-
1
-
-
0034685604
-
Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
-
Clementi, C.; Nymeyer, H.; Onuchic, J.N. Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J. Mol. Biol. 2000, 298, 937-953.
-
(2000)
J. Mol. Biol
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
2
-
-
0036785556
-
-
Karanicolas, J.; Brooks, C.L., III. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci. 2002, 11, 2351-2361.
-
Karanicolas, J.; Brooks, C.L., III. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci. 2002, 11, 2351-2361.
-
-
-
-
3
-
-
0035850732
-
Roles of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model
-
Koga, N.; Takada, S. Roles of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model. J. Mol. Biol. 2001, 313, 171-180.
-
(2001)
J. Mol. Biol
, vol.313
, pp. 171-180
-
-
Koga, N.1
Takada, S.2
-
4
-
-
0036928148
-
Validity of Go models: Comparison with a solvent- shielded empirical energy decomposition
-
Paci, E.; Vendruscolo, M.; Karplus, M. Validity of Go models: Comparison with a solvent- shielded empirical energy decomposition. Biophys. J. 2002, 83, 3032-3038.
-
(2002)
Biophys. J
, vol.83
, pp. 3032-3038
-
-
Paci, E.1
Vendruscolo, M.2
Karplus, M.3
-
5
-
-
34247861746
-
Thermodynamics of Go-type models for protein folding
-
Prieto, L.; de Sancho, D.; Rey, A. Thermodynamics of Go-type models for protein folding. J. Chem. Phys. 2005, 123, 154903.
-
(2005)
J. Chem. Phys
, vol.123
, pp. 154903
-
-
Prieto, L.1
de Sancho, D.2
Rey, A.3
-
6
-
-
34247890044
-
Influence of the chain stiffness on the thermodynamics of a Go-type model for protein folding
-
Prieto, L.; Rey, A. Influence of the chain stiffness on the thermodynamics of a Go-type model for protein folding. J. Chem. Phys. 2007, 126, 166103.
-
(2007)
J. Chem. Phys
, vol.126
, pp. 166103
-
-
Prieto, L.1
Rey, A.2
-
7
-
-
33645406972
-
On the role of chemical detail in simulating protein folding kinetics
-
Rhee, Y.M.; Pande, V.S. On the role of chemical detail in simulating protein folding kinetics. Chem. Phys. 2006, 323, 66-77.
-
(2006)
Chem. Phys
, vol.323
, pp. 66-77
-
-
Rhee, Y.M.1
Pande, V.S.2
-
8
-
-
0033607208
-
Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A
-
Shea, J.E.; Onuchic, J.N.; Brooks, C.L., III. Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A. Proc. Natl. Acad. Sci. USA 1999, 96, 12512-12517.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 12512-12517
-
-
Shea, J.E.1
Onuchic, J.N.2
Brooks III, C.L.3
-
9
-
-
0032443390
-
Discrete molecular dynamics studies of the folding of a protein-like model
-
Dokholyan, N.V.; Buldyrev, S.V.; Stanley, H.E.; Shakhnovich, E.I. Discrete molecular dynamics studies of the folding of a protein-like model. Fold. Des. 1998, 3, 577-587. +
-
(1998)
Fold. Des
, vol.3
, pp. 577-587
-
-
Dokholyan, N.V.1
Buldyrev, S.V.2
Stanley, H.E.3
Shakhnovich, E.I.4
-
10
-
-
0242368163
-
Exploring the interplay between topology and secondary structural formation in the protein folding problem
-
11193-1120 0
-
Cheung, M.S.; Finke, J.M.; Callahan, B.; Onuchic, J.N. Exploring the interplay between topology and secondary structural formation in the protein folding problem. J. Phys. Chem. B 2003, 707, 11193-1120 0.
-
(2003)
J. Phys. Chem. B
, vol.707
-
-
Cheung, M.S.1
Finke, J.M.2
Callahan, B.3
Onuchic, J.N.4
-
11
-
-
35148817913
-
Parallel foldng pathways in the SH3 domain protein
-
Lam, A.R.; Borreguero, J.M.; Ding, F.; Dokholyan, N.V.; Buldyrev, S.V.; Stanley, H.E.; Shakhnovich, E. Parallel foldng pathways in the SH3 domain protein. J. Mol. Biol. 2007, 373, 1348-1360.
-
(2007)
J. Mol. Biol
, vol.373
, pp. 1348-1360
-
-
Lam, A.R.1
Borreguero, J.M.2
Ding, F.3
Dokholyan, N.V.4
Buldyrev, S.V.5
Stanley, H.E.6
Shakhnovich, E.7
-
12
-
-
55949109149
-
Selection of optimal variants of Go-like models of proteins through studies of stretching
-
Sulkowska, J.I.; Cieplak, M. Selection of optimal variants of Go-like models of proteins through studies of stretching. Biophys. J. 2008, 95, 3174-3191.
-
(2008)
Biophys. J
, vol.95
, pp. 3174-3191
-
-
Sulkowska, J.I.1
Cieplak, M.2
-
13
-
-
0036923039
-
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism
-
Ding, F.; Dokholyan, N.V.; Buldyrev, S.V.; Stanley, H.E.; Shakhnovich, E.I. Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J. Mol. Biol. 2002, 324, 851-857.
-
(2002)
J. Mol. Biol
, vol.324
, pp. 851-857
-
-
Ding, F.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Stanley, H.E.4
Shakhnovich, E.I.5
-
14
-
-
34548510580
-
The length dependence of the PolyQ-mediated protein aggregation
-
Barton, S.; Jacak, R.; Khare, S.D.; Ding, F.; Dokholyan, N.V. The length dependence of the PolyQ-mediated protein aggregation. J. Biol. Chem. 2007, 252, 25487-25492.
-
(2007)
J. Biol. Chem
, vol.252
, pp. 25487-25492
-
-
Barton, S.1
Jacak, R.2
Khare, S.D.3
Ding, F.4
Dokholyan, N.V.5
-
16
-
-
0028963219
-
A test of lattice protein folding algorithms
-
Yue, K.; Fiebig, K.M.; Thomas, P.D.; Chan, H.S.; Shakhnovich, E.I.; Dill, K.A. A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci. USA 1995, 92, 325-329.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 325-329
-
-
Yue, K.1
Fiebig, K.M.2
Thomas, P.D.3
Chan, H.S.4
Shakhnovich, E.I.5
Dill, K.A.6
-
17
-
-
58149250463
-
Toward a coarse-grained protein model coupled with a coarsegrained solvent model: Solvation free energies of amino acid side chains
-
Han, W.; Wan, C.K.; Wu, Y.D. Toward a coarse-grained protein model coupled with a coarsegrained solvent model: Solvation free energies of amino acid side chains. J. Chem. Theory Comput. 2008, 4, 1891-1901.
-
(2008)
J. Chem. Theory Comput
, vol.4
, pp. 1891-1901
-
-
Han, W.1
Wan, C.K.2
Wu, Y.D.3
-
18
-
-
36649024127
-
Coarse-grained protein model coupled with a coarse-grained water model: Molecular dynamics study of polyalanine-based peptides
-
Han, W.; Wu, Y.D. Coarse-grained protein model coupled with a coarse-grained water model: Molecular dynamics study of polyalanine-based peptides. J. Chem. Theory Comput. 2007, 3, 2146-2161.
-
(2007)
J. Chem. Theory Comput
, vol.3
, pp. 2146-2161
-
-
Han, W.1
Wu, Y.D.2
-
19
-
-
53249098376
-
Multiscale methods for macromolecular simulations
-
Sherwood, P.; Brooks, B.R.; Sansom, M.S.P. Multiscale methods for macromolecular simulations. Curr. Opin. Struct. Biol. 2008, 75, 630-640.
-
(2008)
Curr. Opin. Struct. Biol
, vol.75
, pp. 630-640
-
-
Sherwood, P.1
Brooks, B.R.2
Sansom, M.S.P.3
-
20
-
-
17044393884
-
Coarse-grained models for proteins
-
Tozzini, V. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 2005, 75, 144-150.
-
(2005)
Curr. Opin. Struct. Biol
, vol.75
, pp. 144-150
-
-
Tozzini, V.1
-
21
-
-
33644644163
-
Insertion and assembly of membrane proteins via simulation
-
Bond, P.J.; Sansom, M.S.P. Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 2006, 725, 2697-2704.
-
(2006)
J. Am. Chem. Soc
, vol.725
, pp. 2697-2704
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
22
-
-
49449113010
-
The MARTINI coarse-grained force field: Extension to proteins
-
Monticelli, L.; Kandasamy, S.K.; Periole, X.; Larson, R.G.; Tieleman, D.P.; Marrink, S.J. The MARTINI coarse-grained force field: Extension to proteins. J. Chem. Theory Comput. 2008, 4, 819-834.
