Quinary lattice model of secondary structures of polymers

TL;DR

This paper introduces a new quinary lattice model for polymers that incorporates non-local cooperative interactions, successfully capturing secondary structures like alpha-helices and beta-strands at a qualitative level.

Contribution

The novel quinary lattice model based on five-monomer fragment energies explains secondary structures, overcoming limitations of nearest neighbor interaction models.

Findings

Model describes secondary structures qualitatively.

All minimal energy conformations include alpha-helix and beta-strand features.

Applicable to polymers up to 38 monomers in length.

Abstract

In the standard approach to lattice proteins the models based on nearest neighbor interaction are used. In this kind of models it is difficult to explain the existence of secondary structures --- special preferred conformations of protein chains. In the present paper a new lattice model of proteins is proposed which is based on non-local cooperative interactions. In this model the energy of a conformation of a polymer is equal to the sum of energies of conformations of fragments of the polymer chain of the length five. It is shown that this quinary lattice model is able to describe at qualitative level secondary structures of proteins: for this model all conformations with minimal energy are combinations of lattice models of alpha--helix and beta--strand. Moreover for lattice polymers of the length not longer that 38 monomers we can describe all conformations with minimal energy.