Identifying the protein folding nucleus using molecular dynamics

TL;DR

This study uses molecular dynamics simulations to identify the protein folding nucleus, showing that specific contacts in the transition state ensemble are crucial for folding cooperativity and successful folding.

Contribution

It introduces a nucleation-based model of protein folding, highlighting the role of key contacts in the transition state ensemble.

Findings

Identification of well-defined contacts in the transition state ensemble

These contacts determine folding cooperativity

They drive the protein into its folded conformation

Abstract

Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model protein into its folded conformation.