-
1
-
-
0033117763
-
Matching theory and experiment in protein folding
-
Alm, E. and Baker, D. 1999a. Matching theory and experiment in protein folding. Curr. Opin. Struct. Biol. 9: 189-196.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 189-196
-
-
Alm, E.1
Baker, D.2
-
2
-
-
0033613255
-
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
-
-, 1999b. 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
-
-
-
3
-
-
0036500833
-
Protein folding - Making a network of hydrophobic clusters
-
Baldwin, R.E. 2002. Protein folding - Making a network of hydrophobic clusters. Science 295: 1657-1658.
-
(2002)
Science
, vol.295
, pp. 1657-1658
-
-
Baldwin, R.E.1
-
4
-
-
0033080081
-
Is protein folding hierarchic? II. Folding intermediates and transition states
-
Baldwin, R.L. and Rose, G.D. 1999. 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
-
-
Baldwin, R.L.1
Rose, G.D.2
-
5
-
-
0000248317
-
Sequential collapse model for protein folding pathways
-
Bergasa-Caceres, F., Ronneberg, T.A., and Rabitz, H.A. 1999. Sequential collapse model for protein folding pathways. J. Phys. Chem. B 103: 9749-9758.
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 9749-9758
-
-
Bergasa-Caceres, F.1
Ronneberg, T.A.2
Rabitz, H.A.3
-
6
-
-
0033578370
-
The speed limit for protein folding measured by triplet-triplet energy transfer
-
Bieri, O., Wirz, J., Hellrung, B., Schutkowski, M., Drewello, M., and Kiefhaber, T. 1999. The speed limit for protein folding measured by triplet-triplet energy transfer. Proc. Natl. Acad. Sci. 96: 9597-9601
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 9597-9601
-
-
Bieri, O.1
Wirz, J.2
Hellrung, B.3
Schutkowski, M.4
Drewello, M.5
Kiefhaber, T.6
-
7
-
-
0023449962
-
Spin-glasses and the statisticalmechanics of protein folding
-
Bryngelson, J.D. and Wolynes, P.G. 1987. Spin-glasses and the statisticalmechanics of protein folding. Proc. Natl. Acad. Sci. 84: 7524-7528.
-
(1987)
Proc. Natl. Acad. Sci.
, vol.84
, pp. 7524-7528
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
8
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein-folding - A synthesis
-
Bryngelson, J.D., Onuchic, J.N., Socci, N.D., and Wolynes, P.G. 1995. Funnels, pathways, and the energy landscape of protein-folding - A synthesis. Prot. Sruct. Func. Gen. 21: 167-195.
-
(1995)
Prot. Sruct. Func. Gen.
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
9
-
-
0035906728
-
Rescuing a destabilized protein fold through backbone cyclization
-
Camarero, J.A., Fushman, D., Sato, S., Giriat, I., Cowburn, D., Raleigh, D.P., and Muir, T.W. 2001. Rescuing a destabilized protein fold through backbone cyclization. J. Mol. Biol. 308: 1045-1062.
-
(2001)
J. Mol. Biol.
, vol.308
, pp. 1045-1062
-
-
Camarero, J.A.1
Fushman, D.2
Sato, S.3
Giriat, I.4
Cowburn, D.5
Raleigh, D.P.6
Muir, T.W.7
-
10
-
-
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
-
11
-
-
0035906650
-
Calculation of ensembles of structures representing the unfolded state of an SH3 domain
-
Choy, W.Y. and Forman-Kay, J. 2000. Calculation of ensembles of structures representing the unfolded state of an SH3 domain. J. Mol. Biol. 308: 1011-1032.
-
(2000)
J. Mol. Biol.
, vol.308
, pp. 1011-1032
-
-
Choy, W.Y.1
Forman-Kay, J.2
-
12
-
-
0033200251
-
Folding studies of immunoglobulin-like β-sandwich proteins suggest that they share a common folding pathway
-
Clarke, J., Cota, E., Fowler, S.B., and Hamill, S.J. 1999. Folding studies of immunoglobulin-like β-sandwich proteins suggest that they share a common folding pathway. Structure 7: 1145-1153.
