-
1
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman K, Kern D (2007) Dynamic personalities of proteins. Nature 450: 964-972.
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
2
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y, Kollman PA (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282: 740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
3
-
-
34547902820
-
Mechanism of Na+/H+ antiporting
-
Arkin IT, Xu HF, Jensen MO, Arbely E, Bennett ER, et al. (2007) Mechanism of Na+/H+ antiporting. Science 317: 799-803.
-
(2007)
Science
, vol.317
, pp. 799-803
-
-
Arkin, I.T.1
Xu, H.F.2
Jensen, M.O.3
Arbely, E.4
Bennett, E.R.5
-
4
-
-
32344434479
-
The changing landscape of protein allostery
-
Swain JF, Gierasch LM (2006) The changing landscape of protein allostery. Curr Opin Struct Biol 16: 102-108.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 102-108
-
-
Swain, J.F.1
Gierasch, L.M.2
-
5
-
-
0343415156
-
The way things move: Looking under the hood of molecular motor proteins
-
Vale RD, Milligan RA (2000) The way things move: looking under the hood of molecular motor proteins. Science 288: 88-95.
-
(2000)
Science
, vol.288
, pp. 88-95
-
-
Vale, R.D.1
Milligan, R.A.2
-
6
-
-
0035312645
-
Steered molecular dynamics and mechanical functions of proteins
-
Isralewitz B, Gao M, Schulten K (2001) Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol 11: 224-230.
-
(2001)
Curr Opin Struct Biol
, vol.11
, pp. 224-230
-
-
Isralewitz, B.1
Gao, M.2
Schulten, K.3
-
10
-
-
14844300852
-
Maturation dynamics of bacteriophage HK97 capsid
-
Rader AJ, Vlad DH, Bahar I (2005) Maturation dynamics of bacteriophage HK97 capsid. Structure 13: 413-421.
-
(2005)
Structure
, vol.13
, pp. 413-421
-
-
Rader, A.J.1
Vlad, D.H.2
Bahar, I.3
-
11
-
-
0029000872
-
Dynamics of the flexible loop of triosephosphate isomerase: The loop motion is not ligand-gated
-
Williams JC, Mcdermott AE (1995) Dynamics of the flexible loop of triosephosphate isomerase: the loop motion is not ligand-gated. Biochemistry 34: 8309-8319.
-
(1995)
Biochemistry
, vol.34
, pp. 8309-8319
-
-
Williams, J.C.1
Mcdermott, A.E.2
-
12
-
-
0026779802
-
Segmental movement: Definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase
-
Sampson NS, Knowles JR (1992) Segmental movement: definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase. Biochemistry 31: 8482-8487.
-
(1992)
Biochemistry
, vol.31
, pp. 8482-8487
-
-
Sampson, N.S.1
Knowles, J.R.2
-
13
-
-
17044401342
-
Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis
-
McElheny D, Schnell JR, Lansing JC, Dyson HJ, Wright PE (2005) Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis. Proc Natl Acad Sci U S A 102: 5032-5037.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 5032-5037
-
-
McElheny, D.1
Schnell, J.R.2
Lansing, J.C.3
Dyson, H.J.4
Wright, P.E.5
-
14
-
-
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 (2001) Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism. Biochemistry 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
-
15
-
-
0029618368
-
Steroid hormone receptors: Many actors in search of a plot
-
Beato M, Herrlich P, Schutz G (1995) Steroid hormone receptors: many actors in search of a plot. Cell 83: 851-857.
-
(1995)
Cell
, vol.83
, pp. 851-857
-
-
Beato, M.1
Herrlich, P.2
Schutz, G.3
-
16
-
-
0032446607
-
The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen
-
Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, et al. (1998) The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 95: 927-937.
-
(1998)
Cell
, vol.95
, pp. 927-937
-
-
Shiau, A.K.1
Barstad, D.2
Loria, P.M.3
Cheng, L.4
Kushner, P.J.5
-
17
-
-
0025015392
-
Anatomy of a conformational change: Hinged lid motion of the triosephosphate isomerase loop
-
Joseph D, Petsko GA, Karplus M (1990) Anatomy of a conformational change: hinged lid motion of the triosephosphate isomerase loop. Science 249: 1425-1428.
