-
1
-
-
0028049327
-
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
-
2
-
-
0029102089
-
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
-
3
-
-
0031443372
-
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
-
4
-
-
0035928796
-
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
-
6
-
-
0037117555
-
Catalysis of cis/trans isomerization in native HIV-1 capsid by human cyclophilin A
-
Bosco DA, Eisenmesser EZ, Pochapsky S, Sundquist WI, Kern D. Catalysis of cis/trans isomerization in native HIV-1 capsid by human cyclophilin A. Proc Natl Acad Sci USA 2002;99:5247-5252.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 5247-5252
-
-
Bosco, D.A.1
Eisenmesser, E.Z.2
Pochapsky, S.3
Sundquist, W.I.4
Kern, D.5
-
7
-
-
0037076522
-
Evidence for flexibility in the function of ribonuclease A
-
Cole R, Loria JP. Evidence for flexibility in the function of ribonuclease A. Biochemistry 2002;41:6072-6081.
-
(2002)
Biochemistry
, vol.41
, pp. 6072-6081
-
-
Cole, R.1
Loria, J.P.2
-
8
-
-
0034636990
-
A view of dynamics changes in the molten globule native folding step by quasielastic neutron scattering
-
Bu ZM, Neumann DA, Lee SH, Brown CM, Engelman DM, Han CC. A view of dynamics changes in the molten globule native folding step by quasielastic neutron scattering. J Mol Biol 2000;301:525-536.
-
(2000)
J Mol Biol
, vol.301
, pp. 525-536
-
-
Bu, Z.M.1
Neumann, D.A.2
Lee, S.H.3
Brown, C.M.4
Engelman, D.M.5
Han, C.C.6
-
9
-
-
0035807881
-
Fast dynamics of halophilic malate dehydrogenase and BSA measured by neutron scattering under various solvent conditions influencing protein stability
-
Tehei M, Madern D, Pfister C, Zaccai G. Fast dynamics of halophilic malate dehydrogenase and BSA measured by neutron scattering under various solvent conditions influencing protein stability. Proc Natl Acad Sci USA 2001;98:14356-14361.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 14356-14361
-
-
Tehei, M.1
Madern, D.2
Pfister, C.3
Zaccai, G.4
-
10
-
-
0036880187
-
Protein dynamics studied by neutron scattering
-
Gabel F, Bicout D, Lehnert U, Tehei M, Weik M, Zaccai G. Protein dynamics studied by neutron scattering. Q Rev Biophys 2002;35:327-367.
-
(2002)
Q Rev Biophys
, vol.35
, pp. 327-367
-
-
Gabel, F.1
Bicout, D.2
Lehnert, U.3
Tehei, M.4
Weik, M.5
Zaccai, G.6
-
11
-
-
0037137214
-
Temperature dependence of the internal dynamics of a calmodulin-peptide complex
-
Lee AL, Sharp KA, Kranz JK, Song XJ, Wand AJ. Temperature dependence of the internal dynamics of a calmodulin-peptide complex. Biochemistry 2002;41:13814-13825.
-
(2002)
Biochemistry
, vol.41
, pp. 13814-13825
-
-
Lee, A.L.1
Sharp, K.A.2
Kranz, J.K.3
Song, X.J.4
Wand, A.J.5
-
12
-
-
0029000872
-
Dynamics of the flexible loop of triosephosphate isomerase: The loop motion is not ligand gated
-
Williams JC, McDermott AE. Dynamics of the flexible loop of triosephosphate isomerase: the loop motion is not ligand gated. Biochemistry 1995;34:8309-8319.
-
(1995)
Biochemistry
, vol.34
, pp. 8309-8319
-
-
Williams, J.C.1
McDermott, A.E.2
-
13
-
-
0034724392
-
Millisecond time scale conformational flexibility in a hyperthermophile protein at ambient temperature
-
Hernandez G, Jenney FE, Adams MWW, LeMaster DM. Millisecond time scale conformational flexibility in a hyperthermophile protein at ambient temperature. Proc Natl Acad Sci USA 2000;97:3166-3170.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 3166-3170
-
-
Hernandez, G.1
Jenney, F.E.2
Adams, M.W.W.3
LeMaster, D.M.4
-
14
-
-
0032560505
-
Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins
-
Zavodszky P, Kardos J, Svingor A, Petsko GA. Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins. Proc Natl Acad Sci USA 1998;95:7406-7411.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 7406-7411
-
-
Zavodszky, P.1
Kardos, J.2
Svingor, A.3
Petsko, G.A.4
-
15
-
-
0025358007
-
Structure of yeast triosephosphate isomerase at 1.9-Å resolution
-
Lolis E, Alber T, Davenport RC, Rose D, Hartman FC. Petsko GA. Structure of yeast triosephosphate isomerase at 1.9-Å resolution. Biochemistry 1990;29:6609-6618.
