Tightening of knots in proteins

TL;DR

This study uses a coarse-grained model to analyze how protein knots behave under stretching, revealing sequential end jumps, temperature effects on jump stochasticity, and differences from homopolymer behavior.

Contribution

It provides new insights into the dynamics of protein knots during stretching, highlighting sequential end jumps and temperature-dependent stochasticity.

Findings

Knot ends jump to specific locations associated with sharp turns.

Jump stochasticity increases with temperature.

Larger knots do not revert to native positions after stretching.

Abstract

We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they diffuse around and eventually slide off. The waiting times of the jumps are increasingly stochastic as the temperature is raised. Larger knots do not return to their native locations when a protein is released after stretching.