Properties and Origins of Protein Secondary Structure

TL;DR

This paper investigates the properties and origins of protein secondary structures by defining them through local correlations, examining the roles of energy and entropy, and testing the hypothesis that compaction alone can induce secondary structure using simple models.

Contribution

It introduces a generic definition of secondary structure based on local correlations and tests the role of compaction in secondary structure formation with simple protein models.

Findings

Compaction can induce secondary structure in proteins.

Energy and entropy balance influence secondary structure formation.

A simple model can replicate key features of secondary structures.

Abstract

Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain. Using this definition and a simple model for proteins, the forces driving the formation of secondary structure are explored. The relative role of energy and entropy are examined. Recent work has indicated that compaction is sufficient to create secondary structure. We test this hypothesis, using simple non-lattice protein models.