Comparing the Temperature-Dependent Conductance of the Two Structurally Similar E. coli Porins OmpC and OmpF

Abstract

The temperature-dependent ion conductance of OmpC, a major outer membrane channel of Escherichia coli, is predicted using all-atom molecular dynamics simulations and experimentally verified. To generalize previous results, OmpC is compared to its structural homolog OmpF at different KCl concentrations, pH values, and a broad temperature range. At low salt concentrations and up to room temperature, the molecular modeling predicts the experimental conductance accurately. At high salt concentrations above 1 M KCl and above room temperature, the simulations underestimate the conductance. Moreover, the temperature dependence of the channel conductance is different from that of the bulk, both in experiment and simulation, indicating a strong contribution of surface effects to the ion conductance. With respect to OmpC, subconductance levels can be observed in experiments only. Subconductance and gating levels can be clearly distinguished by their differences in conductance values and temperature-dependent behavior. With increasing temperature, the probability of a subconductance state to occur, increases, while the dwell time is decreased. The open probability, frequency, and dwell time of such states is largely pH- and KCl concentration-independent, while their amplitudes show a lower increase with increasing salt concentration than gating amplitudes. Voltage dependence of subconductance has been found to be negligible within the uncertainty of the measurements.

Kinetics and thermodynamics of binding reactions as exemplified by anthrax toxin channel blockage with a cationic cyclodextrin derivative

“…The increase in the on-and off-rates of the reaction manifests itself in the decrease of the average times spent by the channel in both open and blocked states. As temperature is elevated from 15 to 40°C the conductance of the channel grows by a factor of 2, which is close to the effect of the temperature on ionic conductance of other large channels (9). Fig.…”

“…K eq = Q ch ; [9] and the van't Hoff equation is dln K eq dβ = ΔH N A = ( ∂ ∂β ½ln Aðx; βÞ − βUðx; βÞ ) B ; [10] where N A is the Avogadro number and the angular brackets denote Boltzmann averaging over the channel,…”

Entropy–enthalpy compensation at the single protein level: pH sensing in the bacterial channel OmpF

“…4a) has two clusters of charge with two acidic residues D113 and E117 facing directly three positive arginines (R42, R82, and R132). [16][17][18][19] Site-directed mutagenesis experiments corroborate that these acidic residues control the channel sensitivity to pH. 15 We propose a scheme involving several quasiparticles (an unoccupied site, a site with bound protons, and a site with bound cations) and the pair of interacting acidic residues as the key sites in the low pH regime (Fig.…”

“…Calculated free energy profiles show a single free energy barrier located in the central constriction acting as the rate-limiting step for ion conduction. [14][15][16][17][18][19] The current through the channel is proportional to the limiting rate constant for ion translocation 13 and then the temperature dependence of the channel conductance is…”

How do the protonation states of E296 and D312 in OmpF and D299 and D315 in homologous OmpC affect protein structure and dynamics? Simulation studies

“…Later, protonating either E296 or D312 and deprotonating both residues were also employed in some simulations [14,27,28]. Nonetheless, based on a previous patch clamp study, deprotonating D312 only becomes more reasonable [20].…”