ArticleBiophysical journal2003
Calculation of mutational free energy changes in transition states for protein folding.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- The mechanism of amyloid fibril growth from Φ-value analysis.Nature chemistry · 2025Article
- Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction.Proteins · 2021Article
- The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations.BMC structural biology · 2011Article
- The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints.Nature structural & molecular biology · 2009Article
- Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.Protein engineering, design & selection : PEDS · 2008Article
- The protein folding problem.Annual review of biophysics · 2008Review
- Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Change of the unbinding mechanism upon a mutation: a molecular dynamics study of an antibody-hapten complex.Protein science : a publication of the Protein Society · 2005Article
- Phi values in protein-folding kinetics have energetic and structural components.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Prediction of water and metal binding sites and their affinities by using the Fold-X force field.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- The FoldX web server: an online force field.Nucleic acids research · 2005Article
- Phi value versus psi analysis.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
- Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
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5 authors.
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Abstract
Recent advances in experimental and computational methods have made it possible to determine with considerable accuracy the structures whose formation is rate limiting for the folding of some small proteins-the transition state ensemble, or TSE. We present a method to analyze and validate all-atom models of such structures. The method is based on the comparison of experimental data with the computation of the change in free energy of the TSE resulting from specific mutations. Each mutation is modeled individually in all members of an ensemble of transition state structures using a method originally developed to predict mutational changes in the stability of native proteins. We first apply this method to six proteins for which we have determined the TSEs with a technique that uses experimental mutational data (Phi-values) as restraints in the structure determination and find a highly significant correlation between the calculated free energy changes and those derived from experimental kinetic data. We then use the procedure to analyze transition state structures determined by molecular dynamics simulations of unfolding, again finding a high correlation. Finally, we use the method to estimate changes in folding rates of several hydrophobic core mutants of Fyn SH3. Taken together, these results show that the procedure developed here is a tool of general validity for analyzing, assessing, and improving the quality of the structures of transition states for protein folding.
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