Multi-Dimensional Theory of Protein Folding

TL;DR

This paper develops a multi-dimensional free energy surface theory for protein folding, classifying folding scenarios and analyzing specific proteins to better understand pathways, intermediates, and transition states.

Contribution

It introduces a multi-dimensional framework for protein folding analysis using structural order parameters and applies it to several proteins for detailed pathway insights.

Findings

Multi-dimensional representation clarifies folding pathways.

Finer description achieved with higher-dimensional models.

Application to various proteins demonstrates model effectiveness.

Abstract

Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in terms of cooperativity within individual regions and interactions among multiple regions and thus obtained classification is used to analyze the folding process of several example proteins. Ribosomal protein S6, src-SH3 domain, CheY, barnase, and BBL domain are analyzed with the two-dimensional representation by using a structure-based Hamiltonian model. Extension to the higher dimensional representation leads to the finer description of the folding process. Barnase, NtrC, and an ankyrin repeat protein are examined with the three-dimensional representation. The multi-dimensional representation allows us to directly address questions on folding pathways, intermediates, and transition states.