-
1
-
-
0028024928
-
Specific nucleus as the transition state for protein folding: Evidence from the lattice model
-
Abkevich, V. I., A. M. Gutin, and E. I. Shakhnovich. 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
-
2
-
-
36849126204
-
Studies in molecular dynamics. I. General method
-
Alder, B. J., and T. E. Wainwright. 1959. Studies in molecular dynamics. I. General method. J. Chem. Phys. 31:459-466.
-
(1959)
J. Chem. Phys.
, vol.31
, pp. 459-466
-
-
Alder, B.J.1
Wainwright, T.E.2
-
3
-
-
0035895436
-
Apparent two-state tendamistat folding is a sequential process along a defined route
-
Bachmann, A., and T. Kiefhaber. 2001. Apparent two-state tendamistat folding is a sequential process along a defined route. J. Mol. Biol. 306:375-386.
-
(2001)
J. Mol. Biol.
, vol.306
, pp. 375-386
-
-
Bachmann, A.1
Kiefhaber, T.2
-
4
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
5
-
-
0036308818
-
Thermodynamics and folding kinetics analysis of the SH3 domain from discrete molecular dynamics
-
Borreguero, J. M., N. V. Dokholyan, S. V. Buldyrev, E. I. Shakhnovich, and H. E. Stanley. 2002. Thermodynamics and folding kinetics analysis of the SH3 domain from discrete molecular dynamics. J. Mol. Biol. 318:863-876.
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 863-876
-
-
Borreguero, J.M.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Shakhnovich, E.I.4
Stanley, H.E.5
-
7
-
-
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
-
8
-
-
0036183221
-
Im7 folding mechanism: Misfolding on a path to the native state
-
Capaldi, A. P., C. Kleanthous, and S. E. Radford. 2002. Im7 folding mechanism: misfolding on a path to the native state. Nat. Struct. Biol. 9:209-216.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 209-216
-
-
Capaldi, A.P.1
Kleanthous, C.2
Radford, S.E.3
-
9
-
-
0037154268
-
Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
-
Cheung, M. S., A. E. García, and J. N. Onuchic. 2002. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl. Acad. Sci. USA. 99:685-690.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 685-690
-
-
Cheung, M.S.1
García, A.E.2
Onuchic, J.N.3
-
10
-
-
0032514727
-
Folding kinetics of villin 14T, a protein domain with a central β-sheet and two hydrophobic cores
-
Choe, S. E., P. T. Matsudaira, J. Osterhout, G. Wagner, and E. I. Shakhnovich. 1998. Folding kinetics of villin 14T, a protein domain with a central β-sheet and two hydrophobic cores. Biochemistry. 37:14508-14518.
-
(1998)
Biochemistry
, vol.37
, pp. 14508-14518
-
-
Choe, S.E.1
Matsudaira, P.T.2
Osterhout, J.3
Wagner, G.4
Shakhnovich, E.I.5
-
11
-
-
0037459022
-
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein L
-
Clementi, C., A. E. García, and J. N. Onuchic. 2003. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. J. Mol. Biol. 326:933-954.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 933-954
-
-
Clementi, C.1
García, A.E.2
Onuchic, J.N.3
-
12
-
-
0036927818
-
Direct molecular dynamics observation of protein folding transition state ensemble
-
Ding, F., N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich. 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.E.4
Shakhnovich, E.I.5
-
13
-
-
0032443390
-
Molecular dynamics studies of folding of a protein-like model
-
Dokholyan, N. V., S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich. 1998. Molecular dynamics studies of folding of a protein-like model. Fold. Des. 3:577-587.
-
(1998)
Fold. Des.
, vol.3
, pp. 577-587
-
-
Dokholyan, N.V.1
Buldyrev, S.V.2
Stanley, H.E.3
Shakhnovich, E.I.4
-
14
-
-
41349116508
-
Glassy behavior of a homopolymer from molecular dynamics simulations
-
Dokholyan, N. V., E. Pitard, S. V. Buldyrev, and H. E. Stanley. 2002. Glassy behavior of a homopolymer from molecular dynamics simulations. Phys. Rev. E. 65:030801:1-030801:4.