-
(1990)
Biochemistry
, vol.29
, pp. 6609-6618
-
-
Lolis, E.1
Alber, T.2
Davenport, R.C.3
Rose, D.4
Hartman, F.C.5
Petsko, G.A.6
-
16
-
-
0025331920
-
Crystallographic analysis of the complex between triosephosphate isomerase and 2 phosphoglycolate at 2.5-A resolution: Implications for catalysis
-
Lolis E, Petsko GA. Crystallographic analysis of the complex between triosephosphate isomerase and 2 phosphoglycolate at 2.5-A resolution: implications for catalysis. Biochemistry 1990;29:6619-6625.
-
(1990)
Biochemistry
, vol.29
, pp. 6619-6625
-
-
Lolis, E.1
Petsko, G.A.2
-
17
-
-
0031015737
-
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
-
18
-
-
0030877587
-
Conformational substates in enzyme mechanism: The 120 K structure of α-lytic protease at 1.5 Å resolution
-
Rader SD, Agard DA. Conformational substates in enzyme mechanism: the 120 K structure of α-lytic protease at 1.5 Å resolution. Protein Sci 1997;6:1375-1386.
-
(1997)
Protein Sci
, vol.6
, pp. 1375-1386
-
-
Rader, S.D.1
Agard, D.A.2
-
19
-
-
0033955055
-
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
-
20
-
-
0037012441
-
Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase
-
Caratzoulas S, Mincer JS, Schwartz SD. Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase. J Am Chem Soc 2002;124:3270-3276.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 3270-3276
-
-
Caratzoulas, S.1
Mincer, J.S.2
Schwartz, S.D.3
-
21
-
-
0037022683
-
Network of coupled promoting motions in enzyme catalysis
-
Agarwal PK, Billeter SR, Rajagopalan PTR, Benkovic SJ, Hammes-Schiffer S. Network of coupled promoting motions in enzyme catalysis. Proc Natl Acad Sci USA 2002;99:2794-2799.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 2794-2799
-
-
Agarwal, P.K.1
Billeter, S.R.2
Rajagopalan, P.T.R.3
Benkovic, S.J.4
Hammes-Schiffer, S.5
-
22
-
-
0037188007
-
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
-
23
-
-
0344391945
-
Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase
-
Garcia-Viloca M, Truhlar DG, Gao JL. 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.L.3
-
25
-
-
0021159379
-
Cyclophilin: A specific cytosolic binding protein for cyclosporin A
-
Handschumacher RE, Harding MW, Rice J, Drugge RJ. Cyclophilin: a specific cytosolic binding protein for cyclosporin A. Science 1984;226:544-547.
-
(1984)
Science
, vol.226
, pp. 544-547
-
-
Handschumacher, R.E.1
Harding, M.W.2
Rice, J.3
Drugge, R.J.4
-
26
-
-
0024959451
-
Peptidyl-prolyl cis-trans isomerase is the cyclosporin A-binding protein cyclophilin
-
Takahashi N, Hayano T, Suzuki M. Peptidyl-prolyl cis-trans isomerase is the cyclosporin A-binding protein cyclophilin. Nature 1989;337:473-475.
-
(1989)
Nature
, vol.337
, pp. 473-475
-
-
Takahashi, N.1
Hayano, T.2
Suzuki, M.3
-
27
-
-
0032926319
-
Peptidyl-prolyl cis-trans isomerases, a superfamily of ubiquitous folding catalysts
-
Gothel SF, Marahiel MA. Peptidyl-prolyl cis-trans isomerases, a superfamily of ubiquitous folding catalysts. Cell Mol Life Sci 1999;55:423-436.
-
(1999)
Cell Mol Life Sci
, vol.55
, pp. 423-436
-
-
Gothel, S.F.1
Marahiel, M.A.2
-
28
-
-
0034129915
-
The impact of immunosuppressive drugs on the analysis of T cell activation
-
Rovira P, Mascarell L, Truffa-Bachi P. The impact of immunosuppressive drugs on the analysis of T cell activation. Curr Med Chem 2000;7:673-692.
