-
1
-
-
0019571422
-
Noninteracting local-structure model of folding and unfolding transition in globular proteins. II. Application to two-dimensional lattice proteins
-
Abe, H. and Go, N. 1981. Noninteracting local-structure model of folding and unfolding transition in globular proteins. II. Application to two-dimensional lattice proteins. Biopolymers 20: 1013-1031.
-
(1981)
Biopolymers
, vol.20
, pp. 1013-1031
-
-
Abe, H.1
Go, N.2
-
2
-
-
0028024928
-
Specific nucleus as the transition state for protein folding: Evidence from the lattice model
-
Abkevich, V.I., Gutin, A.M., and Shakhnovich, E.I. 1994. Specific nucleus as the transition state for protein folding: Evidence from the lattice model. Biochemistry 33: 10026-10036.
-
(1994)
Biochemistry
, vol.33
, pp. 10026-10036
-
-
Abkevich, V.I.1
Gutin, A.M.2
Shakhnovich, E.I.3
-
3
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen, C. 1973. Principles that govern the folding of protein chains. Science 181: 223-230.
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.1
-
4
-
-
0032972986
-
Is protein folding hierarchic? I. Local structure and peptide folding
-
Baldwin, R.L. and Rose, G.D. 1999a. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem. Sci. 24: 26-33.
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 26-33
-
-
Baldwin, R.L.1
Rose, G.D.2
-
5
-
-
0033080081
-
Is protein folding hierarchic? II. Folding intermediates and transition states
-
-. 1999b. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem. Sci. 24: 77-83.
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 77-83
-
-
-
6
-
-
0000370391
-
The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
-
Becker, O.M. and Karplus, M. 1997. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics. J. Chem. Phys. 106: 1495-1517.
-
(1997)
J. Chem. Phys.
, vol.106
, pp. 1495-1517
-
-
Becker, O.M.1
Karplus, M.2
-
7
-
-
0037166875
-
Exact solution of the Munoz-Eaton model for protein folding
-
Bruscolini, P. and Pelizzola, A. 2002. Exact solution of the Munoz-Eaton model for protein folding. Phys. Rev. Lett. 88: 258101.
-
(2002)
Phys. Rev. Lett.
, vol.88
, pp. 258101
-
-
Bruscolini, P.1
Pelizzola, A.2
-
9
-
-
0003166498
-
Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics
-
Chan, H.S., and Dill, K.A. 1998. Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics. Proteins 30: 2-33.
-
(1998)
Proteins
, vol.30
, pp. 2-33
-
-
Chan, H.S.1
Dill, K.A.2
-
10
-
-
0000239504
-
Master equation approach to protein folding and kinetic traps
-
Cieplak, M., Henkel, M., Karbowski, J., and Banavar, J.R. 1998. Master equation approach to protein folding and kinetic traps. Phys. Rev. Lett. 80: 3654-3657.
-
(1998)
Phys. Rev. Lett.
, vol.80
, pp. 3654-3657
-
-
Cieplak, M.1
Henkel, M.2
Karbowski, J.3
Banavar, J.R.4
-
12
-
-
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., and Onuchic, J.N. 2000. 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. 298: 937-953.
-
(2000)
J. Mol. Biol.
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
13
-
-
0032570532
-
Folding intermediates of wild-type and mutants of barnase. I. Use of φ-value analysis and m values to probe the cooperative nature of the folding pre-equilibrium
-
Dalby, P.A., Oliveberg, M., and Fersht, A.R. 1998. Folding intermediates of wild-type and mutants of barnase. I. Use of φ-value analysis and m values to probe the cooperative nature of the folding pre-equilibrium. J. Mol. Biol. 276: 625-646.
-
(1998)
J. Mol. Biol.
, vol.276
, pp. 625-646
-
-
Dalby, P.A.1
Oliveberg, M.2
Fersht, A.R.3
-
14
-
-
0036927818
-
Direct molecular dynamics observation of protein folding transition state ensemble
-
Ding, F., Dokholyan, N.V., Buldyrev, S.V., Stanley, H.H., and Shakhnovich, E.I. 2002. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys. J. 83: 3525-3532.
-
(2002)
Biophys. J.
