-
1
-
-
0033613255
-
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
-
Alm, E. and Baker, D. 1999. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures, Proc. Natl. Acad. Sci. 96: 11305-11310.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 11305-11310
-
-
Alm, E.1
Baker, D.2
-
2
-
-
0036384269
-
Simple physical models connect theory and experiment in protein folding kinetics
-
Alm, E., Morozov, A.V., Kortemme, T., and Baker, D. 2002. Simple physical models connect theory and experiment in protein folding kinetics. J. Mol. Biol. 322: 463-476.
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 463-476
-
-
Alm, E.1
Morozov, A.V.2
Kortemme, T.3
Baker, D.4
-
3
-
-
0043270288
-
Mean-field approach for a statistical mechanical model of proteins
-
Bruscolini, P. and Cecconi, F. 2003. Mean-field approach for a statistical mechanical model of proteins. J. Chem. Phys. 119: 1248-1256.
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 1248-1256
-
-
Bruscolini, P.1
Cecconi, F.2
-
4
-
-
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
-
5
-
-
0032241430
-
Fast events in protein folding: The time evolution of primary processes
-
Callender, R.H., Dyer, R.B., Gilmanshin, R., and Woodruff, W.H. 1998. Fast events in protein folding: The time evolution of primary processes. Annu. Rev. Phys. Chem. 49: 173-202.
-
(1998)
Annu. Rev. Phys. Chem.
, vol.49
, pp. 173-202
-
-
Callender, R.H.1
Dyer, R.B.2
Gilmanshin, R.3
Woodruff, W.H.4
-
6
-
-
0001193711
-
The effects of internal constraints on the configurations of chain molecules
-
Chan, H.S. and Dill, K.A. 1990. The effects of internal constraints on the configurations of chain molecules. J. Chem. Phys. 92: 3118-3135.
-
(1990)
J. Chem. Phys.
, vol.92
, pp. 3118-3135
-
-
Chan, H.S.1
Dill, K.A.2
-
7
-
-
36449008575
-
Energy landscapes and the collapse dynamics of homopolymers
-
-. 1993. Energy landscapes and the collapse dynamics of homopolymers. J. Chem. Phys. 99: 2116-2127.
-
(1993)
J. Chem. Phys
, vol.99
, pp. 2116-2127
-
-
-
8
-
-
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
-
9
-
-
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
-
10
-
-
0036280655
-
Molecular dynamics simulations of the protein unfolding/folding reaction
-
Daggett, V. 2002. Molecular dynamics simulations of the protein unfolding/folding reaction. Acc. Chem. Res. 35: 422-429.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 422-429
-
-
Daggett, V.1
-
11
-
-
0033521194
-
First principles prediction of protein folding rates
-
Debe, D.A. and Goddard III, W.A. 1999. First principles prediction of protein folding rates. J. Mol. Biol. 294: 619-625.
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 619-625
-
-
Debe, D.A.1
Goddard III, W.A.2
-
12
-
-
1842298212
-
From Levinthal to pathways to funnels
-
Dill, K.A. and Chan, H.S. 1997. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4: 10-19.
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
13
-
-
0027405357
-
Cooperativity in protein-folding kinetics
-
Dill, K.A., Fiebig, K.M., and Chan, H.S. 1993. Cooperativity in protein-folding kinetics. Proc. Natl. Acad. Sci. 90: 1942-1946.
-
(1993)
Proc. Natl. Acad. Sci.
, vol.90
, pp. 1942-1946
-
-
Dill, K.A.1
Fiebig, K.M.2
Chan, H.S.3
-
14
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan, Y. and Kollman, P.A. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282: 740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
15
-
-
0542397796
-
Kinetics and dynamics of loops, α-helices, β-hairpins, and fast-folding proteins
-
Eaton, W.A., Munoz, V., Thompson, P.A., Henry, E.R., and Hofrichter, J. 1998. Kinetics and dynamics of loops, α-helices, β-hairpins, and fast-folding proteins. Acc. Chem. Res. 31: 741-753.
-
(1998)
Acc. Chem. Res.
, vol.31
, pp. 741-753
-
-
Eaton, W.A.1
Munoz, V.2
Thompson, P.A.3
Henry, E.R.4
Hofrichter, J.5
-
16
-
-
0033871781
-
Protein folding intermediates and pathways studied by hydrogen exchange
-
Englander, S.W. 2000. Protein folding intermediates and pathways studied by hydrogen exchange. Annu. Rev. Biophys. Biomol. Struct. 29: 213-238.
