From polymers to proteins -- novel phases of short compact tubes

TL;DR

This paper introduces a novel framework modeling proteins as tubes of nonzero thickness, bridging polymer physics with biological structures, and explaining the prevalence of helices and sheets through geometric and continuum considerations.

Contribution

It proposes a continuum tube model for proteins that incorporates many-body interactions, providing a new perspective on protein folding and structure formation.

Findings

Proteins can be modeled as tubes of nonzero thickness.

The model explains the prevalence of helices and sheets.

Protein structures are selected based on geometric considerations at the edge of compaction.

Abstract

A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed characteristics of protein structures. The authors show here that proteins may be regarded as tubes of nonzero thickness. This approach allows one to bridge the conventional compact polymer phase with a novel phase employed by Nature to house biomolecular structures. The continuum description of a tube (or a sheet) of arbitrary thickness entails using appropriately chosen many-body interactions rather than two-body interactions. The authors suggest that the structures of folded proteins are selected based on geometrical considerations and are poised at the edge of compaction, thus accounting for their versatility and flexibility. This approach also offers an explanation for why helices and sheets are the building blocks of protein structures.