ArticleProtein engineering, design & selection : PEDS2008
Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.
Article in Protein engineering, design & selection : PEDS, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 14 citations in OpenAlex.
- Mitochondrial Transmembrane β-Barrels: Deducing Thermodynamic Regulators of Folding and Stability.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Stability of an aggregation-prone partially folded state of human profilin-1 correlates with aggregation propensity.The Journal of biological chemistry · 2018Article
- pKID Binds to KIX via an Unstructured Transition State with Nonnative Interactions.Biophysical journal · 2017Article
- The Folding process of Human Profilin-1, a novel protein associated with familial amyotrophic lateral sclerosis.Scientific reports · 2015Article
- Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- How quickly can a β-hairpin fold from its transition state?The journal of physical chemistry. B · 2014Article
- Folding pathways of proteins with increasing degree of sequence identities but different structure and function.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Constrained proper sampling of conformations of transition state ensemble of protein folding.The Journal of chemical physics · 2011Article
- The folding trajectory of RNase H is dominated by its topology and not local stability: a protein engineering study of variants that fold via two-state and three-state mechanisms.Journal of molecular biology · 2009Article
- Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
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4 authors at 1 institution in 1 country.
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Abstract
It has been suggested that Phi-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Phi-values indicate almost completely folded regions in the TS, intermediate Phi-values regions with a detectable amount of structure and low Phi-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Phi-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Phi-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Phi-values can provide sufficient information for characterising the architecture of a TS for folding of a protein.
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