A First Look at Lattice Effects in Coarse-Grained Protein Models via Wang-Landau Simulations

Abstract

In order to study the effects of lattice constraints on coarse-grained protein models, we apply Wang-Landau sampling to the continuum analogue of the hydrophobic-polar (HP) lattice protein model. The continuum version is inspired by the AB polymer model but incorporates potentials chosen specifically to mimic those of the lattice case. Because of their relative simplicity, both the lattice and continuum models offer significant computational advantage over all-atom simulations, but the impact of the additional lattice constraint on generic folding behavior is unknown. In this preliminary study, we compare and contrast thermodynamics during the folding process of the continuum model to the original HP lattice protein model for sequences mapped from Crambin, a 46 amino acid plant protein. We find that the folding process for both of these coarse-grained models is quite similar, with major structural transitions occurring at almost exactly the same temperatures.