title: A kinetic model for molecular diffusion through pores.
abstract: The number of pathogens developing multiple drug resistance is ever increasing. The impact on healthcare systems is huge and the need for novel antibiotics as well a new way to develop them is urgent, especially against Gram-negative bacteria. The first defense of these bacteria is the outer membrane, where unspecific protein channels (porins) modulate nutrients passive diffusion. Also polar antibiotics enter through this path and down-regulation and/or mutation of porins are very common in drug resistant strains. Our inability to come up with novel effective antibiotics mostly relies upon the insufficient comprehension of the key molecular features enabling better penetration through porins. Molecular dynamics simulations offer an extraordinary tool in the study of the dynamics of biological systems; however, one of the major drawbacks of this method is that its use is currently restricted to study time scales of the order of microsecond. Enhanced sampling methods like Metadynamics have been recently used to investigate the diffusion of antibiotics through bacterial porins. The main limitation is that dynamical properties cannot be estimated because of the different potential that the systems under study are experiencing. Recently, the scope of Metadynamics has been extended. By applying an a posteriori analysis one can obtain rates of transitions and rate-limiting steps of the process under study, directly comparable with kinetic data extracted from electrophysiology experiments. In this work, we apply this method to the study of the permeability of Escherichia coli's OmpF with respect to Meropenem, finding good agreement with the residence time obtained analyzing experimental current noise. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
authors.affiliation: Department of Physics, University of Cagliari, Italy.
authors.forename: Tommaso
authors.initials: T
authors.lastname: D'Agostino
authors.affiliation: Department of Physics, University of Cagliari, Italy.
authors.forename: Samuele
authors.initials: S
authors.lastname: Salis
authors.affiliation: Department of Physics, University of Cagliari, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Ceccarelli
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D001665:Binding Sites; D002462:Cell Membrane / Q000737:chemistry* / Q000648:ultrastructure; D002463:Cell Membrane Permeability; D004058:Diffusion; D006090:Gram-Negative Bacteria / Q000737:chemistry / Q000648:ultrastructure; D015640:Ion Channel Gating; D007473:Ion Channels / Q000737:chemistry* / Q000648:ultrastructure*; D008051:Lipid Bilayers / Q000737:chemistry; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D016062:Porosity; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D000900:Anti-Bacterial Agents; D001425:Bacterial Outer Membrane Proteins; D007473:Ion Channels; D008051:Lipid Bilayers
keywords: Kinetics; Molecular dynamics; Porins; Transport