Small‐Molecule Permeation across Membrane Channels: Chemical Modification to Quantify Transport across OmpF

Abstract

Biological channels facilitate the exchange of molecules across membranes,b ut general tools to quantify transport are missing. Electrophysiology is the method of choice to study the functional properties of channels.However, analyzing the current fluctuation of channelstypically does not identify successful transport, that is,d istinguishing translocation from binding.T odistinguish both processes,weadded an additional barrier at the channel exit acting as am olecular counter.T oi dentify permeation, we compare the molecule residence time in the native channel with one that is chemically modified at the exit. We use the well-studied outer membrane channel from E. coli, OmpF.P osition 181, whichi sb elowt he constriction region, was subsequently mutated into cysteine (E181C) in an otherwise cysteine-free system, then functionalized by covalent binding with one of the two blockers MTSES or GLT. We measured the passage of model peptides, mono-, tri-, hepta-arginine and of norfloxacin, as an example for antibiotic permeation.

Permeation eines 5.1‐kDa‐Peptides durch einen Proteinkanal: Molekulare Basis der Translokation von Protamin durch CymA aus Klebsiella Oxytoca**

“…In Figure S7 of the SI, a linear fit of the rates at lower voltages is shown on a semi-log scale, suggesting a permeation rate of 1-2 Ptm molecules per second for a 1 µM gradient at 0 V, where the permeation time for individual events is estimated from a logarithmic plot as 20-25 ms. Astonishingly, this flux rate agrees nicely with that estimated from the initial rates obtained by the ensemble fluorescence assays in vesicles (see above). In a second set of electrophysiological measurements, we characterized the concentration-driven relative permeation by using the so-called reversal potential measurement technique [31,32] (see Section 2 in the SI for details on Material and Methods). Starting with two compartments having 0.1 mM potassium sulfate separated by a ΔCymA channel embedded in a DPhPC bilayer, a concentration gradient of 0.25 mM Ptm sulphate was introduced on the cis side.…”

“…Studien wurde ein ähnlicher Tr end fürd ie Permeation kürzerer Polyargininmoleküle durch hetero-oligomere Kanäle und durch den allgemeinen Diffusionskanal OmpF beobachtet. [28] In einer zweiten Serie elektrophysiologischer Messungen haben wir die konzentrationsbedingte relative Permeation mithilfe der so genannten Umkehrpotential-Messtechnik charakterisiert [29,30] (Einzelheiten in Material und Methoden, siehe Abschnitt 2d er SI). Ausgehend von zwei Kompartimenten mit 0,1 mm Kaliumsulfat, die durch einen in eine DPhPC-Doppelschicht eingebetteten DCymA-Kanal getrennt waren, wurde auf der cis-Seite ein Konzentrationsgradient von 0,25 mm Ptm-Sulfat angelegt.…”

Ionic Diffusion, Nanoparticle Formation and Trapping Within Sol‐Gel Made Pillared Planar Nanochannels in a Simple Microfluidic Device

“…The material of choice is of paramount importance for the nanochannel surface characteristics, which can, eventually, be modified through inorganic, [50] organic [50] or biological molecules. [51] Finally, the bonding step, which is needed to close the top-down fabricated nanofluidic channels can easily destroy the devices.…”

“…Moreover, the top‐down techniques require a limited set of materials (mainly PDMS, SiO 2 , Si, selected photoresists and a few others). The material of choice is of paramount importance for the nanochannel surface characteristics, which can, eventually, be modified through inorganic, organic or biological molecules . Finally, the bonding step, which is needed to close the top‐down fabricated nanofluidic channels can easily destroy the devices.…”

Electrophysiological Characterization of Transport Across Outer‐Membrane Channels from Gram‐Negative Bacteria in Presence of Lipopolysaccharides

“…[8,9] In particular, major outer membrane channels such as OmpF and OmpC from E. coli are part of the pathway of antimicrobial influx. [10][11][12][13][14] The high-resolution crystal structure showed that OmpF is composed of three identical water-filled monomers. [15] Each monomer contains 16-antiparallel b-sheets spanning in the membrane domain.…”