Anion Translocation in a Brush-Like Nanopore: Simulations of the Outer Membrnae Protein OprP

Abstract

The outer membrane protein OprP from Pseudomonas aeruginosa forms an anion-selective pore, especially selective for phosphate ions. The protein is homo-trimeric, with each pore lined by three positively charged loops (L3, L5, and T7) folded into its lumen. OprP plays a key role in high-affinity phosphate uptake under the condition of phosphate starvation. To better understand the mechanism of phosphate-selective permeation, we employed three simulation techniques: (i) equilibrium molecular dynamics simulations (MD); (ii) steered MD (SMD); (iii) umbrella sampling to calculate a potential of mean force (PMF) for phosphate and chloride ions. The PMFs reveal a deep energy well midway along the OprP channel. Two adjacent phosphate-binding sites (W1 and W2), each with a well depth of ∼8kT, are identified close to the L3 loop in the most constricted region of the pore. The transfer of phosphate between sites W1 and W2 is correlated with changes in conformation of the sidechain of K121, which serves as a ‘charged brush’ to facilitate phosphate passage between the two subsites. The PMF for chloride has also been computed and can be compared with that of phosphate. Our simulations suggest that OprP does not conform to the conventional picture of a channel with a relatively flat energy landscape for permeant ions, but rather resembles a membrane-inserted binding protein with a high specificity that allows access to a centrally located binding site from both the extracellular and the periplasmic spaces.