-
1
-
-
0032921026
-
Is cooperative oxygen binding by hemoglobin really understood?
-
Eaton W.A., Henry E.R., Hofrichter J., and Mozzarelli A. Is cooperative oxygen binding by hemoglobin really understood?. Nat Struct Biol 6 4 (1999) 351-358
-
(1999)
Nat Struct Biol
, vol.6
, Issue.4
, pp. 351-358
-
-
Eaton, W.A.1
Henry, E.R.2
Hofrichter, J.3
Mozzarelli, A.4
-
2
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder H., Sligar S.G., and Wolynes P.G. The energy landscapes and motions of proteins. Science 254 5038 (1991) 1598-1603
-
(1991)
Science
, vol.254
, Issue.5038
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
3
-
-
0028963362
-
Toward an outline of the topography of a realistic protein-folding funnel
-
Onuchic J.N., Wolynes P.G., Luthey-Schulten Z., and Socci N.D. Toward an outline of the topography of a realistic protein-folding funnel. Proc Natl Acad Sci U S A 92 8 (1995) 3626-3630
-
(1995)
Proc Natl Acad Sci U S A
, vol.92
, Issue.8
, pp. 3626-3630
-
-
Onuchic, J.N.1
Wolynes, P.G.2
Luthey-Schulten, Z.3
Socci, N.D.4
-
4
-
-
0034338307
-
Heteropolymer freezing and design: towards physical models of protein folding
-
Pande V.S., Grosberg A.Y., and Tanaka T. Heteropolymer freezing and design: towards physical models of protein folding. Rev Mod Phys 72 (2000) 259-314
-
(2000)
Rev Mod Phys
, vol.72
, pp. 259-314
-
-
Pande, V.S.1
Grosberg, A.Y.2
Tanaka, T.3
-
5
-
-
34249930405
-
Protein-folding dynamics: overview of molecular simulation techniques
-
Scheraga H.A., Khalili M., and Liwo A. Protein-folding dynamics: overview of molecular simulation techniques. Annu Rev Phys Chem 58 (2007) 57-83
-
(2007)
Annu Rev Phys Chem
, vol.58
, pp. 57-83
-
-
Scheraga, H.A.1
Khalili, M.2
Liwo, A.3
-
7
-
-
36749084004
-
Protein folding: then and now
-
Chen Y., Ding F., Nie H., Serohijos A.W., Sharma S., Wilcox K.C., Yin S., and Dokholyan N.V. Protein folding: then and now. Arch Biochem Biophys 469 (2008) 4-19
-
(2008)
Arch Biochem Biophys
, vol.469
, pp. 4-19
-
-
Chen, Y.1
Ding, F.2
Nie, H.3
Serohijos, A.W.4
Sharma, S.5
Wilcox, K.C.6
Yin, S.7
Dokholyan, N.V.8
-
8
-
-
0344301982
-
Protein folding: a perspective from theory and experiment
-
Dobson C.M., Sali A., and Karplus M. Protein folding: a perspective from theory and experiment. Angew Chem Int Ed 37 (1998) 868-893
-
(1998)
Angew Chem Int Ed
, vol.37
, pp. 868-893
-
-
Dobson, C.M.1
Sali, A.2
Karplus, M.3
-
9
-
-
0027234766
-
Engineering of stable and fast-folding sequences of model proteins
-
Shakhnovich E.I., and Gutin A.M. Engineering of stable and fast-folding sequences of model proteins. Proc Natl Acad Sci U S A 90 15 (1993) 7195-7199
-
(1993)
Proc Natl Acad Sci U S A
, vol.90
, Issue.15
, pp. 7195-7199
-
-
Shakhnovich, E.I.1
Gutin, A.M.2
-
10
-
-
0023449962
-
Spin glasses and the statistical mechanics of protein folding
-
Bryngelson J.D., and Wolynes P.G. Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci U S A 84 21 (1987) 7524-7528
-
(1987)
Proc Natl Acad Sci U S A
, vol.84
, Issue.21
, pp. 7524-7528
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
12
-
-
0032574827
-
Dynamics and function of proteins: the search for general concepts
-
Frauenfelder H., and McMahon B. Dynamics and function of proteins: the search for general concepts. Proc Natl Acad Sci U S A 95 9 (1998) 4795-4797