-
(2008)
J. Chem. Theory Comput
, vol.4
, pp. 819-834
-
-
Monticelli, L.1
Kandasamy, S.K.2
Periole, X.3
Larson, R.G.4
Tieleman, D.P.5
Marrink, S.J.6
-
23
-
-
33644893631
-
Coarse grained protein-lipid model with application to lipoprotein particles
-
Shih, A.Y.; Arkhipov, A.; Freddolino, P.L.; Schulten, K. Coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B 2006, 770, 3674-3684.
-
(2006)
J. Phys. Chem. B
, vol.770
, pp. 3674-3684
-
-
Shih, A.Y.1
Arkhipov, A.2
Freddolino, P.L.3
Schulten, K.4
-
24
-
-
38549133951
-
A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding
-
Yap, E.H.; Fawzi, N.L.; Head-Gordon, T. A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding. Proteins 2008, 70, 626-638.
-
(2008)
Proteins
, vol.70
, pp. 626-638
-
-
Yap, E.H.1
Fawzi, N.L.2
Head-Gordon, T.3
-
25
-
-
55149087047
-
Peptide folding using multiscale coarse-grained models
-
Thorpe, I.F.; Zhou, J.; Voth, G.A. Peptide folding using multiscale coarse-grained models. J. Phys. Chem. B 2008, 772, 13079-13090.
-
(2008)
J. Phys. Chem. B
, vol.772
, pp. 13079-13090
-
-
Thorpe, I.F.1
Zhou, J.2
Voth, G.A.3
-
26
-
-
52349118400
-
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains
-
Makowski, M.; Sobolewski, E.; Czaplewski, C.; Oldziej, S.; Liwo, A.; Scheraga, H.A. Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains. J. Phys. Chem. B 2008, 772, 11385-11395.
-
(2008)
J. Phys. Chem. B
, vol.772
, pp. 11385-11395
-
-
Makowski, M.1
Sobolewski, E.2
Czaplewski, C.3
Oldziej, S.4
Liwo, A.5
Scheraga, H.A.6
-
27
-
-
59849093382
-
Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins
-
da Silveira, C.H.; Pires, D.E.V.; Minardi, R.C.; Ribeiro, C.; Veloso, C.J.M.; Lopes, J.C.D.; Meira, W.; Neshich, G.; Ramos, C.H.I.; Habesch, R.; Santoro, M.M. Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Proteins 2009, 74, 727-743.
-
(2009)
Proteins
, vol.74
, pp. 727-743
-
-
da Silveira, C.H.1
Pires, D.E.V.2
Minardi, R.C.3
Ribeiro, C.4
Veloso, C.J.M.5
Lopes, J.C.D.6
Meira, W.7
Neshich, G.8
Ramos, C.H.I.9
Habesch, R.10
Santoro, M.M.11
-
28
-
-
0016696599
-
Studies on protein folding, unfolding and fluctuations by computer simulation. 1. Effect of specific amino acid sequence represented by specific inter-unit interactions
-
Taketomi, H.; Ueda, Y.; Go, N. Studies on protein folding, unfolding and fluctuations by computer simulation. 1. Effect of specific amino acid sequence represented by specific inter-unit interactions. Int. J. Pept. Protein Res. 1975, 7, 445-459.
-
(1975)
Int. J. Pept. Protein Res
, vol.7
, pp. 445-459
-
-
Taketomi, H.1
Ueda, Y.2
Go, N.3
-
29
-
-
18344362394
-
On the use of classical statistical mechanics in the treatment of polymer chain conformations
-
Go, N.; Scheraga, H.A. On the use of classical statistical mechanics in the treatment of polymer chain conformations. Macromolecules 1976, 9, 535-542.
-
(1976)
Macromolecules
, vol.9
, pp. 535-542
-
-
Go, N.1
Scheraga, H.A.2
-
30
-
-
0017131655
-
Theory of large-amplitude conformational fluctuations in native globular proteins: Independent fluctuating site model
-
Ueda, Y.; Go, N. Theory of large-amplitude conformational fluctuations in native globular proteins: Independent fluctuating site model. Int. J. Pept. Protein Res. 1976, 8, 551-558.
-
(1976)
Int. J. Pept. Protein Res
, vol.8
, pp. 551-558
-
-
Ueda, Y.1
Go, N.2
-
31
-
-
0000355428
-
Respective roles of short-range and long-range interactions in protein folding
-
Go, N.; Taketomi, H. Respective roles of short-range and long-range interactions in protein folding. Proc. Natl. Acad. Sci. USA 1978, 75, 559-563.
-
(1978)
Proc. Natl. Acad. Sci. USA
, vol.75
, pp. 559-563
-
-
Go, N.1
Taketomi, H.2
-
32
-
-
0017842051
-
Studies on protein folding, unfolding and fluctuations by computer simulation. 2. A three-dimensional lattice model of lysozyme
-
Ueda, Y.; Taketomi, H.; Go, N. Studies on protein folding, unfolding and fluctuations by computer simulation. 2. A three-dimensional lattice model of lysozyme. Biopolymers 1978, 17, 1531-1548.
-
(1978)
Biopolymers
, vol.17
, pp. 1531-1548
-
-
Ueda, Y.1
Taketomi, H.2
Go, N.3
-
33
-
-
0018344672
-
Studies on protein folding, unfolding and fluctuations by computer simulation. 3. Effect of short-range interactions
-
Go, N.; Taketomi, H. Studies on protein folding, unfolding and fluctuations by computer simulation. 3. Effect of short-range interactions. Int. J. Pept. Protein Res. 1979, 13, 235-252.
-
(1979)
Int. J. Pept. Protein Res
, vol.13
, pp. 235-252
-
-
Go, N.1
Taketomi, H.2
-
34
-
-
0018475814
-
Studies on protein folding, unfolding and fluctuations by computer simulation. 4. Hydrophobic interactions
-
Go, N.; Taketomi, H. Studies on protein folding, unfolding and fluctuations by computer simulation. 4. Hydrophobic interactions. Int. J. Pept. Protein Res. 1979, 13, 447-461.
-
(1979)
Int. J. Pept. Protein Res
, vol.13
, pp. 447-461
-
-
Go, N.1
Taketomi, H.2
-
35
-
-
0020972782
-
Theoretical studies of protein folding
-
Go, N. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 1983, 12, 183-210.
-
(1983)
Annu. Rev. Biophys. Bioeng
, vol.12
, pp. 183-210
-
-
Go, N.1
-
36
-
-
0023991155
-
The effect of amino acid substitution on protein folding and protein unfolding transition studied by computer simulation
-
Taketomi, H.; Kano, F.; Go, N. The effect of amino acid substitution on protein folding and protein unfolding transition studied by computer simulation. Biopolymers 1988, 27, 527-559.
-
(1988)
Biopolymers
, vol.27
, pp. 527-559
-
-
Taketomi, H.1
Kano, F.2
Go, N.3
-
37
-
-
0035958744
-
Statistical thermodynamics: Taking a walk on a landscape
-
Brooks, C.L., III; Onuchic, J.N.; Wales, D.J. Statistical thermodynamics: Taking a walk on a landscape. Science 2001, 293, 612-613.
-
(2001)
Science
, vol.293
, pp. 612-613
-
-
Brooks III, C.L.1
Onuchic, J.N.2
Wales, D.J.3
-
38
-
-
48249134448
-
The protein folding problem
-
Dill, K.A.; Ozkan, S.B.; Shell, M.S.; Weikl, T.R. The protein folding problem. Ann. Rev. Biophys. 2008, 37, 289-316.
-
(2008)
Ann. Rev. Biophys
, vol.37
, pp. 289-316
-
-
Dill, K.A.1
Ozkan, S.B.2
Shell, M.S.3
Weikl, T.R.4
-
40
-
-
34547551805
-
Protein folding by zipping and assembly
-
Ozkan, S.B.; Wu, G.A.; Chodera, J.D.; Dill, K.A. Protein folding by zipping and assembly. Proc. Natl. Acad. Sci. USA 2007, 104, 11987-11992.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 11987-11992
-
-
Ozkan, S.B.1
Wu, G.A.2
Chodera, J.D.3
Dill, K.A.4
-
41
-
-
36049028001
-
Influence of the native topology on the folding barrier for small proteins
-
Prieto, L.; Rey, A. Influence of the native topology on the folding barrier for small proteins. J. Chem. Phys. 2007, 127, 175101.
-
(2007)
J. Chem. Phys
, vol.127
, pp. 175101
-
-
Prieto, L.1
Rey, A.2
-
42
-
-
50049118547
-
-
Hills, R.D., Jr.; Brooks, C.L., III. Subdomain competition, cooperativity, and topological frustration in the folding of Che Y. J. Mol. Biol. 2008, 382, 485-495.
