Steric constraints in model proteins

TL;DR

This paper introduces a lattice protein model with variable amino acid sizes, revealing that certain structures are highly designable and encodable, with hydrophobicity further improving model features.

Contribution

The study presents a novel lattice model accounting for amino acid size differences and hydrophobicity, highlighting the concepts of designability and encodability of protein structures.

Findings

Many conformations are unique ground states for specific sequences.

Some structures are highly designable, being ground states for multiple sequences.

Inclusion of hydrophobicity enhances model's realism and features.

Abstract

A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable. Furthermore, several of the encodable structures are highly designable and are the non-degenerate ground state of several sequences. Even though the native state conformations are typically compact, not all compact conformations are encodable. The incorporation of the hydrophobic and polar nature of amino acids further enhances the attractive features of the model.