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, Issue.9
, pp. 4795-4797
-
-
Frauenfelder, H.1
McMahon, B.2
-
13
-
-
5144223810
-
Bulk-solvent and hydration-shell fluctuations, similar to alpha- and beta-fluctuations in glasses, control protein motions and functions
-
Fenimore P.W., Frauenfelder H., McMahon B.H., and Young R.D. Bulk-solvent and hydration-shell fluctuations, similar to alpha- and beta-fluctuations in glasses, control protein motions and functions. Proc Natl Acad Sci U S A 101 40 (2004) 14408-14413
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, Issue.40
, pp. 14408-14413
-
-
Fenimore, P.W.1
Frauenfelder, H.2
McMahon, B.H.3
Young, R.D.4
-
14
-
-
69749119200
-
The spectrum of biomolecular states and motions
-
Hegler J.A., Weinkam P., and Wolynes P.G. The spectrum of biomolecular states and motions. HFSP J 2 6 (2008) 307-313
-
(2008)
HFSP J
, vol.2
, Issue.6
, pp. 307-313
-
-
Hegler, J.A.1
Weinkam, P.2
Wolynes, P.G.3
-
15
-
-
63549096871
-
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics
-
Grant B.J., Gorfe A.A., and McCammon J.A. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol 5 3 (2009) e1000325
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.3
-
-
Grant, B.J.1
Gorfe, A.A.2
McCammon, J.A.3
-
16
-
-
56649083699
-
Computing the stability diagram of the Trp-cage miniprotein
-
Paschek D., Hempel S., and Garcia A.E. Computing the stability diagram of the Trp-cage miniprotein. Proc Natl Acad Sci U S A 105 46 (2008) 17754-17759
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, Issue.46
, pp. 17754-17759
-
-
Paschek, D.1
Hempel, S.2
Garcia, A.E.3
-
17
-
-
61949273856
-
Apo adenylate kinase encodes its holo form: a principal component and varimax analysis
-
Cukier R.I. Apo adenylate kinase encodes its holo form: a principal component and varimax analysis. J Phys Chem B 113 6 (2009) 1662-1672
-
(2009)
J Phys Chem B
, vol.113
, Issue.6
, pp. 1662-1672
-
-
Cukier, R.I.1
-
18
-
-
49449086650
-
Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions
-
A 330 ns CHARMM explicit solvent molecular dynamics trajectory of eglin c was run and analyzed using dihedral principal component analysis. PCA indicated that the basins of attraction split forming an hierarchical tree. A table of contacts, in particular water-mediated contacts and salt-bridges present in various sub-basins reveals the role of these contacts in sculpting eglin c's energy landscape.
-
Materese C.K., Goldmon C.C., and Papoian G.A. Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions. Proc Natl Acad Sci U S A 105 31 (2008) 10659-10664. A 330 ns CHARMM explicit solvent molecular dynamics trajectory of eglin c was run and analyzed using dihedral principal component analysis. PCA indicated that the basins of attraction split forming an hierarchical tree. A table of contacts, in particular water-mediated contacts and salt-bridges present in various sub-basins reveals the role of these contacts in sculpting eglin c's energy landscape.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, Issue.31
, pp. 10659-10664
-
-
Materese, C.K.1
Goldmon, C.C.2
Papoian, G.A.3
-
19
-
-
67249126712
-
How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?