, vol.83
, pp. 3525-3532
-
-
Ding, F.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Stanley, H.H.4
Shakhnovich, E.I.5
-
15
-
-
0033529946
-
Understanding β-hairpin formation
-
Dinner, A., Lazardis, T., and Karplus, M. 1999. Understanding β-hairpin formation. Proc. Natl. Acad. Sci. 96: 9068-9073.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 9068-9073
-
-
Dinner, A.1
Lazardis, T.2
Karplus, M.3
-
16
-
-
0344301982
-
Protein folding: A perspective from theory and experiment
-
Dobson, C.M., Sali, A., and Karplus, M. 1998. Protein folding: A perspective from theory and experiment. Angew. Chem. Int. Ed. 37: 868-893.
-
(1998)
Angew. Chem. Int. Ed.
, vol.37
, pp. 868-893
-
-
Dobson, C.M.1
Sali, A.2
Karplus, M.3
-
17
-
-
0034628914
-
Identifying the protein folding nucleus using molecular dynamics simulations
-
Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E., and Shakhnovich, E.I. 2000. Identifying the protein folding nucleus using molecular dynamics simulations. J. Mol. Biol. 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
-
18
-
-
0000346442
-
The application of the theory of absolute reaction rates to proteins
-
Eyring, H. and Stern, A.E. 1939. The application of the theory of absolute reaction rates to proteins. Chem. Rev. 24: 253-270.
-
(1939)
Chem. Rev.
, vol.24
, pp. 253-270
-
-
Eyring, H.1
Stern, A.E.2
-
19
-
-
0031043161
-
Nucleation mechanisms in protein folding
-
Fersht, A.R. 1997. Nucleation mechanisms in protein folding. Curr. Opin. Struct. Biol. 7: 3-9.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 3-9
-
-
Fersht, A.R.1
-
21
-
-
0037062047
-
Energy landscape and native-state structure of proteins - A simplified model
-
Flammini, A., Banavar, J.R., and Maritan, A. 2002. Energy landscape and native-state structure of proteins-A simplified model. Europhys. Lett. 58: 623-629.
-
(2002)
Europhys. Lett.
, vol.58
, pp. 623-629
-
-
Flammini, A.1
Banavar, J.R.2
Maritan, A.3
-
22
-
-
0028868995
-
The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
-
Itzhaki, L.S., Otzen, D.E., and Fersht, A.R. 1995. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254: 260-288.
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 260-288
-
-
Itzhaki, L.S.1
Otzen, D.E.2
Fersht, A.R.3
-
23
-
-
0026345750
-
Folding of chymoptrypsin inhibitor 2. 1. Evidence for a two-state transition
-
Jackson, S.E. and Fersht, A.R. 1991. Folding of chymoptrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30: 10428-10435.
-
(1991)
Biochemistry
, vol.30
, pp. 10428-10435
-
-
Jackson, S.E.1
Fersht, A.R.2
-
24
-
-
0035836687
-
Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution
-
Kazmirski, S.L., Wong, K.-B., Freund, S.M.V., Tan, Y.-J., Fersht, A.R., and Daggett, V. 2001. Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution. Proc. Natl. Acad. Sci. 98: 4349-4354.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 4349-4354
-
-
Kazmirski, S.L.1
Wong, K.-B.2
Freund, S.M.V.3
Tan, Y.-J.4
Fersht, A.R.5
Daggett, V.6
-
25
-
-
0035370662
-
Multiple protein folding nuclei and the transition state ensemble in two-state proteins
-
Klimov, D.K. and Thirumalai, D. 2001. Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins 43: 465-475.
-
(2001)
Proteins
, vol.43
, pp. 465-475
-
-
Klimov, D.K.1
Thirumalai, D.2
-
26
-
-
0035956901
-
Solvent effects on the energy landscapes and folding kinetics of polyalanine
-
Levy, Y., Jortner, J., and Becker, O.M. 2001. Solvent effects on the energy landscapes and folding kinetics of polyalanine. Proc. Natl. Acad. Sci. 98: 2188-2193.
-
(2001)
Proc. Natl. Acad. Sci
, vol.98
, pp. 2188-2193
-
-
Levy, Y.1
Jortner, J.2
Becker, O.M.3
-
27
-
-
0028143603
-
Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2
-
Li, A. and Daggett, V. 1994. Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. 91: 10430-10434.
-
(1994)
Proc. Natl. Acad. Sci.
, vol.91
, pp. 10430-10434
-
-
Li, A.1
Daggett, V.2
-
28
-
-
0034112774
-
Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
-
Li, L., Mirny, A.L., and Shakhnovich, E.I. 2000. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat. Struct. Biol. 7: 336-342.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 336-342
-
-
Li, L.1
Mirny, A.L.2
Shakhnovich, E.I.3
-
29
-
-
0024358426
-
Mapping the transition state and pathway of protein folding by protein engineering
-
Matouschek, A., Kellis Jr., J.T., Serrano, L., and Fersht, A.R. 1989. Mapping the transition state and pathway of protein folding by protein engineering. Nature 342: 122-126.
