The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Transition states and folding dynamics of proteins and heteropolymers
Abstract
We study the folding dynamics of short two-dimensional self-avoiding lattice model proteins and copolymers with specific HP sequences (H, hydrophobic, P, polar) that fold to unique native structures. HH contacts are favorable. The conformational landscape is found by exhaustive enumeration using two different move sets, and time evolution is modeled by a transition matrix with the Metropolis criterion. The kinetic sequence of folding events depends strongly on both the monomer sequence and on the move set. But certain features are common to all sequences with both move sets. Beginning with open conformations, chains fold through multiple paths, are slowed by kinetic traps, and accumulate in compact nonnative conformations. Most chains must surmount energy barriers, which we identify as the transition state. Strikingly, the transition state involves a chain expansion, due to the breaking of HH contacts of compact denatured conformations. Mutations can significantly affect the energy landscape and folding dynamics, but in ways that appear too subtle to predict just from knowledge of native structures. Consistent with other models, we find that sequences with a large energy gap between the native and the next higher energy level can be stable and fold rapidly.
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Cites
Equation of State Calculations by Fast Computing Machines
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., & Teller, E. (1953) · The Journal of Chemical Physics · doi:10.1063/1.1699114 · Cited by 37,192
The Design and Analysis of Computer Algorithms
Aho, A. V., & Hopcroft, J. E. (1974) · CERN Document Server (European Organization for Nuclear Research) · Cited by 9,403
The Energy Landscapes and Motions of Proteins
Frauenfelder, H., Sligar, S. G., & Wolynes, P. G. (1991) · Science · doi:10.1126/science.1749933 · Cited by 3,250
Are there pathways for protein folding?
Levinthal, C. (1968) · Journal de Chimie Physique · doi:10.1051/jcp/1968650044 · Cited by 1,517
Kuwajima, K. (1989) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340060202 · Cited by 1,439
A lattice statistical mechanics model of the conformational and sequence spaces of proteins
Lau, K. F., & Dill, K. A. (1989) · Macromolecules · doi:10.1021/ma00200a030 · Cited by 957
Self-citationProtein folding funnels: a kinetic approach to the sequence-structure relationship.
Leopold, P. E., Montal, M., & Onuchic, J. N. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.18.8721 · Cited by 921
Nucleation, Rapid Folding, and Globular Intrachain Regions in Proteins
Wetlaufer, D. B. (1973) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.70.3.697 · Cited by 831
Intermediates and barrier crossing in a random energy model (with applications to protein folding)
Bryngelson, J. D., & Wolynes, P. G. (1989) · The Journal of Physical Chemistry · doi:10.1021/j100356a007 · Cited by 755
Diffusion Constants near the Critical Point for Time-Dependent Ising Models. I
Kawasaki, K. (1966) · Physical Review · doi:10.1103/physrev.145.224 · Cited by 613
Cited by
Funnels, pathways, and the energy landscape of protein folding: A synthesis
Bryngelson, J. D., Onuchic, J. N., Socci, N. D., & Wolynes, P. G. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340210302 · Cited by 2,648
“Protein folding is completely different from these simple reactions [5, 40, 41, 71].”
BackgroundFrom Levinthal to pathways to funnels
Dill, K. A., & Chan, H. S. (1997) · Nature Structural & Molecular Biology · doi:10.1038/nsb0197-10 · Cited by 2,293
Self-citationPrinciples of protein folding — A perspective from simple exact models
Dill, K. A., Bromberg, S., Yue, K., Chan, H. S., Fiebig, K. M., Yee, D. P., & Thomas, P. D. (1995) · Protein Science · doi:10.1002/pro.5560040401 · Cited by 1,525
Self-citationDill, K. A., Ozkan, S. B., Shell, M. S., & Weikl, T. R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092707.153558 · Cited by 1,163
Self-citationFolding funnels, binding funnels, and protein function
Tsai, C., Kumar, S., Ma, B., & Nussinov, R. (1999) · Protein Science · doi:10.1110/ps.8.6.1181 · Cited by 648
Metadata
- Authors
- Chan, H. S., & Dill, K. A.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 1994-06-15
- Volume
- 100
- Issue
- 12
- Pages
- 9238-9257
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2009467983
- Cited by
- 281
- References
- 39
- FWCI
- 8.09
- Type
- journal article
- Language
- en
- Open access
- closed
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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