-
Maisuradze G.G., Liwo A., and Scheraga H.A. How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?. Phys Rev Lett 102 23 (2009) 238102
-
(2009)
Phys Rev Lett
, vol.102
, Issue.23
, pp. 238102
-
-
Maisuradze, G.G.1
Liwo, A.2
Scheraga, H.A.3
-
20
-
-
0000580978
-
Proteins and pressure
-
Frauenfelder H., Alberding N.A., Ansari A., Braunstein D., Cowen B.R., Hong M.K., Iben IET J.B., Johnson S., and Luck. Proteins and pressure. J Phys Chem 94 3 (1990) 1024-1037
-
(1990)
J Phys Chem
, vol.94
, Issue.3
, pp. 1024-1037
-
-
Frauenfelder, H.1
Alberding, N.A.2
Ansari, A.3
Braunstein, D.4
Cowen, B.R.5
Hong, M.K.6
Iben IET, J.B.7
Johnson, S.8
Luck9
-
21
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman K., and Kern D. Dynamic personalities of proteins. Nature 450 7172 (2007) 964-972
-
(2007)
Nature
, vol.450
, Issue.7172
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
22
-
-
58549104541
-
Folding energy landscape and network dynamics of small globular proteins
-
Free energy surfaces for src SH3 domain and protein G were constructed using principal components based on a contact map and a coarse-grained implicit solvent force field. The funnel shape of the folding landscapes was confirmed. In addition, conformations sampled in the simulation were structured into a network. Grouping of the conformations into nodes and assigning rates to edges was based on the contact map. Hierarchical nature of the network was discussed.
-
Hori N., Chikenji G., Berry R.S., and Takada S. Folding energy landscape and network dynamics of small globular proteins. Proc Natl Acad Sci U S A 106 (2009) 73-78. Free energy surfaces for src SH3 domain and protein G were constructed using principal components based on a contact map and a coarse-grained implicit solvent force field. The funnel shape of the folding landscapes was confirmed. In addition, conformations sampled in the simulation were structured into a network. Grouping of the conformations into nodes and assigning rates to edges was based on the contact map. Hierarchical nature of the network was discussed.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 73-78
-
-
Hori, N.1
Chikenji, G.2
Berry, R.S.3
Takada, S.4
-
23
-
-
66849091890
-
Reactive flux and folding pathways in network models of coarse-grained protein dynamics
-
Berezhkovskii A., Hummer G., and Szabo A. Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J Chem Phys 130 20 (2009) 205102
-
(2009)
J Chem Phys
, vol.130
, Issue.20
, pp. 205102
-
-
Berezhkovskii, A.1
Hummer, G.2
Szabo, A.3
-
24
-
-
40549128343
-
Pathways for conformational change in nitrogen regulatory protein c from discrete path sampling
-
Khalili M., and Wales D. Pathways for conformational change in nitrogen regulatory protein c from discrete path sampling. J Phys Chem B (2008)
-
(2008)
J Phys Chem B
-
-
Khalili, M.1
Wales, D.2
-
25
-
-
44949178407
-
Coarse master equations for peptide folding dynamics
-
Buchete N.V., and Hummer G. Coarse master equations for peptide folding dynamics. J Phys Chem B 112 19 (2008) 6057-6069
-
(2008)
J Phys Chem B
, vol.112
, Issue.19
, pp. 6057-6069
-
-
Buchete, N.V.1
Hummer, G.2
-
26
-
-
34547341247
-
Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics
-
Hinrichs N.S., and Pande V.S. Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics. J Chem Phys 126 24 (2007) 244101
-
(2007)
J Chem Phys
, vol.126
, Issue.24
, pp. 244101
-
-
Hinrichs, N.S.1
Pande, V.S.2
-
27
-
-
34247338100
-
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
-
Chodera J.D., Singhal N., Pande V.S., Dill K.A., and Swope W.C. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys 126 15 (2007) 155101
-
(2007)
J Chem Phys
, vol.126
, Issue.15
, pp. 155101
-
-
Chodera, J.D.1
Singhal, N.2
Pande, V.S.3
Dill, K.A.4
Swope, W.C.5
-
28
-
-
32344450229
-
Network and graph analyses of folding free energy surfaces
-
Caflisch A. Network and graph analyses of folding free energy surfaces. Curr Opin Struct Biol 16 (2006) 71-78
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 71-78
-
-
Caflisch, A.1
-
29
-
-
49149121255
-
One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process
-
Krivov S.V., Muff S., Caflisch A., and Karplus M. One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process. J Phys Chem B 112 (2008) 8701-8714
-
(2008)
J Phys Chem B
, vol.112
, pp. 8701-8714
-
-
Krivov, S.V.1
Muff, S.2
Caflisch, A.3
Karplus, M.4
-
30
-
-
44149101188
-
21 - 30 peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions
-
21 - 30 peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions. J Mol Biol 379 (2008) 815-829
-
(2008)
J Mol Biol
, vol.379
, pp. 815-829
-
-
Tarus, B.1
Straub, J.E.2
Thirumalai, D.3
-
31
-
-
58749100487
-
High resolution approach to the native state ensemble kinetics and thermodynamics
-
2 coordinates, where the latter refer to two native-like conformations. Brownian dynamics was run on the resulting FES and borderline behavior between diffusive and activated protein dynamics was found. Role of solvent in smoothing the energy landscape and preventing partial unfolding was shown.