-
Hills, R.D., Jr.; Brooks, C.L., III. Subdomain competition, cooperativity, and topological frustration in the folding of Che Y. J. Mol. Biol. 2008, 382, 485-495.
-
-
-
-
43
-
-
2542599277
-
Phi-Value analysis and the nature of protein-folding transition states
-
Fersht, A.R.; Sato, S. Phi-Value analysis and the nature of protein-folding transition states. Proc. Natl. Acad. Sci. USA 2004, 101, 7976-7981.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 7976-7981
-
-
Fersht, A.R.1
Sato, S.2
-
44
-
-
33745931359
-
Multiple routes lead to the native state in the energy landscape of the beta-trefoil family
-
Chavez, L.L.; Gosavi, S.; Jennings, P.A.; Onuchic, J.N. Multiple routes lead to the native state in the energy landscape of the beta-trefoil family. Proc. Natl. Acad. Sci. USA 2006, 103, 10254-10258.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 10254-10258
-
-
Chavez, L.L.1
Gosavi, S.2
Jennings, P.A.3
Onuchic, J.N.4
-
45
-
-
0034628914
-
Identifying the protein folding nucleus using molecular dynamics
-
Dokholyan, N.V.; Buldyrev, S.V.; Stanley, H.E.; Shakhnovich, E.I. Identifying the protein folding nucleus using molecular dynamics. J. Mol. Biol. 2000, 296, 1183-1188.
-
(2000)
J. Mol. Biol
, vol.296
, pp. 1183-1188
-
-
Dokholyan, N.V.1
Buldyrev, S.V.2
Stanley, H.E.3
Shakhnovich, E.I.4
-
46
-
-
27744531924
-
The energy landscape of modular repeat proteins: Topology determines folding mechanism in the ankyrin family
-
Ferreiro, D.U.; Cho, S.S.; Komives, E.A.; Wolynes, P.G. The energy landscape of modular repeat proteins: Topology determines folding mechanism in the ankyrin family. J. Mol. Biol. 2005, 354, 679-692.
-
(2005)
J. Mol. Biol
, vol.354
, pp. 679-692
-
-
Ferreiro, D.U.1
Cho, S.S.2
Komives, E.A.3
Wolynes, P.G.4
-
47
-
-
33645030244
-
Topological frustration and the folding of interleukin-1 beta
-
Gosavi, S.; Chavez, L.L.; Jennings, P.A.; Onuchic, J.N. Topological frustration and the folding of interleukin-1 beta. J. Mol. Biol. 2006, 357, 986-996.
-
(2006)
J. Mol. Biol
, vol.357
, pp. 986-996
-
-
Gosavi, S.1
Chavez, L.L.2
Jennings, P.A.3
Onuchic, J.N.4
-
48
-
-
2942590388
-
Simulation, experiment, and evolution: Understanding nucleation in protein S6 folding
-
Hubner, I.A.; Oliveberg, M.; Shakhnovich, E.I. Simulation, experiment, and evolution: Understanding nucleation in protein S6 folding. Proc. Natl. Acad. Sci. USA 2004, 707, 8354-8359.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.707
, pp. 8354-8359
-
-
Hubner, I.A.1
Oliveberg, M.2
Shakhnovich, E.I.3
-
49
-
-
0242383943
-
Improved Go-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions
-
Karanicolas, J.; Brooks, C.L., III. Improved Go-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions. J. Mol. Biol. 2003, 334, 309-325.
-
(2003)
J. Mol. Biol
, vol.334
, pp. 309-325
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
50
-
-
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.; Wolynes, P.G. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J. Mol. Biol. 2005, 346, 1121-1145.
-
(2005)
J. Mol. Biol
, vol.346
, pp. 1121-1145
-
-
Levy, Y.1
Cho, S.S.2
Onuchic, J.N.3
Wolynes, P.G.4
-
51
-
-
0345743709
-
Protein topology determines binding mechanism
-
Levy, Y.; Wolynes, P.G.; Onuchic, J.N. Protein topology determines binding mechanism. Proc. Natl. Acad. Sci. USA 2004, 707, 511-516.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.707
, pp. 511-516
-
-
Levy, Y.1
Wolynes, P.G.2
Onuchic, J.N.3
-
52
-
-
16244417212
-
The native energy landscape for interleukin-1 beta. Modulation of the population ensemble through native- state topology
-
Roy, M.; Chavez, L.L.; Finke, J.M.; Heidary, D.K.; Onuchic, J.N.; Jennings, P.A. The native energy landscape for interleukin-1 beta. Modulation of the population ensemble through native- state topology. J. Mol. Biol. 2005, 345, 335-347.
-
(2005)
J. Mol. Biol
, vol.345
, pp. 335-347
-
-
Roy, M.1
Chavez, L.L.2
Finke, J.M.3
Heidary, D.K.4
Onuchic, J.N.5
Jennings, P.A.6
-
53
-
-
0036931525
-
Folding pathways of prion and doppel
-
Settanni, G.; Hoang, T.X.; Micheletti, C.; Maritan, A. Folding pathways of prion and doppel. Biophys. J. 2002, 53, 3533-3541.
-
(2002)
Biophys. J
, vol.53
, pp. 3533-3541
-
-
Settanni, G.1
Hoang, T.X.2
Micheletti, C.3
Maritan, A.4
-
54
-
-
33645019703
-
Folding with downhill behavior and low cooperativity of proteins
-
Zuo, G.H.; Wang, J.; Wang, W. Folding with downhill behavior and low cooperativity of proteins. Proteins 2006, 63, 165-173.
-
(2006)
Proteins
, vol.63
, pp. 165-173
-
-
Zuo, G.H.1
Wang, J.2
Wang, W.3
-
55
-
-
31544472338
-
Effect of finite size on cooperativity and rates of protein folding
-
Kouza, M.; Li, M.S.; O'Brien, E.P.; Hu, C.K.; Thirumalai, D. Effect of finite size on cooperativity and rates of protein folding. J. Phys. Chem. A 2006, 770, 671-676.
-
(2006)
J. Phys. Chem. A
, vol.770
, pp. 671-676
-
-
Kouza, M.1
Li, M.S.2
O'Brien, E.P.3
Hu, C.K.4
Thirumalai, D.5
-
56
-
-
3042677501
-
The effects of nonnative interactions on protein folding rates: Theory and simulation
-
Clementi, C.; Plotkin, S.S. The effects of nonnative interactions on protein folding rates: Theory and simulation. Protein Sci. 2004, 73, 1750-1766.
-
(2004)
Protein Sci
, vol.73
, pp. 1750-1766
-
-
Clementi, C.1
Plotkin, S.S.2
-
57
-
-
22544446147
-
Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes
-
Das, P.; Matysiak, S.; Clementi, C. Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes. Proc. Natl. Acad. Sci. USA 2005, 702, 10141-10146.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.702
, pp. 10141-10146
-
-
Das, P.1
Matysiak, S.2
Clementi, C.3
-
58
-
-
35548965931
-
Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Go model simulation
-
Gu, Z.; Rao, M.K.; Forsyth, W.R.; Finke, J.M.; Matthews, C.R. Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Go model simulation. J. Mol. Biol. 2007, 374, 528-546.
-
(2007)
J. Mol. Biol
, vol.374
, pp. 528-546
-
-
Gu, Z.1
Rao, M.K.2
Forsyth, W.R.3
Finke, J.M.4
Matthews, C.R.5
-
59
-
-
0037093654
-
Native and non-native interactions along protein folding and unfolding pathways
-
Paci, E.; Vendruscolo, M.; Karplus, M. Native and non-native interactions along protein folding and unfolding pathways. Proteins 2002, 47, 379-392.
-
(2002)
Proteins
, vol.47
, pp. 379-392
-
-
Paci, E.1
Vendruscolo, M.2
Karplus, M.3
-
60
-
-
48249138078
-
Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding
-
Zarrine-Afsart, A.; Wallin, S.; Neculai, A.M.; Neudecker, P.; Howell, P.L.; Davidson, A.R.; Chan, H.S. Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding. Proc. Natl. Acad. Sci. USA 2008, 705, 9999-10004.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.705
, pp. 9999-10004
-
-
Zarrine-Afsart, A.1
Wallin, S.2
Neculai, A.M.3
Neudecker, P.4
Howell, P.L.5
Davidson, A.R.6
Chan, H.S.7
-
61
-
-
61549141060
-
Native topology of the designed protein Top7 is not conducive to cooperative folding
-
Zhang, Z.; Chan, H.S. Native topology of the designed protein Top7 is not conducive to cooperative folding. Biophys. J. 2009, 96, L25-L27.