-
(2002)
Phys. Rev. E
, vol.65
-
-
Dokholyan, N.V.1
Pitard, E.2
Buldyrev, S.V.3
Stanley, H.E.4
-
15
-
-
0033624685
-
Fast kinetics and mechanisms in protein folding
-
Eaton, W. A., V. Muñoz, J. 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
Muñoz, V.2
Hagen, J.S.J.3
Jas, G.S.4
Lapidus, L.J.5
Henry, E.R.6
Hofrichter, J.7
-
16
-
-
0041305985
-
Natural selection of more designable folds: A mechanism for thermophilic adaptation
-
England, J. L., B. E. Shakhnovich, and E. I. Shakhnovich. 2003. Natural selection of more designable folds: a mechanism for thermophilic adaptation. Proc. Natl. Acad. Sci. USA. 100:8727-8731.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 8727-8731
-
-
England, J.L.1
Shakhnovich, B.E.2
Shakhnovich, E.I.3
-
17
-
-
0033548553
-
Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9
-
Ferguson, N., A. P. Capaldi, R. James, C. Kleanthous, and S. E. Radford. 1999. Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9. J. Mol. Biol. 286:1597-1608.
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 1597-1608
-
-
Ferguson, N.1
Capaldi, A.P.2
James, R.3
Kleanthous, C.4
Radford, S.E.5
-
18
-
-
0028958601
-
Characterizing transition states in protein-folding - An essential step in the puzzle
-
Fersht, A. R. 1995. Characterizing transition states in protein-folding - an essential step in the puzzle. Curr. Opin. Struct. Biol. 5:79-84.
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, pp. 79-84
-
-
Fersht, A.R.1
-
19
-
-
0034687686
-
A kinetically significant intermediate in the folding of barnase
-
Fersht, A. R. 2000. A kinetically significant intermediate in the folding of barnase. Proc. Natl. Acad. Sci. USA. 97:14121-14126.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 14121-14126
-
-
Fersht, A.R.1
-
20
-
-
0034652206
-
Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
-
Fersht, A. R. 2000b. 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. USA. 97:1525-1529.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 1525-1529
-
-
Fersht, A.R.1
-
21
-
-
0037154980
-
Protein folding and unfolding at atomic resolution
-
Fersht, A. R., and V. Daggett. 2002. Protein folding and unfolding at atomic resolution. Cell. 108:573-582.
-
(2002)
Cell
, vol.108
, pp. 573-582
-
-
Fersht, A.R.1
Daggett, V.2
-
22
-
-
0033045105
-
A thermodynamic analysis of a family of small globular proteins: SH3 domains
-
Filimonov, V. V., A. I. Azuaga, A. R. Viguera, L. Serrano, and P. L. Mateo. 1999. A thermodynamic analysis of a family of small globular proteins: SH3 domains. Biophys. Chem. 77:195-208.
-
(1999)
Biophys. Chem.
, vol.77
, pp. 195-208
-
-
Filimonov, V.V.1
Azuaga, A.I.2
Viguera, A.R.3
Serrano, L.4
Mateo, P.L.5
-
23
-
-
0019569599
-
Non-interacting local-structure model of folding and unfolding transition in globular proteins. I. Formulation
-
Gō, N., and H. Abe. 1981. Non-interacting local-structure model of folding and unfolding transition in globular proteins. I. Formulation. Biopolymers. 20:991-1011.
-
(1981)
Biopolymers
, vol.20
, pp. 991-1011
-
-
Go, N.1
Abe, H.2
-
24
-
-
0035017534
-
NMR and SAXS characterization of the denatured state of the chemotactic protein CheY: Implications for protein folding initiation
-
García, P., L. Serrano, D. Durand, M. Rico, and M. Bruix. 2001. NMR and SAXS characterization of the denatured state of the chemotactic protein CheY: implications for protein folding initiation. Prot. Sci. 10:1100-1112.
-
(2001)
Prot. Sci.
, vol.10
, pp. 1100-1112
-
-
García, P.1
Serrano, L.2
Durand, D.3
Rico, M.4
Bruix, M.5
-
25
-
-
0037340910
-
Folding of a highly conserved diverging turn motif from the SH3 domain
-
Gnanakaran, S., and A. E. García. 2003. Folding of a highly conserved diverging turn motif from the SH3 domain. Biophys. J. 84:1548-1562.
