-
1
-
-
0346220393
-
The role of dynamics in allosteric regulation
-
Kern, D., and E. R. Zuiderweg. 2003. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13:748-757.
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 748-757
-
-
Kern, D.1
Zuiderweg, E.R.2
-
3
-
-
53149126899
-
Protein dynamics explain the allosteric behaviors of hemoglobin
-
Yonetani, T., and M. Laberge. 2008. Protein dynamics explain the allosteric behaviors of hemoglobin. Biochim. Biophys. Acta. 1784; 1146-1158.
-
(2008)
Biochim. Biophys. Acta.
, vol.1784
, pp. 1146-1158
-
-
Yonetani, T.1
Laberge, M.2
-
4
-
-
41149104308
-
Allostery: Absence of a change in shape does not imply that allostery is not at play
-
Tsai, C. J., A. del Sol, and R. Nussinov. 2008. Allostery: absence of a change in shape does not imply that allostery is not at play. J. Mol. Biol. 378:1-11.
-
(2008)
J. Mol. Biol.
, vol.378
, pp. 1-11
-
-
Tsai, C.J.1
Del Sol, A.2
Nussinov, R.3
-
5
-
-
47649125643
-
Allosteric regulation and catalysis emerge via a common route
-
Goodey, N. M., and S. J. Benkovic. 2008. Allosteric regulation and catalysis emerge via a common route. Nat. Chem. Biol. 4:474-482.
-
(2008)
Nat. Chem. Biol.
, vol.4
, pp. 474-482
-
-
Goodey, N.M.1
Benkovic, S.J.2
-
6
-
-
78651189765
-
On the nature of allosteric transitions: A plausible model
-
Monod, J., J. Wyman, and J. P. Changeux. 1965. On the nature of allosteric transitions: a plausible model. J. Mol., Biol. 12:88-118.
-
(1965)
J. Mol., Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
7
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
Koshland, Jr., D. E, G. Némethy, and D. Filmer. 1966. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry. 5:365-385.
-
(1966)
Biochemistry.
, vol.5
, pp. 365-385
-
-
Koshland Jr., D.E.1
Némethy, G.2
Filmer, D.3
-
8
-
-
0033621118
-
The propagation of binding interactions to remote sites in proteins: Analysis of the binding of the monoclonal antibody D1.3 to tysozyme
-
Freire, E. 1999. The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody D1.3 to tysozyme. Proc Natl. Acad. Sci. USA. 96:10118-10122.
-
(1999)
Proc Natl. Acad. Sci. USA.
, vol.96
, pp. 10118-10122
-
-
Freire, E.1
-
9
-
-
0030433170
-
Protein dynamics and conformational transitions in allosteric proteins
-
Jardetzky, O. 1996. Protein dynamics and conformational transitions in allosteric proteins. Prog. Biophys. Mol. Biol. 65:171-219.
-
(1996)
Prog. Biophys. Mol. Biol.
, vol.65
, pp. 171-219
-
-
Jardetzky, O.1
-
10
-
-
33746911627
-
Dynamic coupling and allosteric behavior in a nonallosteric protein
-
Clarkson, M. W., S. A. Gilmore, ..., A. L. Lee. 2006. Dynamic coupling and allosteric behavior in a nonallosteric protein. Biochemistry. 45:7693-7699.
-
(2006)
Biochemistry.
, vol.45
, pp. 7693-7699
-
-
Clarkson, M.W.1
Gilmore, S.A.2
Lee, A.L.3
-
11
-
-
0242585455
-
Configurational entropy and cooperativity between ligand binding and dimerization in glycopeptide antibiotics
-
Jusuf, S., P. J. Loll, and P. H. Axelsen. 2003. Configurational entropy and cooperativity between ligand binding and dimerization in glycopeptide antibiotics. J. Am. Chem. Soc. 125:3988-3994.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 3988-3994
-
-
Jusuf, S.1
Loll, P.J.2
Axelsen, P.H.3
-
12
-
-
0035915354
-
Cooperativity in drug-DNA recognition: A molecular dynamics study
-
Harris, S. A., E. Gavathiotis, ...., A. Laughton. 2001. Cooperativity in drug-DNA recognition: a molecular dynamics study. J. Am. Chem. Soc. 123:12658-12663.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 12658-12663
-
-
Harris, S.A.1
Gavathiotis, E.2
Laughton, A.3
-
13
-
-
0021658956
-
Allostery without conformational change. A plausible model
-
Cooper, A., and D. T. Dryden. 1984. Allostery without conformational change. A plausible model. Eur. Biophys. J. 11:103-109.
-
(1984)
Eur. Biophys. J.
, vol.11
, pp. 103-109
-
-
Cooper, A.1
Dryden, D.T.2
-
15
-
-
38949190032
-
Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design
-
Liu, J., and R. Nussinov. 2008. Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design. Proc. Natl. Acad. Sci. USA. 105:901-906.
-
(2008)
Proc. Natl. Acad. Sci. USA.