-
(2009)
Biophys. J
, vol.96
-
-
Zhang, Z.1
Chan, H.S.2
-
62
-
-
34547362785
-
Effects of frustration, confinement, and surface interactions on the dimerization of an off-lattice beta-barrel protein
-
Griffin, M.A.; Friedel, M.; Shea, J.E. Effects of frustration, confinement, and surface interactions on the dimerization of an off-lattice beta-barrel protein. J. Chem. Phys. 2005, 723, 174707.
-
(2005)
J. Chem. Phys
, vol.723
, pp. 174707
-
-
Griffin, M.A.1
Friedel, M.2
Shea, J.E.3
-
63
-
-
0031475159
-
Folding thermodynamics of a model hree-helix-bundle protein
-
Zhou, Y.Q.; Karplus, M. Folding thermodynamics of a model hree-helix-bundle protein. Proc. Natl. Acad. Sci. USA 1997, 94, 14429-14432.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 14429-14432
-
-
Zhou, Y.Q.1
Karplus, M.2
-
64
-
-
4644340168
-
Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: How far can a minimalist model go?
-
Matysiak, S.; Clementi, C. Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: How far can a minimalist model go? J. Mol. Biol. 2004, 343, 235-248.
-
(2004)
J. Mol. Biol
, vol.343
, pp. 235-248
-
-
Matysiak, S.1
Clementi, C.2
-
65
-
-
0000007199
-
On the role of conformational geometry in protein folding
-
Du, R.; Pande, V.S.; Grosberg, A.Y.; Tanaka, T.; Shakhnovich, E. On the role of conformational geometry in protein folding. J. Chem. Phys. 1999, 111, 10375-10380.
-
(1999)
J. Chem. Phys
, vol.111
, pp. 10375-10380
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, E.5
-
66
-
-
0042510944
-
Contact order revisited: Influence of protein size on the folding rate
-
Ivankov, D.N.; Garbuzynskiy, S.O.; Alm, E.; Plaxco, K.W.; Baker, D.; Finkelstein, A.V. Contact order revisited: Influence of protein size on the folding rate. Protein Sci. 2003, 12, 2057-2062.
-
(2003)
Protein Sci
, vol.12
, pp. 2057-2062
-
-
Ivankov, D.N.1
Garbuzynskiy, S.O.2
Alm, E.3
Plaxco, K.W.4
Baker, D.5
Finkelstein, A.V.6
-
67
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco, K.W.; Simons, K.T.; Baker, D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 1998, 277, 985-994.
-
(1998)
J. Mol. Biol
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
68
-
-
14644435825
-
Intrinsically unstructured proteins and their functions
-
Dyson, H.J.; Wright, P.E. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 2005, 6, 197-208.
-
(2005)
Nat. Rev. Mol. Cell Biol
, vol.6
, pp. 197-208
-
-
Dyson, H.J.1
Wright, P.E.2
-
69
-
-
0037397705
-
Emerging ideas on the molecular basis of protein and peptide aggregation
-
Thirumalai, D.; Klimov, D.K.; Dima, R.I. Emerging ideas on the molecular basis of protein and peptide aggregation. Curr. Opin. Struct. Biol. 2003, 13, 146-159.
-
(2003)
Curr. Opin. Struct. Biol
, vol.13
, pp. 146-159
-
-
Thirumalai, D.1
Klimov, D.K.2
Dima, R.I.3
-
70
-
-
33745712768
-
Sequence of events in folding mechanism: Beyond the Go model
-
Sutto, L.; Tiana, G.; Broglia, R.A. Sequence of events in folding mechanism: Beyond the Go model. Protein Sci. 2006, 15, 1638-1652.
-
(2006)
Protein Sci
, vol.15
, pp. 1638-1652
-
-
Sutto, L.1
Tiana, G.2
Broglia, R.A.3
-
71
-
-
0242662235
-
Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis
-
Khare, S.D.; Ding, F.; Dokholyan, N.V. Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis. J. Mol. Biol. 2003, 334, 515-525.
-
(2003)
J. Mol. Biol
, vol.334
, pp. 515-525
-
-
Khare, S.D.1
Ding, F.2
Dokholyan, N.V.3
-
72
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
Miyazawa, S.; Jernigan, R.L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 1996, 256, 623-644.
-
(1996)
J. Mol. Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
73
-
-
51849142374
-
Crystallographic B-factors highlight energetic frustration in aldolase folding
-
Rao, M.K.; Chapman, T.R.; Finke, J.M. Crystallographic B-factors highlight energetic frustration in aldolase folding. J. Phys. Chem. B 2008, 112, 10417-10431.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 10417-10431
-
-
Rao, M.K.1
Chapman, T.R.2
Finke, J.M.3
-
74
-
-
9944258521
-
New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate
-
Dixon, R.D.S.; Chen, Y.W.; Feng, D.; Khare, S.D.; Prutzman, K.C.; Schaller, M.D.; Campbell, S.L.; Dokholyan, N.V. New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate. Structure 2004, 12, 2161-2171.
-
(2004)
Structure
, vol.12
, pp. 2161-2171
-
-
Dixon, R.D.S.1
Chen, Y.W.2
Feng, D.3
Khare, S.D.4
Prutzman, K.C.5
Schaller, M.D.6
Campbell, S.L.7
Dokholyan, N.V.8
-
75
-
-
0037459022
-
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein L
-
Clementi, C.; Garcia, A.E.; Onuchic, J.N. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein L. J. Mol. Biol. 2003, 326, 933-954.
-
(2003)
J. Mol. Biol
, vol.326
, pp. 933-954
-
-
Clementi, C.1
Garcia, A.E.2
Onuchic, J.N.3
-
76
-
-
33947642689
-
The mechanical unfolding of ubiquitin through all-atom Monte Carlo simulation with a Go-type potential
-
Kleiner, A.; Shakhnovich, E. The mechanical unfolding of ubiquitin through all-atom Monte Carlo simulation with a Go-type potential. Biophys. J. 2007, 92, 2054-2061.
-
(2007)
Biophys. J
, vol.92
, pp. 2054-2061
-
-
Kleiner, A.1
Shakhnovich, E.2
-
77
-
-
33745570919
-
The equilibrium properties and folding kinetics of an all- atom Go model of the Trp-cage
-
Linhananta, A.; Boer, J.; MacKay, I. The equilibrium properties and folding kinetics of an all- atom Go model of the Trp-cage. J. Chem. Phys. 2005, 122, 114901.
-
(2005)
J. Chem. Phys
, vol.122
, pp. 114901
-
-
Linhananta, A.1
Boer, J.2
MacKay, I.3
-
78
-
-
0037113227
-
The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Go model of fragment B of Staphylococcal protein A
-
Linhananta, A.; Zhou, Y.Q. The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Go model of fragment B of Staphylococcal protein A. J. Chem. Phys. 2002, 117, 8983-8995.
-
(2002)
J. Chem. Phys
, vol.117
, pp. 8983-8995
-
-
Linhananta, A.1
Zhou, Y.Q.2
-
79
-
-
34547662125
-
Protein simulations combining an all-atom force field with a Go term
-
Meinke, J.H.; Hansmann, U.H.E. Protein simulations combining an all-atom force field with a Go term. J. Phys.-Condes. Matter 2007, 19, 285215.
-
(2007)
J. Phys.-Condes. Matter
, vol.19
, pp. 285215
-
-
Meinke, J.H.1
Hansmann, U.H.E.2
-
80
-
-
0035917318
-
The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation
-
Shimada, J.; Kussell, E.L.; Shakhnovich, E.I. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J. Mol. Biol. 2001, 308, 79-95.
-
(2001)
J. Mol. Biol
, vol.308
, pp. 79-95
-
-
Shimada, J.1
Kussell, E.L.2
Shakhnovich, E.I.3
-
81
-
-
0037143694
-
The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation
-
Shimada, J.; Shakhnovich, E.I. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc. Natl. Acad. Sci. USA 2002, 99, 11175-11180.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 11175-11180
-
-
Shimada, J.1
Shakhnovich, E.I.2
-
82
-
-
0037075457
-
Thermodynamics of an all-atom off-lattice model of the fragment B of Staphylococcal protein A: Implication for the origin of the cooperativity of protein folding
-
Zhou, Y.Q.; Linhananta, A. Thermodynamics of an all-atom off-lattice model of the fragment B of Staphylococcal protein A: Implication for the origin of the cooperativity of protein folding. J. Phys. Chem. B 2002, 706, 1481-1485.
-
(2002)
J. Phys. Chem. B
, vol.706
, pp. 1481-1485
-
-
Zhou, Y.Q.1
Linhananta, A.2
-
83
-
-
34548778164
-
Temperature-dependent folding pathways of pin1 WW domain: An all-atom molecular dynamics simulation of a Go model
-
Luo, Z.L.; Ding, J.D.; Zhou, Y.Q. Temperature-dependent folding pathways of pin1 WW domain: An all-atom molecular dynamics simulation of a Go model. Biophys. J. 2007, 93, 2152-2161.