-
(1999)
Structure
, vol.7
, pp. 1145-1153
-
-
Clarke, J.1
Cota, E.2
Fowler, S.B.3
Hamill, S.J.4
-
13
-
-
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
-
14
-
-
0033521194
-
First principles prediction of protein folding rates
-
Debe, D.A. and Goddard, 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, W.A.2
-
15
-
-
0032980496
-
The topomer-sampling model of protein folding
-
Debe, D.A., Carlson, M.J., and Goddard, W.A. 1999. The topomer-sampling model of protein folding. Proc. Natl. Acad. Sci. 96: 2596-2601.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 2596-2601
-
-
Debe, D.A.1
Carlson, M.J.2
Goddard, W.A.3
-
16
-
-
1842298212
-
From Levinthal to pathways to funnels
-
Dill, K.A. and Chan, H.S. 1997. From Levinthal to pathways to funnels. Nat. Struc. Biol. 4: 10-19.
-
(1997)
Nat. Struc. Biol.
, vol.4
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
17
-
-
0009586942
-
Understanding protein folding via free-energy surfaces from theory and experiment
-
Dinner, A.R., Sali, A., Smith, L.J., Dobson, C.M., and Karplus, M. 2000. Understanding protein folding via free-energy surfaces from theory and experiment. Trend. Bioch. Sci. 25: 331-339.
-
(2000)
Trend. Bioch. Sci.
, vol.25
, pp. 331-339
-
-
Dinner, A.R.1
Sali, A.2
Smith, L.J.3
Dobson, C.M.4
Karplus, M.5
-
18
-
-
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. Ang. Chem. Int. Ed. 37: 868-893.
-
(1998)
Ang. Chem. Int. Ed.
, vol.37
, pp. 868-893
-
-
Dobson, C.M.1
Sali, A.2
Karplus, M.3
-
19
-
-
0033624685
-
Fast kinetics and mechanisms in protein folding
-
Eaton, W.A., Munoz, V., Hagen, S.J., Jas, G.S., Lapidus, L.J., Henry, E.R., and Hofrichter, J. 2000. Fast kinetics and mechanisms in protein folding. Annu. Rev. Biomol. Struct. 29: 327-359.
-
(2000)
Annu. Rev. 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
-
20
-
-
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
-
-
0034652206
-
Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
-
- . 2000. Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism. Proc. Natl. Acad. Sci. 97: 1525-1529.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 1525-1529
-
-
-
22
-
-
0026543378
-
Truncated staphylococcal nuclease is compact but disordered
-
Flanagan, J.M., Kataoka, M., Shortle, D., and Engelman, D.M. 1992. Truncated staphylococcal nuclease is compact but disordered. Proc. Natl. Acad. Sci. 89: 748-752.
-
(1992)
Proc. Natl. Acad. Sci.
, vol.89
, pp. 748-752
-
-
Flanagan, J.M.1
Kataoka, M.2
Shortle, D.3
Engelman, D.M.4
-
23
-
-
33947466111
-
Theory of elastic mechanisms in fibrous proteins
-
Flory, P.J. 1956, Theory of elastic mechanisms in fibrous proteins. J. Am. Chem. Soc. 78: 5222-5234.
-
(1956)
J. Am. Chem. Soc.
, vol.78
, pp. 5222-5234
-
-
Flory, P.J.1
-
24
-
-
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
-
25
-
-
0034710944
-
Non-glassy kinetics in the folding of a simple, single domain protein
-
Gillespie, B. and Plaxco, K.W. 2000. Non-glassy kinetics in the folding of a simple, single domain protein. Proc. Natl. Acad. Sci. 97: 12014-12019.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 12014-12019
-
-
Gillespie, B.1
Plaxco, K.W.2
-
26
-
-
0035936689
-
Circularization changes the folding transition state of the src SH3 domain
-
Grantcharova, V.P. and Baker, D. 2001. Circularization changes the folding transition state of the src SH3 domain. J. Mol. Biol. 306: 555-563.
