Movement of arginine through OprD: The energetics of permeation and the role of lipopolysaccharide in directing arginine to the protein

Abstract

The outer membrane channel OprD from Pseudomonas aeruginosa transports basic amino acids and clinically relevant carbapenem antibiotics. Understanding the molecular basis of substrate permeation across this channel will therefore lead to better therapeutic designs to treat infections. Using umbrella sampling simulations, we calculated the potential of mean force (PMF) for the arginine permeation pathway through OprD. The PMF reveals a deep free energy well of ~6 kT around the putative substrate binding site followed by a shallower well of ~4 kT close to the most constricted region of the pore. Despite becoming partially dehydrated during translocation, some water molecules are retained to shield the guanidinium side chain of arginine from the ladder of basic residues in the protein. Sugars of the lipopolysaccharide headgroups form contacts with arginine and could potentially play an important role in transferring substrate from the external medium to OprD. The PMF through bulk membrane shows a large energetic barrier of ~45 kT within the hydrophobic core of the membrane, suggesting that spontaneous translocation without OprD is highly unlikely. This significant energetic penalty is likely caused by the extensive distortion of the lower leaflet of the outer membrane as phospholipid headgroups sink inwards to interact with charged groups of arginine. Our results provide quantitative insights into solute permeation across bacterial outer membrane.

More information

Identifiers

ORCID for Firdaus Samsudin: orcid.org/0000-0003-2766-4459

ORCID for Syma Khalid: orcid.org/0000-0002-3694-5044

Catalogue record

Export record

Altmetrics