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

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.

Special Issue—The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder

“…A detailed molecular-level knowledge not only of the native but also of the diverse non-native conformational states, which are accessible to a protein in solution (i.e., its denatured state ensemble (DSE)), is necessary to fully comprehend its function. Several investigations employed short peptides as models to obtain the canonical features of the DSE [ 6 ]. Short peptides are advantageous within this context as, being too short to assume a compact fold, they can sample unfolded states under folding conditions.…”

“…Short peptides are advantageous within this context as, being too short to assume a compact fold, they can sample unfolded states under folding conditions. Different peptide structural studies showed the strong tendency for the polyproline II (PPII) backbone conformation, which consequently could be a dominant component of the DSE [ 6 ]. Another structural model for the DSE is represented by the protein coil library that was built up from the segments of protein structure in the Protein Data Bank (PDB) that are located outside the α-helix and β-strand domains.…”

“…In order to assess structural preferences in unfolded states under non-denaturing conditions, IDPs can also be employed as an additional experimental model system. An interesting review by Steven T. Whitten and collaborators critically analyzes spectroscopic and calorimetric works on short peptides, structures in the protein coil library and sequence and temperature-based investigations of IDP hydrodynamic sizes; they demonstrate how the three model systems used for describing unfolded proteins under folding conditions deliver a consistent structural and energetic view of the DSE [ 6 ]. Results from analyses of the three model systems (i.e., peptides, the coil library and IDPs) highlight that the structural and energetic features of the DSE at normal temperatures can be predicted by a PPII-dominant ensemble.…”