-
(2001)
J. Mol. Biol.
, vol.306
, pp. 555-563
-
-
Grantcharova, V.P.1
Baker, D.2
-
27
-
-
0034691039
-
Long-range order in the src SH3 folding transition state
-
Grantcharova, V.P., Riddle, D.S., and Baker, D. 2000. Long-range order in the src SH3 folding transition state. Proc. Natl. Acad. Sci. 97: 7084-7089.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 7084-7089
-
-
Grantcharova, V.P.1
Riddle, D.S.2
Baker, D.3
-
28
-
-
0035252683
-
Mechanisms of protein folding
-
Grantcharova, V.P., Alm. E.J., Baker, D., and Horowitz, A.L. 2001. Mechanisms of protein folding. Curr. Opin. Struct. Biol. 11: 70-82.
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 70-82
-
-
Grantcharova, V.P.1
Alm, E.J.2
Baker, D.3
Horowitz, A.L.4
-
29
-
-
0035967862
-
Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Application of long-range order to folding rate prediction
-
Gromiha, M.M. and Selvaraj, S. 2001. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Application of long-range order to folding rate prediction. J. Mol. Biol. 310: 27-32.
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 27-32
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
30
-
-
0030605814
-
Linguistic analysis of protein folding
-
Gross, M. 1996. Linguistic analysis of protein folding. FEBS Lett. 390: 249-252.
-
(1996)
FEBS Lett.
, vol.390
, pp. 249-252
-
-
Gross, M.1
-
31
-
-
0032570543
-
Folding kinetics of the SH3 domain of PI3 by real-time NMR and optical techniques
-
Guijarro, J.I., Morton, C.J., Plaxco, K.W., Campbell, I.D., and Dobson, C.M. 1998. Folding kinetics of the SH3 domain of PI3 by real-time NMR and optical techniques. J. Mol. Biol. 275: 657-667.
-
(1998)
J. Mol. Biol.
, vol.275
, pp. 657-667
-
-
Guijarro, J.I.1
Morton, C.J.2
Plaxco, K.W.3
Campbell, I.D.4
Dobson, C.M.5
-
32
-
-
0030967896
-
Exploring the folding free energy surface of a three-helix bundle protein
-
Guo, Z.Y., Brooks, C.L., and Boczko, E.M. 1997. Exploring the folding free energy surface of a three-helix bundle protein. Proc. Natl. Acad. Sci. 94: 10161-10166.
-
(1997)
Proc. Natl. Acad. Sci.
, vol.94
, pp. 10161-10166
-
-
Guo, Z.Y.1
Brooks, C.L.2
Boczko, E.M.3
-
33
-
-
36448999542
-
Statistical mechanics of polymers with distance constraints
-
Gutin, A.M. and Shakhnovich, E.I. 1994. Statistical mechanics of polymers with distance constraints. J. Chem. Phys. 100: 5290-5293.
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 5290-5293
-
-
Gutin, A.M.1
Shakhnovich, E.I.2
-
34
-
-
4243416989
-
Chain length scaling of protein folding time
-
Gutin, A.M., Abkevich, V.I., and Shakhnovich, E.I. 1996. Chain length scaling of protein folding time. Phys. Rev. Lett. 77: 5433-5436.
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 5433-5436
-
-
Gutin, A.M.1
Abkevich, V.I.2
Shakhnovich, E.I.3
-
35
-
-
0029964867
-
Diffusion-limited contact formation in unfolded cytochrome c: Estimating the maximum rate of protein folding
-
Hagen, S.J., Hofrichter, J., Szabo, A., and Eaton, W.A. 1996. Diffusion-limited contact formation in unfolded cytochrome c: Estimating the maximum rate of protein folding. Proc. Natl. Acad. Sci. 93: 11615-11617.
-
(1996)
Proc. Natl. Acad. Sci.
