673-5682. (Pubitemid 46697657)
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.17
, pp. 5673-5682
-
-
Naganathan, A.N.1
Doshi, U.2
Munoz, V.3
-
43
-
-
22244493867
-
Determination of barrier heights and prefactors from protein folding rate data
-
Plotkin SS (2005) Determination of barrier heights and prefactors from protein folding rate data. Biophys J 88:3762-3769.
-
(2005)
Biophys J
, vol.88
, pp. 3762-3769
-
-
Plotkin, S.S.1
-
44
-
-
0017275569
-
A Fourier method for the analysis of exponential decay curves
-
Provencher SW (1976) A Fourier method for the analysis of exponential decay curves. Biophys J 16:27-41.
-
(1976)
Biophys J
, vol.16
, pp. 27-41
-
-
Provencher, S.W.1
-
45
-
-
36749107621
-
An eigenfunction expansion method for the analysis of exponential decay curves
-
Provencher SW (1976) An eigenfunction expansion method for the analysis of exponential decay curves. J Chem Phys 64:2772-2777.
-
(1976)
J Chem Phys
, vol.64
, pp. 2772-2777
-
-
Provencher, S.W.1
|