Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins

dc.contributor.authorPaiz, Elisia
dc.contributor.authorLewis, Karen A.
dc.contributor.authorWhitten, Steven T.
dc.description.abstractThe α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained.
dc.description.departmentChemistry and Biochemistry
dc.format.extent22 pages
dc.format.medium1 file (.pdf)
dc.identifier.citationPaiz, E. A., Lewis, K. A., & Whitten, S. T. (2021). Structural and energetic characterization of the denatured state from the perspectives of peptides, the coil library, and intrinsically disordered proteins. Molecules, 26(3), 634.
dc.publisherMultidisciplinary Digital Publishing Institute
dc.rights.holder© 2021 The Authors.
dc.rights.licenseThis work is licensed under a Creative Commons Attribution 4.0 International License.
dc.sourceMolecules, 2021, Vol. 26, No. 3, Article 634.
dc.subjectdenatured state ensemble
dc.subjectprotein coil library
dc.subjectintrinsically disordered proteins
dc.subjectChemistry and Biochemistry
dc.titleStructural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins


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