Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins
Date
2021-01-26
Authors
Paiz, Elisia
Lewis, Karen A.
Whitten, Steven T.
Journal Title
Journal ISSN
Volume Title
Publisher
Multidisciplinary Digital Publishing Institute
Abstract
The 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.
Description
Keywords
denatured state ensemble, protein coil library, peptides, intrinsically disordered proteins, Chemistry and Biochemistry
Citation
Paiz, 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.
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© 2021 The Authors.
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This work is licensed under a Creative Commons Attribution 4.0 International License.