-
(2007)
Biophys. J
, vol.93
, pp. 2152-2161
-
-
Luo, Z.L.1
Ding, J.D.2
Zhou, Y.Q.3
-
84
-
-
45449083495
-
Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations
-
Luo, Z.L.; Ding, J.D.; Zhou, Y.Q. Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations. J. Chem. Phys. 2008, 725, 225103.
-
(2008)
J. Chem. Phys
, vol.725
, pp. 225103
-
-
Luo, Z.L.1
Ding, J.D.2
Zhou, Y.Q.3
-
85
-
-
63449135082
-
An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields
-
In press, doi:10.1002/prot.22253
-
Whitford, P.C.; Noel, J.K.; Gosavi, S.; Schug, A.; Sanbonmatsu, K.Y.; Onuchic, J.N. An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields. Proteins. In press, 2009, doi:10.1002/prot.22253.
-
(2009)
Proteins
-
-
Whitford, P.C.1
Noel, J.K.2
Gosavi, S.3
Schug, A.4
Sanbonmatsu, K.Y.5
Onuchic, J.N.6
-
86
-
-
58149173184
-
-
Hills, R.D., Jr.; Brooks, C.L., III. Coevolution of function and the folding landscape: Correlation with density of native contacts. Biophys. J. 2008, 95, L57-L59.
-
Hills, R.D., Jr.; Brooks, C.L., III. Coevolution of function and the folding landscape: Correlation with density of native contacts. Biophys. J. 2008, 95, L57-L59.
-
-
-
-
87
-
-
84898207973
-
-
Hills, R.D., Jr.; Kathuria, S.V.; Wallace, L.A.; Matthews, C.R.; Brooks, C.L., III. Functional diversity and shifting cores of stability modulate the folding mechanisms of flavodoxin fold proteins. J. Mol. Biol. 2009, Pending publication.
-
Hills, R.D., Jr.; Kathuria, S.V.; Wallace, L.A.; Matthews, C.R.; Brooks, C.L., III. Functional diversity and shifting cores of stability modulate the folding mechanisms of flavodoxin fold proteins. J. Mol. Biol. 2009, Pending publication.
-
-
-
-
88
-
-
50049084050
-
Kinetic traps in the folding of beta alpha-repeat proteins: CheY initially misfolds before accessing the native conformation
-
Kathuria, S.V.; Day, I.J.; Wallace, L.A.; Matthews, C.R. Kinetic traps in the folding of beta alpha-repeat proteins: CheY initially misfolds before accessing the native conformation. J. Mol. Biol. 2008, 352, 467-484.
-
(2008)
J. Mol. Biol
, vol.352
, pp. 467-484
-
-
Kathuria, S.V.1
Day, I.J.2
Wallace, L.A.3
Matthews, C.R.4
-
89
-
-
0030334834
-
Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2
-
LopezHernandez, E.; Serrano, L. Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. Fold. Des. 1996, 7, 43-55.
-
(1996)
Fold. Des
, vol.7
, pp. 43-55
-
-
LopezHernandez, E.1
Serrano, L.2
-
90
-
-
0001563395
-
On the transition coordinate for protein folding
-
Du, R.; Pande, V.S.; Grosberg, A.Y.; Tanaka, T.; Shakhnovich, E.S. On the transition coordinate for protein folding. J. Chem. Phys. 1998, 705, 334-350.
-
(1998)
J. Chem. Phys
, vol.705
, pp. 334-350
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, E.S.5
-
91
-
-
33745744079
-
Kinetic definition of protein folding transition state ensembles and reaction coordinates
-
Snow, C.D.; Rhee, Y.M.; Pande, V.S. Kinetic definition of protein folding transition state ensembles and reaction coordinates. Biophys. J. 2006, 97, 14-24.
-
(2006)
Biophys. J
, vol.97
, pp. 14-24
-
-
Snow, C.D.1
Rhee, Y.M.2
Pande, V.S.3
-
92
-
-
31444452031
-
P versus Q: Structural reaction coordinates capture protein folding on smooth landscapes
-
Cho, S.S.; Levy, Y.; Wolynes, P.G. P versus Q: Structural reaction coordinates capture protein folding on smooth landscapes. Proc. Natl. Acad. Sci. USA 2006, 703, 586-591.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.703
, pp. 586-591
-
-
Cho, S.S.1
Levy, Y.2
Wolynes, P.G.3
-
93
-
-
56249105081
-
Advillin folding takes place on a hypersurface of small dimensionality
-
Piana, S.; Laio, A. Advillin folding takes place on a hypersurface of small dimensionality. Phys. Rev. Lett. 2008, 707, 208101.
-
(2008)
Phys. Rev. Lett
, vol.707
, pp. 208101
-
-
Piana, S.1
Laio, A.2
-
94
-
-
58149146888
-
Rate constant and reaction coordinate of Trp-cage folding in explicit water
-
Juraszek, J.; Bolhuis, P.G. Rate constant and reaction coordinate of Trp-cage folding in explicit water. Biophys. J. 2008, 95, 4246-4257.
-
(2008)
Biophys. J
, vol.95
, pp. 4246-4257
-
-
Juraszek, J.1
Bolhuis, P.G.2
-
95
-
-
33646931471
-
Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
-
Shakhnovich, E. Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet. Chem. Rev. 2006, 706, 1559-1588.
-
(2006)
Chem. Rev
, vol.706
, pp. 1559-1588
-
-
Shakhnovich, E.1
-
96
-
-
0000630681
-
Protein folding bottlenecks: A lattice Monte-Carlo simulation
-
Shakhnovich, E.; Farztdinov, G.; Gutin, A.M.; Karplus, M. Protein folding bottlenecks: A lattice Monte-Carlo simulation. Phys. Rev. Lett. 1991, 67, 1665-1668.
-
(1991)
Phys. Rev. Lett
, vol.67
, pp. 1665-1668
-
-
Shakhnovich, E.1
Farztdinov, G.2
Gutin, A.M.3
Karplus, M.4
-
97
-
-
56349146048
-
Characterization of protein folding by dominant reaction pathways
-
Faccioli, P. Characterization of protein folding by dominant reaction pathways. J. Phys. Chem. B 2008, 772, 13756-13764.
-
(2008)
J. Phys. Chem. B
, vol.772
, pp. 13756-13764
-
-
Faccioli, P.1
-
98
-
-
0034692882
-
Towards understanding a molecular switch mechanism: Thermodynamic and crystallographic studies of the signal transduction protein CheY
-
Sola, M.; Lopez-Hernandez, E.; Cronet, P.; Lacroix, E.; Serrano, L.; Coll, M.; Parraga, A. Towards understanding a molecular switch mechanism: Thermodynamic and crystallographic studies of the signal transduction protein CheY. J. Mol. Biol. 2000, 303, 213-225.
-
(2000)
J. Mol. Biol
, vol.303
, pp. 213-225
-
-
Sola, M.1
Lopez-Hernandez, E.2
Cronet, P.3
Lacroix, E.4
Serrano, L.5
Coll, M.6
Parraga, A.7
-
99
-
-
33750478377
-
A new perspective on response regulator activation
-
Stock, A.M.; Guhaniyogi, J. A new perspective on response regulator activation. J. Bacteriol.2006, 188, 7328-7330.
-
(2006)
J. Bacteriol
, vol.188
, pp. 7328-7330
-
-
Stock, A.M.1
Guhaniyogi, J.2
-
100
-
-
33745471490
-
The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state
-
Varughese, K.I.; Tsigelny, I.; Zhao, H.Y. The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state. J. Bacteriol. 2006, 188, 4970-4977.
-
(2006)
J. Bacteriol
, vol.188
, pp. 4970-4977
-
-
Varughese, K.I.1
Tsigelny, I.2
Zhao, H.Y.3
-
101
-
-
0035937443
-
Two-state allosteric behavior in a single- domain signaling protein
-
Volkman, B.F.; Lipson, D.; Wemmer, D.E.; Kern, D. Two-state allosteric behavior in a single- domain signaling protein. Science 2001, 291, 2429-2433.
-
(2001)
Science
, vol.291
, pp. 2429-2433
-
-
Volkman, B.F.1
Lipson, D.2
Wemmer, D.E.3
Kern, D.4
-
102
-
-
34247639886
-
Exploring subdomain cooperativity in T4 lysozyme II: Uncovering the C-terminal subdomain as a hidden intermediate in the kinetic folding pathway
-
Cellitti, J.; Bernstein, R.; Marqusee, S. Exploring subdomain cooperativity in T4 lysozyme II: Uncovering the C-terminal subdomain as a hidden intermediate in the kinetic folding pathway. Protein Sci. 2007, 16, 852-862.
