Mechanism of OmpG pH-Dependent Gating from Loop Ensemble and Single Channel Studies

Abstract

Outer membrane protein G (OmpG) from Escherichia coli has exhibited pH-dependent gating that can be employed by bacteria to alter the permeability of their outer membranes in response to environmental changes. We developed a computational model, Protein Topology of Zoetic Loops (Pretzel), to investigate the roles of OmpG extracellular loops implicated in gating. The key interactions predicted by our model were verified by single-channel recording data. Our results indicate that the gating equilibrium is primarily controlled by an electrostatic interaction network formed between the gating loop and charged residues on the lumen. The results shed light on the mechanism of OmpG gating and will provide a fundamental basis for the engineering of OmpG as a nanopore sensor. Our computational Pretzel model could be applied to other outer membrane proteins that contain intricate dynamic loops that are functionally important.

Giant single molecule chemistry events observed from a tetrachloroaurate(III) embedded Mycobacterium smegmatis porin A nanopore

“…The locations of these adaptors within a conically shaped biological nanopore may also be slightly dispersed so that the signal amplitude from different analyte may be tuned to assist full discrimination. Similar pore engineering may be performed by taking the monomeric channel protein OmpG 48–50 as a template for metal embedding. Other ion-amino acid combinations within a variety of biological nanopores such as Cytolysin A 51 , phi29 motor protein 52 or aerolysin 2,53 could also be adapted for different applications.…”

The Utility of Nanopore Technology for Protein and Peptide Sensing

“…Often, segments of a protein can be captured by a pore and manipulated with proteins outside the pore . While the above papers use rigid pore forming toxins, it is sometimes advantageous to use channels that produce significant conformational fluctuations like OmpG . By anchoring a tether with recognition elements to OmpG, characteristic fluctuations can be observed for several proteins with different binding strength including antibodies …”

Lipid Headgroup Charge and Acyl Chain Composition Modulate Closure of Bacterial β-Barrel Channels

“…Voltage gating of β-barrel channels is notoriously complex [9] and the mechanism that rules it is particularly elusive. Gating models point into different directions, from reversible protein denaturation [5], to electrostatic interaction networks [10], or to the concerted movement of a soft or flexible part of the barrel [11,12]. The physiological role of voltage gating in general diffusion porins has been a matter of intense debate.…”

“…The possibility that electrical voltage, among other external factors, may regulate the transport across the membrane by promoting the transitions to pore closed states opens a new scenario. In fact, changes in the permeability of outer membrane proteins are found in some antibiotic-resistant pathogenic bacteria [10].…”