, vol.93
, pp. 11615-11617
-
-
Hagen, S.J.1
Hofrichter, J.2
Szabo, A.3
Eaton, W.A.4
-
36
-
-
0031095826
-
Rate of intrachain diffusion of unfolded cytochrome c
-
Hagen, S.J., Hofrichter, J., and Eaton, W.A. 1997. Rate of intrachain diffusion of unfolded cytochrome c. J. Phys. Chem. B 101: 2352-2365.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 2352-2365
-
-
Hagen, S.J.1
Hofrichter, J.2
Eaton, W.A.3
-
37
-
-
0035793222
-
Rate of intrachain contact formation in an unfolded protein: Temperature and denaturant effects
-
Hagen, S.J., Carswell, C.W., and Sjolander, E.M. 2001. Rate of intrachain contact formation in an unfolded protein: Temperature and denaturant effects. J. Mol. Biol. 305: 1161-1171.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 1161-1171
-
-
Hagen, S.J.1
Carswell, C.W.2
Sjolander, E.M.3
-
38
-
-
0035936551
-
Intestinal fatty acid binding protein: The folding mechanism as determined by NMR studies
-
Hodsdon, M.E. and Frieden, C. 2001. Intestinal fatty acid binding protein: The folding mechanism as determined by NMR studies. Biochemistry 40: 732-742.
-
(2001)
Biochemistry
, vol.40
, pp. 732-742
-
-
Hodsdon, M.E.1
Frieden, C.2
-
39
-
-
0036307683
-
Application of the diffusioncollision model to the folding of three-helix bundle proteins
-
Islam, S.A., Karplus, M., and Weaver, D.L. 2002. Application of the diffusioncollision model to the folding of three-helix bundle proteins. J. Mol. Biol. 318: 199-215.
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 199-215
-
-
Islam, S.A.1
Karplus, M.2
Weaver, D.L.3
-
40
-
-
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
-
41
-
-
0031815749
-
How do small single domain proteins fold?
-
Jackson, S.E. 1998. How do small single domain proteins fold? Fold. Des. 3: R81-R91.
-
(1998)
Fold. Des.
, vol.3
-
-
Jackson, S.E.1
-
42
-
-
0026345750
-
The folding of chymotrypsin inhibitor-2. 1. Evidence for a two-state transition
-
Jackson, S.E. and Fersht, A.R. 1991. The 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
-
43
-
-
3843114319
-
Intramolecular reaction in polycondensations. 1. The theory of linear systems
-
Jacobson, H. and Stockmayer, W.H. 1950. Intramolecular reaction in polycondensations. 1. The theory of linear systems. J. Chem. Phys. 18: 1600-1606.
-
(1950)
J. Chem. Phys.
, vol.18
, pp. 1600-1606
-
-
Jacobson, H.1
Stockmayer, W.H.2
-
44
-
-
84985656311
-
Diffusion-collision model or protein folding
-
Karplus, M. and Weaver, D.L. 1979. Diffusion-collision model or protein folding. Biopolymers 18: 1421-1437.
-
(1979)
Biopolymers
, vol.18
, pp. 1421-1437
-
-
Karplus, M.1
Weaver, D.L.2
-
45
-
-
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 Chan. H.S. 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
-
46
-
-
18244364614
-
Long-range interactions within a nonnative protein
-
Klein-Seetharaman, J., Oikawa, M., Grimshaw, S.B., Wirmer, J., Duchardt, E., Ueda, T., Imoto, T., Smith, L.J., Dobson, C.M., and Schwalbe, H. 2002. Long-range interactions within a nonnative protein. Science 295: 1719-1722.
-
(2002)
Science
, vol.295
, pp. 1719-1722
-
-
Klein-Seetharaman, J.1
Oikawa, M.2
Grimshaw, S.B.3
Wirmer, J.4
Duchardt, E.5
Ueda, T.6
Imoto, T.7
Smith, L.J.8
Dobson, C.M.9
Schwalbe, H.10
-
47
-
-
0000542656
-
Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteins
-
Kolinski, A., Galazka, W., and Skolnick, J. 1998. Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteins. J. Chem. Phys. 108: 2608-2617.