-
2 coordinates, where the latter refer to two native-like conformations. Brownian dynamics was run on the resulting FES and borderline behavior between diffusive and activated protein dynamics was found. Role of solvent in smoothing the energy landscape and preventing partial unfolding was shown.
-
(2008)
Biophys J
, vol.95
, Issue.12
, pp. 5524-5532
-
-
Wu, S.1
Zhuravlev, P.I.2
Papoian, G.A.3
-
32
-
-
70350453758
-
Enzyme millisecond conformational dynamics do not catalyze the chemical step
-
Multiscale simulations, namely all-atom → coarse-grained → Brownian dynamics on a 2D free energy surface with a chemical and conformational coordinates were used to investigate the connection between conformational and catalytic step in adenylate kinase enzymatic activity. The authors found no significant coupling between the chemical and conformational coordinates.
-
Pisliakov A., Cao J., Kamerlin S., and Warshel A. Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc Natl Acad Sci U S A 106 (2009) 17359-17364. Multiscale simulations, namely all-atom → coarse-grained → Brownian dynamics on a 2D free energy surface with a chemical and conformational coordinates were used to investigate the connection between conformational and catalytic step in adenylate kinase enzymatic activity. The authors found no significant coupling between the chemical and conformational coordinates.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 17359-17364
-
-
Pisliakov, A.1
Cao, J.2
Kamerlin, S.3
Warshel, A.4
-
33
-
-
36849010909
-
Mechanical control of the directional stepping dynamics of the kinesin motor
-
From coarse-grained simulations, a potential of mean field for the tethered head of kinesin motor on a microtubule was calculated, helping to identify the preferential place on the microtubule for the next binding of the head and showing that the motor stays on the same protofilament. Partial unfolding of the binding motif in the head was noted and discussed.
-
Hyeon C., and Onuchic J.N. Mechanical control of the directional stepping dynamics of the kinesin motor. Proc Natl Acad Sci U S A 104 44 (2007) 17382-17387. From coarse-grained simulations, a potential of mean field for the tethered head of kinesin motor on a microtubule was calculated, helping to identify the preferential place on the microtubule for the next binding of the head and showing that the motor stays on the same protofilament. Partial unfolding of the binding motif in the head was noted and discussed.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, Issue.44
, pp. 17382-17387
-
-
Hyeon, C.1
Onuchic, J.N.2
-
34
-
-
33747065536
-
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: structure-based molecular dynamics simulations
-
Okazaki K., Koga N., Takada S., Onuchic J.N., and Wolynes P.G. Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: structure-based molecular dynamics simulations. Proc Natl Acad Sci U S A 103 32 (2006) 11844-11849
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, Issue.32
, pp. 11844-11849
-
-
Okazaki, K.1
Koga, N.2
Takada, S.3
Onuchic, J.N.4
Wolynes, P.G.5
-
35
-
-
62549167040
-
Ligand-induced global transitions in the catalytic domain of protein kinase A
-
Hyeon C., Jennings P.A., Adams J.A., and Onuchic J.N. Ligand-induced global transitions in the catalytic domain of protein kinase A. Proc Natl Acad Sci U S A 106 9 (2009) 3023-3028
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.9
, pp. 3023-3028
-
-
Hyeon, C.1
Jennings, P.A.2
Adams, J.A.3
Onuchic, J.N.4
-
36
-
-
61949448788
-
Energy landscape along an enzymatic reaction trajectory: hinges or cracks?
