Protein Folding: A New Geometric Analysis

TL;DR

This paper introduces a geometric framework for understanding protein folding, modeling the process with differential geometry and solitons, revealing how amino acid geometry influences the final folded structure.

Contribution

It presents a novel geometric analysis of protein folding using differential geometry and soliton theory, independent of energy considerations.

Findings

Identification of sine-Gordon torsion solitons in protein folding

Quantitative link between amino acid geometry and folded structure

Folding modeled as shape change driven by local geometry

Abstract

A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it is possible that so many initial configurations proceed to fold to a unique final configuration. We put energy and dynamical considerations temporarily aside and focus upon the geometry alone. We parameterize the structure of an idealized protein using the concept of a ribbon from differential geometry. The deformation of the ribbon is described by introducing a generic twisting Ansatz. The folding process in this picture entails a change in shape guided by the local amino acid geometry. The theory is reparamaterization invariant from the start, so the final shape is independent of folding time. We develop differential equations for the changing shape. For some parameter ranges, a sine-Gordon torsion soliton is found. This purely geometric waveform has properties similar to dynamical solitons. Namely: A threshold distortion of the molecule is required to initiate the soliton, after which, small additional distortions do not change the waveform. In this analysis, the soliton twists the molecule until bonds form. The analysis reveals a quantitative relationship between the geometry of the amino acids and the folded form.