-
(1989)
Nature
, vol.342
, pp. 122-126
-
-
Matouschek, A.1
Kellis Jr., J.T.2
Serrano, L.3
Fersht, A.R.4
-
30
-
-
0025698613
-
Transient folding intermediates characterized by protein engineering
-
Matouschek, A., Kellis Jr., J.T., Serrano, L., Bycroft, M., and Fersht, A.R. 1990. Transient folding intermediates characterized by protein engineering. Nature 346: 440-445.
-
(1990)
Nature
, vol.346
, pp. 440-445
-
-
Matouschek, A.1
Kellis Jr., J.T.2
Serrano, L.3
Bycroft, M.4
Fersht, A.R.5
-
31
-
-
0026550397
-
The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analyzed by a protein engineering procedure
-
Matouschek, A., Serrano, L., and Fersht, A.R. 1992. The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analyzed by a protein engineering procedure. J. Mol. Biol. 224: 819-835.
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 819-835
-
-
Matouschek, A.1
Serrano, L.2
Fersht, A.R.3
-
32
-
-
0033613165
-
A simple model for calculating the kinetics of protein folding from three-dimensional structures
-
Munoz, V. and Eaton, W.A. 1999. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl. Acad. Sci. 96: 11311-11316.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 11311-11316
-
-
Munoz, V.1
Eaton, W.A.2
-
33
-
-
0038502170
-
Folding dynamics and mechanism of β-hairpin formation
-
Munoz, V., Thompson, P.A., Hofrichter, J., and Eaton, W.A. 1997. Folding dynamics and mechanism of β-hairpin formation. Nature 390: 196-199.
-
(1997)
Nature
, vol.390
, pp. 196-199
-
-
Munoz, V.1
Thompson, P.A.2
Hofrichter, J.3
Eaton, W.A.4
-
34
-
-
0032568537
-
A statistical mechanical model for β-hairpin kinetics
-
Munoz, V., Henry, E.R., Hofrichter, J., and Eaton, W.A. 1998. A statistical mechanical model for β-hairpin kinetics. Proc. Natl. Acad. Sci. 95: 5872-5879.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 5872-5879
-
-
Munoz, V.1
Henry, E.R.2
Hofrichter, J.3
Eaton, W.A.4
-
35
-
-
0035252685
-
Characterisation of the transition states for protein folding: Towards a new level of mechanistic detail in protein engineering analysis
-
Oliveberg, M. 2001. Characterisation of the transition states for protein folding: Towards a new level of mechanistic detail in protein engineering analysis. Curr. Op. Str. Biol. 11: 94-100.
-
(2001)
Curr. Op. Str. Biol.
, vol.11
, pp. 94-100
-
-
Oliveberg, M.1
-
36
-
-
0028981210
-
Negative activation enthalpies in the kinetics of protein folding
-
Oliveberg, M., Tan, Y.-J., and Fersht, A.R. 1995. Negative activation enthalpies in the kinetics of protein folding. Proc. Natl. Acad. Sci. 92: 8926-8929.
-
(1995)
Proc. Natl. Acad. Sci.
, vol.92
, pp. 8926-8929
-
-
Oliveberg, M.1
Tan, Y.-J.2
Fersht, A.R.3
-
37
-
-
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. 1995. Toward an outline of the topography of a realistic protein-folding funnel. Proc. Natl. Acad Sci. 92: 3626-3630.
-
(1995)
Proc. Natl. Acad Sci.
, vol.92
, pp. 3626-3630
-
-
Onuchic, J.N.1
Wolynes, P.G.2
Luthey-Schulten, Z.3
Socci, N.D.4
-
38
-
-
0027948175
-
The structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding
-
Otzen, D.S., ElMasry, N., Jackson, S.E., and Fersht, A.R. 1994. The structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. Proc. Natl. Acad. Sci. 91: 10422-10425.
-
(1994)
Proc. Natl. Acad. Sci.
