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

Anders Irbäck·Erik Sandelin
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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 $κ$ of the local interactions; $κ=0$ 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 $κ$. Also, we find that the number of designable structures can differ widely for the two lattices at a given $κ$. This is the case, for example, at $κ=0$, 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.

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Anders Irbäck, Erik Sandelin. 1997-11-02. Local Interactions and Protein Folding: A Model Study on the Square and Triangular Lattices. https://doi.org/10.1063/1.475605

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