Conjecture on the Design of Helical Proteins

Abstract

In an important advance in our understanding of protein folding, Wolynes and Onuchic found that the frustration ratio, T_f/T_s, for funneled energy landscapes is T_f/T_s ∼1.6. In our recent work on four heme proteins, we showed that when a protein unfolds from the native state to an early unfolded state, the degree of departure is characterized by a ratio f ∼1.6, where f is a measure of the elongation of n-residue segments of the polypeptide chain. Our analysis, which accounts for this apparent similarity in calculated signatures, is based on a logistic-map model of unfolding. We offer an important take home for the de novo protein synthesis community: in order to increase the probability of obtaining good quality crystals, nearest-neighbor repulsive interactions between adjacent residues (or sequences of residues) in the polypeptide chain must be propagated correctly.