-
1
-
-
4444324627
-
The nature of the free energy barriers to two state folding
-
Akmal, A., and V. Munoz. 2004. The nature of the free energy barriers to two state folding. Proteins. 57:142-152.
-
(2004)
Proteins
, vol.57
, pp. 142-152
-
-
Akmal, A.1
Munoz, V.2
-
2
-
-
0028947257
-
Funnels, pathways and the energy landscape of protein folding
-
Bryngelson, J. D., J. N. Onuchic, N. D. Socci, and P. G. Wolynes. 1995. Funnels, pathways and the energy landscape of protein folding. Proteins. 21:167-195.
-
(1995)
Proteins
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
3
-
-
0024733407
-
Intermediates and barrier crossing in a random energy model (with applications to protein folding)
-
Bryngelson, J. D., and P. G. Wolynes. 1989. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93:6902-6915.
-
(1989)
J. Phys. Chem.
, vol.93
, pp. 6902-6915
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
5
-
-
0029900846
-
The magnitude of the backbone conformational entropy change in protein folding
-
D'Aquino, J. A., J. Gomez, V. J. Hilser, K. H. Lee, L. M. Amzel, and E. Freire. 1996. The magnitude of the backbone conformational entropy change in protein folding. Proteins Struct. Funct. Gen. 25:143-156.
-
(1996)
Proteins Struct. Funct. Gen.
, vol.25
, pp. 143-156
-
-
D'Aquino, J.A.1
Gomez, J.2
Hilser, V.J.3
Lee, K.H.4
Amzel, L.M.5
Freire, E.6
-
6
-
-
0033624685
-
Fast kinetics and mechanisms in protein folding
-
Eaton, W. A., V. Munoz, S. J. Hagen, G. S. Jas, L. J. Lapidus, E. R. Henry, and J. Hofrichter. 2000. Fast kinetics and mechanisms in protein folding. Annu. Rev. Biophys. Biomol. Struct. 29:327-359.
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 327-359
-
-
Eaton, W.A.1
Munoz, V.2
Hagen, S.J.3
Jas, G.S.4
Lapidus, L.J.5
Henry, E.R.6
Hofrichter, J.7
-
7
-
-
4644259872
-
Three-body interactions improve the prediction of rate and mechanism in protein folding models
-
Ejtehadi, M. R., S. P. Avall, and S. S. Plotkin. 2004. Three-body interactions improve the prediction of rate and mechanism in protein folding models. Proc. Natl. Acad. Sci., USA. 101:15088-15093.
-
(2004)
Proc. Natl. Acad. Sci., USA
, vol.101
, pp. 15088-15093
-
-
Ejtehadi, M.R.1
Avall, S.P.2
Plotkin, S.S.3
-
9
-
-
0345133287
-
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
-
Garcia, A. E., and J. N. Onuchic. 2003. Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proc. Natl. Acad. Sci. USA. 100:13898-13903.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13898-13903
-
-
Garcia, A.E.1
Onuchic, J.N.2
-
10
-
-
0347193736
-
Reaction-rate theory: Fifty years after Kramers
-
Hanggi, P., P. Talkner, and M. Borkevec. 1990. Reaction-rate theory: fifty years after Kramers. Rev. Mod. Phys. 62:251-341.
-
(1990)
Rev. Mod. Phys.
, vol.62
, pp. 251-341
-
-
Hanggi, P.1
Talkner, P.2
Borkevec, M.3
-
11
-
-
0026345750
-
Folding of chymotrypsin inhibitor 2. 1. Evidence for a two state transition
-
Jackson, S. E., and A. R. Fersht. 1991. Folding of chymotrypsin 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
-
12
-
-
0000399469
-
Viscosity dependence of the folding rates of proteins
-
Klimov, D. K., and D. Thirumalai. 1997. Viscosity dependence of the folding rates of proteins. Phys. Rev. Lett. 79:317-320.
-
(1997)
Phys. Rev. Lett.
, vol.79
, pp. 317-320
-
-
Klimov, D.K.1
Thirumalai, D.2
-
13
-
-
0032545150
-
Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein 19
-
Kuhlman, B., D. L. Luisi, P. A. Evans, and D. P. Raleigh. 1998. Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein 19. J. Mol. Biol. 284:1661-1670.
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 1661-1670
-
-
Kuhlman, B.1
Luisi, D.L.2
Evans, P.A.3
Raleigh, D.P.4
-
14
-
-
0034691198
-
Measuring the rate of intramolecular contact formation in polypeptides
-
Lapidus, L. J., W. A. Eaton, and J. Hofrichter. 2000. Measuring the rate of intramolecular contact formation in polypeptides. Proc. Natl. Acad. Sci. USA. 97:7220-7225.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 7220-7225
-
-
Lapidus, L.J.1
Eaton, W.A.2
Hofrichter, J.3
-
15
-
-
0013900792
-
Computation of sterically allowed conformations of peptides
-
Leach, S. J., G. Nemethy, and H. A. Scheraga. 1966. Computation of sterically allowed conformations of peptides. Biopolymers. 4:369-407.
-
(1966)
Biopolymers
, vol.4
, pp. 369-407
-
-
Leach, S.J.1
Nemethy, G.2
Scheraga, H.A.3
-
16
-
-
0347123330
-
Thermal denaturation and folding rates of single domain proteins: Size matters
-
Li, M. S., D. K. Klimov, and D. Thirumalai. 2004. Thermal denaturation and folding rates of single domain proteins: size matters. Polym. 45: 573-579.
-
(2004)
Polym.
