Lipid Flipping, O-antigen Shielding, and Water Dynamics Revealed by 100-200 μs Coarse-Grained Simulations of E. coli Outer Membrane Proteins

Abstract

Gram-negative (GN) bacterial infections are a major global health concern, with antibiotic-resistant strains representing a growing problem. The outer membrane (OM) of GN bacteria is the primary interface between the cell and its environment, and it plays a crucial role in regulating how GN bacteria interact with a hosts immune system and with antimicrobial drugs. Consequently, understanding the structural details of the GN OM is an essential step toward addressing the pressing threat of GN organisms. One way to gain insights into complex molecular structures like the GN OM is to use coarse-grained molecular dynamics (MD) simulations. In this work, we use the Martini3 coarse-grained force field to model and simulate ten different OM proteins (OMPs) from E. coli embedded in four different OM models that each contain lipopolysaccharides (LPS) with different O-antigen lengths. We extensively assess OMP-phospholipid interactions and demonstrate that TolC, in particular, shows a strong preference for binding cardiolipin. We also uncover a phenomenon that, to our knowledge, has not been previously described in the simulation literature--i.e., the ability of OMPs to serve as sites of phospholipid flipping from the OM inner leaflet to the outer leaflet. Finally, we show that longer LPS O-antigen chains occlude OMPs, and we provide a detailed characterization of water and ion movement throughout our simulations.