Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

TL;DR

This study explores a mean-field HP model on a lattice, revealing that peptides favor structures with many surface-core switches, especially alpha-helices, aligning with real protein sequences.

Contribution

It introduces a mean-field HP model that links geometric properties of protein structures to sequence preferences, highlighting alpha-helices as favored configurations.

Findings

Structures with many surface-core switches are favored by peptides.

High correlation between model peptides and real protein alpha-helices.

Alpha-helices are identified as energetically favorable in the model.

Abstract

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.