The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

TL;DR

This study models the folding pathways and kinetics of a knotted protein using energy landscape analysis, revealing how topological constraints influence folding intermediates and rate-limiting steps, with significantly slower folding compared to similar proteins.

Contribution

It introduces a detailed energy landscape and transition network analysis for a knotted protein, highlighting the role of topological constraints in folding pathways.

Findings

Folding involves early N-terminus knot formation

C-terminus incorporation is the rate-determining step

Folding is over six orders of magnitude slower than similar proteins

Abstract

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.