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 2608-2617
-
-
Kolinski, A.1
Galazka, W.2
Skolnick, J.3
-
48
-
-
0031576337
-
Glutamine, alanine, or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates
-
Ladurner, A.G. and Fersht, A.R. 1997. Glutamine, alanine, or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates. J. Mol. Biol. 273: 330-337.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 330-337
-
-
Ladurner, A.G.1
Fersht, A.R.2
-
49
-
-
0031576341
-
Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2
-
Ladurner, A.G., Itzhaki, L.S., Gay, G.D., and Fersht, A.R. 1997. Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2. J. Mol. Biol. 273: 317-329.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 317-329
-
-
Ladurner, A.G.1
Itzhaki, L.S.2
Gay, G.D.3
Fersht, A.R.4
-
50
-
-
0034691198
-
Measuring the rate of intramolecular contact formation in polypeptides
-
Lapidus, L.J., Eaton, W.A., and Hofrichter, J. 2000. Measuring the rate of intramolecular contact formation in polypeptides. Proc. Natl. Acad. Sci. 97: 7220-7225.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 7220-7225
-
-
Lapidus, L.J.1
Eaton, W.A.2
Hofrichter, J.3
-
51
-
-
0035824886
-
Folding of circular permutants with decreased contact order: General trend balanced by protein stability
-
Lindberg, M.O., Tangrot, J., Otzen, D.E., Dolgikh, D.A., Finkelstein, A.V., and Oliveberg, M. 2001. Folding of circular permutants with decreased contact order: General trend balanced by protein stability. J. Mol. Biol. 314: 891-900.
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 891-900
-
-
Lindberg, M.O.1
Tangrot, J.2
Otzen, D.E.3
Dolgikh, D.A.4
Finkelstein, A.V.5
Oliveberg, M.6
-
52
-
-
0037155403
-
A model for the kinetics of protein folding: Kinetic Monte Carlo simulations and analytical results
-
Makarov, D.E. and Metiu, H. 2002. A model for the kinetics of protein folding: Kinetic Monte Carlo simulations and analytical results. J. Chem. Phys. 116: 5205-5216.
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 5205-5216
-
-
Makarov, D.E.1
Metiu, H.2
-
53
-
-
0037133574
-
How the folding rate constant of simple-single domain proteins depends on number of native contacts
-
Makarov, D.E., Keller, C.A., Plaxco, K.W., and Metiu, H. 2002. How the folding rate constant of simple-single domain proteins depends on number of native contacts. Proc. Natl. Acad. Sci. 99: 3535-3539.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 3535-3539
-
-
Makarov, D.E.1
Keller, C.A.2
Plaxco, K.W.3
Metiu, H.4
-
54
-
-
0034610360
-
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
-
Mayor, U., Johnson, C.M., Daggett, V., and Fersht. A.R. 2000. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl. Acad. Sci. 97: 13518-13522.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 13518-13522
-
-
Mayor, U.1
Johnson, C.M.2
Daggett, V.3
Fersht, A.R.4
-
55
-
-
0036678120
-
Experimental evaluation of topological parameters determining protein-folding rates
-
Miller, E.J., Fischer, K.F., and Marqusee, S. 2002. Experimental evaluation of topological parameters determining protein-folding rates. Proc. Natl. Acad. Sci. 99: 10359-10363.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 10359-10363
-
-
Miller, E.J.1
Fischer, K.F.2
Marqusee, S.3
-
56
-
-
0037039440
-
Equilibrium collapse and the kinetic 'foldability' of proteins
-
Millet, I.S., Townsley, L., Chiti, F., Doniach, S., and Plaxco, K.W. 2002. Equilibrium collapse and the kinetic 'foldability' of proteins. Biochemistry 41: 321-325.
-
(2002)
Biochemistry
, vol.41
, pp. 321-325
-
-
Millet, I.S.1
Townsley, L.2
Chiti, F.3
Doniach, S.4
Plaxco, K.W.5
-
57
-
-
0034984144
-
Protein folding theory: From lattice to all-atom models
-
Mirny, L. and Shakhnovich, E. 2001. Protein folding theory: From lattice to all-atom models. Annu. Rev. Biophys. Biomol. Struc. 30: 361-396.
-
(2001)
Annu. Rev. Biophys. Biomol. Struc.
