Bridging timescales and length scales: from macroscopic flux to the molecular mechanism of antibiotic diffusion through porins.
Our aim in this study was to provide an atomic description of ampicillin translocation through OmpF, the major outer membrane channel in Escherichia coli and main entry point for beta-lactam antibiotics. By applying metadynamics simulations, we also obtained the energy barriers along the diffusion pathway. We then studied the effect of mutations that affect the charge and size at the channel constriction zone, and found that in comparison to the wild-type, much lower energy barriers are required for translocation. The expected higher translocation rates were confirmed on the macroscopic scale by liposome-swelling assays. A microscopic view on the millisecond timescale was obtained by analysis of temperature-dependent ion current fluctuations in the presence of ampicillin and provide the enthalpic part of the energy barrier. By studying antibiotic translocation over various timescales and length scales, we were able to discern its molecular mechanism and rate-limiting interactions, and draw biologically relevant conclusions that may help in the design of drugs with enhanced permeation rates.
Hajjar
Eric
E
Department of Physics, Universita degli Studi di Cagliari and Sardinian Laboratory for Computational Materials Science, Monserrato, Italy.
Mahendran
Kozhinjampara R
KR
Kumar
Amit
A
Bessonov
Andrey
A
Petrescu
Mircea
M
Weingart
Helge
H
Ruggerone
Paolo
P
Winterhalter
Mathias
M
Ceccarelli
Matteo
M
D000667:Ampicillin / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000378:metabolism*; D004058:Diffusion; D055724:Electrophysiological Phenomena; D008081:Liposomes / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009154:Mutation; D010539:Permeability; D018272:Porins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011487:Protein Conformation; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors
D000900:Anti-Bacterial Agents; D008081:Liposomes; C109237:OmpF protein; D018272:Porins; D000667:Ampicillin