Thermodynamic Mechanism and Consequences of the Polyproline II (P_II) Structural Bias in the Denatured States of Proteins

Abstract

A quantitative characterization of the structure and energy of the denatured states of proteins represents the cornerstone to a molecular-level understanding of both protein stability and fold specificity. Recent studies have revealed a significant bias in unstructured peptides toward the polyproline II (P(II)) conformation, even when no prolines are present in the sequence. This indicates that the P(II) conformation is a dominant component of the denatured states of proteins, although a quantitative description of the component enthalpy and entropy functions associated with this conformation (i.e., the thermodynamic mechanism) has thus far proven elusive. An experimental system has been designed that, when analyzed with high-precision isothermal titration calorimetry, provides direct access to the residue-specific thermodynamics of the P(II) structure formation in disordered proteins and peptides. Here, it is shown that the P(II) bias is driven by a favorable and significant enthalpy (Deltah) of -1.7 kcal mol(-1) residue(-1), which is partially offset by an unfavorable entropy (TDeltas) of -0.7 kcal mol(-1) residue(-1), relative to the ensemble of disordered conformations of the molecule. In addition to impacting dramatically the interpretation of thermal denaturation experiments, these experimental values form the framework of a quantitative energetic description of the denatured states of proteins.

Experimental and Computational Studies of Polyproline II Propensity

“…As discussed previously by Hamburger et al in the context of a funnel -shaped folding landscape [83] , an apparently small bias of an unfolded peptide toward a conformation (PII) can have a signifi cant impact on the size of the denatured state ensemble. Indeed, the difference in the number of states adopted by a 100 amino acid protein with a smooth (unbiased) folding landscape ( ∼ 10 90 possible conformations) compared with a peptide with a rugged ( ∼ 30% PII biased) landscape (10 20 possible conformations) is profound [83] .…”

“…Indeed, the difference in the number of states adopted by a 100 amino acid protein with a smooth (unbiased) folding landscape ( ∼ 10 90 possible conformations) compared with a peptide with a rugged ( ∼ 30% PII biased) landscape (10 20 possible conformations) is profound [83] . However, this reduction in conformational search space caused by PII bias does not necessarily mean that proteins fold through PII mechanistically.…”

Binding Mechanism of the N-Terminal SH3 Domain of CrkII and Proline-Rich Motifs in cAbl

“…The absence of correlation between PPII propensity and thermodynamic parameters has been observed for other SH3:PRM interactions (66-68). However, the effect of PPII propensity to binding thermodynamics was shown in the binding of PRM Sos to Sem-5 cSH3 domain (69,70). Because we tested only three PRMs in this study, the effect of PPII helix propensity on binding affinity should be further tested with a larger data set.…”

A backbone-based theory of protein folding

“…Polyproline II in the unfolded state. In addition to organization imposed by systematic local steric restrictions, there is also a substantial population of left-handed polyproline II (P II ) conformation in unfolded proteins (64)(65)(66)(67), as proposed by Tiffany and Krimm (68) more than three decades ago. Even earlier, Schellman and Schellman (69) had already argued that the spectrum of unfolded proteins was unlikely to be that of a true random coil.…”