-
(2003)
Biophys. J.
, vol.84
, pp. 1548-1562
-
-
Gnanakaran, S.1
García, A.E.2
-
26
-
-
0035965128
-
Acidic conditions stabilise intermediates populated during the folding of Im7 and Im9
-
Gorski, S. A., A. P. Capaldi, C. Kleanthous, and S. E. Radford. 2001. Acidic conditions stabilise intermediates populated during the folding of Im7 and Im9. J. Mol. Biol. 312:849-863.
-
(2001)
J. Mol. Biol.
, vol.312
, pp. 849-863
-
-
Gorski, S.A.1
Capaldi, A.P.2
Kleanthous, C.3
Radford, S.E.4
-
27
-
-
0031444104
-
Folding dynamics of the Src SH3 domain
-
Grantcharova, V. P., and D. Baker. 1997. Folding dynamics of the Src SH3 domain. Biochemistry. 36:15685-15692.
-
(1997)
Biochemistry
, vol.36
, pp. 15685-15692
-
-
Grantcharova, V.P.1
Baker, D.2
-
28
-
-
0031853167
-
Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain
-
Grantcharova, V. P., D. S. Riddle, J. N. Santiago, and D. Baker. 1998. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nat. Struct. Biol. 8:714-720.
-
(1998)
Nat. Struct. Biol.
, vol.8
, pp. 714-720
-
-
Grantcharova, V.P.1
Riddle, D.S.2
Santiago, J.N.3
Baker, D.4
-
29
-
-
0034671177
-
The SH3-fold family: Experimental evidence and prediction of variations in the folding pathways
-
Guerois, R., and L. Serrano. 2000. The SH3-fold family: experimental evidence and prediction of variations in the folding pathways. J. Mol. Biol. 304:967-982.
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 967-982
-
-
Guerois, R.1
Serrano, L.2
-
30
-
-
0001229818
-
Temperature dependence of the folding rate in a simple protein model: Search for a "glass" transition
-
Gutin, A., A. Sali, V. Abkevich, M. Karplus, and E. I. Shakhnovich. 1998. Temperature dependence of the folding rate in a simple protein model: search for a "glass" transition. J. Chem. Phys. 108:6466-6483.
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 6466-6483
-
-
Gutin, A.1
Sali, A.2
Abkevich, V.3
Karplus, M.4
Shakhnovich, E.I.5
-
31
-
-
0034705052
-
An essential intermediate in the folding of dihydrofolate reductase
-
Heidary, D. K., J. C. O'Neill, M. Roy, and P. A. Jennings. 2000. An essential intermediate in the folding of dihydrofolate reductase. Proc. Natl. Acad. Sci. USA. 97:5866-5870.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 5866-5870
-
-
Heidary, D.K.1
O'Neill, J.C.2
Roy, M.3
Jennings, P.A.4
-
32
-
-
0029785147
-
Mapping the protein universe
-
Holm, L., and C. Sander. 1996. Mapping the protein universe. Science. 273:595-602.
-
(1996)
Science
, vol.273
, pp. 595-602
-
-
Holm, L.1
Sander, C.2
-
33
-
-
0015918856
-
Kinetics of unfolding and refolding of proteins. I. Mathematical analysis
-
Ikai, A., and C. Tandford. 1973. Kinetics of unfolding and refolding of proteins. I. Mathematical analysis. J. Mol. Biol. 73:145-163.
-
(1973)
J. Mol. Biol.
, vol.73
, pp. 145-163
-
-
Ikai, A.1
Tandford, C.2
-
34
-
-
0033613236
-
Equilibria and kinetics of folding of gelsolin domain 2 and mutants involved in familial amyloidosis-Finnish type
-
Isaacson, R. L., A. G. Weedsdagger, and A. R. Fersht. 1999. Equilibria and kinetics of folding of gelsolin domain 2 and mutants involved in familial amyloidosis-Finnish type. Proc. Natl. Acad. Sci. USA. 96:11247-11252.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11247-11252
-
-
Isaacson, R.L.1
Weedsdagger, A.G.2
Fersht, A.R.3
-
35
-
-
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
-
36
-
-
0037176861
-
Characterization of the unfolding of ribonuclease A by a pulsed hydrogen exchange study: Evidence for competing pathways for unfolding
-
Juneja, J., and J. B. Udgaonkar. 2002. Characterization of the unfolding of ribonuclease A by a pulsed hydrogen exchange study: evidence for competing pathways for unfolding. Biochemistry. 41:2641-2654.
