ArticleJournal of molecular biology2009
Psi-constrained simulations of protein folding transition states: implications for calculating.
Article in Journal of molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Piecewise All-Atom SMD Simulations Reveal Key Secondary Structures in Luciferase Unfolding Pathway.Biophysical journal · 2020Article
- Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different.Journal of molecular biology · 2020Review
- Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized).Journal of molecular biology · 2012Article
- A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable.Protein science : a publication of the Protein Society · 2012Article
- Ubiquitin is a novel substrate for human insulin-degrading enzyme.Journal of molecular biology · 2011Article
- The folding of single domain proteins--have we reached a consensus?Current opinion in structural biology · 2011Review
- Protein vivisection reveals elusive intermediates in folding.Journal of molecular biology · 2010Article
- Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates.Biochemistry · 2009Article
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Authors and funding
3 authors.
Funding
Abstract
Psi-analysis has been used to identify interresidue contacts in the transition state ensemble (TSE) of ubiquitin and other proteins. The magnitude of psi depends on the degree to which an inserted bihistidine (biHis) metal ion binding site is formed in the TSE. A psi equal to zero or one indicates that the biHis site is absent or fully native-like, respectively, while a fractional psi implies that in the TSE, the biHis site recovers only part of the binding-induced stabilization of the native state. All-atom Langevin dynamics simulations of the TSE are performed with restrictions imposed only on the distances between the pairs of residues with experimentally determined psi of unity. When a site with a fractional psi lies adjacent to a site with psi = 1, the fractional psi generally signifies that the "fractional site" has a distorted geometry in the TSE. When a fractional site is distal to the sites with psi = 1, however, the histidines sample configurations in which the site is absent. The simulations indicate that the psi = 1 sites by themselves can be used to generate a well-defined TSE having near-native topology. values calculated from the TS simulations exhibit mixed agreement with the experimental values. The origin and implication of the disparities are discussed.
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