-
1
-
-
36448999595
-
Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations
-
Abkevich, V. I., A. M. Gutin, and E. I. Shakhnovich. 1994. Free energy landscape for protein folding kinetics: intermediates, traps, and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101:6052-6062.
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 6052-6062
-
-
Abkevich, V.I.1
Gutin, A.M.2
Shakhnovich, E.I.3
-
2
-
-
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
-
3
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein-folding - A synthesis
-
Bryngelson, J. D., J. O. Onuchic, N. D. Socci, and P. G. Wolynes. 1995. Funnels, pathways, and the energy landscape of protein-folding - a synthesis. Proteins Struct. Funct. Genet. 21:167-195.
-
(1995)
Proteins Struct. Funct. Genet.
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.O.2
Socci, N.D.3
Wolynes, P.G.4
-
4
-
-
36449000646
-
Transition states and folding dynamics of proteins and heteropolymers
-
Chan, H. S., and K. A. Dill. 1994. Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100:9238-9257.
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9238-9257
-
-
Chan, H.S.1
Dill, K.A.2
-
5
-
-
1542319916
-
Cooperativity principles in protein folding
-
Chan, H. S., S. Shimizu, and H. Kaya. 2004. Cooperativity principles in protein folding. Meth. Enzymol. 380:350-379.
-
(2004)
Meth. Enzymol.
, vol.380
, pp. 350-379
-
-
Chan, H.S.1
Shimizu, S.2
Kaya, H.3
-
6
-
-
0000301323
-
Scaling of folding properties in simple models of proteins
-
Cieplak, M., T. X. Hoang, and M. S. Li. 1999. Scaling of folding properties in simple models of proteins. Phys. Rev. Lett. 83:1684-1687.
-
(1999)
Phys. Rev. Lett.
, vol.83
, pp. 1684-1687
-
-
Cieplak, M.1
Hoang, T.X.2
Li, M.S.3
-
7
-
-
4243861085
-
Random-energy model: An exactly solvable model of disordered systems
-
Derrida, B. 1981. Random-energy model: an exactly solvable model of disordered systems. Phys. Rev. B. 24:2613-2626.
-
(1981)
Phys. Rev. B
, vol.24
, pp. 2613-2626
-
-
Derrida, B.1
-
9
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder, H., S. G. Sligar, and P. G. Wolynes. 1991. The energy landscapes and motions of proteins. Science. 254:1598-1603.
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
11
-
-
0028868995
-
The structure of the transition state for folding of chymotrypsin inhibitor-2 analyzed by protein engineering methods - Evidence for a nucleation-condensation mechanism for protein-folding
-
Itzhaki, L. S., D. E. Otzen, and A. R. Fersht. 1995. The structure of the transition state for folding of chymotrypsin inhibitor-2 analyzed 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
-
12
-
-
0033462513
-
Folding dynamics of single GCN-4 peptides by fluorescence resonant energy transfer confocal microscopy
-
Jia, Y. W., D. S. Talaga, W. L. Lau, H. S. M. Lu, W. F. DeGrado, and R. M. Hochstrasser. 1999. Folding dynamics of single GCN-4 peptides by fluorescence resonant energy transfer confocal microscopy. Chem. Phys. 247:69-83.
-
(1999)
Chem. Phys.
, vol.247
, pp. 69-83
-
-
Jia, Y.W.1
Talaga, D.S.2
Lau, W.L.3
Lu, H.S.M.4
DeGrado, W.F.5
Hochstrasser, R.M.6
-
13
-
-
0034310589
-
Energetic components of cooperative protein folding
-
Kaya, H., and H. S. Chan. 2000. Energetic components of cooperative protein folding. Phys. Rev. Lett. 85:4823-4826.
-
(2000)
Phys. Rev. Lett.
, vol.85
, pp. 4823-4826
-
-
Kaya, H.1
Chan, H.S.2
-
14
-
-
0036304480
-
Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: How applicable is the transition state picture to folding and unfolding?
