ArticleBiophysical journal2008
Transition states in protein folding kinetics: modeling phi-values of small beta-sheet proteins.
Article in Biophysical journal, 2008. 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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11 citing papers in PubMed, 21 citations in OpenAlex.
- Protein misfolding involving entanglements providesa structural explanation for the origin of stretched-exponential refolding kinetics.Science advances · 2025Article
- Information Bottleneck Approach for Markov Model Construction.Journal of chemical theory and computation · 2024Article
- Article
- An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes.Journal of chemical theory and computation · 2023Article
- How Similar Are Proteins and Origami?Biomolecules · 2022Article
- The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate.Journal of the American Chemical Society · 2016Article
- High-Resolution Mapping of the Folding Transition State of a WW Domain.Journal of molecular biology · 2016Article
- The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations.Biomolecules · 2013Review
- Characterization of folding mechanisms of Trp-cage and WW-domain by network analysis of simulations with a hybrid-resolution model.The journal of physical chemistry. B · 2013Article
- Dominant folding pathways of a WW domain.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
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1 author at 1 institution in 1 country.
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Abstract
Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived from the mutational data. In this article, we model and structurally interpret mutational Phi-values for two small beta-sheet proteins, the PIN and the FBP WW domains. The native structure of these WW domains comprises two beta-hairpins that form a three-stranded beta-sheet. In our model, we assume that the transition state consists of two conformations in which either one of the hairpins is formed. Such a transition state has been recently observed in molecular dynamics folding-unfolding simulations of a small designed three-stranded beta-sheet protein. We obtain good agreement with the experimental data 1), by splitting up the mutation-induced free-energy changes into terms for the two hairpins and for the small hydrophobic core of the proteins; and 2), by fitting a single parameter, the relative degree to which hairpins 1 and 2 are formed in the transition state. The model helps us to understand how mutations affect the folding kinetics of WW domains, and captures also negative Phi-values that have been difficult to interpret.
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