title: Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations.
abstract: In this paper we investigate the structural and dynamical properties of the two major porins (OmpF and OmpC) in Escherichia coli, using molecular dynamics (MD) simulations. In particular we characterized the atomic fluctuations, correlated motions, temperature dependence, solvent-accessible cross-sectional area and water dynamics in the key regions of the two channels. Our in-depth analysis allows us to highlight the importance of both the key conserved and substituted residues between OmpF and OmpC. The latter is characterized by a narrower and longer constriction region with respect to OmpF. OmpC also showed a higher stability upon increasing temperature. We then present the results of transport properties by using accelerated MD simulations to probe the diffusion of norfloxacin (a fluoroquinolone antibiotic) through the two porins OmpF/OmpC. Our study constitutes a step forward towards understanding the structure-function relationship of the two porins' channels. This will benefit the research of antibacterials with improved permeation properties and nanopores that aim to use these porins as sensing systems.
authors.affiliation: Istituto Officina dei Materiali/CNR UOS SLACS, c/o Department of Physics, University of Cagliari, SP Monserrato-Sestu Km 0.700, Monserrato I-09042, Italy.
authors.forename: Amit
authors.initials: A
authors.lastname: Kumar
authors.forename: Eric
authors.initials: E
authors.lastname: Hajjar
authors.forename: Paolo
authors.initials: P
authors.lastname: Ruggerone
authors.forename: Matteo
authors.initials: M
authors.lastname: Ceccarelli
mesh_terms: D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D018272:Porins / Q000737:chemistry* / Q000648:ultrastructure*; D011487:Protein Conformation
chemical_list: C113724:OmpC protein; C109237:OmpF protein; D018272:Porins