-
Kaya, H., and H. S. Chan. 2002. Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: how applicable is the transition state picture to folding and unfolding? J. Mol. Biol. 315:899-909.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 899-909
-
-
Kaya, H.1
Chan, H.S.2
-
15
-
-
0042631521
-
Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences
-
Kaya, H., and H. S. Chan. 2003. Contact order dependent protein folding rates: kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins. 52:524-533.
-
(2003)
Proteins
, vol.52
, pp. 524-533
-
-
Kaya, H.1
Chan, H.S.2
-
16
-
-
33744873820
-
Stable and metastable states in mean-field Potts and structural glasses
-
Kirkpatrick, T. R., and P. G. Wolynes. 1987. Stable and metastable states in mean-field Potts and structural glasses. Phys. Rev. B. 36:8552-8564.
-
(1987)
Phys. Rev. B
, vol.36
, pp. 8552-8564
-
-
Kirkpatrick, T.R.1
Wolynes, P.G.2
-
17
-
-
18344378985
-
Scaling concepts for the dynamics of viscous liquids near an ideal glassy state
-
Kirkpatrick, T. R., D. Thirumalai, and P. G. Wolynes. 1989. Scaling concepts for the dynamics of viscous liquids near an ideal glassy state. Phys. Rev. A. 40:1045-1054.
-
(1989)
Phys. Rev. A
, vol.40
, pp. 1045-1054
-
-
Kirkpatrick, T.R.1
Thirumalai, D.2
Wolynes, P.G.3
-
18
-
-
0001337986
-
Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics
-
Klimov, D. K., and D. Thirumalai. 1998. Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics. J. Chem. Phys. 109:4119-4125.
-
(1998)
J. Chem. Phys.
, vol.109
, pp. 4119-4125
-
-
Klimov, D.K.1
Thirumalai, D.2
-
19
-
-
85003318612
-
Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules
-
Lee, C. L., C. T. Lin, G. Stell, and J. Wang. 2003. Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules. Phys. Rev. E. 67:041905.
-
(2003)
Phys. Rev. E
, vol.67
, pp. 041905
-
-
Lee, C.L.1
Lin, C.T.2
Stell, G.3
Wang, J.4
-
20
-
-
0037425662
-
First-passage time distribution and non-Markovian diffusion dynamics of protein folding
-
Lee, C. L., G. Stell, and J. Wang. 2003. First-passage time distribution and non-Markovian diffusion dynamics of protein folding. J. Chem. Phys. 118:959-968.
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 959-968
-
-
Lee, C.L.1
Stell, G.2
Wang, J.3
-
21
-
-
0001861319
-
-
P. DeBrunner, J. Tsibris, and E. Munck, editors. University of Illinois Press, Urbana, IL
-
Levinthal, C. 1969. Proceedings in Mössbauer Spectroscopy in Biological Systems. P. DeBrunner, J. Tsibris, and E. Munck, editors. University of Illinois Press, Urbana, IL. p22.
-
(1969)
Proceedings in Mössbauer Spectroscopy in Biological Systems
, pp. 22
-
-
Levinthal, C.1
-
22
-
-
0041321045
-
Single-molecule measurement of protein folding kinetics
-
Lipman, E. A., B. Schuler, O. Bakajin, and W. A. Eaton. 2003. Single-molecule measurement of protein folding kinetics. Science. 301:1233-1235.
-
(2003)
Science
, vol.301
, pp. 1233-1235
-
-
Lipman, E.A.1
Schuler, B.2
Bakajin, O.3
Eaton, W.A.4
-
23
-
-
0032484096
-
Single-molecule enzymatic dynamics
-
Lu, H. P., L. Y. Xun, and X. S. Xie. 1998. Single-molecule enzymatic dynamics. Science. 282:1877-1882.
-
(1998)
Science
, vol.282
, pp. 1877-1882
-
-
Lu, H.P.1
Xun, L.Y.2
Xie, X.S.3
-
24
-
-
0000650835
-
High-resolution optical spectroscopy of single molecules in solids
-
Moerner, W. E. 1996. High-resolution optical spectroscopy of single molecules in solids. Acc. Chem. Res. 29:563-571.
