Polyproline II propensities from GGXGG peptides reveal an anticorrelation with β-sheet scales

Abstract

There is growing appreciation of the functional relevance of unfolded proteins in biology. However, unfolded states of proteins have proven inaccessible to the usual techniques for high-resolution structural and energetic characterization. Unfolded states are still generally conceived of as statistical coils, based on the pioneering work of Flory [(1969) Statistical Mechanics of Chain Molecules (Wiley, New York)] and Tanford [(1968) Adv. Protein Chem. 23, 121–282]. Recently, several lines of independent evidence have raised doubts about the random coil model and offer support for alternative views. Here, we show that polyproline II conformation is dominant in a host–guest peptide model AcGGXGGNH 2 (X ≠ glycine), in equilibrium predominantly with β-structure. This result is inconsistent with a random coil model and the general view that these peptides are unstructured. By calculating a set of apparent Δ G values from the measured coupling constants of the backbone amides, we can construct a polyproline II scale that correlates negatively with β-sheet scales.