Structural determinants of antibiotic translocations in OMPF

In Gram-negative bacteria membrane-protein channels, also known as porins, constitute the entry point of various classes of antibiotics. With the advent of bacterial resistance to antibiotics, porins are becoming a prime target. The outer membrane porin F (OmpF) is the major outer membrane protein component of Escherichia coli and bacterial strains resistant to antibiotics showed either underexpression or mutations of OmpF. To study antibiotic translocation at a molecular scale, we performed molecular dynamics (MD) simulations combined with the metadynamics algorithm. This recently designed algorithm overcomes the time scale problem of classical MD by accelerating some reaction coordinates. We compared the following methodologies: modeling (i) OmpF in its monomeric or trimeric form and (ii) membranes as surrounding detergent molecules or as lipid bilayers. Furthermore, we considered antibiotics of different structural, chemical and physical properties (penicillins, fluorokinolones, cephalosporines). Earlier MD studies on the OmpF trimer reported structural differences between each monomer. Differences arising from some key mutations were also investigated. However, the influence of such differences on antibiotic translocation is not clear. To answer this question we performed a careful structural analysis of our simulations in the different conditions stated above. We reveal the reciprocal influence of each monomer and the role of single residues and loops L2–L3. We also calculated the cross sectional surface area at the pore constriction zone and determined the preferred binding sites for the antibiotics. Overall, our results are in good agreement with experiments. This work directly benefits the design of new antibiotics with improved transport properties.