-
(1990)
Science
, vol.249
, pp. 1425-1428
-
-
Joseph, D.1
Petsko, G.A.2
Karplus, M.3
-
18
-
-
0345540195
-
Brownian dynamics simulation of diffusional encounters between triose phosphate isomerase and D-glyceraldehyde phos- phate
-
Madura JD, Mccammon JA (1989) Brownian dynamics simulation of diffusional encounters between triose phosphate isomerase and D-glyceraldehyde phos- phate. J Phys Chem 93: 7285-7287.
-
(1989)
J Phys Chem
, vol.93
, pp. 7285-7287
-
-
Madura, J.D.1
Mccammon, J.A.2
-
19
-
-
0031972864
-
The loop opening/closing motion of the enzyme triosephosphate isomerase
-
Derreumaux P, Schlick T (1998) The loop opening/closing motion of the enzyme triosephosphate isomerase. Biophys J 74: 72-81.
-
(1998)
Biophys J
, vol.74
, pp. 72-81
-
-
Derreumaux, P.1
Schlick, T.2
-
20
-
-
35348942279
-
Allosteric communication in dihydrofolate reductase: Signaling network and pathways for closed to occluded transition and back
-
Chen J, Dima RI, Thirumalai D (2007) Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. J Mol Biol 374: 250-266.
-
(2007)
J Mol Biol
, vol.374
, pp. 250-266
-
-
Chen, J.1
Dima, R.I.2
Thirumalai, D.3
-
21
-
-
0031557394
-
Domain motions in dihydrofolate reductase: A molecular dynamics study
-
Verma CS, Caves LSD, Hubbard RE, Roberts GCK (1997) Domain motions in dihydrofolate reductase: a molecular dynamics study. J Mol Biol 266: 776-796.
-
(1997)
J Mol Biol
, vol.266
, pp. 776-796
-
-
Verma, C.S.1
Caves, L.S.D.2
Hubbard, R.E.3
Roberts, G.C.K.4
-
22
-
-
0033955055
-
Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase
-
Radkiewicz JL, Brooks CL (2000) Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase. J Am Chem Soc 122: 225-231.
-
(2000)
J Am Chem Soc
, vol.122
, pp. 225-231
-
-
Radkiewicz, J.L.1
Brooks, C.L.2
-
23
-
-
0038810233
-
Correlated motion and the effect of distal mutations in dihydrofolate reductase
-
Rod TH, Radkiewicz JL, Brooks CL (2003) Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc Natl Acad Sci U S A 100: 6980-6985.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 6980-6985
-
-
Rod, T.H.1
Radkiewicz, J.L.2
Brooks, C.L.3
-
24
-
-
6344294816
-
-
Thorpe IF, Brooks CL 3rd (2004) The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins 57: 444-457.
-
Thorpe IF, Brooks CL 3rd (2004) The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins 57: 444-457.
-
-
-
-
25
-
-
0034966704
-
Enzyme specificity under dynamic control II: Principal component analysis of alpha-lytic protease using global and local solvent boundary conditions
-
Ota N, Agard DA (2001) Enzyme specificity under dynamic control II: principal component analysis of alpha-lytic protease using global and local solvent boundary conditions. Protein Sci 10: 1403-1414.
-
(2001)
Protein Sci
, vol.10
, pp. 1403-1414
-
-
Ota, N.1
Agard, D.A.2
-
26
-
-
1842532008
-
A hierarchical approach to all-atom protein loop prediction
-
Jacobson MP, Pincus DL, Rapp CS, Day TJF, Honig B, et al. (2004) A hierarchical approach to all-atom protein loop prediction. Proteins 55: 351-367.
-
(2004)
Proteins
, vol.55
, pp. 351-367
-
-
Jacobson, M.P.1
Pincus, D.L.2
Rapp, C.S.3
Day, T.J.F.4
Honig, B.5
-
27
-
-
47349128896
-
Toward better refinement of comparative models: Predicting loops in inexact environments
-
Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP (2008) Toward better refinement of comparative models: predicting loops in inexact environments. Proteins 72: 959-971.
-
(2008)
Proteins
, vol.72
, pp. 959-971
-
-
Sellers, B.D.1
Zhu, K.2
Zhao, S.3
Friesner, R.A.4
Jacobson, M.P.5
-
28
-
-
45649083705
-
A simple model of backbone flexibility improves modeling of side-chain conformational variability
-
Friedland GD, Linares AJ, Smith CA, Kortemme T (2008) A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol 380: 757-774.
