Discrete molecular dynamics studies of the folding of a protein-like model

TL;DR

This paper demonstrates that discrete molecular dynamics can effectively simulate the folding and unfolding processes of a protein-like model, providing insights into its thermodynamics and kinetics.

Contribution

It introduces the use of a discrete time molecular dynamics algorithm to study protein folding, addressing limitations of previous models.

Findings

Successfully resolves folding-unfolding transition over time

Able to study the protein core dynamics

Serves as a tool for thermodynamic and kinetic analysis

Abstract

Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical properties of the proteins (lattice models), while others are computationally heavy (traditional MD). Results: We use a recently-proposed approach of Zhou and Karplus to study the folding of the protein model based on the discrete time molecular dynamics algorithm. We show that this algorithm resolves with respect to time the folding --- unfolding transition. In addition, we demonstrate the ability to study the coreof the model protein. Conclusion: The algorithm along with the model of inter-residue interactions can serve as a tool to study the thermodynamics and kinetics of protein models.