-
(2002)
Biochemistry
, vol.41
, pp. 2641-2654
-
-
Juneja, J.1
Udgaonkar, J.B.2
-
37
-
-
0042887400
-
Multiple parallel-pathway folding of proline-free staphylococcal nuclease
-
Kamagata, K., Y. Sawano, M. Tanokura, and K. Kuwajima. 2003. Multiple parallel-pathway folding of proline-free staphylococcal nuclease. J. Mol. Biol. 332:1143-1153.
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 1143-1153
-
-
Kamagata, K.1
Sawano, Y.2
Tanokura, M.3
Kuwajima, K.4
-
38
-
-
0037386699
-
The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: Lessons for protein design?
-
Karanicolas, J., and C. L. Brooks, III. 2003. The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proc. Natl. Acad. Sci. USA. 100:3954-3959.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3954-3959
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
39
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M., and J. A. McCammon. 2002. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9:646-652.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
40
-
-
0030057477
-
Evidence for a three-state model of protein folding from kinetics analysis of ubiquitin variants with altered core residues
-
Khorasanizadeh, S., I. D. Peters, and H. Roder. 1996. Evidence for a three-state model of protein folding from kinetics analysis of ubiquitin variants with altered core residues. Nature Struct. Biol. 3:193-205.
-
(1996)
Nature Struct. Biol.
, vol.3
, pp. 193-205
-
-
Khorasanizadeh, S.1
Peters, I.D.2
Roder, H.3
-
41
-
-
0029025915
-
Kinetics traps in lysozyme folding
-
Kiefhaber, T. 1995. Kinetics traps in lysozyme folding. Proc. Natl. Acad. Sci. USA. 92:9029-9033.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 9029-9033
-
-
Kiefhaber, T.1
-
42
-
-
0037452877
-
Close identity of a pressure-stabilized intermediate with a kinetic intermediate in protein folding
-
Kitahara, R., and K. Akasaka. 2003. Close identity of a pressure-stabilized intermediate with a kinetic intermediate in protein folding. Proc. Natl. Acad. Sci. USA. 100:3167-3172.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3167-3172
-
-
Kitahara, R.1
Akasaka, K.2
-
43
-
-
0036295960
-
Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains
-
Klimov, D. K., and D. Thirumalai. 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
-
44
-
-
0032525298
-
Thermal unfolding of small proteins with SH3 domain folding pattern
-
Knapp, S., P. T. Mattson, P. Christova, K. D. Berndt, A. Karshikoff, M. Vihinen, C. I. Smith, and R. Ladenstein. 1998. Thermal unfolding of small proteins with SH3 domain folding pattern. PSFG. 23:309-319.
-
(1998)
PSFG
, vol.23
, pp. 309-319
-
-
Knapp, S.1
Mattson, P.T.2
Christova, P.3
Berndt, K.D.4
Karshikoff, A.5
Vihinen, M.6
Smith, C.I.7
Ladenstein, R.8
-
45
-
-
0034646562
-
Similarities between the spectrin SH3 domain denatured state and its folding transition state
-
Kortemme, T., M. J. S. Kelly, L. E. Kay, J. Forman-Kay, and L. Serrano. 2000. Similarities between the spectrin SH3 domain denatured state and its folding transition state. J. Mol. Biol. 297:1217-1229.
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 1217-1229
-
-
Kortemme, T.1
Kelly, M.J.S.2
Kay, L.E.3
Forman-Kay, J.4
Serrano, L.5
-
46
-
-
0030334834
-
Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2
-
Lopez-Hernandez, E., and L. Serrano. 1996. Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. Fold. Des. 1:43-55.