-
(1996)
Acc. Chem. Res.
, vol.29
, pp. 563-571
-
-
Moerner, W.E.1
-
25
-
-
0013496963
-
Folding kinetics of proteins and copolymers
-
Miller, R., C. A. Danko, M. J. Fasolka, A. C. Balazs, H. S. Chan, and K. A. Dill. 1992. Folding kinetics of proteins and copolymers. J. Chem. Phys. 96:768-780.
-
(1992)
J. Chem. Phys.
, vol.96
, pp. 768-780
-
-
Miller, R.1
Danko, C.A.2
Fasolka, M.J.3
Balazs, A.C.4
Chan, H.S.5
Dill, K.A.6
-
26
-
-
0001071357
-
Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation
-
Nguyen, H., M. Jäger, A. Moretto, M. Gruebele, and J. W. Kelly. 2003. Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation. Proc. Natl. Acad. Sci. USA. 100:3948-3953.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3948-3953
-
-
Nguyen, H.1
Jäger, M.2
Moretto, A.3
Gruebele, M.4
Kelly, J.W.5
-
27
-
-
0033437006
-
Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions
-
Onuchic, J. N., J. Wang, and P. G. Wolynes. 1999. Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions. Chem. Phys. 247:175-184.
-
(1999)
Chem. Phys.
, vol.247
, pp. 175-184
-
-
Onuchic, J.N.1
Wang, J.2
Wolynes, P.G.3
-
28
-
-
0001482546
-
Non-Markovian configurational diffusion and reaction coordinates for protein folding
-
Plotkin, S. S., and P. G. Wolynes. 1998. Non-Markovian configurational diffusion and reaction coordinates for protein folding. Phys. Rev. Lett. 80:5015-5018.
-
(1998)
Phys. Rev. Lett.
, vol.80
, pp. 5015-5018
-
-
Plotkin, S.S.1
Wolynes, P.G.2
-
29
-
-
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. Quar. Rev. Biophys. 35:111-167.
-
(2002)
Quar. Rev. Biophys.
, vol.35
, pp. 111-167
-
-
Plotkin, S.S.1
Onuchic, J.N.2
-
30
-
-
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. Quar. Rev. Biophys. 35:205-286.
-
(2002)
Quar. Rev. Biophys.
, vol.35
, pp. 205-286
-
-
Plotkin, S.S.1
Onuchic, J.N.2
-
32
-
-
0001081429
-
Kinetics of protein folding: The dynamics of globally connected rough energy landscapes with biases
-
Saven, J. G., J. Wang, and P. G. Wolynes. 1994. Kinetics of protein folding: the dynamics of globally connected rough energy landscapes with biases. J. Chem. Phys. 101:11037-11043.
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 11037-11043
-
-
Saven, J.G.1
Wang, J.2
Wolynes, P.G.3
-
33
-
-
0001600697
-
Variational approach to protein design and extraction of interaction potentials
-
Seno, F., C. Micheletti, A. Maritan, and J. R. Banavar. 1998. Variational approach to protein design and extraction of interaction potentials. Phys. Rev. Lett. 81:2172-2175.
-
(1998)
Phys. Rev. Lett.
, vol.81
, pp. 2172-2175
-
-
Seno, F.1
Micheletti, C.2
Maritan, A.3
Banavar, J.R.4
-
34
-
-
0001248634
-
Statistical analyses and theoretical models of single-molecule enzymatic dynamics
-
Schemer, G. K., H. P. Lu, and X. S. Xie. 1999. Statistical analyses and theoretical models of single-molecule enzymatic dynamics. J. Phys. Chem. A. 103:10477-10488.
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 10477-10488
-
-
Schemer, G.K.1
Lu, H.P.2
Xie, X.S.3
-
35
-
-
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
-
36
-
-
0007725036
-
Folding kinetics of proteinlike heteropolymers
-
Socci, N. D., and J. N. Onuchic. 1994. Folding kinetics of proteinlike heteropolymers. J. Chem. Phys. 101:1519-1528.