, vol.45
, pp. 573-579
-
-
Li, M.S.1
Klimov, D.K.2
Thirumalai, D.3
-
17
-
-
0036829967
-
Complete change of the protein folding transition state upon circular permutation
-
Lindberg, M., J. Tangrot, and M. Oliveberg. 2002. Complete change of the protein folding transition state upon circular permutation. Nat. Struct. Biol. 9:818-822.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 818-822
-
-
Lindberg, M.1
Tangrot, J.2
Oliveberg, M.3
-
18
-
-
0030154861
-
Cytochrome-c folding triggered by electron transfer
-
Mines, G. A., T. Pascher, S. C. L. J. R. Winkler, and H. B. Gray. 1996. Cytochrome-c folding triggered by electron transfer. Chem. Biol. 3: 491-497.
-
(1996)
Chem. Biol.
, vol.3
, pp. 491-497
-
-
Mines, G.A.1
Pascher, T.2
Winkler, S.C.L.J.R.3
Gray, H.B.4
-
21
-
-
0037007489
-
Thermodynamics of a diffusional protein folding reaction
-
Perl, D., M. Jacob, M. Bano, M. Stupak, M. Antalik, and F. X. Schmid. 2002. Thermodynamics of a diffusional protein folding reaction. Biophys. Chem. 96:173-190.
-
(2002)
Biophys. Chem.
, vol.96
, pp. 173-190
-
-
Perl, D.1
Jacob, M.2
Bano, M.3
Stupak, M.4
Antalik, M.5
Schmid, F.X.6
-
22
-
-
0034612228
-
Investigation of routes and funnels in protein folding by free energy functional methods
-
Plotkin, S. S., and J. N. Onuchic. 2000. Investigation of routes and funnels in protein folding by free energy functional methods. Proc. Natl. Acad. Sci. USA. 97:6509-6514.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 6509-6514
-
-
Plotkin, S.S.1
Onuchic, J.N.2
-
23
-
-
0036023918
-
Understanding protein folding with energy landscape theory. I. Basic concepts
-
Plotkin, S. S., and J. N. Onuchic. 2002a. Understanding protein folding with energy landscape theory. I. Basic concepts. Q. Rev. Biophys. 35: 111-167.
-
(2002)
Q. Rev. Biophys.
, vol.35
, pp. 111-167
-
-
Plotkin, S.S.1
Onuchic, J.N.2
-
24
-
-
0036706015
-
Understanding protein folding with energy landscape theory. II. Quantitative aspects
-
Plotkin, S. S., and J. N. Onuchic. 2002b. Understanding protein folding with energy landscape theory. II. Quantitative aspects. Q. Rev. Biophys. 35:205-286.
-
(2002)
Q. Rev. Biophys.
, vol.35
, pp. 205-286
-
-
Plotkin, S.S.1
Onuchic, J.N.2
-
25
-
-
0035868526
-
Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics
-
Portman, J. J., S. Takada, and P. G. Wolynes. 2001. Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics. J. Chem. Phys. 114:5082-5096.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 5082-5096
-
-
Portman, J.J.1
Takada, S.2
Wolynes, P.G.3
-
26
-
-
0030984109
-
Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability
-
Scalley, M., and D. Baker. 1997. Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability. Proc. Natl. Acad. Sci. USA. 94:10636-10640.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 10636-10640
-
-
Scalley, M.1
Baker, D.2
-
27
-
-
0030450051
-
Thermodynamic properties of an extremely rapid protein folding reaction
-
Schindler, T., and F. X. Schmid. 1996. Thermodynamic properties of an extremely rapid protein folding reaction. Biochemistry. 35:16833-16842.
-
(1996)
Biochemistry
, vol.35
, pp. 16833-16842
-
-
Schindler, T.1
Schmid, F.X.2
-
28
-
-
0037126290
-
Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
-
Schuler, B., E. A. Lipman, and W. A. Eaton. 2002. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature. 419:743-747.
-
(2002)
Nature
, vol.419
, pp. 743-747
-
-
Schuler, B.1
Lipman, E.A.2
Eaton, W.A.3
-
29
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
Shea, J. E., and C. L. Brooks III. 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
-
30
-
-
0033515615
-
Exploring structures in protein folding funnels with free energy functionals: The transition state ensemble
-
Shoemaker, B. A., J. Wang, and P. G. Wolynes. 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
-
31
-
-
0000710672
-
Diffusive dynamics of the reaction coordinate for protein folding funnels
-
Socci, N. D., J. N. Onuchic, and P. G. Wolynes. 1996. Diffusive dynamics of the reaction coordinate for protein folding funnels. J. Chem. Phys. 104:5860-5868.
-
(1996)
J. Chem. Phys.
, vol.104
, pp. 5860-5868
-
-
Socci, N.D.1
Onuchic, J.N.2
Wolynes, P.G.3
-
32
-
-
0031098769
-
Configurational diffusion on a locally connected correlated energy landscape; application to finite, random heteropolymers
-
Wang, J., S. S. Plotkin, and P. G. Wolynes. 1997. Configurational diffusion on a locally connected correlated energy landscape; application to finite, random heteropolymers. J. Phys. I (Fr.). 7:395-421.
-
(1997)
J. Phys. I (Fr.)
, vol.7
, pp. 395-421
-
-
Wang, J.1
Plotkin, S.S.2
Wolynes, P.G.3
-
33
-
-
0037612553
-
Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second β-hairpin fragment of protein-G
-
Zhou, Y., C. Zhang, G. Stell, and J. Wang. 2003. Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second β-hairpin fragment of protein-G. J. Am. Chem. Soc. 125:6300-6305.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 6300-6305
-
-
Zhou, Y.1
Zhang, C.2
Stell, G.3
Wang, J.4
|