, vol.30
, pp. 361-396
-
-
Mirny, L.1
Shakhnovich, E.2
-
58
-
-
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
-
59
-
-
0038502170
-
Folding dynamics and mechanism of β-hairpin formation
-
Muñoz, 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
-
-
Muñoz, V.1
Thompson, P.A.2
Hofrichter, J.3
Eaton, W.A.4
-
60
-
-
0035005366
-
Preorganized secondary structure as an important determinant of fast protein folding
-
Myers, J.K. and Oas, T.G. 2001. Preorganized secondary structure as an important determinant of fast protein folding. Nat. Struct. Biol. 8: 552-558.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 552-558
-
-
Myers, J.K.1
Oas, T.G.2
-
61
-
-
0034964196
-
Computer-based redesign of a protein folding pathway
-
Nauli, S., Kuhlman, B., and Baker, D. 2001. Computer-based redesign of a protein folding pathway. Nat. Struct. Biol. 8: 602-605.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 602-605
-
-
Nauli, S.1
Kuhlman, B.2
Baker, D.3
-
62
-
-
0030628825
-
Theory of protein folding: The energy landscape perspective
-
Onuchic, J.N., Luthey-Schulten, Z., and Wolynes, P.G. 1997. Theory of protein folding: The energy landscape perspective. Annu. Rev. Phys. Chem. 48: 545-600.
-
(1997)
Annu. Rev. Phys. Chem.
, vol.48
, pp. 545-600
-
-
Onuchic, J.N.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
63
-
-
0032474460
-
Folding of circular and permuted chymotrypsin inhibitor 2: Retention of the folding nucleus
-
Otzen, D.E. and Fersht, A.R. 1998. Folding of circular and permuted chymotrypsin inhibitor 2: Retention of the folding nucleus. Biochemistry 37: 8139-8146.
-
(1998)
Biochemistry
, vol.37
, pp. 8139-8146
-
-
Otzen, D.E.1
Fersht, A.R.2
-
64
-
-
0032374091
-
Structural and dynamical characterization of a biologically active unfolded fibronectin-binding protein from Staphylococus aureus
-
Penkett, C.J., Redfield, C., Jones, J.A., Dodd, I., Hubbard, J., Smith, R.A.G., Smith, L.J., and Dobson, C.M. 1998. Structural and dynamical characterization of a biologically active unfolded fibronectin-binding protein from Staphylococus aureus. Biochemistry 37: 17054-17067.
-
(1998)
Biochemistry
, vol.37
, pp. 17054-17067
-
-
Penkett, C.J.1
Redfield, C.2
Jones, J.A.3
Dodd, I.4
Hubbard, J.5
Smith, R.A.G.6
Smith, L.J.7
Dobson, C.M.8
-
65
-
-
0034886552
-
Unfolded, yes, but random? Never!
-
Plaxco, K.W. and Gross, M. 2001. Unfolded, yes, but random? Never! Nat. Struct. Biol. 8: 659-670.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 659-670
-
-
Plaxco, K.W.1
Gross, M.2
-
66
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco, K.W., Simons, K.T., and Baker, D. 1998. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277: 985-994.
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
67
-
-
0032978994
-
Polypeptide chain collapse can occur concomitantly with the rate limiting step in protein folding
-
Plaxco, K.W., Millett, I.S., Segel, D.J., Doniach, S., and Baker, D. 1999. Polypeptide chain collapse can occur concomitantly with the rate limiting step in protein folding. Nat. Struct. Biol. 6: 554-557.
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 554-557
-
-
Plaxco, K.W.1
Millett, I.S.2
Segel, D.J.3
Doniach, S.4
Baker, D.5
-
68
-
-
0034687123
-
Topology. Stability, sequence, and length: Defining the determinants of two-state protein folding kinetics
-
Plaxco, K.W., Simons, K.T., Ruczinski, I., and Baker, D. 2000. Topology. Stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry 37: 11177-11183.
-
(2000)
Biochemistry
, vol.37
, pp. 11177-11183
-
-
Plaxco, K.W.1
Simons, K.T.2
Ruczinski, I.3
Baker, D.4
-
69
-
-
0030165480
-
Correlated energy landscape model for finite, random heteropolymers
-
Plotkin, S.S., Wang, J, and Wolynes, P.G. 1996. Correlated energy landscape model for finite, random heteropolymers. Phys. Rev. E 53: 6271-6296.
-
(1996)
Phys. Rev. E
, vol.53
, pp. 6271-6296
-
-
Plotkin, S.S.1
Wang, J.2
Wolynes, P.G.3
-
70
-
-
84984087977
-
Statistical mechanics of noncovalent bonds in polyamino acids. 8. Covalent loops in proteins
-
Poland, D.C. and Scheraga, H.A. 1965. Statistical mechanics of noncovalent bonds in polyamino acids. 8. Covalent loops in proteins. Biopolymers 3: 379-385.
