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

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 usin...

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Bibliographic Details
Published in:arXiv.org 2024-11
Main Authors: Begun, A M, Korneev, A A, Zorina, A V
Format: Article
Language:English
Subjects:
Biological activity
Biological effects
Computer simulation
Dynamic structural analysis
High temperature
Knots
Molecular dynamics
Molecular structure
Monte Carlo simulation
Proteins
Thermal stability
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Summary: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.
ISSN:2331-8422