-
(2007)
Protein Sci
, vol.16
, pp. 852-862
-
-
Cellitti, J.1
Bernstein, R.2
Marqusee, S.3
-
103
-
-
58849083668
-
Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics
-
Cho, S.S.; Levy, Y.; Wolynes, P.G. Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics. Proc. Natl. Acad. Sci. USA 2009, 106, 434-439.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 434-439
-
-
Cho, S.S.1
Levy, Y.2
Wolynes, P.G.3
-
104
-
-
0037022347
-
Flexibility and packing in proteins
-
Halle, B. Flexibility and packing in proteins. Proc. Natl. Acad. Sci. USA 2002, 99, 1274-1279.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 1274-1279
-
-
Halle, B.1
-
105
-
-
34047157022
-
Hydrophobic cooperativity as a mechanism for amyloid nucleation
-
Hills, R.D., Jr.; Brooks, C.L., III. Hydrophobic cooperativity as a mechanism for amyloid nucleation. J. Mol. Biol. 2007, 368, 894-901.
-
(2007)
J. Mol. Biol
, vol.368
, pp. 894-901
-
-
Hills Jr., R.D.1
Brooks III, C.L.2
-
106
-
-
34447270231
-
Hydrophobic, hydrophilic, and charged amino acid networks within protein
-
Aftabuddin, M.; Kundu, S. Hydrophobic, hydrophilic, and charged amino acid networks within protein. Biophys. J. 2007, 93, 225-231.
-
(2007)
Biophys. J
, vol.93
, pp. 225-231
-
-
Aftabuddin, M.1
Kundu, S.2
-
107
-
-
0346057951
-
Small-world communication of residues and significance for protein dynamics
-
Atilgan, A.R.; Akan, P.; Baysal, C. Small-world communication of residues and significance for protein dynamics. Biophys. J. 2004, 86, 85-91.
-
(2004)
Biophys. J
, vol.86
, pp. 85-91
-
-
Atilgan, A.R.1
Akan, P.2
Baysal, C.3
-
108
-
-
34249910312
-
Network analysis of protein dynamics
-
Bode, C.; Kovacs, I.A.; Szalay, M.S.; Palotai, R.; Korcsmaros, T.; Csermely, P. Network analysis of protein dynamics. FEBS Lett. 2007, 581, 2776-2782.
-
(2007)
FEBS Lett
, vol.581
, pp. 2776-2782
-
-
Bode, C.1
Kovacs, I.A.2
Szalay, M.S.3
Palotai, R.4
Korcsmaros, T.5
Csermely, P.6
-
109
-
-
0037173002
-
Topological determinants of protein folding
-
Dokholyan, N.V.; Li, L.; Ding, F.; Shakhnovich, E.I. Topological determinants of protein folding. Proc. Natl. Acad. Sci. USA 2002, 99, 8637-8641.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 8637-8641
-
-
Dokholyan, N.V.1
Li, L.2
Ding, F.3
Shakhnovich, E.I.4
-
110
-
-
0242720597
-
Uncovering network systems within protein structures
-
Greene, L.H.; Higman, V.A. Uncovering network systems within protein structures. J. Mol. Biol. 2003, 334, 781-791.
-
(2003)
J. Mol. Biol
, vol.334
, pp. 781-791
-
-
Greene, L.H.1
Higman, V.A.2
-
111
-
-
33744827386
-
Elucidation of conserved long-range interaction networks in proteins and their significance in determining protein topology
-
Higman, V.A.; Greene, L.H. Elucidation of conserved long-range interaction networks in proteins and their significance in determining protein topology. Physica A 2006, 368, 595-606.
-
(2006)
Physica A
, vol.368
, pp. 595-606
-
-
Higman, V.A.1
Greene, L.H.2
-
112
-
-
41349118690
-
Small-world view of the amino acids that play a key role in protein folding
-
061910-1-4
-
Vendruscolo, M.; Dokholyan, N.V.; Paci, E.; Karplus, M. Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E 2002, 65, 061910-1-4.
-
(2002)
Phys. Rev. E
, vol.65
-
-
Vendruscolo, M.1
Dokholyan, N.V.2
Paci, E.3
Karplus, M.4
-
113
-
-
63449085279
-
-
113, Pending publication
-
113.Kathuria, S.V.; Matthews, C.R. Clusters of isoleucine, leucine and valine side chains define cores of stability in globular proteins: Sequence determinants of structure, stability and folding. 2009, Pending publication.
-
(2009)
Clusters of isoleucine, leucine and valine side chains define cores of stability in globular proteins: Sequence determinants of structure, stability and folding
-
-
Kathuria, S.V.1
Matthews, C.R.2
-
114
-
-
33846829720
-
A tightly packed hydrophobic cluster directs the formation of an off-pathway sub-millisecond folding intermediate in the alpha subunit of tryptophan synthase, a TIM barrel protein
-
Wu, Y.; Vadrevu, R.; Kathuria, S.; Yang, X.Y.; Matthews, C.R. A tightly packed hydrophobic cluster directs the formation of an off-pathway sub-millisecond folding intermediate in the alpha subunit of tryptophan synthase, a TIM barrel protein. J. Mol. Biol. 2007, 366, 1624-1638.
-
(2007)
J. Mol. Biol
, vol.366
, pp. 1624-1638
-
-
Wu, Y.1
Vadrevu, R.2
Kathuria, S.3
Yang, X.Y.4
Matthews, C.R.5
-
115
-
-
0030580089
-
Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors
-
Hilser, V.J.; Freire, E. Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J. Mol. Biol. 1996, 262, 756-772.
-
(1996)
J. Mol. Biol
, vol.262
, pp. 756-772
-
-
Hilser, V.J.1
Freire, E.2
-
116
-
-
0033613255
-
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
-
Alm, E.; Baker, D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl. Acad. Sci. USA 1999, 96, 11305-11310.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11305-11310
-
-
Alm, E.1
Baker, D.2
-
117
-
-
0033613131
-
A theoretical search for folding/unfolding nuclei in three- dimensional protein structures
-
Galzitskaya, O.V.; Finkelstein, A.V. A theoretical search for folding/unfolding nuclei in three- dimensional protein structures. Proc. Natl. Acad. Sci. USA 1999, 96, 11299-11304.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11299-11304
-
-
Galzitskaya, O.V.1
Finkelstein, A.V.2
-
118
-
-
0242330738
-
The importance of explicit chain representation in protein folding models: An examination of Ising-like models
-
Karanicolas, J.; Brooks, C.L., III. The importance of explicit chain representation in protein folding models: An examination of Ising-like models. Proteins 2003, 53, 740-747.
-
(2003)
Proteins
, vol.53
, pp. 740-747
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
119
-
-
0033613165
-
A simple model for calculating the kinetics of protein folding from three-dimensional structures
-
Munoz, V.; Eaton, W.A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl. Acad. Sci. USA 1999, 96, 11311-11316.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11311-11316
-
-
Munoz, V.1
Eaton, W.A.2
-
120
-
-
0032742688
-
Go-ing for the prediction of protein folding mechanisms
-
Takada, S. Go-ing for the prediction of protein folding mechanisms. Proc. Natl. Acad. Sci. USA 1999, 96, 11698-11700.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11698-11700
-
-
Takada, S.1
-
121
-
-
0037079578
-
Dynamics of large proteins through hierarchical levels of coarse-grained structures
-
Doruker, P.; Jernigan, R.L.; Bahar, I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 2002, 23, 119-127.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 119-127
-
-
Doruker, P.1
Jernigan, R.L.2
Bahar, I.3
-
122
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama, F.; Sanejouand, Y.H. Conformational change of proteins arising from normal mode calculations. Protein Eng. 2001, 74, 1-6.
-
(2001)
Protein Eng
, vol.74
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
123
-
-
33646145523
-
Can conformational change be described by only a few normal modes?
-
Petrone, P.; Pande, V.S. Can conformational change be described by only a few normal modes? Biophys. J. 2006, 90, 1583-1593.
-
(2006)
Biophys. J
, vol.90
, pp. 1583-1593
-
-
Petrone, P.1
Pande, V.S.2
-
124
-
-
33745024278
-
Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
-
Tama, F.; Brooks, C.L., III. Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines. Annu. Rev. Biophys. Biomolec. Struct. 2006, 35, 115-133.
-
(2006)
Annu. Rev. Biophys. Biomolec. Struct
, vol.35
, pp. 115-133
-
-
Tama, F.1
Brooks III, C.L.2
-
125
-
-
34547666968
-
How well can we understand large-scale protein motions using normal modes of elastic network models?
-
Yang, L.; Song, G.; Jernigan, R.L. How well can we understand large-scale protein motions using normal modes of elastic network models? Biophys. J. 2007, 93, 920-929.
