Protein-Protein Interaction Studies Using Molecular Dynamics Simulation

Veerendra Kumar; Shivani Yaduvanshi

doi:10.1007/978-1-0716-3147-8_16

Protein-Protein Interaction Studies Using Molecular Dynamics Simulation

Methods Mol Biol. 2023:2652:269-283. doi: 10.1007/978-1-0716-3147-8_16.

Authors

Veerendra Kumar¹, Shivani Yaduvanshi²

Affiliations

¹ Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India. vkumar34@amity.edu.
² Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India.

PMID: 37093482
DOI: 10.1007/978-1-0716-3147-8_16

Abstract

Protein-protein interaction (PPI) is a crucial event for many biological functions. Studying the molecular details of PPI requires structure determination using X-ray crystallography, nuclear magnetic resistance (NMR), and single particle Cryo-EM. However, sometimes it is not easy to solve the complex structure for various reasons. For example, complex may be unstable, not enough protein expression for structural studies, etc. Further, PPI are intricate processes, and its molecular details cannot be fully explained by experimental observations. Here, we describe a quick and simple method to study the PPI using the combinatorial approach of molecular dynamics simulation and biophysical methods.

Keywords: Force fields; GROMACS; Molecular dynamics simulations; Protein-protein interactions; Structural biology.

MeSH terms

Cryoelectron Microscopy / methods
Crystallography, X-Ray
Molecular Dynamics Simulation*