-
1
-
-
64049102289
-
Binding of small-molecule ligands to proteins: " what you see" is not always " what you get"
-
Mobley D.L., Dill K.A. Binding of small-molecule ligands to proteins: " what you see" is not always " what you get" Structure 2009, 17:489-498.
-
(2009)
Structure
, vol.17
, pp. 489-498
-
-
Mobley, D.L.1
Dill, K.A.2
-
2
-
-
0034919305
-
Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules
-
Palmer A.G., Kroenke C.D., Loria J.P. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol 2001, 339:204-238.
-
(2001)
Methods Enzymol
, vol.339
, pp. 204-238
-
-
Palmer, A.G.1
Kroenke, C.D.2
Loria, J.P.3
-
3
-
-
33645834303
-
New tools provide new insights in NMR studies of protein dynamics
-
Mittermaier A., Kay L.E. New tools provide new insights in NMR studies of protein dynamics. Science 2006, 312:224-228.
-
(2006)
Science
, vol.312
, pp. 224-228
-
-
Mittermaier, A.1
Kay, L.E.2
-
4
-
-
33646911358
-
Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences
-
Jarymowycz V.A., Stone M.J. Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem Rev 2006, 106:1624-1671.
-
(2006)
Chem Rev
, vol.106
, pp. 1624-1671
-
-
Jarymowycz, V.A.1
Stone, M.J.2
-
5
-
-
33646945580
-
Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution
-
Igumenova T.I., Frederick K.K., Wand A.J. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev 2006, 106:1672-1699.
-
(2006)
Chem Rev
, vol.106
, pp. 1672-1699
-
-
Igumenova, T.I.1
Frederick, K.K.2
Wand, A.J.3
-
7
-
-
33646719091
-
Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules 1. Theory and range of validity
-
Lipari G., Szabo A. Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules 1. Theory and range of validity. J Am Chem Soc 1982, 104:4546-4559.
-
(1982)
J Am Chem Soc
, vol.104
, pp. 4546-4559
-
-
Lipari, G.1
Szabo, A.2
-
8
-
-
33845553743
-
Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules 2. Analysis of experimental results
-
Lipari G., Szabo A. Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules 2. Analysis of experimental results. J Am Chem Soc 1982, 104:4559-4570.
-
(1982)
J Am Chem Soc
, vol.104
, pp. 4559-4570
-
-
Lipari, G.1
Szabo, A.2
-
9
-
-
0028282555
-
Backbone dynamics of a free and a phosphopeptide-complexed src homology-2 domain studied by N-15 NMR relaxation
-
Farrow N.A., Muhandiram R., Singer A.U., Pascal S.M., Kay C.M., Gish G., Shoelson S.E., Pawson T., Forman Kay J.D., Kay L.E. Backbone dynamics of a free and a phosphopeptide-complexed src homology-2 domain studied by N-15 NMR relaxation. Biochemistry 1994, 33:5984-6003.
-
(1994)
Biochemistry
, vol.33
, pp. 5984-6003
-
-
Farrow, N.A.1
Muhandiram, R.2
Singer, A.U.3
Pascal, S.M.4
Kay, C.M.5
Gish, G.6
Shoelson, S.E.7
Pawson, T.8
Forman Kay, J.D.9
Kay, L.E.10
-
10
-
-
0028941877
-
Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme
-
Mandel A.M., Akke M., Palmer A.G. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J Mol Biol 1995, 246:144-163.
-
(1995)
J Mol Biol
, vol.246
, pp. 144-163
-
-
Mandel, A.M.1
Akke, M.2
Palmer, A.G.3
-
11
-
-
0034048847
-
Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data
-
Dosset P., Hus J.C., Blackledge M., Marion D. Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J Biomol NMR 2000, 16:23-28.
-
(2000)
J Biomol NMR
, vol.16
, pp. 23-28
-
-
Dosset, P.1
Hus, J.C.2
Blackledge, M.3
Marion, D.4
-
12
-
-
0037266991
-
The use of model selection in the model-free analysis of protein dynamics
-
d'Auvergne E.J., Gooley P.R. The use of model selection in the model-free analysis of protein dynamics. J Biomol NMR 2003, 25:25-39.