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 213-238
-
-
Englander, S.W.1
-
18
-
-
0000381972
-
Protein core assembly processes
-
Fiebig, K.M. and Dill, K.A. 1993. Protein core assembly processes. J. Chem. Phys. 98: 3475-3487.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 3475-3487
-
-
Fiebig, K.M.1
Dill, K.A.2
-
19
-
-
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
-
20
-
-
0033613131
-
A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
-
Galzitskaya, O.V. and Finkelstein, A.V. 1999, A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc. Natl. Acad. Sci. 96: 11299-11304.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 11299-11304
-
-
Galzitskaya, O.V.1
Finkelstein, A.V.2
-
21
-
-
0037073934
-
Experimental identification of downhill protein folding
-
Garcia-Mira, M.M., Sadqi, M., Fischer, N., Sanchez-Ruiz, J.M., and Munoz, V. 2002. Experimental identification of downhill protein folding. Science 298: 2191-2195.
-
(2002)
Science
, vol.298
, pp. 2191-2195
-
-
Garcia-Mira, M.M.1
Sadqi, M.2
Fischer, N.3
Sanchez-Ruiz, J.M.4
Munoz, V.5
-
22
-
-
0000346308
-
Laser temperature jump induced protein refolding
-
Gruebele, M., Sabelko, J., Ballew, R., and Ervin, J. 1998. Laser temperature jump induced protein refolding. Acc. Chem. Res. 31: 699-707.
-
(1998)
Acc. Chem. Res.
, vol.31
, pp. 699-707
-
-
Gruebele, M.1
Sabelko, J.2
Ballew, R.3
Ervin, J.4
-
23
-
-
0034319711
-
Sequencing of folding events in Go-type proteins
-
Hoang, T.X. and Cieplak, M. 2000. Sequencing of folding events in Go-type proteins. J. Chem. Phys. 113: 8319-8328.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 8319-8328
-
-
Hoang, T.X.1
Cieplak, M.2
-
24
-
-
0015220649
-
Kinetic evidence for incorrectly folded intermediate states in the refolding of denatured proteins
-
Ikai, A. and Tanford, C. 1971. Kinetic evidence for incorrectly folded intermediate states in the refolding of denatured proteins. Nature 230: 100-102.
-
(1971)
Nature
, vol.230
, pp. 100-102
-
-
Ikai, A.1
Tanford, C.2
-
25
-
-
0035928731
-
Theoretical study of a landscape of protein folding-unfolding pathways. Folding rates at midtransition
-
Ivankov, D.N. and Finkelstein, A.V. 2001. Theoretical study of a landscape of protein folding-unfolding pathways. Folding rates at midtransition. Biochemistry 40: 9957-9961.
-
(2001)
Biochemistry
, vol.40
, pp. 9957-9961
-
-
Ivankov, D.N.1
Finkelstein, A.V.2
-
26
-
-
0017251893
-
Protein-folding dynamics
-
Karplus, M. and Weaver, D.L. 1976. Protein-folding dynamics. Nature 260: 404-406.
-
(1976)
Nature
, vol.260
, pp. 404-406
-
-
Karplus, M.1
Weaver, D.L.2
-
27
-
-
0028327236
-
Protein-folding dynamics: The diffusion-collision model and experimental data
-
-. 1994. Protein-folding dynamics: The diffusion-collision model and experimental data. Protein Sci. 3: 650-668.
-
(1994)
Protein Sci.
, vol.3
, pp. 650-668
-
-
-
28
-
-
0036295960
-
Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains
-
Klimov, D.K. and Thirumalai, D. 2002. Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J. Mol. Biol. 317: 721-737.
-
(2002)
J. Mol. Biol.
, vol.317
, pp. 721-737
-
-
Klimov, D.K.1
Thirumalai, D.2
-
29
-
-
0026723063
-
Protein folding funnels: A kinetic approach to the sequence-structure relationship
-
Leopold, P.E., Montal, M., and Onuchic, J.N. 1992. Protein folding funnels: A kinetic approach to the sequence-structure relationship. Proc. Natl. Acad. Sci. 89: 8721-8725.
-
(1992)
Proc. Natl. Acad. Sci.