-
(2007)
Biophys. J
, vol.93
, pp. 920-929
-
-
Yang, L.1
Song, G.2
Jernigan, R.L.3
-
126
-
-
0036470527
-
Residue packing in proteins: Uniform distribution on a coarse-grained scale
-
Bagci, Z.; Jernigan, R.L.; Bahar, I. Residue packing in proteins: Uniform distribution on a coarse-grained scale. J. Chem. Phys. 2002, 776, 2269-2276.
-
(2002)
J. Chem. Phys
, vol.776
, pp. 2269-2276
-
-
Bagci, Z.1
Jernigan, R.L.2
Bahar, I.3
-
127
-
-
0034029144
-
Proteins with similar architecture exhibit similar large-scale dynamic behavior
-
Keskin, O.; Jernigan, R.L.; Bahar, I. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys. J. 2000, 75, 2093-2106.
-
(2000)
Biophys. J
, vol.75
, pp. 2093-2106
-
-
Keskin, O.1
Jernigan, R.L.2
Bahar, I.3
-
128
-
-
25844525600
-
The role of shape in determining molecular motions
-
Lu, M.Y.; Ma, J.P. The role of shape in determining molecular motions. Biophys. J. 2005, 59, 2395-2401.
-
(2005)
Biophys. J
, vol.59
, pp. 2395-2401
-
-
Lu, M.Y.1
Ma, J.P.2
-
129
-
-
24644483073
-
Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
-
Maragakis, P.; Karplus, M. Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase. J. Mol. Biol. 2005, 352, 807-822.
-
(2005)
J. Mol. Biol
, vol.352
, pp. 807-822
-
-
Maragakis, P.1
Karplus, M.2
-
130
-
-
36849057606
-
Coarse-grained free energy functions for studying protein conformational changes: A double-well network model
-
Chu, J.W.; Voth, G.A. Coarse-grained free energy functions for studying protein conformational changes: A double-well network model. Biophys. J. 2007, 93, 3860-3871.
-
(2007)
Biophys. J
, vol.93
, pp. 3860-3871
-
-
Chu, J.W.1
Voth, G.A.2
-
131
-
-
28844466824
-
Slow protein conformational dynamics from multiple experimental structures: The helix/sheet transition of arc repressor
-
Best, R.B.; Chen, Y.G.; Hummer, G. Slow protein conformational dynamics from multiple experimental structures: The helix/sheet transition of arc repressor. Structure 2005, 73, 1755-1763.
-
(2005)
Structure
, vol.73
, pp. 1755-1763
-
-
Best, R.B.1
Chen, Y.G.2
Hummer, G.3
-
132
-
-
33645770731
-
Folding-based molecular simulations reveal mechanisms of the rotary motor F-1-ATPase
-
Koga, N.; Takada, S. Folding-based molecular simulations reveal mechanisms of the rotary motor F-1-ATPase. Proc. Natl. Acad. Sci. USA 2006, 703, 5367-5372.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.703
, pp. 5367-5372
-
-
Koga, N.1
Takada, S.2
-
133
-
-
36849006430
-
Structural change and nucleotide dissociation of myosin motor domain: Dual Go model simulation
-
Takagi, F.; Kikuchi, M. Structural change and nucleotide dissociation of myosin motor domain: Dual Go model simulation. Biophys. J. 2007, 93, 3820-3827.
-
(2007)
Biophys. J
, vol.93
, pp. 3820-3827
-
-
Takagi, F.1
Kikuchi, M.2
-
134
-
-
0037216990
-
Universality classes in folding times of proteins
-
Cieplak, M.; Hoang, T.X. Universality classes in folding times of proteins. Biophys. J. 2003, 54, 475-488.
-
(2003)
Biophys. J
, vol.54
, pp. 475-488
-
-
Cieplak, M.1
Hoang, T.X.2
-
135
-
-
0037459035
-
Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling?
-
Kaya, H.; Chan, H.S. Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling? J. Mol. Biol. 2003, 326, 911-931.
-
(2003)
J. Mol. Biol
, vol.326
, pp. 911-931
-
-
Kaya, H.1
Chan, H.S.2
-
136
-
-
19444381093
-
Chevron Behavior and isostable enthalpic barriers in protein folding: Successes and limitations of simple Go-like modeling
-
Kaya, H.; Liu, Z.R.; Chan, H.S. Chevron Behavior and isostable enthalpic barriers in protein folding: Successes and limitations of simple Go-like modeling. Biophys. J. 2005, 89, 520-535.
-
(2005)
Biophys. J
, vol.89
, pp. 520-535
-
-
Kaya, H.1
Liu, Z.R.2
Chan, H.S.3
-
137
-
-
52649084160
-
Simulations of the protein folding process using topology-based models depend on the experimental structure
-
Prieto, L.; Rey, A. Simulations of the protein folding process using topology-based models depend on the experimental structure. J. Chem. Phys. 2008, 129, 115101.
-
(2008)
J. Chem. Phys
, vol.129
, pp. 115101
-
-
Prieto, L.1
Rey, A.2
-
138
-
-
63449085891
-
Topology-based models and NMR structures in protein folding simulations
-
In press, doi:10.1002/jcc.21149
-
Rey-Stolle, M.F.; Enciso, M.; Rey, A. Topology-based models and NMR structures in protein folding simulations. J. Comp. Chem. In press. 2009, doi:10.1002/jcc.21149.
-
(2009)
J. Comp. Chem
-
-
Rey-Stolle, M.F.1
Enciso, M.2
Rey, A.3
-
139
-
-
0034753250
-
Role of native-state topology in the stabilization of intracellular antibodies
-
Settanni, G.; Cattaneo, A.; Maritan, A. Role of native-state topology in the stabilization of intracellular antibodies. Biophys. J. 2001, 81, 2935-2945.
-
(2001)
Biophys. J
, vol.81
, pp. 2935-2945
-
-
Settanni, G.1
Cattaneo, A.2
Maritan, A.3
-
140
-
-
0037154268
-
Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
-
Cheung, M.S.; Garcia, A.E.; Onuchic, J.N. Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl. Acad. Sci. USA 2002, 99, 685-690.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 685-690
-
-
Cheung, M.S.1
Garcia, A.E.2
Onuchic, J.N.3
-
141
-
-
34547251863
-
Self-assembly of beta-sheet forming peptides into chiral fibrillar aggregates
-
Bellesia, G.; Shea, J.E. Self-assembly of beta-sheet forming peptides into chiral fibrillar aggregates. J. Chem. Phys. 2007, 126, 245104.
-
(2007)
J. Chem. Phys
, vol.126
, pp. 245104
-
-
Bellesia, G.1
Shea, J.E.2
-
142
-
-
44049099816
-
Protofibril assemblies of the arctic, dutch, and flemish mutants of the Alzheimer's A beta(1-40) peptide
-
Fawzi, N.L.; Kohlstedt, K.L.; Okabe, Y.; Head-Gordon, T. Protofibril assemblies of the arctic, dutch, and flemish mutants of the Alzheimer's A beta(1-40) peptide. Biophys. J. 2008, 94, 2007-2016.
-
(2008)
Biophys. J
, vol.94
, pp. 2007-2016
-
-
Fawzi, N.L.1
Kohlstedt, K.L.2
Okabe, Y.3
Head-Gordon, T.4
-
143
-
-
33244456166
-
Spontaneous fibril formation by polyalanines; Discontinuous molecular dynamics simulations
-
Nguyen, H.D.; Hall, C.K. Spontaneous fibril formation by polyalanines; Discontinuous molecular dynamics simulations. J. Am. Chem. Soc. 2006, 128, 1890-1901.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 1890-1901
-
-
Nguyen, H.D.1
Hall, C.K.2
-
144
-
-
33847712647
-
Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids
-
Nguyen, H.D.; Reddy, V.S.; Brooks, C.L., III. Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids. Nano Lett. 2007, 7, 338-344.
-
(2007)
Nano Lett
, vol.7
, pp. 338-344
-
-
Nguyen, H.D.1
Reddy, V.S.2
Brooks III, C.L.3
-
145
-
-
33747095897
-
Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment
-
Cieplak, M.; Filipek, S.; Janovjak, H.; Krzysko, K.A. Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochim. Biophys. Acta-Biomembr. 2006, 1758, 537-544.
-
(2006)
Biochim. Biophys. Acta-Biomembr
, vol.1758
, pp. 537-544
-
-
Cieplak, M.1
Filipek, S.2
Janovjak, H.3
Krzysko, K.A.4
-
146
-
-
0036783398
-
Folding and stretching in a Go-like model of titin
-
Cieplak, M.; Hoang, T.X.; Robbins, M.O. Folding and stretching in a Go-like model of titin. Proteins 2002, 49, 114-124.