, vol.105
, pp. 901-906
-
-
Liu, J.1
Nussinov, R.2
-
17
-
-
0019873707
-
Dimeric and tetrameric hemoglobins from the mollusk Scapharca inaequivalis
-
Chaiancone, E., P. Vecchini, ...,E. Antonini. 1981. Dimeric and tetrameric hemoglobins from the mollusk Scapharca inaequivalis. J. Mol. Biol, 152:577-592.
-
(1981)
J. Mol. Biol
, vol.152
, pp. 577-592
-
-
Chaiancone, E.1
Vecchini, P.2
Antonini, E.3
-
18
-
-
0029867028
-
Crystal structure of the T state of allosteric yeast chorismate mutase and comparison with the R state
-
Strater, N., K. Hakansson, ..., W. N. Lipscomb. 1996. Crystal structure of the T state of allosteric yeast chorismate mutase and comparison with the R state. Proc Natl. Acad. Sci. USA. 93:3330-3334.
-
(1996)
Proc Natl. Acad. Sci. USA.
, vol.93
, pp. 3330-3334
-
-
Strater, N.1
Hakansson, K.2
Lipscomb, W.N.3
-
19
-
-
33751248527
-
Structural basis for proteinprotein interactions in the 14-3-3 protein family
-
Yang, X., W. H. Lee, ..., J. M. Elkins. 2006. Structural basis for proteinprotein interactions in the 14-3-3 protein family. Proc. Natl. Acad. Sci. USA. 103:17237-17242.
-
(2006)
Proc. Natl. Acad. Sci. USA.
, vol.103
, pp. 17237-17242
-
-
Yang, X.1
Lee, W.H.2
Elkins, J.M.3
-
20
-
-
33847326238
-
Dissecting the thermodynamics and cooperativity of ligand binding in cytochrome P450eryF
-
Muralidhara, B. K., S. S. Negi, and J. R. Halpert. 2007. Dissecting the thermodynamics and cooperativity of ligand binding in cytochrome P450eryF. J. Am. Chem. Soc: 129:2015-2024.
-
(2007)
J. Am. Chem. Soc
, vol.129
, pp. 2015-2024
-
-
Muralidhara, B.K.1
Negi, S.S.2
Halpert, J.R.3
-
21
-
-
67650079187
-
The two active sites of Thermotoga maritima CheA dimers bind ATP with, dramatically different affinities
-
Eaton, A. K., and R. C. Stewart. 2009. The two active sites of Thermotoga maritima CheA dimers bind ATP with, dramatically different affinities. Biochemistry. 48:6412-6422.
-
(2009)
Biochemistry.
, vol.48
, pp. 6412-6422
-
-
Eaton, A.K.1
Stewart, R.C.2
-
22
-
-
60649109828
-
Protein allostery, signal transmission and dynamics: A classification scheme of allosteric mechanisms
-
Tsai, C. J., A. Del Sol, and R. Nussinov. 2009. Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol. Biosyst. 5:207-216.
-
(2009)
Mol. Biosyst.
, vol.5
, pp. 207-216
-
-
Tsai, C.J.1
Del Sol, A.2
Nussinov, R.3
-
23
-
-
0036385839
-
Elastic properties of proteins: Insight on the folding process and evolutionary selection of native structures
-
Micheletti, C., G. Lattanzi, and A. Maritan. 2002. Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures. J. Mol. Biol. 321:909-921.
-
(2002)
J. Mol. Biol.
, vol.321
, pp. 909-921
-
-
Micheletti, C.1
Lattanzi, G.2
Maritan, A.3
-
24
-
-
33748442882
-
Coupling of global and local vibrational modes in dynamic allostery of proteins
-
Hawkins, R. J., and T. C McLeish. 2006. Coupling of global and local vibrational modes in dynamic allostery of proteins. Biophys. J. 91:2055-2062.
-
(2006)
Biophys. J.
, vol.91
, pp. 2055-2062
-
-
Hawkins, R.J.1
McLeish, T.C.2
-
25
-
-
19544377327
-
Coarse-grained model of entropic allostery
-
Hawkins, R., and T. McLeish. 2004. Coarse-grained model of entropic allostery. Phys. Rev. Lett. 93:098104.
-
(2004)
Phys. Rev. Lett.
, vol.93
, pp. 098104
-
-
Hawkins, R.1
McLeish, T.2
-
26
-
-
33747137334
-
Dynamical allostery of protein α-helical coiled-coils
-
Hawkins, R., and T. McLeish. 2005. Dynamical allostery of protein α-helical coiled-coils. J. R. Sot: Interface. 3:125-138.
-
(2005)
J. R. Sot: Interface
, vol.3
, pp. 125-138
-
-
Hawkins, R.1
McLeish, T.2
-
27
-
-
64849111005
-
Sending signals dynamically
-
Smock, R. G., and L. M. Gierasch. 2009. Sending signals dynamically. Science, 324:198-203.
-
(2009)
Science
, vol.324
, pp. 198-203
-
-
Smock, R.G.1
Gierasch, L.M.2
-
28
-
-
0000197372
-
Large amplitude elastic motions in proteins from single-parameter, atomic analysis
-
Tirion, M. M. 1996. Large amplitude elastic motions in proteins from single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
29
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-181.