-
(1965)
Biopolymers
, vol.3
, pp. 379-385
-
-
Poland, D.C.1
Scheraga, H.A.2
-
71
-
-
0035868526
-
Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics
-
Portman, J.J., Takada, S., and Wolynes, P.G. 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
-
72
-
-
0032568591
-
Optimizing the stability of single-chain proteins by linker length and composition mutagenasis
-
Robinson, C.R. and Sauer, R.T. 1998. Optimizing the stability of single-chain proteins by linker length and composition mutagenasis. Proc. Natl. Acad. Sci. 95: 5929-5934.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 5929-5934
-
-
Robinson, C.R.1
Sauer, R.T.2
-
73
-
-
0018782641
-
Hierarchic organization of domains in globular-proteins
-
Rose, G.D. 1979. Hierarchic organization of domains in globular-proteins. J. Mol. Biol. 134: 447-470.
-
(1979)
J. Mol. Biol.
, vol.134
, pp. 447-470
-
-
Rose, G.D.1
-
74
-
-
0030759665
-
Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea
-
Schwalbe, H., Fiebig, J.M., Buck, M., Jones, J.A., Grimshaw, S.B., Spencer, A., Glaser, S.J., Smith, L.J., and Dobson, C.M. 1997. Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea. Biochemistry 36: 8977-8991.
-
(1997)
Biochemistry
, vol.36
, pp. 8977-8991
-
-
Schwalbe, H.1
Fiebig, J.M.2
Buck, M.3
Jones, J.A.4
Grimshaw, S.B.5
Spencer, A.6
Glaser, S.J.7
Smith, L.J.8
Dobson, C.M.9
-
75
-
-
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., and Brooks, C.L. 1999. Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A. Proc. Natl. Acad. Sci. 96: 12512-12517.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 12512-12517
-
-
Shea, J.E.1
Onuchic, J.N.2
Brooks, C.L.3
-
76
-
-
0032539561
-
Molecular picture of folding of a small α/β protein
-
Sheinerman, F.B. and Brooks, C.L. 1998. Molecular picture of folding of a small α/β protein. Proc. Natl. Acad. Sci. 95: 1562-1567.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 1562-1567
-
-
Sheinerman, F.B.1
Brooks, C.L.2
-
77
-
-
0033515614
-
Exploring structures in protein folding funnels with free energy functionals: The denatured ensemble
-
Shoemaker, B.A. and Wolynes, P.G. 1999. Exploring structures in protein folding funnels with free energy functionals: The denatured ensemble. J. Mol. Biol. 287: 657-674.
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 657-674
-
-
Shoemaker, B.A.1
Wolynes, P.G.2
-
78
-
-
0035919635
-
Persistence of native-like topology in a denatured protein in 8 M urea
-
Shortle, D. and Ackerman, M.S. 2001. Persistence of native-like topology in a denatured protein in 8 M urea. Science 293: 487-489.
-
(2001)
Science
, vol.293
, pp. 487-489
-
-
Shortle, D.1
Ackerman, M.S.2
-
79
-
-
0032147243
-
Protein folding mechanisms and the multidimensional folding funnel
-
Socci, N.D., Onuchic, J.N., and Wolynes, P.G. 1998. Protein folding mechanisms and the multidimensional folding funnel. Prot. Struc. Func. Gen. 32: 136-158.
-
(1998)
Prot. Struc. Func. Gen.
, vol.32
, pp. 136-158
-
-
Socci, N.D.1
Onuchic, J.N.2
Wolynes, P.G.3
-
80
-
-
0028402689
-
The barriers in protein folding
-
Sosnick, T.R., Mayne, L., Hiller, R., and Englander, S.W. 1994. The barriers in protein folding. Nat. Struct. Biol. 1: 149-156.
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 149-156
-
-
Sosnick, T.R.1
Mayne, L.2
Hiller, R.3
Englander, S.W.4
-
81
-
-
0029940033
-
Molecular collapse: The rate-limiting step in two-state cytochrome c folding
-
Sosnick, T.R., Mayne, L., and Englander, S.W. 1996. Molecular collapse: The rate-limiting step in two-state cytochrome c folding. Proteins 24: 413-426.