-
(2003)
J Biomol NMR
, vol.25
, pp. 25-39
-
-
d'Auvergne, E.J.1
Gooley, P.R.2
-
13
-
-
43949084048
-
Quantitative lid dynamics of MDM2 reveals differential ligand binding modes of the p53-binding cleft
-
Showalter S.A., Bruschweiler-Li L., Johnson E., Zhang F., Bruschweiler R. Quantitative lid dynamics of MDM2 reveals differential ligand binding modes of the p53-binding cleft. J Am Chem Soc 2008, 130:6472-6478.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 6472-6478
-
-
Showalter, S.A.1
Bruschweiler-Li, L.2
Johnson, E.3
Zhang, F.4
Bruschweiler, R.5
-
14
-
-
0037028988
-
An effective method for the discrimination of motional anisotropy and chemical exchange
-
Kneller J.M., Lu M., Bracken C. An effective method for the discrimination of motional anisotropy and chemical exchange. J Am Chem Soc 2002, 124:1852-1853.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 1852-1853
-
-
Kneller, J.M.1
Lu, M.2
Bracken, C.3
-
15
-
-
3042763969
-
Prediction of methyl-side chain dynamics in proteins
-
Ming D., Bruschweiler R. Prediction of methyl-side chain dynamics in proteins. J Biomol NMR 2004, 29:363-368.
-
(2004)
J Biomol NMR
, vol.29
, pp. 363-368
-
-
Ming, D.1
Bruschweiler, R.2
-
16
-
-
0037622537
-
Insights into the mobility of methyl-bearing side chains in proteins from (3)J(CC) and (3)J(CN) couplings
-
Chou J.J., Case D.A., Bax A. Insights into the mobility of methyl-bearing side chains in proteins from (3)J(CC) and (3)J(CN) couplings. J Am Chem Soc 2003, 125:8959-8966.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 8959-8966
-
-
Chou, J.J.1
Case, D.A.2
Bax, A.3
-
17
-
-
23344451429
-
Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR
-
Hu H., Hermans J., Lee A.L. Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR. J Biomol NMR 2005, 32:151-162.
-
(2005)
J Biomol NMR
, vol.32
, pp. 151-162
-
-
Hu, H.1
Hermans, J.2
Lee, A.L.3
-
18
-
-
0029176895
-
Measurement of H-2 T-1 and T-1p relaxation-times in uniformly C-13-labeled and fractionally H-2-labeled proteins in solution
-
Muhandiram D.R., Yamazaki T., Sykes B.D., Kay L.E. Measurement of H-2 T-1 and T-1p relaxation-times in uniformly C-13-labeled and fractionally H-2-labeled proteins in solution. J Am Chem Soc 1995, 117:11536-11544.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 11536-11544
-
-
Muhandiram, D.R.1
Yamazaki, T.2
Sykes, B.D.3
Kay, L.E.4
-
19
-
-
0037024180
-
Deuterium spin probes of side-chain dynamics in proteins. 1. Measurement of five relaxation rates per deuteron in (13)C-labeled and fractionally (2)H-enriched proteins in solution
-
Millet O., Muhandiram D.R., Skrynnikov N.R., Kay L.E. Deuterium spin probes of side-chain dynamics in proteins. 1. Measurement of five relaxation rates per deuteron in (13)C-labeled and fractionally (2)H-enriched proteins in solution. J Am Chem Soc 2002, 124:6439-6448.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 6439-6448
-
-
Millet, O.1
Muhandiram, D.R.2
Skrynnikov, N.R.3
Kay, L.E.4
-
20
-
-
74349122308
-
Experimental approaches for NMR studies of side-chain dynamics in high-molecular-weight proteins
-
Sheppard D., Sprangers R., Tugarinov V. Experimental approaches for NMR studies of side-chain dynamics in high-molecular-weight proteins. Progr Nucl Magn Reson Spectrosc 2010, 56:1-45.