, vol.91
, pp. 10422-10425
-
-
Otzen, D.S.1
ElMasry, N.2
Jackson, S.E.3
Fersht, A.R.4
-
40
-
-
0034872511
-
Transition states and the meaning of φ values in protein folding kinetics
-
Ozkan, S.B., Bahar, I., and Dill, K.A. 2001. Transition states and the meaning of φ values in protein folding kinetics. Nat. Struct. Biol. 8: 765-769.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 765-769
-
-
Ozkan, S.B.1
Bahar, I.2
Dill, K.A.3
-
41
-
-
0036074173
-
Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model
-
Ozkan, S.B., Dill, K.A., and Bahar, I. 2002. Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model. Protein Sci. 11: 1971-1977.
-
(2002)
Protein Sci.
, vol.11
, pp. 1971-1977
-
-
Ozkan, S.B.1
Dill, K.A.2
Bahar, I.3
-
42
-
-
0037457892
-
Self-consistent determination of the transition state for protein folding: Application to a fibronectin type III domain
-
Paci, E., Clarke, J., Steward, A., Vendruscolo, M., and Karplus, M. 2003. Self-consistent determination of the transition state for protein folding: Application to a fibronectin type III domain. Proc. Natl. Acad. Sci. 100: 394-399.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 394-399
-
-
Paci, E.1
Clarke, J.2
Steward, A.3
Vendruscolo, M.4
Karplus, M.5
-
43
-
-
0033574069
-
Folding pathway of a lattice model for proteins
-
Pande, V.S. and Rokhsar, D.S. 1999a. Folding pathway of a lattice model for proteins. Proc. Natl. Acad. Sci. 96: 1273-1278.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 1273-1278
-
-
Pande, V.S.1
Rokhsar, D.S.2
-
44
-
-
0033529908
-
Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G
-
-. 1999b. Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G. Proc. Natl. Acad. Sci. 96: 9062-9067.
-
(1999)
Proc. Natl. Acad. Sci
, vol.96
, pp. 9062-9067
-
-
-
45
-
-
0032005143
-
Pathways for protein folding: Is a new view needed?
-
Pande, V.S., Grosberg, A.Yu., Tanaka, T., and Rokhsar, D.S. 1998. Pathways for protein folding: Is a new view needed? Curr. Opin. Struct. Biol. 8: 68-79.
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 68-79
-
-
Pande, V.S.1
Grosberg, A.Yu.2
Tanaka, T.3
Rokhsar, D.S.4
-
47
-
-
0034321011
-
Energetic frustration and the nature of the transition state in protein folding
-
Shea, J.E., Onuchic, J.N., and Brooks, C.L. 2000. Energetic frustration and the nature of the transition state in protein folding. J. Chem. Phys. 113: 7663-7671.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 7663-7671
-
-
Shea, J.E.1
Onuchic, J.N.2
Brooks, C.L.3
-
48
-
-
0033592876
-
From snapshot to movie: φ Analysis of protein folding transition states taken one step further
-
Ternstroem, T., Mayor, U., Akke, M., and Oliveberg, M. 1999. From snapshot to movie: φ analysis of protein folding transition states taken one step further. Proc. Natl. Acad. Sci. 96: 14854-14859.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 14854-14859
-
-
Ternstroem, T.1
Mayor, U.2
Akke, M.3
Oliveberg, M.4
-
49
-
-
0030067976
-
Importance of two buried salt bridges in the stability and folding pathway of barnase
-
Tissot, A.C., Vuilleumier, S., and Fersht, A.R. 1996. Importance of two buried salt bridges in the stability and folding pathway of barnase. Biochemistry 35: 6786-6794.
-
(1996)
Biochemistry
, vol.35
, pp. 6786-6794
-
-
Tissot, A.C.1
Vuilleumier, S.2
Fersht, A.R.3
-
50
-
-
0035252350
-
Three key residues form a critical contact network in a protein folding transition state
-
Vendruscolo, M., Paci, E., Dobson, C.M., and Karplus, M. 2001. Three key residues form a critical contact network in a protein folding transition state. Nature 409: 641-645.
-
(2001)
Nature
, vol.409
, pp. 641-645
-
-
Vendruscolo, M.1
Paci, E.2
Dobson, C.M.3
Karplus, M.4
-
51
-
-
0002971332
-
Energy landscapes: From clusters to biomolecules
-
Wales, D.J., Doye, J.P.K., Miller, M.A., Mortenson, P.N., and Walsh, T.R. 2000. Energy landscapes: From clusters to biomolecules. Adv. Chem. Phys. 115: 1-111.
-
(2000)
Adv. Chem. Phys.
, vol.115
, pp. 1-111
-
-
Wales, D.J.1
Doye, J.P.K.2
Miller, M.A.3
Mortenson, P.N.4
Walsh, T.R.5
|