Unraveling Biomolecular Functionality: Molecular Dynamics Insights

EasyChair Preprint no. 12005

Abstract

Understanding the functionality of biomolecules at the molecular level is pivotal for advancing our knowledge in fields such as drug design, enzyme catalysis, and protein engineering. Molecular dynamics (MD) simulations have emerged as a powerful tool for elucidating the dynamic behavior of biomolecules and their interactions with ligands or substrates. In this study, we present a comprehensive review of recent advances in MD simulations aimed at unraveling biomolecular functionality. We begin by discussing the principles underlying MD simulations and their applications in studying biomolecular systems. Subsequently, we delve into case studies highlighting the use of MD simulations in elucidating the conformational dynamics of proteins, nucleic acids, and lipids. We explore how MD simulations have provided insights into the mechanisms of enzyme catalysis, protein-ligand binding, and allosteric regulation. Additionally, we discuss the role of enhanced sampling techniques in overcoming timescale limitations inherent to MD simulations, thus enabling the exploration of rare events and transitions critical for biomolecular functionality. Furthermore, we examine the integration of MD simulations with experimental techniques such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM) to refine structural models and validate simulation predictions. We highlight the synergy between computational and experimental approaches in elucidating complex biomolecular mechanisms.

Keyphrases: Biomolecular functionality, molecular dynamics, simulation

@Booklet{EasyChair:12005,
  author = {Basit Amir and Jane Elsa},
  title = {Unraveling Biomolecular Functionality: Molecular Dynamics Insights},
  howpublished = {EasyChair Preprint no. 12005},

  year = {EasyChair, 2024}}