-
(2010)
Progr Nucl Magn Reson Spectrosc
, vol.56
, pp. 1-45
-
-
Sheppard, D.1
Sprangers, R.2
Tugarinov, V.3
-
21
-
-
36849039429
-
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
-
Henzler-Wildman K.A., Lei M., Thai V., Kerns S.J., Karplus M., Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 2007, 450:913-916.
-
(2007)
Nature
, vol.450
, pp. 913-916
-
-
Henzler-Wildman, K.A.1
Lei, M.2
Thai, V.3
Kerns, S.J.4
Karplus, M.5
Kern, D.6
-
22
-
-
0026748968
-
15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible
-
15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. Biochemistry 1992, 31:5269-5278.
-
(1992)
Biochemistry
, vol.31
, pp. 5269-5278
-
-
Barbato, G.1
Ikura, M.2
Kay, L.E.3
Pastor, R.W.4
Bax, A.5
-
23
-
-
0036147844
-
Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations
-
Freedberg D.I., Ishima R., Jacob J., Wang Y.X., Kustanovich I., Louis J.M., Torchia D.A. Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations. Protein Sci 2002, 11:221-232.
-
(2002)
Protein Sci
, vol.11
, pp. 221-232
-
-
Freedberg, D.I.1
Ishima, R.2
Jacob, J.3
Wang, Y.X.4
Kustanovich, I.5
Louis, J.M.6
Torchia, D.A.7
-
24
-
-
3142657230
-
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes
-
Kalodimos C.G., Biris N., Bonvin A.M., Levandoski M.M., Guennuegues M., Boelens R., Kaptein R. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 2004, 305:386-389.
-
(2004)
Science
, vol.305
, pp. 386-389
-
-
Kalodimos, C.G.1
Biris, N.2
Bonvin, A.M.3
Levandoski, M.M.4
Guennuegues, M.5
Boelens, R.6
Kaptein, R.7
-
25
-
-
14844326275
-
The structural and dynamic basis of Ets-1 DNA binding autoinhibition
-
Lee G.M., Donaldson L.W., Pufall M.A., Kang H.S., Pot I., Graves B.J., McIntosh L.P. The structural and dynamic basis of Ets-1 DNA binding autoinhibition. J Biol Chem 2005, 280:7088-7099.
-
(2005)
J Biol Chem
, vol.280
, pp. 7088-7099
-
-
Lee, G.M.1
Donaldson, L.W.2
Pufall, M.A.3
Kang, H.S.4
Pot, I.5
Graves, B.J.6
McIntosh, L.P.7
-
26
-
-
34547460183
-
Molecular evolution of affinity and flexibility in the immune system
-
Thorpe I.F., Brooks C.L. Molecular evolution of affinity and flexibility in the immune system. Proc Natl Acad Sci U S A 2007, 104:8821-8826.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 8821-8826
-
-
Thorpe, I.F.1
Brooks, C.L.2
-
27
-
-
33748797691
-
Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics
-
Zimmermann J., Oakman E.L., Thorpe I.F., Shi X., Abbyad P., Brooks C.L., Boxer S.G., Romesberg F.E. Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc Natl Acad Sci U S A 2006, 103:13722-13727.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 13722-13727
-
-
Zimmermann, J.1
Oakman, E.L.2
Thorpe, I.F.3
Shi, X.4
Abbyad, P.5
Brooks, C.L.6
Boxer, S.G.7
Romesberg, F.E.8
-
28
-
-
69949167518
-
Dynamically driven ligand selectivity in cyclic nucleotide binding domains
-
Das R., Chowdhury S., Mazhab-Jafari M.T., Sildas S., Selvaratnam R., Melacini G. Dynamically driven ligand selectivity in cyclic nucleotide binding domains. J Biol Chem 2009, 284:23682-23696.
-
(2009)
J Biol Chem
, vol.284
, pp. 23682-23696
-
-
Das, R.1
Chowdhury, S.2
Mazhab-Jafari, M.T.3
Sildas, S.4
Selvaratnam, R.5
Melacini, G.6
-
29
-
-
34247180580
-
Sequence-specific dynamics modulate recognition specificity in WW domains
-
Peng T., Zintsmaster J.S., Namanja A.T., Peng J.W. Sequence-specific dynamics modulate recognition specificity in WW domains. Nat Struct Mol Biol 2007, 14:325-331.
