Simulating Gas Permeation Through the Central Pore of AQP5

Aquaporins (AQPs), a family of integral membrane proteins that serve as water channels, have been hypothesized to facilitate the permeation of metabolic gases (O₂ and CO₂) via their central pore (CP) formed in the middle of AQP tetramers. Our examination of aquaporin-5 (AQP5), an isoform expressed in lung epithelial cells, using atomistic molecular dynamics (MD) simulations suggests that gas can indeed permeate through the protein. Free energy calculations by implicit ligand sampling (ILS) predict that gas molecules favorably partition into the hydrophobic interior of the CP. Following up, we performed concentration gradient simulations of membrane-embedded AQP5 with CO₂. Concentration profiles predict that CO₂ partitions favorably within the CP cavity, to greater levels than even the lipid bilayer core. Additional analysis showed that the CP facilitates a greater number of permeations than the four monomeric pores combined and that permeations through the CP occurred with a mean residence time 88.1 ns. Altogether, the results indicate that AQPs may facilitate the permeation of gas across membranes, with the CP playing a key role. Understanding the impact of proteins on gas permeation across membranes contributes to a more complete picture of cellular gas transport and may lead to the discovery of therapeutic targets in disease states involving altered gas transport.