Thermodynamics of hydrophobic-polar model proteins on the face-centered cubic lattice.

Abstract

The HP model, a coarse-grained protein representation with only hydrophobic (H) and polar (P) amino acids, has already been extensively studied on the simple cubic (SC) lattice. However, this geometry severely restricts possible bond angles, and a simple improvement is to instead use the face-centered cubic (fcc) lattice. In this paper, the density of states and ground state energies are calculated for several benchmark HP sequences on the fcc lattice using the replica-exchange Wang-Landau algorithm and a powerful set of Monte Carlo trial moves. Results from the fcc lattice proteins are directly compared with those obtained from a previous lattice protein folding study with a similar methodology on the SC lattice. A thermodynamic analysis shows comparable folding behavior between the two lattice geometries, but with a greater rate of hydrophobic-core formation persisting into lower temperatures on the fcc lattice.