-
Whitford P., Onuchic J.N., and Wolynes P.G. Energy landscape along an enzymatic reaction trajectory: hinges or cracks?. HFSP J 2 2 (2008) 61-64
-
(2008)
HFSP J
, vol.2
, Issue.2
, pp. 61-64
-
-
Whitford, P.1
Onuchic, J.N.2
Wolynes, P.G.3
-
37
-
-
33846847773
-
Conformational transitions of adenylate kinase: switching by cracking
-
Whitford P.C., Miyashita O., Levy Y., and Onuchic J.N. Conformational transitions of adenylate kinase: switching by cracking. J Mol Biol 366 5 (2007) 1661-1671
-
(2007)
J Mol Biol
, vol.366
, Issue.5
, pp. 1661-1671
-
-
Whitford, P.C.1
Miyashita, O.2
Levy, Y.3
Onuchic, J.N.4
-
38
-
-
0037438606
-
Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor
-
Papoian G.A., DeGrado W.F., and Klein M.L. Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor. J Am Chem Soc 125 2 (2003) 560-569
-
(2003)
J Am Chem Soc
, vol.125
, Issue.2
, pp. 560-569
-
-
Papoian, G.A.1
DeGrado, W.F.2
Klein, M.L.3
-
39
-
-
16244419691
-
Enzyme dynamics during catalysis measured by NMR spectroscopy
-
Kern D., Eisenmesser E.Z., and Wolf-Watz M. Enzyme dynamics during catalysis measured by NMR spectroscopy. Method Enzymol 394 (2005) 507-524
-
(2005)
Method Enzymol
, vol.394
, pp. 507-524
-
-
Kern, D.1
Eisenmesser, E.Z.2
Wolf-Watz, M.3
-
40
-
-
36849048228
-
Intrinsic motions along an enzymatic reaction trajectory
-
Henzler-Wildman K.A., Thai V., Lei M., Ott M., Wolf-Watz M., Fenn T., Pozharski E., Wilson M.A., Petsko G.A., Karplus M., Hübner C.G., and Kern D. Intrinsic motions along an enzymatic reaction trajectory. Nature 450 7171 (2007) 838-844
-
(2007)
Nature
, vol.450
, Issue.7171
, pp. 838-844
-
-
Henzler-Wildman, K.A.1
Thai, V.2
Lei, M.3
Ott, M.4
Wolf-Watz, M.5
Fenn, T.6
Pozharski, E.7
Wilson, M.A.8
Petsko, G.A.9
Karplus, M.10
Hübner, C.G.11
Kern, D.12
-
41
-
-
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., and Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450 7171 (2007) 913-916
-
(2007)
Nature
, vol.450
, Issue.7171
, pp. 913-916
-
-
Henzler-Wildman, K.A.1
Lei, M.2
Thai, V.3
Kerns, S.J.4
Karplus, M.5
Kern, D.6
-
42
-
-
49649084492
-
Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms
-
Okazaki K., and Takada S. Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms. Proc Natl Acad Sci U S A 105 32 (2008) 11182-11187
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, Issue.32
, pp. 11182-11187
-
-
Okazaki, K.1
Takada, S.2
-
43
-
-
48749120889
-
An allosteric circuit in caspase-1
-
Alanine mutation scanning study of the residues forming hydrogen bond networks in caspase-1 was carried out. The two H-bond networks interconvert upon ligand binding and conformational change, which shows their importance for allosteric switching. Four important residues were identified. Mutations of either of two residues in this set change the enzymatic rate by a factor of 4-7, while mutations of either of the other two that form salt bridge decrease the rate 100-200-fold.
-
Datta D., Scheer J.M., Romanowski M.J., and Wells J.A. An allosteric circuit in caspase-1. J Mol Biol 381 5 (2008) 1157-1167. Alanine mutation scanning study of the residues forming hydrogen bond networks in caspase-1 was carried out. The two H-bond networks interconvert upon ligand binding and conformational change, which shows their importance for allosteric switching. Four important residues were identified. Mutations of either of two residues in this set change the enzymatic rate by a factor of 4-7, while mutations of either of the other two that form salt bridge decrease the rate 100-200-fold.
