Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α / β proteins

Abstract

Employing a high coordination lattice model and conformational sampling based on dynamic and entropy sampling Monte Carlo protocols, computer experiments were performed on three small globular proteins, each representing one of the three secondary structure classes. The goal was to explore the thermodynamic character of the conformational transition and possible mechanisms of topology assembly. Depending on the stability of isolated elements of secondary structure, topology assembly can proceed by various mechanisms. For the three-helix bundle, protein A, which exhibits substantial helix content in the denatured state, a diffusion–collision mechanism of topology assembly dominates, and here, the conformational transition is predicted to be continuous. In contrast, a model β protein, which possesses little intrinsic denatured state secondary structure, exhibits a sequential "on-site" assembly mechanism and a conformational transition that is well described by a two-state model. Augmenting the cooperativity of tertiary interactions led to a slight shift toward the diffusion–collision model of assembly. Finally, simulations of the folding of the α / β protein G, while only partially successful, suggest that the C-terminal β hairpin should be an early folding conformation and that the N-terminal β hairpin is considerably less stable in isolation. Implications of these results for our general understanding of the process of protein folding and their utility for de novo structure prediction are briefly discussed.