-
(1996)
Proteins
, vol.24
, pp. 413-426
-
-
Sosnick, T.R.1
Mayne, L.2
Englander, S.W.3
-
83
-
-
0000050196
-
From minimal models to real proteins: Time scales for protein folding
-
Thirumalai, D. 1995. From minimal models to real proteins: Time scales for protein folding. J. Physique 15: 1457-1467.
-
(1995)
J. Physique
, vol.15
, pp. 1457-1467
-
-
Thirumalai, D.1
-
84
-
-
0030789351
-
Laser temperature jump study of the helix reversible arrow coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model
-
Thompson, P.A., Eaton. W.A., and Hofrichter, J. 1997. Laser temperature jump study of the helix reversible arrow coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model. Biochemistry 36: 9200-9210.
-
(1997)
Biochemistry
, vol.36
, pp. 9200-9210
-
-
Thompson, P.A.1
Eaton, W.A.2
Hofrichter, J.3
-
85
-
-
0032491565
-
Slow folding of muscle acylphosphatase in the absence of intermediates
-
Van Nuland, N.A.J., Chiti, F., Taddei, N., Raugei, G., Ramponi, G., and Dobson, C.M. 1998. Slow folding of muscle acylphosphatase in the absence of intermediates. J. Mol. Biol. 283: 883-891.
-
(1998)
J. Mol. Biol.
, vol.283
, pp. 883-891
-
-
Van Nuland, N.A.J.1
Chiti, F.2
Taddei, N.3
Raugei, G.4
Ramponi, G.5
Dobson, C.M.6
-
86
-
-
0030663205
-
Loop length, intramolecular diffusion and protein folding
-
Viguera, A.R. and Serrano, L. 1997. Loop length, intramolecular diffusion and protein folding. Nat. Struct. Biol. 4: 939-946.
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 939-946
-
-
Viguera, A.R.1
Serrano, L.2
-
87
-
-
0033535839
-
Cytochrome b562 folding triggered by electron transfer: Approaching the speed limit for formation of a four-helix-bundle protein
-
Wittung-Stafshede, P., Lee, J.C., Winkler, J.R., and Gray, H.B. 1999. Cytochrome b562 folding triggered by electron transfer: Approaching the speed limit for formation of a four-helix-bundle protein. Proc. Natl. Acad. Sci. 96: 6587-6590.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 6587-6590
-
-
Wittung-Stafshede, P.1
Lee, J.C.2
Winkler, J.R.3
Gray, H.B.4
-
88
-
-
0036394906
-
Native-like mean structure in the unfolded ensemble of small proteins
-
in press
-
Zagrovic, B., Snow, C., Khaliq, S., Shirts, M., and Pande. V. 2002. Native-like mean structure in the unfolded ensemble of small proteins. J. Mol. Biol. (in press)
-
(2002)
J. Mol. Biol.
-
-
Zagrovic, B.1
Snow, C.2
Khaliq, S.3
Shirts, M.4
Pande, V.5
-
89
-
-
0000177440
-
Folding time of ideal β-sheets vs. chain length
-
Zhdanaov, V.P. 1998. Folding time of ideal β-sheets vs. chain length. Europhys. Lett. 42: 577-581.
-
(1998)
Europhys. Lett.
, vol.42
, pp. 577-581
-
-
Zhdanaov, V.P.1
-
90
-
-
0036215854
-
Folding rate prediction using total contact distance
-
Zhou, H.Y. and Zhou, Y.Q. 2002. Folding rate prediction using total contact distance. Biophys. J. 82: 458-463.
-
(2002)
Biophys. J.
, vol.82
, pp. 458-463
-
-
Zhou, H.Y.1
Zhou, Y.Q.2
-
91
-
-
0033598375
-
Interpreting the folding kinetics of helical proteins
-
Zhou, Y.Q. and Karplus, M. 1999. Interpreting the folding kinetics of helical proteins. Nature 401: 400-403.
-
(1999)
Nature
, vol.401
, pp. 400-403
-
-
Zhou, Y.Q.1
Karplus, M.2
|