-
(2008)
J Mol Biol
, vol.381
, Issue.5
, pp. 1157-1167
-
-
Datta, D.1
Scheer, J.M.2
Romanowski, M.J.3
Wells, J.A.4
-
44
-
-
36749008588
-
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
-
Arora K., and Brooks C.L. Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci U S A 104 47 (2007) 18496-18501
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, Issue.47
, pp. 18496-18501
-
-
Arora, K.1
Brooks, C.L.2
-
45
-
-
65549153301
-
Conformational change path between closed and open forms of C2 domain of coagulation factor V on a two-dimensional free-energy surface
-
Wu S., Lee C.J., and Pedersen L.G. Conformational change path between closed and open forms of C2 domain of coagulation factor V on a two-dimensional free-energy surface. Phys Rev E 79 4 Pt 1 (2009) 041909
-
(2009)
Phys Rev E
, vol.79
, Issue.4 PART 1
, pp. 041909
-
-
Wu, S.1
Lee, C.J.2
Pedersen, L.G.3
-
46
-
-
62649161772
-
Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories
-
Yang S., Banavali N.K., and Roux B. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc Natl Acad Sci U S A 106 10 (2009) 3776-3781
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.10
, pp. 3776-3781
-
-
Yang, S.1
Banavali, N.K.2
Roux, B.3
-
47
-
-
58149354711
-
Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement
-
Clore G.M. Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement. Mol Biosyst 4 11 (2008) 1058-1069
-
(2008)
Mol Biosyst
, vol.4
, Issue.11
, pp. 1058-1069
-
-
Clore, G.M.1
-
48
-
-
53349152834
-
Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease
-
Tang C., Louis J.M., Aniana A., Suh J.Y., and Clore G.M. Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease. Nature 455 7213 (2008) 693-696
-
(2008)
Nature
, vol.455
, Issue.7213
, pp. 693-696
-
-
Tang, C.1
Louis, J.M.2
Aniana, A.3
Suh, J.Y.4
Clore, G.M.5
-
49
-
-
46849122649
-
Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition
-
Thielges M.C., Zimmermann J., Yu W., Oda M., and Romesberg F.E. Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition. Biochemistry 47 27 (2008) 7237-7247
-
(2008)
Biochemistry
, vol.47
, Issue.27
, pp. 7237-7247
-
-
Thielges, M.C.1
Zimmermann, J.2
Yu, W.3
Oda, M.4
Romesberg, F.E.5
-
50
-
-
33749316614
-
Biomolecule large-amplitude motion and solvation dynamics: modelling and probes from THz to X-rays
-
Leitner D.M., Havenith M., and Gruebele M. Biomolecule large-amplitude motion and solvation dynamics: modelling and probes from THz to X-rays. Int Rev Phys Chem 25 4 (2008) 553-582
-
(2008)
Int Rev Phys Chem
, vol.25
, Issue.4
, pp. 553-582
-
-
Leitner, D.M.1
Havenith, M.2
Gruebele, M.3
-
51
-
-
0036468397
-
Coupling of folding and binding for unstructured proteins
-
Dyson H.J., and Wright P.E. Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 12 (2002) 54-60
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 54-60
-
-
Dyson, H.J.1
Wright, P.E.2
-
52
-
-
0037346726
-
The physics and bioinformatics of binding and folding - an energy landscape perspective
-
Papoian G.A., and Wolynes P.G. The physics and bioinformatics of binding and folding - an energy landscape perspective. Biopolymers 68 3 (2003) 333-349
-
(2003)
Biopolymers
, vol.68
, Issue.3
, pp. 333-349
-
-
Papoian, G.A.1
Wolynes, P.G.2
-
53
-
-
33646350033
-
Dominant kinetic paths on biomolecular binding-folding energy landscape
-
Wang J., Zhang K., Lu H., and Wang E. Dominant kinetic paths on biomolecular binding-folding energy landscape. Phys Rev Lett 96 16 (2006) 168101
-
(2006)
Phys Rev Lett
, vol.96
, Issue.16
, pp. 168101
-
-
Wang, J.1
