Effects of Stiffness on Low Energy States in a Lattice Protein Model for Crambin

Abstract

Many studies inspired by the HP lattice protein model have helped to confirm the importance of the hydrophobic “driving force” during folding. Unfortunately, the high level of coarse-graining inherent to this model leads to significant limitations; results from proteins studied under the framework of the HP model fail to reproduce many, sometimes significant, details of the folding process, and the obtained ground states are usually highly degenerate. We propose simple modifications to the original HP model, with the goal of reducing degeneracy and gaining insight into how other interaction parameters influence the folding, while retaining the computational simplicity of lattice models. Namely, we introduce a “neutral” monomer (0) to further divide the hydrophobicity scale and an energetic penalty for “bends” in the protein to account for rigidity. Using replica-exchange Wang-Landau (REWL) sampling and suitable Monte Carlo trial moves, we obtain a unique (non-degenerate) ground state for the new lattice mapping of Crambin (a small, 46 amino acid plant protein), and investigate the effects of stiffness on the folding and the low energy structures.