-
(2000)
Curr Med Chem
, vol.7
, pp. 673-692
-
-
Rovira, P.1
Mascarell, L.2
Truffa-Bachi, P.3
-
29
-
-
0034419296
-
Chemical aspects of peptide bond isomerisation
-
Fischer G. Chemical aspects of peptide bond isomerisation. Chem Soc Rev 2000;29:119-127.
-
(2000)
Chem Soc Rev
, vol.29
, pp. 119-127
-
-
Fischer, G.1
-
30
-
-
0030448994
-
Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid
-
Gamble TR, Vajdos FF, Yoo SH, Worthylake DK, Houseweart M, Sundquist WI, Hill CP. Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid. Cell 1996;87:1285-1294.
-
(1996)
Cell
, vol.87
, pp. 1285-1294
-
-
Gamble, T.R.1
Vajdos, F.F.2
Yoo, S.H.3
Worthylake, D.K.4
Houseweart, M.5
Sundquist, W.I.6
Hill, C.P.7
-
31
-
-
0031588011
-
Molecular recognition in the HIV-1 capsid/cyclophilin A complex
-
Yoo SH, Myszka DG, Yeh CY, McMurray M, Hill CP, Sundquist WI. Molecular recognition in the HIV-1 capsid/cyclophilin A complex. J Mol Biol 1997;269:780-795.
-
(1997)
J Mol Biol
, vol.269
, pp. 780-795
-
-
Yoo, S.H.1
Myszka, D.G.2
Yeh, C.Y.3
McMurray, M.4
Hill, C.P.5
Sundquist, W.I.6
-
32
-
-
0036168738
-
trans-complementation rescue of cyclophilin A-deficient viruses reveals that the requirement for cyclophilin A in human immunodeficiency virus type 1 replication is independent of its isomerase activity
-
Saphire ACS, Bobardt MD, Gallay PA. trans-Complementation rescue of cyclophilin A-deficient viruses reveals that the requirement for cyclophilin A in human immunodeficiency virus type 1 replication is independent of its isomerase activity. J Virol 2002;76:2255-2262.
-
(2002)
J Virol
, vol.76
, pp. 2255-2262
-
-
Saphire, A.C.S.1
Bobardt, M.D.2
Gallay, P.A.3
-
33
-
-
0038780573
-
Structural insights into the catalytic mechanism of cyclophilin A
-
Howard BR, Vajdos FF, Li S, Sundquist WI, Hill CP. Structural insights into the catalytic mechanism of cyclophilin A. Nature Struct Biol 2003;10:475-481.
-
(2003)
Nature Struct Biol
, vol.10
, pp. 475-481
-
-
Howard, B.R.1
Vajdos, F.F.2
Li, S.3
Sundquist, W.I.4
Hill, C.P.5
-
34
-
-
0029887104
-
Cyclophilin A is required for the replication of group M human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus SIV(CPZ) GAB but not group O HIV-1 or other primate immunodeficiency viruses
-
Braaten D, Franke EK, Luban J. Cyclophilin A is required for the replication of group M human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus SIV(CPZ) GAB but not group O HIV-1 or other primate immunodeficiency viruses. J Virol 1996;70:4220-4227.
-
(1996)
J Virol
, vol.70
, pp. 4220-4227
-
-
Braaten, D.1
Franke, E.K.2
Luban, J.3
-
35
-
-
0036061001
-
Differential dependence of the infectivity of HIV-1 group O isolates on the cellular protein cyclophilin A
-
Wiegers K, Krausslich HG. Differential dependence of the infectivity of HIV-1 group O isolates on the cellular protein cyclophilin A. Virology 2002;294:289-295.
-
(2002)
Virology
, vol.294
, pp. 289-295
-
-
Wiegers, K.1
Krausslich, H.G.2
-
36
-
-
0027940713
-
Specific incorporation of cyclophilin A into HIV-1 virions
-
Franke EK, Yuan HEH, Luban J. Specific incorporation of cyclophilin A into HIV-1 virions. Nature 1994;372:359-362.
