The polyproline II conformation in short alanine peptides is noncooperative

The finding that short alanine peptides possess a high fraction of polyproline II (PII) structure (Φ = -75°, Ψ = +145°) at low temperature has broad implications for unfolded states of proteins. An important question concerns whether or not this structure is locally determined or cooperative. We have monitored the conformation of alanine in a series of model peptides AcGG(A)n-GGNH₂ (n = 1-3) over a temperature range from -10°C to +80°C. Use of ¹⁵N-labeled alanine substitutions makes it possible to measure ³J_αN coupling constants accurately over the full temperature range. Based on a 1D next-neighbor model, the cooperative parameter σ of PII nucleation is evaluated from the coupling constant data. The finding that σ is close to unity (1 ± 0.2) indicates a noncooperative role for alanine in PII structure formation, consistent with statistical surveys of the Protein Data Bank that suggest that most PII structure occurs in isolated residues. Lack of cooperativity in these models implies that hydration effects that influence PII conformation in water are highly localized. Using a nuclear Overhauser effect ratio strategy to define the alanine Ψ angle, we estimate that, at 40°C, the time-averaged alanine conformation (Φ = -80°, Ψ = +170°) deviates from canonical PII structure, indicating that PII melts at high temperature. Thus, the high-temperature state of short alanine peptides seems to be an unfolded ensemble with higher distribution in the extended β structure basin, but not a coil.