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 1519-1528
-
-
Socci, N.D.1
Onuchic, J.N.2
-
37
-
-
0001669870
-
Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique
-
Socci, N. D., and J. N. Onuchic. 1995. Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique. J. Chem. Phys. 103:4732-4744.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 4732-4744
-
-
Socci, N.D.1
Onuchic, J.N.2
-
38
-
-
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
-
39
-
-
9644263074
-
Intermittency of single molecule reaction dynamics in fluctuating environments
-
Wang, J., and P. G. Wolynes. 1995. Intermittency of single molecule reaction dynamics in fluctuating environments. Phys. Rev. Lett. 74:4317-4320.
-
(1995)
Phys. Rev. Lett.
, vol.74
, pp. 4317-4320
-
-
Wang, J.1
Wolynes, P.G.2
-
40
-
-
0001209011
-
Statistics of kinetic pathways on biased rough energy landscapes with applications to protein folding
-
Wang, J., J. Onuchic, and P. Wolynes. 1996a. Statistics of kinetic pathways on biased rough energy landscapes with applications to protein folding. Phys. Rev. Lett. 76:4861-4864.
-
(1996)
Phys. Rev. Lett.
, vol.76
, pp. 4861-4864
-
-
Wang, J.1
Onuchic, J.2
Wolynes, P.3
-
41
-
-
0000788389
-
Kinetics in a globally connected, correlated random energy model
-
Wang, J., J. G. Saven, and P. G. Wolynes. 1996b. Kinetics in a globally connected, correlated random energy model. J. Chem. Phys. 105:11276-11284.
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 11276-11284
-
-
Wang, J.1
Saven, J.G.2
Wolynes, P.G.3
-
42
-
-
0001548409
-
Intermittency of activated events in single molecules: The reaction diffusion description
-
Wang, J., and P. G. Wolynes. 1999. Intermittency of activated events in single molecules: the reaction diffusion description. J. Chem. Phys. 110:4812-4819.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 4812-4819
-
-
Wang, J.1
Wolynes, P.G.2
-
43
-
-
0037425692
-
Statistics, pathways and dynamics of single molecule protein folding
-
Wang, J. 2003. Statistics, pathways and dynamics of single molecule protein folding. J. Chem. Phys. 118:952-958.
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 952-958
-
-
Wang, J.1
-
44
-
-
0036829458
-
Statistical approaches for probing single-molecule dynamics photon by photon
-
Yang, H., and X. S. Xie. 2002a. Statistical approaches for probing single-molecule dynamics photon by photon. Chem. Phys. 284:423-437.
-
(2002)
Chem. Phys.
, vol.284
, pp. 423-437
-
-
Yang, H.1
Xie, X.S.2
-
45
-
-
0037461522
-
Probing single-molecule dynamics photon-by-photon
-
Yang, H., and X. S. Xie. 2002b. Probing single-molecule dynamics photon-by-photon. J. Chem. Phys. 117:10965-10979.
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 10965-10979
-
-
Yang, H.1
Xie, X.S.2
-
46
-
-
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-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-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
-
47
-
-
0034674420
-
A single-molecule study of RNA catalysis and folding
-
Zhuang, X. W., L. E. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu. 2000. A single-molecule study of RNA catalysis and folding. Science. 288:2048-2051.
-
(2000)
Science
, vol.288
, pp. 2048-2051
-
-
Zhuang, X.W.1
Bartley, L.E.2
Babcock, H.P.3
Russell, R.4
Ha, T.5
Herschlag, D.6
Chu, S.7
-
48
-
-
0037165996
-
Correlating structural dynamics and function in single ribozyme molecules
-
Zhuang, X. W., H. Kim, M. J. B. Pereira, H. P. Babcock, N. G. Walter, and S. Chu. 2002. Correlating structural dynamics and function in single ribozyme molecules. Science. 296:1473-1476.
-
(2002)
Science
, vol.296
, pp. 1473-1476
-
-
Zhuang, X.W.1
Kim, H.2
Pereira, M.J.B.3
Babcock, H.P.4
Walter, N.G.5
Chu, S.6
|