Protein Ground State Candidates in a Simple Model: An Exact Enumeration

TL;DR

This paper introduces a method to exactly enumerate native states of proteins in a simplified lattice model, revealing sequences with unique native states and analyzing how these properties scale with sequence length.

Contribution

It presents an exact enumeration approach for protein ground states using reduced contact maps in a lattice model, a novel method for analyzing native state stability.

Findings

Identification of sequences with absolute native states.

Scaling analysis of ground state candidates with sequence length.

Introduction of reduced contact maps for exact enumeration.

Abstract

The concept of the reduced set of contact maps is introduced. Using this concept we find the ground state candidates for Hydrophobic-Polar lattice model on a two dimensional square lattice. Using these results we exactly enumerate the native states of all proteins for a wide range of energy parameters. In this way, we show that there are some sequences, which have an absolute native state. Moreover, we study the scale-dependence of the number of the members of the reduced set, the number of ground state candidates, and the number of perfectly stable sequences by comparing the results for sequences with lengths of 6 up to 20.