A coarse-grained, ``realistic'' model for Protein Folding

TL;DR

This paper introduces a phenomenological, coarse-grained model for protein folding that simplifies the configuration space to secondary structure elements and analytically explores its partition function, offering a new tool for studying real protein folding.

Contribution

It proposes a novel, realistic model focusing on secondary structures, combining local and non-local interactions, and analytically evaluates its partition function.

Findings

Partition function calculated analytically for a simplified model.

Model applied to a synthetic protein with preliminary results.

Highlights the importance of secondary structure interactions in folding.

Abstract

A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the number of secondary structure elements rather than with the number of residues. The hamiltonian presents both local (i.e. single helix, accounting for the stiffness of the chain) and non local (interactions between hydrophobically-charged helices) terms, and is expected to provide a first tool for studying the folding of real proteins. The partition function for a simplified, but by no means trivial, version of the model is calculated almost completely in an analytical way. The latter simplified model is also applied to the study of a synthetic protein, and some preliminary results are shown.