The Molecular Dynamics Simulation of a Multi-domain Outer Membrane Protein A (OmpA) from Shigella flexneri in POPE Lipid Bilayer

Abstract

Shigella flexneri serotype 2a is a major public health concern in the developing and under-developed countries as it contributes to the endemic shigellosis (also known as bacillus dysentery) as well as shigellosis mortality. A 35 kDa antigenic protein from S. flexneri has been shown to be a potential biomarker and the predictive model from earlier studies showed that this protein is a variant of outer membrane protein A (OmpA) that consists of OmpA domain and OmpA-like domain. This study was conducted to further sample and explore the conformation of the OmpA of S. flexneri in POPE lipid bilayer. The trajectories data from molecular dynamics (MD) simulation showed that the OmpA secondary structure is retained and the protein integrity is not impaired. The four extracellular loops are flexible and similar observation was noted for the linker of the two domains. The conformation of the extracellular loops could be useful for possible future development for diagnostics or vaccine of shigellosis.