-
(1996)
Fold. Des.
, vol.1
, pp. 43-55
-
-
Lopez-Hernandez, E.1
Serrano, L.2
-
47
-
-
0036088602
-
The linkage between protein folding and functional cooperativity: Two sides of the same coin?
-
Luque, I., S. A. Leavitt, and E. Freire. 2002. The linkage between protein folding and functional cooperativity: two sides of the same coin? Annu. Rev. Biophys. Biomol. Struct. 31:235-256.
-
(2002)
Annu. Rev. Biophys. Biomol. Struct.
, vol.31
, pp. 235-256
-
-
Luque, I.1
Leavitt, S.A.2
Freire, E.3
-
48
-
-
0039726624
-
Thermodynamic analysis of α-spectrin SH3 and two of its circular permutants with different loop lengths: Discerning the reasons for rapid folding in proteins
-
Martinez, J. C., A. R. Viguera, R. Berisio, M. Wilmanns, P. L. Mateo, V. V. Filimonov, and L. Serrano. 1999. Thermodynamic analysis of α-spectrin SH3 and two of its circular permutants with different loop lengths: discerning the reasons for rapid folding in proteins. Biochemistry. 38:549-559.
-
(1999)
Biochemistry
, vol.38
, pp. 549-559
-
-
Martinez, J.C.1
Viguera, A.R.2
Berisio, R.3
Wilmanns, M.4
Mateo, P.L.5
Filimonov, V.V.6
Serrano, L.7
-
49
-
-
0025698613
-
Transient folding intermediates characterized by protein engineering
-
Matouschek, A., J. T. Kellis, Jr., L. Serrano, M. Bycroft, and A. R. Fersht. 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
-
50
-
-
0036401140
-
Toward a taxonomy of the denatured state: Small angle scattering studies of unfolded proteins
-
Millet, I. S., S. Doniach, and K. W. Plaxco. 2002. Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. Adv. Prot. Chem. 62:241-262.
-
(2002)
Adv. Prot. Chem.
, vol.62
, pp. 241-262
-
-
Millet, I.S.1
Doniach, S.2
Plaxco, K.W.3
-
51
-
-
0030334626
-
Universality and diversity of the protein folding scenarios: A comprehensive analysis with the aid of a lattice model
-
Mirny, L. A., V. Abkevich, and E. I. Shakhnovich. 1996. Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model. Fold. Des. 1:103-116.
-
(1996)
Fold. Des.
, vol.1
, pp. 103-116
-
-
Mirny, L.A.1
Abkevich, V.2
Shakhnovich, E.I.3
-
52
-
-
0036172116
-
Hydrophobic core packing in the SH3 domain folding transition state
-
Northey, J. G. B., A. A. Di Nardo, and A. R. Davidson. 2002. Hydrophobic core packing in the SH3 domain folding transition state. Nat. Struct. Biol. 9:126-130.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 126-130
-
-
Northey, J.G.B.1
Di Nardo, A.A.2
Davidson, A.R.3
-
53
-
-
0033580679
-
Structural changes in the transition state of protein folding: Alternative interpretations of curved chevron plots
-
Otzen, D. E., O. Kristensen, M. Proctor, and M. Oliveberg. 1999. Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots. Biochemistry. 38:6499-6511.
-
(1999)
Biochemistry
, vol.38
, pp. 6499-6511
-
-
Otzen, D.E.1
Kristensen, O.2
Proctor, M.3
Oliveberg, M.4
-
54
-
-
0036074173
-
Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model
-
Ozkan, S. B., K. A. Dill, and I. Bahar. 2002. Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model. Prot. Sci. 11:1958-1970.
-
(2002)
Prot. Sci.
, vol.11
, pp. 1958-1970
-
-
Ozkan, S.B.1
Dill, K.A.2
Bahar, I.3
-
55
-
-
0037093654
-
Native and non-native interactions along protein folding and unfolding pathways
-
Paci, E., M. Vendruscolo, and M. Karplus. 2002. Native and non-native interactions along protein folding and unfolding pathways. Prot. Struct. Func. Genet. 47:379-392.
-
(2002)
Prot. Struct. Func. Genet.
