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Ariel Fernández, A. Colubri (1998)
Microscopic dynamics from a coarsely defined solution to the protein folding problemJournal of Mathematical Physics, 39
G. Huang, T. Oas (1995)
Structure and stability of monomeric lambda repressor: NMR evidence for two-state folding.Biochemistry, 34 12
(1997)
Proc Natl Acad Sci
D. Hamada, Y. Goto (1997)
The equilibrium intermediate of beta-lactoglobulin with non-native alpha-helical structure.Journal of molecular biology, 269 4
K. Kuwata, R. Shastry, Hong Cheng, M. Hoshino, C. Batt, Y. Goto, H. Roder (2001)
Structural and kinetic characterization of early folding events in β-lactoglobulinNature Structural Biology, 8
W. Houry, D. Rothwarf, H. Scheraga (1995)
The nature of the initial step in the conformational folding of disulphide-intact ribonuclease ANature Structural Biology, 2
Rajgopal Srinivasan, G. Rose (1995)
LINUS: A hierarchic procedure to predict the fold of a proteinProteins: Structure, 22
D. Hamada, S. Segawa, Y. Goto (1996)
Non-native α-helical intermediate in the refolding of β-lactoglobulin, a predominantly β-sheet proteinNature Structural Biology, 3
V. Forge, M. Hoshino, K. Kuwata, M. Arai, K. Kuwajima, C. Batt, Y. Goto (2000)
Is folding of beta-lactoglobulin non-hierarchic? Intermediate with native-like beta-sheet and non-native alpha-helix.Journal of molecular biology, 296 4
B. Krantz, T. Sosnick (2000)
Distinguishing between two-state and three-state models for ubiquitin folding.Biochemistry, 39 38
A. Liwo, A. Liwo, A. Liwo, R. Kazmierkiewicz, C. Czaplewski, M. Groth, S. Ołdziej, R. Wawak, S. Rackovsky, Matthew Pincus, H. Scheraga (1998)
United‐residue force field for off‐lattice protein‐structure simulations: III. Origin of backbone hydrogen‐bonding cooperativity in united‐residue potentialsJournal of Computational Chemistry, 19
(2002)
Physica A
S. Jackson (1998)
How do small single-domain proteins fold?Folding & design, 3 4
C. Krittanai, W. Johnson (1997)
The relative order of helical propensity of amino acids changes with solvent environmentProteins: Structure, 39
DISTINGUISHING FOLDABLE PROTEINS FROM NONFOLDERS
Ariel Fernández, A. Colubri, R. Berry (2000)
Topology to geometry in protein folding: β-LactoglobulinProceedings of the National Academy of Sciences of the United States of America, 97
C. Waldburger, Thorlakur Jonsson, Robert Sauer (1996)
Barriers to protein folding: formation of buried polar interactions is a slow step in acquisition of structure.Proceedings of the National Academy of Sciences of the United States of America, 93 7
K. Kuwata, R. Shastry, H. Cheng, M. Hoshino, C. Batt, Y. Goto, H. Roder (2001)
Structural and kinetic characterization of early folding events in beta-lactoglobulin.Nature structural biology, 8 2
D. Hamada, Shigeki Segawa, Yoichiro Goto (1996)
Non-native alpha-helical intermediate in the refolding of beta-lactoglobulin, a predominantly beta-sheet protein.Nature structural biology, 3 10
M. Shastry, H. Roder (1998)
Evidence for barrier-limited protein folding kinetics on the microsecond time scaleNature Structural Biology, 5
S. Akiyama, Satoshi Takahashi, K. Ishimori, I. Morishima (2000)
Stepwise formation of alpha-helices during cytochrome c folding.Nature structural biology, 7 6
A. Kentsis, T. Sosnick (1998)
Trifluoroethanol promotes helix formation by destabilizing backbone exposure: desolvation rather than native hydrogen bonding defines the kinetic pathway of dimeric coiled coil folding.Biochemistry, 37 41
Kibeom Park, M. Vendruscolo, E. Domany (2000)
Toward an energy function for the contact map representation of proteinsProteins: Structure, 40
D. Minor, P. Kim (1994)
Context is a major determinant of beta-sheet propensity.Nature, 371 6494
T. Sosnick, M. Shtilerman, L. Mayne, S. Englander (1997)
Ultrafast signals in protein folding and the polypeptide contracted state.Proceedings of the National Academy of Sciences of the United States of America, 94 16
S. Khorasanizadeh, I. Peters, H. Roder (1996)
Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residuesNature Structural Biology, 3
A. Fernández, A. Colubri, R. Berry (2000)
Topology to geometry in protein folding: beta-lactoglobulin.Proceedings of the National Academy of Sciences of the United States of America, 97 26
Ariel Fernández, A. Colubri, R. Berry (2002)
Three-body correlations in protein folding: the origin of cooperativityPhysica A-statistical Mechanics and Its Applications, 307
(1997)