-
(1997)
Fold. Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
30
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen, K. 1998. Analysis of domain motions by approximate normal mode calculations. Proteins Struct. Fund. Genet. 33:417-429.
-
(1998)
Proteins Struct. Fund. Genet.
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
31
-
-
0034710950
-
Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble
-
Pan, H., J. C. Lee, and V. J. Hilser. 2000. Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble. Proc. Natl. Acad. Sci. USA. 97:12020-12025.
-
(2000)
Proc. Natl. Acad. Sci. USA.
, vol.97
, pp. 12020-12025
-
-
Pan, H.1
Lee, J.C.2
Hilser, V.J.3
-
32
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan, A. R., S. R. Durell, ..., I. Bahar. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-515.
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Bahar, I.3
-
33
-
-
28844456158
-
Allostery in a coarse-grained model of protein, dynamics
-
Ming, D., and M. E. Wall. 2005. Allostery in a coarse-grained model of protein, dynamics. Phys. Rev. Lett. 95:198103.
-
(2005)
Phys. Rev. Lett.
, vol.95
, pp. 198103
-
-
Ming, D.1
Wall, M.E.2
-
34
-
-
33748448490
-
A natural coarse graining for simulating large biomolecular motion
-
Gohlke, H., and M. F. Thorpe. 2006. A natural coarse graining for simulating large biomolecular motion. Biophys. J. 91:2115-2120.
-
(2006)
Biophys. J.
, vol.91
, pp. 2115-2120
-
-
Gohlke, H.1
Thorpe, M.F.2
-
35
-
-
36549005182
-
Coarse-grained biomolecular simulation, with REACH: Realistic extension algorithm via covariance Hessian
-
Moritsugu, K., and J. C. Smith. 2007. Coarse-grained biomolecular simulation, with REACH: realistic extension algorithm via covariance Hessian. Biophys. J. 93:3460-3469.
-
(2007)
Biophys. J.
, vol.93
, pp. 3460-3469
-
-
Moritsugu, K.1
Smith, J.C.2
-
36
-
-
0024462882
-
Escherichia coli cAMP receptor protein: Evidence for three protein conformational states with different promoter binding affinities
-
Heyduk, T., and J. C. Lee. 1989. Escherichia coli cAMP receptor protein: evidence for three protein conformational states with different promoter binding affinities. Biochemistry. 28:6914-6924.
-
(1989)
Biochemistry.
, vol.28
, pp. 6914-6924
-
-
Heyduk, T.1
Lee, J.C.2
-
37
-
-
0034671172
-
Modeling the cAMP-induced allosteric transition using the crystal structure of CAPcAMP at 2.1 Å resolution
-
Passner, J. M., S. C. Schultz, and T. A. Steitz. 2000. Modeling the cAMP-induced allosteric transition using the crystal structure of CAPcAMP at 2.1 Å resolution. J. Mol. Biol. 304:847-859.
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 847-859
-
-
Passner, J.M.1
Schultz, S.C.2
Steitz, T.A.3
-
38
-
-
0026769759
-
Intersubunit communications in Escherichia coli cyclic AMP receptor protein: Studies of the ligand binding domain
-
Heyduk, E., T. Heyduk, and J. C. Lee. 1992. Intersubunit communications in Escherichia coli cyclic AMP receptor protein: studies of the ligand binding domain. Biochemistry. 31:3682-3688.
-
(1992)
Biochemistry.
, vol.31
, pp. 3682-3688
-
-
Heyduk, E.1
Heyduk, T.2
Lee, J.C.3
-
39
-
-
33747829284
-
OGNM: Online computation of structural dynamics using the Gaussian, network model
-
(Web Server issue)
-
Yang, L.-W., A. J. Rader, ..., I. Bahar. 2006. oGNM: online computation of structural dynamics using the Gaussian, network model. Nucleic Acids Res. 34(Web Server issue):W24-W31.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Yang, L.-W.1
Rader, A.J.2
Bahar, I.3
-
40
-
-
38049089909
-
A computational investigation of allostery in the catabolite activator protein
-
Li, L., V. N. Uversky, ..., S.O. Meroueh. 2007. A. computational investigation of allostery in the catabolite activator protein. J. Am. Chem. Soc. 129:15668-15676.
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 15668-15676
-
-
Li, L.1
Uversky, V.N.2
Meroueh, S.O.3
-
41
-
-
66349083528
-
Structural basis for cAMP-mediated allosteric control of the catabolite activator protein
-
Popovych, N., S.-R. Tzeng, ..., C. G. Kalodimos. 2009. Structural basis for cAMP-mediated allosteric control of the catabolite activator protein. Proc. Natl. Acad, Sci. USA. 106:6927-6932.
-
(2009)
Proc. Natl. Acad, Sci. USA
, vol.106
, pp. 6927-6932
-
-
Popovych, N.1
Tzeng, S.-R.2
Kalodimos, C.G.3
|