ArticleJournal of chemical theory and computation2011
Are Peptides Good Two-State Folders?
Article in Journal of chemical theory and computation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Towards a generic prototyping approach for therapeutically-relevant peptides and proteins in a cell-free translation system.Nature communications · 2022Article
- Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields.The journal of physical chemistry. B · 2021Article
- Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides.The Journal of chemical physics · 2018Article
- Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations.The journal of physical chemistry. B · 2018Article
- Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics.Biophysical journal · 2016Article
- Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding.The journal of physical chemistry letters · 2014Article
- Note: network random walk model of two-state protein folding: test of the theory.The Journal of chemical physics · 2013Article
- Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation.Biophysical journal · 2012Article
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Authors and funding
3 authors.
Funding
Abstract
The folding kinetics of proteins is frequently single-exponential, as basins of folded and unfolded conformations are well separated by a high barrier. However, for relatively short peptides, a two-state character of folding is rather the exception than the rule. In this work, we use a Zwanzig-type model of protein conformational dynamics to study the dependence of folding kinetics on the protein chain length, M. The analysis is focused on the gap in the eigenvalue spectrum of the rate matrix that describes the protein's conformational dynamics. When there is a large gap between the two smallest in magnitude nonzero eigenvalues, the corresponding relaxation times have qualitatively different physical interpretations. The longest of these two times characterizes the interbasin equilibration (i.e., folding), whereas the second time characterizes the intrabasin relaxation. We derive approximate analytical solutions for the two eigenvalues that show how they depend on M. From these solutions, we infer that there is a large gap between the two, and thus, the kinetics is essentially single-exponential when M is large enough such that 2(M+1) is much larger than M(2).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.