Folding behavior of model proteins with weak energetic frustration

Abstract

The native structure of fast-folding proteins, albeit a deep local free-energy minimum, may involve a relatively small energetic penalty due to nonoptimal, though favorable, contacts between amino acid residues. The weak energetic frustration that such contacts represent varies among different proteins and may account for folding behavior not seen in unfrustrated models. Minimalist model proteins with heterogeneous contacts—as represented by lattice heteropolymers consisting of three types of monomers—also give rise to weak energetic frustration in their corresponding native structures, and the present study of their equilibrium and nonequilibrium properties reveals some of the breadth in their behavior. In order to capture this range within a detailed study of only a few proteins, four candidate protein structures ~with their cognate sequences! have been selected according to a figure of merit called the winding index—a characteristic of the number of turns the protein winds about an axis. The temperature-dependent heat capacities reveal a high-temperature collapse transition, and an infrequently observed low-temperature rearrangement transition that arises because of the presence of weak energetic frustration. Simulation results motivate the definition of a new measure of folding affinity as a sequence-dependent free energy—a function of both a reduced stability gap and high accessibility to non-native structures—that correlates strongly with folding rates.