, vol.47
, pp. 379-392
-
-
Paci, E.1
Vendruscolo, M.2
Karplus, M.3
-
56
-
-
0034338307
-
Heteropolymer freezing and design: Towards physical models of protein folding
-
Pande, V. S., A. Y. Grosberg, and T. Tanaka. 2000. Heteropolymer freezing and design: towards physical models of protein folding. Rev. Mod. Phys. 72:259-314.
-
(2000)
Rev. Mod. Phys.
, vol.72
, pp. 259-314
-
-
Pande, V.S.1
Grosberg, A.Y.2
Tanaka, T.3
-
57
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco, K. W., K. T. Simons, and D. Baker. 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
-
58
-
-
0034886552
-
Unfolded, yes, but random? Never!
-
Plaxco, K. W., and M. Gross. 2001. Unfolded, yes, but random? Never! Nature. 8:659-660.
-
(2001)
Nature
, vol.8
, pp. 659-660
-
-
Plaxco, K.W.1
Gross, M.2
-
59
-
-
0037155413
-
Structural and energetic heterogeneity in protein folding. I. Theory
-
Plotkin, S. S., and J. N. Onuchic. 2002. Structural and energetic heterogeneity in protein folding. I. Theory. J. Chem. Phys. 116:5263-5283.
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 5263-5283
-
-
Plotkin, S.S.1
Onuchic, J.N.2
-
61
-
-
0032734515
-
Experiment and theory highlight role of native state topology in SH3 folding
-
Riddle, D. S., V. P. Grantcharova, J. V. Santiago, A. L. M. E. Ruczinski, and D. Baker. 1999. Experiment and theory highlight role of native state topology in SH3 folding. Nat. Struct. Biol. 6:1016-1024.
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 1016-1024
-
-
Riddle, D.S.1
Grantcharova, V.P.2
Santiago, J.V.3
Ruczinski, A.L.M.E.4
Baker, D.5
-
62
-
-
0037225280
-
Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding
-
Sanchez, I. E., and T. Kiefhaber. 2003. Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding. J. Mol. Biol. 325:367-376.
-
(2003)
J. Mol. Biol.
, vol.325
, pp. 367-376
-
-
Sanchez, I.E.1
Kiefhaber, T.2
-
63
-
-
0037058992
-
Probing the folding free energy landscape of the src-SH3 protein domain
-
Shea, J. E., J. N. Onuchic, and C. L. Brooks, III. 2002. Probing the folding free energy landscape of the src-SH3 protein domain. Proc. Natl. Acad. Sci. USA. 99:16064-16068.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 16064-16068
-
-
Shea, J.E.1
Onuchic, J.N.2
Brooks III, C.L.3
-
64
-
-
0035919635
-
Persistence of native-like topology in a denatured protein in 8 M urea
-
Shortle, D., and M. S. Ackerman. 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
-
66
-
-
0037065802
-
Characterization of transient protein folding intermediates during myoglobin reconstitution by time-resolved electrospray mass spectrometry with on-line isotopic pulse labeling
-
Simmons, D. A., and L. Konermann. 2002. Characterization of transient protein folding intermediates during myoglobin reconstitution by time-resolved electrospray mass spectrometry with on-line isotopic pulse labeling. Biochemistry. 41:1906-1914.
-
(2002)
Biochemistry
, vol.41
, pp. 1906-1914
-
-
Simmons, D.A.1
Konermann, L.2
-
67
-
-
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. 15:5860-5868.
-
(1996)
J. Chem. Phys.
, vol.15
, pp. 5860-5868
-
-
Socci, N.D.1
Onuchic, J.N.2
Wolynes, P.G.3
-
69
-
-
2242465042
-
Insights into specific problems in protein folding using simple concepts
-
Thirumalai, D., D. K. Klimov, and R. I. Dima. 2002. Insights into specific problems in protein folding using simple concepts. Adv. Chem. Phys. 120:35-76.
-
(2002)
Adv. Chem. Phys.
