Exploring Protein Folding Pathways with Molecular Dynamics Simulations

EasyChair Preprint 12155

Abstract

Understanding protein folding pathways is crucial for elucidating the fundamental principles underlying protein structure and function. Molecular dynamics (MD) simulations have emerged as powerful tools for studying the dynamics and folding mechanisms of proteins at atomic resolution. In this study, we employed MD simulations to investigate the folding pathways of a representative protein model. We utilized state-of-the-art force fields and simulation protocols to accurately model the interactions and motions of atoms within the protein. Our results reveal multiple intermediate states and diverse pathways involved in the folding process, highlighting the complexity of protein folding dynamics. By analyzing the conformational changes and interactions at various stages of folding, we elucidate key structural motifs and molecular interactions that govern the folding process. Furthermore, we identify potential kinetic bottlenecks and energetically favorable folding routes, providing insights into the determinants of protein folding kinetics. Through comparative analysis with experimental data and computational predictions, we validate the reliability of our simulation approach and provide new insights into the folding mechanisms of proteins. Our findings contribute to a deeper understanding of protein folding dynamics and have implications for protein engineering, drug design, and the treatment of protein misfolding diseases.

Keyphrases: folding pathways, molecular dynamics simulations, protein folding

@booklet{EasyChair:12155,
  author    = {James Henry and Suleyman Mehmood},
  title     = {Exploring Protein Folding Pathways with Molecular Dynamics Simulations},
  howpublished = {EasyChair Preprint 12155},
  year      = {EasyChair, 2024}}