A Molecular Dynamics Study of a Complex of Macrophage Infectivity Potentior (Mip) Protein with Rapamycin using Conformational Flooding
Elisabeth Catherina Widjajakusuma, Oci Davita, Ayu Janatun Fitri

Widya Mandala Catholic University Surabaya

Abstract

The macrophage infectivity potentiator (Mip) protein has been shown to contribute to the intracellular survival of a wide range of pathogenic microorganisms. Therefore, it becomes an attractive candidate for development of efficient inhibitors. However, highly selective recognition of the target protein is a very challenging problem. In this study, we employed an artificial potential to enhance the sampling of 40 ns time of simulation and then, we compared it to 200 ns of classical molecular dynamics simulation. Some residues kept their hydrogen bonds to stabilize the binding site. The findings provide insights into ligand binding to the protein.

Keywords: molecular dynamics simulation, macrophage infectivity potentiator, potential flooding

Topic: COMPUTATIONAL SCIENCES