Molecular Dynamics Simulation for Investigating Antigen-Antibody Interaction

Takefumi Yamashita

doi:10.1007/978-1-0716-2609-2_4

Molecular Dynamics Simulation for Investigating Antigen-Antibody Interaction

Methods Mol Biol. 2023:2552:101-107. doi: 10.1007/978-1-0716-2609-2_4.

Author

Takefumi Yamashita¹

Affiliation

¹ Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan. yamashita@lsbm.org.

PMID: 36346587
DOI: 10.1007/978-1-0716-2609-2_4

Abstract

Molecular dynamics (MD) simulation is a computational method which elucidates the protein dynamics. Following analyses characterize the dynamics and structural change as well as interaction energy. To characterize the protein structure effectively, the internal angular coordinates are often useful. Directional analysis provides the averages and variances of those coordinates in a mathematically rigorous way. Here, we describe not only a standard MD simulation procedure for the antigen-antibody system but also an umbrella sampling method following a multistep targeted MD simulation (US/mTMD), which is useful for evaluating the free energy profile along the antigen-antibody dissociation coordinate.

Keywords: Free energy; Interaction energy; Molecular dynamics simulation; Potential of mean force; Structure.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Molecular Dynamics Simulation*
Proteins*

Substances

Proteins