The Biophysics Of Antibiotics Translocation Through OmpF Revealed By Computer Simulations

In Gram-negative bacteria, the outer membrane porin F (OmpF) constitute the preferred entry point of antibiotics. Since bacteria can resist antibiotics by altering the expression or structures of OmpF, it is of fundamental importance to investigate on the permeation mechanisms at a molecular level. A key feature in the structure of OmpF is the presence of a constriction region, characterized by both a spatial (with dimensions as low as 7x11Å) and an electrostatic (a transversal field formed by negative and positive residues facing each others) restriction. To study the translocation process at a molecular scale, we performed molecular dynamic simulations combined with the metadynamic algorithm. This recently designed algorithm overcomes the time scale problem by accelerating properly defined reaction coordinates. We compared the following modeling methodologies: (i) OmpF as monomers or trimers, (ii) membranes as surrounding detergent molecules or lipid bilayers, (iii) antibiotics of different structural and chemical properties (penicillins, fluorokinolones, cephalosporines). We evaluated how site mutations on OmpF alter electrostatic or spatial restriction at the constriction region and affect antibiotics binding and transport. We reconstructed the free energy surface of each antibiotic translocation and compared their preferred path, orientation, affinity sites. We find that translocation is governed by specific (polar, hydrophobic) interactions. This leads us to discuss the applicability of analytical models in this transport. Our results, such as energy barriers for translocations, compared well with the translocation rates obtained by experimental collaborators using electrophysiology and MIC measurements. Furthermore, our methodology suggested new measurements, such as testing novel OmpF variants, low-temperature measurements and liposome swelling assays. This study demonstrates how theory and experiments combined can reveal the mechanism and the molecular basis of OmpF permeation. This work will benefits to the design of antibiotics with improved transport properties