Environmental Influences on the Conformational Dynamics of Tonb-Dependent Transporters: Molecular Dynamics Simulations of Complex Membrane Models

Abstract

The outer membrane of Gram-negative bacteria is a complex mixture of Lipopolysaccharide (LPS) and phospholipids. LPS is distributed in the outer leaflet of this membrane and is composed of Lipid A, which anchors the LPS into the membrane, the core oligosaccharide and the O-antigen. LPS plays a key role in many bacterial functions, such as controlling membrane permeability and providing antibiotic resistance, as well as inducing septic shock upon infection of a mammalian host. In addition to these roles, LPS is vital for the correct functioning of proteins located within the outer membrane of Gram-negative bacteria. Despite reports of numerous simulation studies of bacterial outer membrane proteins, only a limited number of these studies have been performed using membrane models incorporating LPS. In the present work, we have developed atomistic models of rough (Lipid A and core oligosaccharide) mutants of LPS. We have performed a series of molecular dynamics simulations of three TonB-dependent transporters from the outer membrane of E .coli (BtuB, FecA and FhuA) in membrane models containing various LPS mutants in the outer leaflet and mixtures of phospholipids in the inner leaflet. These simulations are compared to our simulations of the same proteins in symmetric phospholipid bilayers. The more detailed representation of the E. coli membrane enables us to study the stability, conformational dynamics and diffusion of these membrane proteins in an environment that more accurately represents the in vivo situation. Furthermore it enables us to identify key protein-LPS and protein-phospholipid interactions that anchor the proteins in the membrane and perhaps may also play a role in mediating interactions with other proteins.