-
(2008)
J Mol Biol
, vol.380
, pp. 757-774
-
-
Friedland, G.D.1
Linares, A.J.2
Smith, C.A.3
Kortemme, T.4
-
29
-
-
0030580089
-
Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors
-
Hilser VJ, Freire E (1996) Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J Mol Biol 262: 756-772.
-
(1996)
J Mol Biol
, vol.262
, pp. 756-772
-
-
Hilser, V.J.1
Freire, E.2
-
30
-
-
33748281380
-
Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations
-
Shehu A, Clementi C, Kavraki LE (2006) Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations. Proteins 65: 164-179.
-
(2006)
Proteins
, vol.65
, pp. 164-179
-
-
Shehu, A.1
Clementi, C.2
Kavraki, L.E.3
-
31
-
-
33847776838
-
On the characterization of protein native state ensembles
-
Shehu A, Kavraki LE, Clementi C (2007) On the characterization of protein native state ensembles. Biophys J 92: 1503-1511.
-
(2007)
Biophys J
, vol.92
, pp. 1503-1511
-
-
Shehu, A.1
Kavraki, L.E.2
Clementi, C.3
-
32
-
-
0030931612
-
Prediction of protein conformational freedom from distance constraints
-
de Groot BL, van Aalten DMF, Scheek RM, Amadei A, Vriend G, et al. (1997) Prediction of protein conformational freedom from distance constraints. Proteins 29: 240-251.
-
(1997)
Proteins
, vol.29
, pp. 240-251
-
-
de Groot, B.L.1
van Aalten, D.M.F.2
Scheek, R.M.3
Amadei, A.4
Vriend, G.5
-
33
-
-
22444450449
-
Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
-
Ota N, Agard DA (2005) Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J Mol Biol 351: 345-354.
-
(2005)
J Mol Biol
, vol.351
, pp. 345-354
-
-
Ota, N.1
Agard, D.A.2
-
34
-
-
33749029273
-
Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
-
Sharp K, Skinner JJ (2006) Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Proteins 65: 347-361.
-
(2006)
Proteins
, vol.65
, pp. 347-361
-
-
Sharp, K.1
Skinner, J.J.2
-
35
-
-
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, et al. (1995) 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 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
-
36
-
-
0025762996
-
The crystal-structure of the open and the closed conformation of the flexible loop of trypanosomal triosephosphate isomerase
-
Wierenga RK, Noble MEM, Postma JPM, Groendijk H, Kalk KH, et al. (1991) The crystal-structure of the open and the closed conformation of the flexible loop of trypanosomal triosephosphate isomerase. Proteins 10: 33-49.
-
(1991)
Proteins
, vol.10
, pp. 33-49
-
-
Wierenga, R.K.1
Noble, M.E.M.2
Postma, J.P.M.3
Groendijk, H.4
Kalk, K.H.5
-
37
-
-
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 (1995) Dynamics of the dihydrofolate- reductase folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features. Biochemistry 34: 11037-11048.
-
(1995)
Biochemistry
, vol.34
, pp. 11037-11048
-
-
Epstein, D.M.1
Benkovic, S.J.2
Wright, P.E.3
-
38
-
-
0037022683
-
Network of coupled promoting motions in enzyme catalysis
-
Agarwal PK, Billeter SR, Rajagopalan PTR, Benkovic SJ, Hammes-Schiffer S (2002) Network of coupled promoting motions in enzyme catalysis. Proc Natl Acad Sci U S A 99: 2794-2799.
-
(2002)
Proc Natl Acad Sci U S A
, 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
-
39
-
-
0032558779
-
Unfolded conformations of alpha-lytic protease are more stable than its native state
-
Sohl JL, Jaswal SS, Agard DA (1998) Unfolded conformations of alpha-lytic protease are more stable than its native state. Nature 395: 817-819.
