Pushing the cell envelope: Simulations at the gram-negative cellular interface

Abstract

Computational simulations of bacterial membrane systems were performed in silico using molecular dynamics to describe the function and interaction of integral, membrane-spanning proteins with their native environment. This was first exemplified for the B12 transporter BtuB, which found that the native membrane environment stabilizes key ligand binding sights as well as creates an allosteric effect within the luminal domain to promote lumen extraction. The second topic supplemented the role of the native environment by validating a method of mass repartitioning for hydrogen atoms in the system to enhance and increase simulation production. Leveraging the success of the native environment and a method to enhance computational output, proteomic and structural databases were utilized to generate a model for the Gram-negative bacterial cell envelope with an accurate representation of all molecules present.