ArticleBiophysical journal2006
Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed.
- The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins.The journal of physical chemistry. B · 2023Article
- Structural Preferences Shape the Entropic Force of Disordered Protein Ensembles.The journal of physical chemistry. B · 2023Article
- The analytical Flory random coil is a simple-to-use reference model for unfolded and disordered proteins.bioRxiv : the preprint server for biology · 2023Article
- Structural preferences shape the entropic force of disordered protein ensembles.bioRxiv : the preprint server for biology · 2023Article
- The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy.Essays in biochemistry · 2022Article
- General Counteraction Exerted by Sugars against Denaturants.Life (Basel, Switzerland) · 2021Article
- Inferring properties of disordered chains from FRET transfer efficiencies.The Journal of chemical physics · 2018Article
- The liquid structure of elastin.eLife · 2017Article
- Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Direct Observation of the Intrinsic Backbone Torsional Mobility of Disordered Proteins.Biophysical journal · 2016Article
- Protein Composition Determines the Effect of Crowding on the Properties of Disordered Proteins.Biophysical journal · 2016Article
- Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation.Journal of the American Chemical Society · 2015Article
- Article
- Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- A quantitative measure for protein conformational heterogeneity.The Journal of chemical physics · 2013Article
- Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Describing sequence-ensemble relationships for intrinsically disordered proteins.The Biochemical journal · 2013Review
- Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study.Journal of chemical theory and computation · 2012Article
- Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
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2 authors.
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Abstract
Our focus is on an appropriate theoretical framework for describing highly denatured proteins. In high concentrations of denaturants, proteins behave like polymers in a good solvent and ensembles for denatured proteins can be modeled by ignoring all interactions except excluded volume (EV) effects. To assay conformational preferences of highly denatured proteins, we quantify a variety of properties for EV-limit ensembles of 23 two-state proteins. We find that modeled denatured proteins can be best described as follows. Average shapes are consistent with prolate ellipsoids. Ensembles are characterized by large correlated fluctuations. Sequence-specific conformational preferences are restricted to local length scales that span five to nine residues. Beyond local length scales, chain properties follow well-defined power laws that are expected for generic polymers in the EV limit. The average available volume is filled inefficiently, and cavities of all sizes are found within the interiors of denatured proteins. All properties characterized from simulated ensembles match predictions from rigorous field theories. We use our results to resolve between conflicting proposals for structure in ensembles for highly denatured states.
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