-
(1998)
Nature
, vol.395
, pp. 817-819
-
-
Sohl, J.L.1
Jaswal, S.S.2
Agard, D.A.3
-
40
-
-
65349192770
-
-
Protein Flexibility from Perturbations PLoS Computational Biology | www.ploscompbiol.org 13 April 2009 | 5 | Issue 4 | e1000343
-
Protein Flexibility from Perturbations PLoS Computational Biology | www.ploscompbiol.org 13 April 2009 | Volume 5 | Issue 4 | e1000343
-
-
-
-
41
-
-
0037122769
-
Energetic landscape of alpha- lytic protease optimizes longevity through kinetic stability
-
Jaswal SS, Sohl JL, Davis JH, Agard DA (2002) Energetic landscape of alpha- lytic protease optimizes longevity through kinetic stability. Nature 415: 343-346.
-
(2002)
Nature
, vol.415
, pp. 343-346
-
-
Jaswal, S.S.1
Sohl, J.L.2
Davis, J.H.3
Agard, D.A.4
-
42
-
-
0034851838
-
The conserved residues of the ligand-binding domains of steroid receptors are located in the core of the molecules
-
Maeda M (2001) The conserved residues of the ligand-binding domains of steroid receptors are located in the core of the molecules. J Mol Graph Model 19: 543-551.
-
(2001)
J Mol Graph Model
, vol.19
, pp. 543-551
-
-
Maeda, M.1
-
43
-
-
33750008686
-
Structural analysis of E-coli hsp90 reveals dramatic nucleotide-dependent conformational rearrange- ments
-
Shiau AK, Harris SF, Southworth DR, Agard DA (2006) Structural analysis of E-coli hsp90 reveals dramatic nucleotide-dependent conformational rearrange- ments. Cell 127: 329-340.
-
(2006)
Cell
, vol.127
, pp. 329-340
-
-
Shiau, A.K.1
Harris, S.F.2
Southworth, D.R.3
Agard, D.A.4
-
44
-
-
33750407288
-
Anisotropic network model: Systematic evaluation and a new web interface
-
Eyal E, Yang LW, Bahar I (2006) Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics 22: 2619.
-
(2006)
Bioinformatics
, vol.22
, pp. 2619
-
-
Eyal, E.1
Yang, L.W.2
Bahar, I.3
-
45
-
-
33748663254
-
THESEUS: Maximum likelihood super- positioning and analysis of macromolecular structures
-
Theobald DL, Wuttke DS (2006) THESEUS: maximum likelihood super- positioning and analysis of macromolecular structures. Bioinformatics 22: 2171.
-
(2006)
Bioinformatics
, vol.22
, pp. 2171
-
-
Theobald, D.L.1
Wuttke, D.S.2
-
46
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9: 646-652.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
47
-
-
0034663710
-
Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to a- amylase inhibitor
-
Doruker P, Atilgan AR, Bahar I (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to a- amylase inhibitor. Proteins 40: 512-524.
-
(2000)
Proteins
, vol.40
, pp. 512-524
-
-
Doruker, P.1
Atilgan, A.R.2
Bahar, I.3
-
48
-
-
2442543557
-
Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models
-
Micheletti C, Carloni P, Maritan A (2004) Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models. Proteins 55: 635-645.
-
(2004)
Proteins
, vol.55
, pp. 635-645
-
-
Micheletti, C.1
Carloni, P.2
Maritan, A.3
-
49
-
-
31544444687
-
Loop motions of triosephosphate isomerase observed with elastic networks
-
Kurkcuoglu O, Jernigan RL, Doruker P (2006) Loop motions of triosephosphate isomerase observed with elastic networks. Biochemistry 45: 1173-1182.
-
(2006)
Biochemistry
, vol.45
, pp. 1173-1182
-
-
Kurkcuoglu, O.1
Jernigan, R.L.2
Doruker, P.3
-
50
-
-
29444446536
-
Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small a/b protein: A unified picture of high probability, fast atomic motions in proteins
-
Clore GM, Schwieters CD (2006) Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small a/b protein: a unified picture of high probability, fast atomic motions in proteins. J Mol Biol 355: 879-886.
-
(2006)
J Mol Biol
, vol.355
, pp. 879-886
-
-
Clore, G.M.1
Schwieters, C.D.2
-
51
-
-
40549107133
-
Conformational selection in silico: Loop latching motions and ligand binding in enzymes
-
Wong S, Jacobson MP (2007) Conformational selection in silico: loop latching motions and ligand binding in enzymes. Proteins 71: 153-164.
-
(2007)
Proteins
, vol.71
, pp. 153-164
-
-
Wong, S.1
Jacobson, M.P.2
|