Ultrafast 22 T.R. SOSNICK ET AL. signals in protein folding and the polypeptide contracted state
S. Hagen, W. Eaton (2000)
Two-state expansion and collapse of a polypeptide.Journal of molecular biology, 301 4
D. Minor, P. Kim (1994)
Context is a major determinant of β-sheet propensityNature, 371
T. Sosnick, L. Mayne, S. Englander (1996)
Molecular collapse: The rate‐limiting step in two‐state cytochrome c foldingProteins: Structure, 24
P. Qi, T. Sosnick, S. Englander (1998)
The burst phase in ribonuclease A folding and solvent dependence of the unfolded stateNature Structural Biology, 5
Ariel Fernández, R. Berry (2000)
Self-organization and mismatch tolerance in protein folding: General theory and an applicationJournal of Chemical Physics, 112
Lois Pollack, M. Tate, Nicholas Darnton, James Knight, S. Gruner, William Eaton, Robert Austin (1999)
Compactness of the denatured state of a fast-folding protein measured by submillisecond small-angle x-ray scattering.Proceedings of the National Academy of Sciences of the United States of America, 96 18
V. Forge, M. Hoshino, K. Kuwata, M. Arai, K. Kuwajima, C. Batt, Y. Goto (2000)
Is folding of β-lactoglobulin non-hierarchic? intermediate with native-like β-sheet and non-native α-helixJournal of Molecular Biology, 296
S. Takada, Z. Luthey-Schulten, P. Wolynes (1999)
Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymerJournal of Chemical Physics, 110
(1998)
Unitedresidue force field for off-lattice protein-structure simulations: Iii. Origin of backbone hydrogen-bonding cooperativity in unitedresidue potentials
Chi-Kin Chan, Yi Hu, S. Takahashi, Satoshi Takahashi, Denis Rousseau, William Eaton, J. Hofrichter (1997)
Submillisecond protein folding kinetics studied by ultrarapid mixing.Proceedings of the National Academy of Sciences of the United States of America, 94 5
Ariel Fernández, A. Colubri, R. Berry (2001)
Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenariosJournal of Chemical Physics, 114
Ariel Fernández (2001)
Conformation-dependent environments in folding proteinsJournal of Chemical Physics, 114
B. Krantz, L. Moran, A. Kentsis, T. Sosnick (2000)
D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein foldingNature Structural Biology, 7
A. Fernández, K. Kostov, R. Berry (1999)
From residue matching patterns to protein folding topographies: general model and bovine pancreatic trypsin inhibitor.Proceedings of the National Academy of Sciences of the United States of America, 96 23
Ariel Fernández (1998)
The Lagrangian Structure of Long-Time Torsional Dynamics Leading to RNA FoldingJournal of Statistical Physics, 92
R. Laskowski, M. MacArthur, D. Moss, J. Thornton (1993)
PROCHECK: a program to check the stereochemical quality of protein structuresJournal of Applied Crystallography, 26
J. Sauder, H. Roder (1998)
Amide protection in an early folding intermediate of cytochrome c.Folding & design, 3 4
When a denatured polypeptide is put into refolding conditions, it undergoes conformational changes on a variety of times scales. We set out here to distinguish the fast events that promote productive folding from other processes that may be generic to any non‐folding polypeptide. We have apply an ab initio folding algorithm to model the folding of various proteins and their compositionally identical, random‐sequence analogues. In the earliest stages, proteins and their scrambled‐sequence counterparts undergo indistinguishable reductions in the extent to which they explore conformation space. For both polypeptides, an early contraction occurs but does not involve the formation of a distinct intermediate. Following this phase, however, the naturally‐occurring sequences are distinguished by an increase in the formation of three‐body correlations wherein a hydrophobic group desolvates and protects an intra‐molecular hydrogen bond. These correlations are manifested in a mild but measurable reduction of the accessible configuration space beyond that of the random‐sequence peptides, and portend the folding to the native structure. Hence, early events reflect a generic response of the denatured ensemble to a change in solvent condition, but the wild‐type sequence develops additional correlations as its structure evolves that can reveal the protein's foldability. Proteins 2002;49:15–23. © 2002 Wiley‐Liss, Inc.
Proteins: Structure Function and Bioinformatics – Wiley
Published: Jan 1, 2002
Keywords: ; ; ; ; ; ; ;
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