Zhang, K.2
Lu, H.3
Wang, E.4
-
54
-
-
13444301037
-
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes
-
Levy Y., Cho S.S., Onuchic J.N., and Wolynes P.G. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J Mol Biol 346 4 (2005) 1121-1145
-
(2005)
J Mol Biol
, vol.346
, Issue.4
, pp. 1121-1145
-
-
Levy, Y.1
Cho, S.S.2
Onuchic, J.N.3
Wolynes, P.G.4
-
55
-
-
68049120378
-
Arc-repressor dimerization on DNA: folding rate enhancement by colocalization
-
Marcovitz A., and Levy Y. Arc-repressor dimerization on DNA: folding rate enhancement by colocalization. Biophys J 96 10 (2009) 4212-4220
-
(2009)
Biophys J
, vol.96
, Issue.10
, pp. 4212-4220
-
-
Marcovitz, A.1
Levy, Y.2
-
56
-
-
38049165543
-
Localizing frustration in native proteins and protein assemblies
-
Ferreiro D.U., Hegler J.A., Komives E.A., and Wolynes P.G. Localizing frustration in native proteins and protein assemblies. Proc Natl Acad Sci U S A 104 50 (2007) 19819-19824
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, Issue.50
, pp. 19819-19824
-
-
Ferreiro, D.U.1
Hegler, J.A.2
Komives, E.A.3
Wolynes, P.G.4
-
57
-
-
36849044219
-
Structure and dynamics of a molten globular enzyme
-
Pervushin K., Vamvaca K., Vögeli B., and Hilvert D. Structure and dynamics of a molten globular enzyme. Nat Struct Mol Biol 14 12 (2007) 1202-1206
-
(2007)
Nat Struct Mol Biol
, vol.14
, Issue.12
, pp. 1202-1206
-
-
Pervushin, K.1
Vamvaca, K.2
Vögeli, B.3
Hilvert, D.4
-
58
-
-
52949128744
-
On the relationship between folding and chemical landscapes in enzyme catalysis
-
Roca M., Messer B., Hilvert D., and Warshel A. On the relationship between folding and chemical landscapes in enzyme catalysis. Proc Natl Acad Sci U S A 105 37 (2008) 13877-13882
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, Issue.37
, pp. 13877-13882
-
-
Roca, M.1
Messer, B.2
Hilvert, D.3
Warshel, A.4
-
59
-
-
55749083564
-
Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm
-
Papoian G.A. Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm. Proc Natl Acad Sci U S A 105 38 (2008) 14237-14238
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, Issue.38
, pp. 14237-14238
-
-
Papoian, G.A.1
-
60
-
-
0034255123
-
Speeding molecular recognition by using the folding funnel: the fly-casting mechanism
-
Shoemaker B.A., Portman J.J., and Wolynes P.G. Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc Natl Acad Sci U S A 97 16 (2000) 8868-8873
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, Issue.16
, pp. 8868-8873
-
-
Shoemaker, B.A.1
Portman, J.J.2
Wolynes, P.G.3
-
61
-
-
42949161558
-
Binding-induced folding of a natively unstructured transcription factor
-
Turjanski A.G., Gutkind J.S., Best R.B., and Hummer G. Binding-induced folding of a natively unstructured transcription factor. PLoS Comput Biol 4 4 (2008) e1000060
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.4
-
-
Turjanski, A.G.1
Gutkind, J.S.2
Best, R.B.3
Hummer, G.4
-
62
-
-
34250821717
-
Mechanism of coupled folding and binding of an intrinsically disordered protein
-
Sugase K., Dyson H.J., and Wright P.E. Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447 7147 (2007) 1021-1025
-
(2007)
Nature
, vol.447
, Issue.7147
, pp. 1021-1025
-
-
Sugase, K.1
Dyson, H.J.2
Wright, P.E.3
-
63
-
-
38349181087
-
Metal-coupled folding of Cys2His2 zinc-finger
-
Li W., Zhang J., Wang J., and Wang W. Metal-coupled folding of Cys2His2 zinc-finger. J Am Chem Soc 130 3 (2008) 892-900
-
(2008)
J Am Chem Soc
, vol.130
, Issue.3
, pp. 892-900
-
-
Li, W.1
Zhang, J.2
Wang, J.3
Wang, W.4
|