Cation-selective Pathway of OmpF Porin Revealed by Anomalous X-ray Diffraction

Abstract

Summary The OmpF porin from the Escherichia coli outer membrane folds into a trimer of β-barrel, each forming a wide aqueous pore allowing the passage of ions and small solutes. A long loop (L3) carrying multiple acidic residues folds into the β-barrel pore to form a narrow “constriction zone”. A strong and highly conserved charge asymmetry is observed at the constriction zone, with multiple basic residues attached to the wall of the β-barrel (Lys16, Arg42, Arg82 and Arg132) on one side, and multiple acidic residues of L3 (Asp107, Asp113, Glu117, Asp121, Asp126, Asp127) on the other side. Several computational studies have suggested that a strong transverse electric field could exist at the constriction zone as a result of such charge asymmetry, giving rise to separate permeation pathways for cations and anions. To examine this question, OmpF was expressed, purified and crystallized in the P63 space group and two different data sets were obtained at 2.6 Å and 3.0 Å resolution with K+ and Rb+, respectively. The Rb+ soaked crystals were collected at the rubidium anomalous wavelength of 0.8149 Å and cation positions were determined. A PEG molecule was observed in the pore region for both the K+ and Rb+ soaked crystals, where it is interacting with the loop L3. The results reveal the separate pathways of anions and cations across the constriction zone of the OmpF pore.

First-passage-time analysis of atomic-resolution simulations of the ionic transport in a bacterial porin

“…As expected, potassium ions are dragged along the direction of the external electric field, whereas chloride ions are dragged in the opposite direction. The slightly different magnitude of both forces is consistent with the observation that anions and cations follow different pathways in the constriction, as has been reported in previous MD studies [22] and in experiment [42]. Assuming that the section of the channel along the z axis is uniform in the constriction (see Fig.…”

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

“…Like earlier studies [15,43,44], this study can also confirm that OmpC is more structurally stable than OmpF. Its pore size is also slightly smaller than that of OmpF.…”

Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi

“…Recent crystal structure (Dhakshnamoorthy et al, 2009) and molecular dynamics study (Im and Roux, 2002a;Schirmer and Phale, 1999) of E. coli OmpF revealed that cations and anions follow separate pathway along the entire length of channel, indicating residues other than those present in the constriction zone might participate in the ion permeation (Vrouenraets and Miedema, 2010). In the crystal structure of S. typhi Ty21a rfOmpF, five basic residues (16K, 20R, 60R, 77R and 130R) from the barrel wall face one acidic residue 108D from loop L3, making it less negative electrostatic potential than E. coli OmpF (Fig.…”