, vol.89
, pp. 8721-8725
-
-
Leopold, P.E.1
Montal, M.2
Onuchic, J.N.3
-
30
-
-
0035818481
-
Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations
-
Li, L. and Shakhnovich, E.I. 2001. Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc. Natl. Acad. Sci. 98: 13014-13018.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 13014-13018
-
-
Li, L.1
Shakhnovich, E.I.2
-
31
-
-
0037325379
-
Mean first-passage time analysis reveals rate-limiting steps, parallel pathways and dead ends in a simple model of protein folding
-
Micheelsen, M.A., Rischel, C., Ferkinghoff-Borg, J., Guerois, R., and Serrano, L. 2003. Mean first-passage time analysis reveals rate-limiting steps, parallel pathways and dead ends in a simple model of protein folding. Europhys. Lett. 61: 561-566.
-
(2003)
Europhys. Lett.
, vol.61
, pp. 561-566
-
-
Micheelsen, M.A.1
Rischel, C.2
Ferkinghoff-Borg, J.3
Guerois, R.4
Serrano, L.5
-
32
-
-
0033613165
-
A simple model for calculating the kinetics of protein folding from three-dimensional structures
-
Muñoz, 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
-
-
Muñoz, V.1
Eaton, W.A.2
-
33
-
-
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
-
34
-
-
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: 1958-1970.
-
(2002)
Protein Sci.
, vol.11
, pp. 1958-1970
-
-
Ozkan, S.B.1
Dill, K.A.2
Bahar, I.3
-
35
-
-
0346003771
-
Computing the transition state populations in simple protein models
-
-. 2003. Computing the transition state populations in simple protein models. Biopolymers 68: 35-46.
-
(2003)
Biopolymers
, vol.68
, pp. 35-46
-
-
-
36
-
-
0034725549
-
A statistical appraisal of native state hydrogen exchange data: Evidence for a burst phase continuum?
-
Parker, M.J. and Marqusee, S. 2000. A statistical appraisal of native state hydrogen exchange data: Evidence for a burst phase continuum? J. Mol. Biol. 300: 1361-1375.
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 1361-1375
-
-
Parker, M.J.1
Marqusee, S.2
-
37
-
-
0035868476
-
Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach
-
Portman, J.J., Takada, S., and Wolynes, P.G. 2001. Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach. J. Chem. Phys. 114: 5069-5081.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 5069-5081
-
-
Portman, J.J.1
Takada, S.2
Wolynes, P.G.3
-
39
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
Shea, J.-E. and Brooks III, C.L. 2001. From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52: 499-535.
-
(2001)
Annu. Rev. Phys. Chem.
, vol.52
, pp. 499-535
-
-
Shea, J.-E.1
Brooks III, C.L.2
-
40
-
-
0033515615
-
Exploring structures in protein folding funnels with free energy functionals: The transition state ensemble
-
Shoemaker, B.A., Wang, J., and Wolynes, P.G. 1999. Exploring structures in protein folding funnels with free energy functionals: The transition state ensemble. J. Mol. Biol. 287: 675-694.
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 675-694
-
-
Shoemaker, B.A.1
Wang, J.2
Wolynes, P.G.3
-
41
-
-
0015155644
-
The sequential unfolding of ribonuclease A: Detection of a fast initial phase in the kinetics of unfolding
-
Tsong, T.Y., Baldwin, R.L., and Elson, E.L. 1971. The sequential unfolding of ribonuclease A: Detection of a fast initial phase in the kinetics of unfolding. Proc. Natl. Acad. Sci. 68: 2712-2715.
-
(1971)
Proc. Natl. Acad. Sci.
, vol.68
, pp. 2712-2715
-
-
Tsong, T.Y.1
Baldwin, R.L.2
Elson, E.L.3
-
43
-
-
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
-
44
-
-
0038630483
-
Folding rates and low-entropy-loss routes of 2-state proteins
-
Weikl, T.R. and Dill, K.A. 2003a. Folding rates and low-entropy-loss routes of 2-state proteins. J. Mol. Biol. 329: 585-598.
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 585-598
-
-
Weikl, T.R.1
Dill, K.A.2
-
45
-
-
0041825363
-
Folding kinetics 2-state proteins: Effect of circularization, permutation, and crosslinks
-
-. 2003b. Folding kinetics 2-state proteins: Effect of circularization, permutation, and crosslinks. J. Mol. Biol. 332: 953-963.
-
(2003)
J. Mol. Biol
, vol.332
, pp. 953-963
-
-
|