-
(2007)
Nat Struct Mol Biol
, vol.14
, pp. 325-331
-
-
Peng, T.1
Zintsmaster, J.S.2
Namanja, A.T.3
Peng, J.W.4
-
31
-
-
0030473440
-
Insights into the local residual entropy of proteins provided by NMR relaxation
-
Li Z., Raychaudhuri S., Wand A.J. Insights into the local residual entropy of proteins provided by NMR relaxation. Protein Sci 1996, 5:2647-2650.
-
(1996)
Protein Sci
, vol.5
, pp. 2647-2650
-
-
Li, Z.1
Raychaudhuri, S.2
Wand, A.J.3
-
32
-
-
0030601792
-
Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding
-
Yang D., Kay L.E. Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J Mol Biol 1996, 263:369-382.
-
(1996)
J Mol Biol
, vol.263
, pp. 369-382
-
-
Yang, D.1
Kay, L.E.2
-
34
-
-
33747508183
-
Characterization of the backbone and side chain dynamics of the CaM-CaMKIp complex reveals microscopic contributions to protein conformational entropy
-
Frederick K.K., Kranz J.K., Wand A.J. Characterization of the backbone and side chain dynamics of the CaM-CaMKIp complex reveals microscopic contributions to protein conformational entropy. Biochemistry 2006, 45:9841-9848.
-
(2006)
Biochemistry
, vol.45
, pp. 9841-9848
-
-
Frederick, K.K.1
Kranz, J.K.2
Wand, A.J.3
-
35
-
-
33746224059
-
Conformational dynamics of calmodulin in complex with the calmodulin-dependent kinase kinase alpha calmodulin-binding domain
-
Marlow M.S., Wand A.J. Conformational dynamics of calmodulin in complex with the calmodulin-dependent kinase kinase alpha calmodulin-binding domain. Biochemistry 2006, 45:8732-8741.
-
(2006)
Biochemistry
, vol.45
, pp. 8732-8741
-
-
Marlow, M.S.1
Wand, A.J.2
-
36
-
-
77951281285
-
The role of conformational entropy in molecular recognition by calmodulin
-
Marlow M.S., Dogan J., Frederick K.K., Valentine K.G., Wand A.J. The role of conformational entropy in molecular recognition by calmodulin. Nat Chem Biol 2010, 6:352-358.
-
(2010)
Nat Chem Biol
, vol.6
, pp. 352-358
-
-
Marlow, M.S.1
Dogan, J.2
Frederick, K.K.3
Valentine, K.G.4
Wand, A.J.5
-
37
-
-
73949098933
-
Absolute single-molecule entropies from quasi-harmonic analysis of microsecond molecular dynamics: correction terms and convergence properties
-
Baron R., Hunenberger P.H., McCammon J.A. Absolute single-molecule entropies from quasi-harmonic analysis of microsecond molecular dynamics: correction terms and convergence properties. J Chem Theory Comput 2009, 5:3150-3160.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 3150-3160
-
-
Baron, R.1
Hunenberger, P.H.2
McCammon, J.A.3
-
38
-
-
43649103922
-
(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding
-
Baron R., McCammon J.A. (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding. Chemphyschem 2008, 9:983-988.
-
(2008)
Chemphyschem
, vol.9
, pp. 983-988
-
-
Baron, R.1
McCammon, J.A.2
-
39
-
-
67650529401
-
A dictionary for protein side-chain entropies from NMR order parameters
-
Li D.W., Bruschweiler R. A dictionary for protein side-chain entropies from NMR order parameters. J Am Chem Soc 2009, 131:7226-7227.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 7226-7227
-
-
Li, D.W.1
Bruschweiler, R.2
-
40
-
-
75749146563
-
Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors
-
Zhang J., Adrian F.J., Jahnke W., Cowan-Jacob S.W., Li A.G., Iacob R.E., Sim T., Powers J., Dierks C., Sun F., et al. Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors. Nature 2010, 463:501-506.