-
(1994)
Nature
, vol.372
, pp. 359-362
-
-
Franke, E.K.1
Yuan, H.E.H.2
Luban, J.3
-
37
-
-
0027971782
-
Functional association of cyclophilin A with HIV-1 virions
-
Thali M, Bukovsky A, Kondo E, Rosenwirth B, Walsh CT, Sodroski J, Gottlinger HG. Functional association of cyclophilin A with HIV-1 virions. Nature 1994;372:363-365.
-
(1994)
Nature
, vol.372
, pp. 363-365
-
-
Thali, M.1
Bukovsky, A.2
Kondo, E.3
Rosenwirth, B.4
Walsh, C.T.5
Sodroski, J.6
Gottlinger, H.G.7
-
38
-
-
0029633186
-
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 1995;91:1-41.
-
(1995)
Comput Phys Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
Debolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
39
-
-
0004195760
-
-
San Francisco, CA: University of California, San Francisco
-
Case DA, Pearlman DA, Caldwell JW, Cheatham III TE, Wang J, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Gohlke H, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Single UC, Weiner PK, Kollman P. AMBER 7. San Francisco, CA: University of California, San Francisco; 2002.
-
(2002)
AMBER 7
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Wang, J.5
Ross, W.S.6
Simmerling, C.L.7
Darden, T.A.8
Merz, K.M.9
Stanton, R.V.10
Cheng, A.L.11
Vincent, J.J.12
Crowley, M.13
Tsui, V.14
Gohlke, H.15
Radmer, R.J.16
Duan, Y.17
Pitera, J.18
Massova, I.19
Seibel, G.L.20
Single, U.C.21
Weiner, P.K.22
Kollman, P.23
more..
-
40
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
41
-
-
36749107785
-
Molecular dynamics simulations at constant pressure and/or temperature
-
Andersen HC. Molecular dynamics simulations at constant pressure and/or temperature. J Chem Phys 1980;72:2384-2393.
-
(1980)
J Chem Phys
, vol.72
, pp. 2384-2393
-
-
Andersen, H.C.1
-
42
-
-
33646940952
-
Numerical integration of Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
43
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Vangunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
44
-
-
0342929614
-
Nonphysical sampling distributions in Monte-Carlo free-energy estimation: Umbrella sampling
-
Torrie GM, Valleau JP. Nonphysical sampling distributions in Monte-Carlo free-energy estimation: umbrella sampling. J Comput Phys 1977;23:187-199.
-
(1977)
J Comput Phys
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
45
-
-
0020160864
-
Dynamical theory of activated processes in globular proteins
-
Northrup SH, Pear MR, Lee CY, McCammon JA, Karplus M. Dynamical theory of activated processes in globular proteins. Proc Natl Acad Sci USA 1982;79:4035-4039.
-
(1982)
Proc Natl Acad Sci USA
, vol.79
, pp. 4035-4039
-
-
Northrup, S.H.1
Pear, M.R.2
Lee, C.Y.3
McCammon, J.A.4
Karplus, M.5
-
46
-
-
0036025446
-
Quantum mechanical methods for enzyme kinetics
-
Gao JL, Truhlar DG. Quantum mechanical methods for enzyme kinetics. Annu Rev Phys Chem 2002;53:467-505.
-
(2002)
Annu Rev Phys Chem
, vol.53
, pp. 467-505
-
-
Gao, J.L.1
Truhlar, D.G.2
-
47
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method
-
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM. The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method. J Comput Chem 1992;13:1011-1021.
-
(1992)
J Comput Chem
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
48
-
-
0000764091
-
Constant temperature free energy surfaces for physical and chemical processes
-
Boczko EM, Brooks CL. Constant temperature free energy surfaces for physical and chemical processes. J Phys Chem 1993;97:4509-4513.
-
(1993)
J Phys Chem
, vol.97
, pp. 4509-4513
-
-
Boczko, E.M.1
Brooks, C.L.2
-
49
-
-
0000092491
-
Promotion of helix formation in peptides dissolved in alcohol and water-alcohol mixtures
-
Brooks CL, Nilsson L. Promotion of helix formation in peptides dissolved in alcohol and water-alcohol mixtures. J Am Chem Soc 1993;115:11034-11035.