, vol.120
, pp. 35-76
-
-
Thirumalai, D.1
Klimov, D.K.2
Dima, R.I.3
-
70
-
-
0034823503
-
Statistical analysis of native contact formation in the folding of designed model proteins
-
Tiana, G., and R. A. Broglia. 2001. Statistical analysis of native contact formation in the folding of designed model proteins. J. Chem. Phys. 114:2503-2510.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 2503-2510
-
-
Tiana, G.1
Broglia, R.A.2
-
71
-
-
0028331876
-
Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition
-
Viguera, A. R., V. V. Filimonov, P. L. Mateo, and L. Serrano. 1994. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. Biochemistry. 33:2142-2150.
-
(1994)
Biochemistry
, vol.33
, pp. 2142-2150
-
-
Viguera, A.R.1
Filimonov, V.V.2
Mateo, P.L.3
Serrano, L.4
-
72
-
-
0038286126
-
Hydrogen-exchange stability analysis of Bergerac-Src homology 3 variants allows the characterization of a folding intermediate in equilibrium
-
Viguera, A. R., and L. Serrano. 2003. Hydrogen-exchange stability analysis of Bergerac-Src homology 3 variants allows the characterization of a folding intermediate in equilibrium. Proc. Natl. Acad. Sci. USA. 100:5730-5735.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 5730-5735
-
-
Viguera, A.R.1
Serrano, L.2
-
74
-
-
0031010618
-
Kinetic evidence for folding and unfolding intermediates in staphylococcal nuclease
-
Walkenhorst, W. F., S. M. Green, and H. Roder. 1997. Kinetic evidence for folding and unfolding intermediates in staphylococcal nuclease. Biochemistry. 36:5795-5805.
-
(1997)
Biochemistry
, vol.36
, pp. 5795-5805
-
-
Walkenhorst, W.F.1
Green, S.M.2
Roder, H.3
-
75
-
-
0029643950
-
Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk
-
Wu, X. D., B. Knudsen, S. M. Feller, J. Sali, D. Cowburn, and H. Hanafusa. 1995. Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk, Structure. 2:215-226.
-
(1995)
Structure
, vol.2
, pp. 215-226
-
-
Wu, X.D.1
Knudsen, B.2
Feller, S.M.3
Sali, J.4
Cowburn, D.5
Hanafusa, H.6
-
76
-
-
0029598779
-
Folding pathway of Escherichia coli ribonuclease HI: A circular dichroism, fluorescence, and NMR study
-
Yamasaki, K., K. Ogasahara, K. Yutani, M. Oobatake, and S. Kanaya. 1995. Folding pathway of Escherichia coli ribonuclease HI: a circular dichroism, fluorescence, and NMR study. Biochemistry. 34:16552-16562.
-
(1995)
Biochemistry
, vol.34
, pp. 16552-16562
-
-
Yamasaki, K.1
Ogasahara, K.2
Yutani, K.3
Oobatake, M.4
Kanaya, S.5
-
77
-
-
0036394906
-
Native-like mean structure in the unfolded ensemble of small proteins
-
Zagrovic, B., C. D. Snow, S. Khaliq, M. R. Shirts, and V. S. Pande. 2002. Native-like mean structure in the unfolded ensemble of small proteins. J. Mol. Biol. 323:153-164.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 153-164
-
-
Zagrovic, B.1
Snow, C.D.2
Khaliq, S.3
Shirts, M.R.4
Pande, V.S.5
-
78
-
-
0031475159
-
Folding thermodynamics of a model three-helix-bundle protein
-
Zhou, Y. Q., and M. Karplus. 1997. Folding thermodynamics of a model three-helix-bundle protein. Proc. Natl. Acad. Sci. USA. 94:14429-14432.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 14429-14432
-
-
Zhou, Y.Q.1
Karplus, M.2
-
79
-
-
0001015060
-
Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions
-
Zhou, Y. Q., M. Karplus, J. M. Wichert, and C. K. Hall. 1997. Equilibrium thermodynamics of homopolymers and clusters: molecular dynamics and Monte Carlo simulations of systems with square-well interactions. J. Chem. Phys. 107:10691-10708.
-
(1997)
J. Chem. Phys.
, vol.107
, pp. 10691-10708
-
-
Zhou, Y.Q.1
Karplus, M.2
Wichert, J.M.3
Hall, C.K.4
|