-
(2002)
Proteins
, vol.49
, pp. 114-124
-
-
Cieplak, M.1
Hoang, T.X.2
Robbins, M.O.3
-
147
-
-
58149374561
-
Stabilizing effect of knots on proteins
-
Sulkowska, J.I.; Sulkowski, P.; Szymczak, P.; Cieplak, M. Stabilizing effect of knots on proteins. Proc. Natl. Acad. Sci. USA 2008, 105, 19714-19719.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 19714-19719
-
-
Sulkowska, J.I.1
Sulkowski, P.2
Szymczak, P.3
Cieplak, M.4
-
148
-
-
40549141130
-
Predicting the order in which contacts are broken during single molecule protein stretching experiments
-
Sulkowska, J.I.; Kloczkowski, A.; Sen, T.Z.; Cieplak, M.; Jernigan, R.L. Predicting the order in which contacts are broken during single molecule protein stretching experiments. Proteins 2008, 71, 45-60.
-
(2008)
Proteins
, vol.71
, pp. 45-60
-
-
Sulkowska, J.I.1
Kloczkowski, A.2
Sen, T.Z.3
Cieplak, M.4
Jernigan, R.L.5
-
149
-
-
33846460423
-
Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin
-
Li, M.S.; Kouza, M.; Hu, C.K. Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin. Biophys. J. 2007, 92, 547-561.
-
(2007)
Biophys. J
, vol.92
, pp. 547-561
-
-
Li, M.S.1
Kouza, M.2
Hu, C.K.3
-
150
-
-
34547673274
-
Mechanical stretching of proteins: A theoretical survey of the Protein Data Bank
-
Sulkowska, J.I.; Cieplak, M. Mechanical stretching of proteins: A theoretical survey of the Protein Data Bank. J. Phys.-Condes. Matter 2007, 19, 283201.
-
(2007)
J. Phys.-Condes. Matter
, vol.19
, pp. 283201
-
-
Sulkowska, J.I.1
Cieplak, M.2
-
151
-
-
33645277151
-
Molecular dynamics simulations of outer-membrane protease T from E-coli based on a hybrid coarse-grained/atomistic potential
-
Neri, M.; Anselmi, C.; Carnevale, V.; Vargiu, A.V.; Carloni, P. Molecular dynamics simulations of outer-membrane protease T from E-coli based on a hybrid coarse-grained/atomistic potential. J. Phys.-Condes. Matter 2006, 18, S347-S355.
-
(2006)
J. Phys.-Condes. Matter
, vol.18
-
-
Neri, M.1
Anselmi, C.2
Carnevale, V.3
Vargiu, A.V.4
Carloni, P.5
-
152
-
-
28844494903
-
Coarse-grained model of proteins incorporating atomistic detail of the active site
-
Neri, M.; Anselmi, C.; Cascella, M.; Maritan, A.; Carloni, P. Coarse-grained model of proteins incorporating atomistic detail of the active site. Phys. Rev. Lett. 2005, 95, 218102.
-
(2005)
Phys. Rev. Lett
, vol.95
, pp. 218102
-
-
Neri, M.1
Anselmi, C.2
Cascella, M.3
Maritan, A.4
Carloni, P.5
-
153
-
-
37749005024
-
Microseconds dynamics simulations of the outer-membrane protease T
-
Neri, M.; Baaden, M.; Carnevale, V.; Anselmi, C.; Maritan, A.; Carloni, P. Microseconds dynamics simulations of the outer-membrane protease T. Biophys. J. 2008, 94, 71-78.
-
(2008)
Biophys. J
, vol.94
, pp. 71-78
-
-
Neri, M.1
Baaden, M.2
Carnevale, V.3
Anselmi, C.4
Maritan, A.5
Carloni, P.6
-
154
-
-
23944448528
-
Protein oligomerization through domain swapping: Role of inter-molecular interactions and protein concentration
-
Yang, S.C.; Levine, H.; Onuchic, J.N. Protein oligomerization through domain swapping: Role of inter-molecular interactions and protein concentration. J. Mol. Biol. 2005, 352, 202-211.
-
(2005)
J. Mol. Biol
, vol.352
, pp. 202-211
-
-
Yang, S.C.1
Levine, H.2
Onuchic, J.N.3
-
155
-
-
50149092143
-
Crowded, celllike environment induces shape changes in aspherical protein
-
Homouz, D.; Perham, M.; Samiotakis, A.; Cheung, M.S.; Wittung-Stafshede, P. Crowded, celllike environment induces shape changes in aspherical protein. Proc. Natl. Acad. Sci. USA 2008, 105, 11754-11759.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 11754-11759
-
-
Homouz, D.1
Perham, M.2
Samiotakis, A.3
Cheung, M.S.4
Wittung-Stafshede, P.5
-
156
-
-
61749097701
-
Crowding effects on the mechanical stability and unfolding pathways of ubiquitin
-
Pincus, D.L.; Thirumalai, D. Crowding effects on the mechanical stability and unfolding pathways of ubiquitin. J. Phys. Chem. B 2009, 113, 359-368.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 359-368
-
-
Pincus, D.L.1
Thirumalai, D.2
-
157
-
-
33846625611
-
Fly-casting in protein-DNA binding: Frustration between protein folding and electrostatics facilitates target recognition
-
Levy, Y.; Onuchic, J.N.; Wolynes, P.G. Fly-casting in protein-DNA binding: Frustration between protein folding and electrostatics facilitates target recognition. J. Am. Chem. Soc. 2007, 129, 738-739.
-
(2007)
J. Am. Chem. Soc
, vol.129
, pp. 738-739
-
-
Levy, Y.1
Onuchic, J.N.2
Wolynes, P.G.3
-
158
-
-
38049165543
-
Localizing frustration in native proteins and protein assemblies
-
Ferreiro, D.U.; Hegler, J.A.; Komives, E.A.; Wolynes, P.G. Localizing frustration in native proteins and protein assemblies. Proc. Natl. Acad. Sci. USA 2007, 104, 19819-19824.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 19819-19824
-
-
Ferreiro, D.U.1
Hegler, J.A.2
Komives, E.A.3
Wolynes, P.G.4
-
159
-
-
48749113763
-
Extracting function from a beta-trefoil folding motif
-
Gosavi, S.; Whitford, P.C.; Jennings, P.A.; Onuchic, J.N. Extracting function from a beta-trefoil folding motif. Proc. Natl. Acad. Sci. USA 2008, 105, 10384-10389.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 10384-10389
-
-
Gosavi, S.1
Whitford, P.C.2
Jennings, P.A.3
Onuchic, J.N.4
-
160
-
-
33746042979
-
Structure-function-folding relationship in a WW domain
-
Jager, M.; Zhang, Y.; Bieschke, J.; Nguyen, H.; Dendle, M.; Bowman, M.E.; Noel, J.P.; Gruebele, M.; Kelly, J.W. Structure-function-folding relationship in a WW domain. Proc. Natl. Acad. Sci. USA 2006, 103, 10648-10653.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 10648-10653
-
-
Jager, M.1
Zhang, Y.2
Bieschke, J.3
Nguyen, H.4
Dendle, M.5
Bowman, M.E.6
Noel, J.P.7
Gruebele, M.8
Kelly, J.W.9
-
161
-
-
0242268469
-
Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
-
Miyashita, O.; Onuchic, J.N.; Wolynes, P.G. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc. Natl. Acad. Sci. USA 2003, 100, 12570-12575.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 12570-12575
-
-
Miyashita, O.1
Onuchic, J.N.2
Wolynes, P.G.3
-
162
-
-
13444305369
-
Simple energy landscape model for the kinetics of functional transitions in proteins
-
Miyashita, O.; Wolynes, P.G.; Onuchic, J.N. Simple energy landscape model for the kinetics of functional transitions in proteins. J. Phys. Chem. B 2005, 109, 1959-1969.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 1959-1969
-
-
Miyashita, O.1
Wolynes, P.G.2
Onuchic, J.N.3
-
163
-
-
33846847773
-
Conformational transitions of adenylate kinase: Switching by cracking
-
Whitford, P.C.; Miyashita, O.; Levy, Y.; Onuchic, J.N. Conformational transitions of adenylate kinase: Switching by cracking. J. Mol. Biol. 2007, 366, 1661-1671.
-
(2007)
J. Mol. Biol
, vol.366
, pp. 1661-1671
-
-
Whitford, P.C.1
Miyashita, O.2
Levy, Y.3
Onuchic, J.N.4
-
164
-
-
1542723482
-
Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain
-
Karanicolas, J.; Brooks, C.L., III. Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain. Proc. Natl. Acad. Sci. USA 2004, 101, 3432-3437.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 3432-3437
-
-
Karanicolas, J.1
Brooks III, C.L.2
|