Molecular dynamics or: How I learned to stop worrying and love the membrane

The rise of antibiotic resistant bacterial species is an international problem. The structure, function and dynamic behaviour of the bacterial cell envelope must be thoroughly understood in order to design novel antimicrobial molecules. This thesis presents the use of molecular dynamics techniques to investigate the function of the Gram-negative outer membrane enzyme LpxR, as well as the subsequent effect of the protein on the dynamics of the outer membrane. LpxR covalently modifies a constituent of the outer membrane, lipopolysaccharide, which can modulate the immune response of the host. Simulations enabled the identification of a putative closed conformation for the protein, as well as a secondary ion binding site. These observations led to the proposition of an evaluated catalytic mechanism for the membrane enzyme.The effect of lipopolysaccharide deacylation on wider membrane properties and dynamics was also investigated. Deacylated lipopolysaccharide induced positive curvature on the membrane when in distinct patches; cardiolipin phospholipids also clustered in areas of the inner leaflet corresponding with the patches of deacylated lipopolysaccharide in the outer leaflet. The application of an electric field to these modified membranes identified structural weaknesses at the interface between deacylated and wildtype lipopolysaccharide. Electroporation of the outer membrane model with OmpA embedded was also performed, and these simulations indicated that the presence of integral proteins may cause localised weakness in the membrane. Finally, the interactions between polymyxin B1, an antimicrobial peptide, and the outer membrane were examined, to gain a further understanding of how the molecule infiltrates the Gram-negative cell envelope. The peptides were observed to permeate through both the outer and inner membrane models, resulting in phospholipid flipflopping, thereby degrading the lipid asymmetry of the outer membrane. Data presented here provide the basis for an updated self-promoted uptake mechanism of cellular infiltration for polymyxin B1