Local Interactions and Protein Folding: A Model Study on the Square and Triangular Lattices

TL;DR

This study explores how local interactions influence protein folding on square and triangular lattices, revealing that such interactions significantly affect the number and nature of unique energy-minimizing structures.

Contribution

It introduces a heteropolymer model with sequence-independent local interactions and compares folding behaviors on different lattice types, highlighting the importance of local properties.

Findings

Number of designable structures varies with local interaction strength.

Lattice type influences the set of stable structures at given interaction parameters.

Local interactions can determine unique folding configurations independently of sequence.

Abstract

We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength $\kappa$ of the local interactions; $\kappa=0$ corresponds to the well-known HP model [K.F. Lau and K.A. Dill, Macromolecules 22, 3986 (1989)]. By exhaustive enumerations for short chains, we obtain all structures which act as a unique and pronounced energy minimum for at least one sequence. We find that the number of such designable structures depends strongly on $\kappa$. Also, we find that the number of designable structures can differ widely for the two lattices at a given $\kappa$. This is the case, for example, at $\kappa=0$, which implies that the HP model exhibits different behavior on the two lattices. Our findings clearly show that sequence-independent local properties of the chains can play an important role in the formation of unique minimum energy structures.