-
(1993)
J Am Chem Soc
, vol.115
, pp. 11034-11035
-
-
Brooks, C.L.1
Nilsson, L.2
-
50
-
-
0141459794
-
Free energy surface, reaction paths, and kinetic isotope effect of short-chain acyl-CoA dehydrogenase
-
Poulsen TD, Garcia-Viloca M, Gao JL, Truhlar DG. Free energy surface, reaction paths, and kinetic isotope effect of short-chain acyl-CoA dehydrogenase. J Phys Chem B 2003;107:9567-9578.
-
(2003)
J Phys Chem B
, vol.107
, pp. 9567-9578
-
-
Poulsen, T.D.1
Garcia-Viloca, M.2
Gao, J.L.3
Truhlar, D.G.4
-
51
-
-
0032996356
-
Simulation analysis of the retinal conformational equilibrium in dark adapted bacteriorhodopsin
-
Baudry J, Crouzy S, Roux B, Smith JC. Simulation analysis of the retinal conformational equilibrium in dark adapted bacteriorhodopsin. Biophys J 1999;76:1909-1917.
-
(1999)
Biophys J
, vol.76
, pp. 1909-1917
-
-
Baudry, J.1
Crouzy, S.2
Roux, B.3
Smith, J.C.4
-
52
-
-
0022419152
-
Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
-
Levitt M, Sander C, Stern PS. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 1985;181:423-447.
-
(1985)
J Mol Biol
, vol.181
, pp. 423-447
-
-
Levitt, M.1
Sander, C.2
Stern, P.S.3
-
53
-
-
0025221847
-
Domain communication in the dynamic structure of human immunodeficiency virus-1 protease
-
Harte WE, Swaminathan S, Mansuri MM, Martin JC, Rosenberg IE, Beveridge DL. Domain communication in the dynamic structure of human immunodeficiency virus-1 protease. Proc Natl Acad Sci USA 1990;87:8864-8868.
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 8864-8868
-
-
Harte, W.E.1
Swaminathan, S.2
Mansuri, M.M.3
Martin, J.C.4
Rosenberg, I.E.5
Beveridge, D.L.6
-
54
-
-
0000561283
-
Investigation of domain structure in proteins via molecular dynamics simulation: Application to HIV-1 protease dimer
-
Swaminathan S, Harte WE, Beveridge DL. Investigation of domain structure in proteins via molecular dynamics simulation: application to HIV-1 protease dimer. J Am Chem Soc 1991;113:2717-2721.
-
(1991)
J Am Chem Soc
, vol.113
, pp. 2717-2721
-
-
Swaminathan, S.1
Harte, W.E.2
Beveridge, D.L.3
-
55
-
-
0000961995
-
Evaluation of the configurational entropy for proteins: Application to molecular dynamics simulations ofan a-helix
-
Levy RM, Karplus M, Kushick J, Perahia D. Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations ofan a-helix. Macromolecules 1984;17:1370-1374.
-
(1984)
Macromolecules
, vol.17
, pp. 1370-1374
-
-
Levy, R.M.1
Karplus, M.2
Kushick, J.3
Perahia, D.4
-
56
-
-
0000118827
-
Harmonic and quasiharmonic descriptions of crambin
-
Teeter MM, Case DA. Harmonic and quasiharmonic descriptions of crambin. J Phys Chem 1990;94:8091-8097.
-
(1990)
J Phys Chem
, vol.94
, pp. 8091-8097
-
-
Teeter, M.M.1
Case, D.A.2
-
57
-
-
0001205818
-
Electrostatic effects in water accessible regions of proteins
-
Mehler EL, Eichele G. Electrostatic effects in water accessible regions of proteins. Biochemistry 1984;23:3887-3891.
-
(1984)
Biochemistry
, vol.23
, pp. 3887-3891
-
-
Mehler, E.L.1
Eichele, G.2
-
58
-
-
0026332547
-
Electrostatic effects in proteins: Comparison of dielectric and charge models
-
Mehler EL, Solmajer T. Electrostatic effects in proteins: comparison of dielectric and charge models. Protein Eng 1991;4:903-910.
-
(1991)
Protein Eng
, vol.4
, pp. 903-910
-
-
Mehler, E.L.1
Solmajer, T.2
-
59
-
-
0025035782
-
Substrate specificity for the human rotamase FKBP: A view of FK506 and rapamycin as leucine-(twisted amide) proline mimics
-
Albers MW, Walsh CT, Schreiber SL. Substrate specificity for the human rotamase FKBP: a view of FK506 and rapamycin as leucine-(twisted amide) proline mimics. J Org Chem 1990;55:4984-4986.