-
(2010)
Nature
, vol.463
, pp. 501-506
-
-
Zhang, J.1
Adrian, F.J.2
Jahnke, W.3
Cowan-Jacob, S.W.4
Li, A.G.5
Iacob, R.E.6
Sim, T.7
Powers, J.8
Dierks, C.9
Sun, F.10
-
41
-
-
77954656514
-
Beneficial effects of combining a type II ATP competitive inhibitor with an allosteric competitive inhibitor of BCR-ABL for the treatment of imatinib-sensitive and imatinib-resistant CML
-
Weisberg E., Deng X., Choi H.G., Barrett R., Adamia S., Ray A., Moreno D., Kung A.L., Gray N., Griffin J.D. Beneficial effects of combining a type II ATP competitive inhibitor with an allosteric competitive inhibitor of BCR-ABL for the treatment of imatinib-sensitive and imatinib-resistant CML. Leukemia 2010, 24:1375-1378.
-
(2010)
Leukemia
, vol.24
, pp. 1375-1378
-
-
Weisberg, E.1
Deng, X.2
Choi, H.G.3
Barrett, R.4
Adamia, S.5
Ray, A.6
Moreno, D.7
Kung, A.L.8
Gray, N.9
Griffin, J.D.10
-
42
-
-
0021658956
-
Allostery without conformational change. A plausible model
-
Cooper A., Dryden D.T. Allostery without conformational change. A plausible model. Eur Biophys J 1984, 11:103-109.
-
(1984)
Eur Biophys J
, vol.11
, pp. 103-109
-
-
Cooper, A.1
Dryden, D.T.2
-
43
-
-
33748363077
-
Dynamically driven protein allostery
-
Popovych N., Sun S., Ebright R.H., Kalodimos C.G. Dynamically driven protein allostery. Nat Struct Mol Biol 2006, 13:831-838.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 831-838
-
-
Popovych, N.1
Sun, S.2
Ebright, R.H.3
Kalodimos, C.G.4
-
44
-
-
70450191983
-
Dynamic activation of an allosteric regulatory protein
-
Tzeng S.R., Kalodimos C.G. Dynamic activation of an allosteric regulatory protein. Nature 2009, 462:368-372.
-
(2009)
Nature
, vol.462
, pp. 368-372
-
-
Tzeng, S.R.1
Kalodimos, C.G.2
-
45
-
-
70849084011
-
Hidden dynamic allostery in a PDZ domain
-
Petit C.M., Zhang J., Sapienza P.J., Fuentes E.J., Lee A.L. Hidden dynamic allostery in a PDZ domain. Proc Natl Acad Sci U S A 2009, 106:18249-18254.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 18249-18254
-
-
Petit, C.M.1
Zhang, J.2
Sapienza, P.J.3
Fuentes, E.J.4
Lee, A.L.5
-
46
-
-
41949132916
-
Flexible ligand docking to multiple receptor conformations: a practical alternative
-
Totrov M., Abagyan R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol 2008, 18:178-184.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
47
-
-
63149162777
-
Managing protein flexibility in docking and its applications
-
B-Rao C., Subramanian J., Sharma S.D. Managing protein flexibility in docking and its applications. Drug Discov Today 2009, 14:394-400.
-
(2009)
Drug Discov Today
, vol.14
, pp. 394-400
-
-
B-Rao, C.1
Subramanian, J.2
Sharma, S.D.3
-
48
-
-
12744263121
-
Simultaneous determination of protein structure and dynamics
-
Lindorff-Larsen K., Best R.B., Depristo M.A., Dobson C.M., Vendruscolo M. Simultaneous determination of protein structure and dynamics. Nature 2005, 433:128-132.
-
(2005)
Nature
, vol.433
, pp. 128-132
-
-
Lindorff-Larsen, K.1
Best, R.B.2
Depristo, M.A.3
Dobson, C.M.4
Vendruscolo, M.5
|