Topological Enhancement of Protein Kinetic Stability

TL;DR

This study uses simulations to demonstrate that protein knots significantly enhance kinetic stability, with deeper knots providing greater resistance to unfolding, and that evolutionary complexity further promotes this stability.

Contribution

It isolates topological effects on protein stability using simulations, showing knots increase kinetic stability and that sequence complexity enhances this effect.

Findings

Knotted proteins exhibit higher kinetic stability than unknotted ones.

Knot depth correlates positively with kinetic stability.

Increased amino-acid diversity further enhances stability.

Abstract

Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using extensive Monte Carlo off-lattice simulations of a simple structure-based model, we isolate the effect of topology by comparing simulations that preserve the linear topology of the chain with simulations that allow chain crossings. This controlled framework enables us to isolate topological effects from sequence, structure and energetic contributions. We show that protein kinetic stability, defined as resistance to unfolding at a fixed temperature, is higher in knotted proteins. Additionally, kinetic stability increases significantly with knot depth, whereas foldability (or folding efficiency) is comparatively less affected. By considering a simple model of protein evolution in which amino-acid alphabet size is used as a proxy for evolutionary time, we find that increasing primary-sequence complexity through the addition of biotic amino acids predominantly enhances kinetic stability. Taken together, these results indicate that kinetic stability is a functional advantage conferred by protein knots and suggest that evolutionary pressure for kinetic stability could contribute to the persistence of knotted proteins.