-
(1990)
J Org Chem
, vol.55
, pp. 4984-4986
-
-
Albers, M.W.1
Walsh, C.T.2
Schreiber, S.L.3
-
60
-
-
0025373627
-
Substrate specificities of the peptidyl prolyl cis-trans isomerase activities of cyclophilin and FK-506 binding-protein: Evidence for the existence of a family of distinct enzymes
-
Harrison RK, Stein RL. Substrate specificities of the peptidyl prolyl cis-trans isomerase activities of cyclophilin and FK-506 binding-protein: evidence for the existence of a family of distinct enzymes. Biochemistry 1990;29:3813-3816.
-
(1990)
Biochemistry
, vol.29
, pp. 3813-3816
-
-
Harrison, R.K.1
Stein, R.L.2
-
61
-
-
0025868143
-
Determination of kinetic constants for peptidyl prolyl cis-trans isomerases by an improved spectrophotometric assay
-
Kofron JL, Kuzmic P, Kishore V, Colonbonilla E, Rich DH. Determination of kinetic constants for peptidyl prolyl cis-trans isomerases by an improved spectrophotometric assay. Biochemistry 1991;30:6127-6134.
-
(1991)
Biochemistry
, vol.30
, pp. 6127-6134
-
-
Kofron, J.L.1
Kuzmic, P.2
Kishore, V.3
Colonbonilla, E.4
Rich, D.H.5
-
62
-
-
0028877264
-
Kinetic analysis of cyclophilin-catalyzed prolyl cis/trans isomerization by dynamic NMR spectroscopy
-
Kern D, Kern G, Scherer G, Fischer G, Drakenberg T. Kinetic analysis of cyclophilin-catalyzed prolyl cis/trans isomerization by dynamic NMR spectroscopy. Biochemistry 1995;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
-
63
-
-
0035827163
-
Inclusion of quantum mechanical vibrational energy in reactive potentials of mean force
-
Garcia-Viloca M, Alhambra C, Truhlar DG, Gao J. Inclusion of quantum mechanical vibrational energy in reactive potentials of mean force. J Chem Phys 2001;114:9953-9958.
-
(2001)
J Chem Phys
, vol.114
, pp. 9953-9958
-
-
Garcia-Viloca, M.1
Alhambra, C.2
Truhlar, D.G.3
Gao, J.4
-
64
-
-
0036282937
-
The incorporation of quantum effects in enzyme kinetics modeling
-
Truhlar DG, Gao JL, Alhambra C, Garcia-Viloca M, Corchado J, Sanchez ML, Villa J. The incorporation of quantum effects in enzyme kinetics modeling. Acc Chem Res 2002;35:341-349.
-
(2002)
Acc Chem Res
, vol.35
, pp. 341-349
-
-
Truhlar, D.G.1
Gao, J.L.2
Alhambra, C.3
Garcia-Viloca, M.4
Corchado, J.5
Sanchez, M.L.6
Villa, J.7
-
65
-
-
0142026621
-
Generalized transition state theory in terms of the potential of mean force
-
Schenter GK, Garrett BC, Truhlar DG. Generalized transition state theory in terms of the potential of mean force. J Chem Phys 2003;119:5828-5833.
-
(2003)
J Chem Phys
, vol.119
, pp. 5828-5833
-
-
Schenter, G.K.1
Garrett, B.C.2
Truhlar, D.G.3
-
66
-
-
0030666230
-
Crystal structure of cyclophilin A complexed with a binding site peptide from the HIV-1 capsid protein
-
Vajdos FE, Yoo SH, Houseweart M, Sundquist WI, Hill CP. Crystal structure of cyclophilin A complexed with a binding site peptide from the HIV-1 capsid protein. Protein Sci 1997;6:2297-2307.
-
(1997)
Protein Sci
, vol.6
, pp. 2297-2307
-
-
Vajdos, F.E.1
Yoo, S.H.2
Houseweart, M.3
Sundquist, W.I.4
Hill, C.P.5
-
67
-
-
0037178118
-
The mechanism of cis-trans isomerization of prolyl peptides by cyclophilin
-
Hur S, Bruice TC. The mechanism of cis-trans isomerization of prolyl peptides by cyclophilin. J Am Chem Soc 2002;124:7303-7313.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 7303-7313
-
-
Hur, S.1
Bruice, T.C.2
|