The Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights from Molecular Dynamics and Monte Carlo Simulations

TL;DR

This study uses molecular dynamics and Monte Carlo simulations to show that a knot in protein MJ0366 enhances its thermal stability by acting as a topological barrier, with implications for its biological function.

Contribution

It provides the first detailed computational analysis of how a protein knot influences thermal stability and folding behavior in a hypothetical protein.

Findings

The knot increases the protein's thermal stability.

The knot acts as a topological barrier preventing unfolding.

Knot presence affects folding and unfolding pathways.

Abstract

Protein MJ0366 is a hypothetical protein from Methanocaldococcus jannaschii that has a rare and complex knot in its structure. The knot is a right-handed trefoil knot that involves about half of the protein's residues. In this article, we investigate the thermal stability of protein MJ0366 using numerical simulations based on molecular dynamics and Monte Carlo methods. We compare the results with those of a similar unknotted protein and analyze the effects of the knot on the folding and unfolding processes. We show that the knot in protein MJ0366 increases its thermal stability by creating a topological barrier that prevents the protein from unfolding at high temperatures. We also discuss the possible biological implications of the knot for the function and evolution of protein MJ0366.