A novel molecular dynamics study of CO₂ permeation through aquaporin-5

Aquaporins (AQPs) are protein channels which facilitate rapid water permeation across cell membrane. The AQPs are very vital for biological organs, as their malfunction causes severe diseases in human body. A particular family of AQPs, that is AQP5, has a significant role in lung fluid transport due to submucosal glands structure. However, it has not been yet well understood whether these protein channels can conduct gas molecules. Here, Molecular Dynamics (MD) simulations are used to investigate the CO₂ permeability and diffusion in AQP5 during a 40-nanosecond period. For the first time, equilibrium and Steered MD (SMD) are used to simulate self and force-induced diffusion of CO₂ molecules across AQP5 and POPE lipid bilayer. According to PMFs profile associated to CO₂ permeation, the hydrophobic central pore provides a more suitable pathway for gas molecules compared to other AQP5 channels. Although CO₂ molecules can also permeate across AQP5 water channels, the rate of CO₂ permeation through four channels of the AQP5 monomers is much lower than the central pore. The rate of CO₂ permeation through four AQP5 water channels is even lower than CO₂ diffusion through POPE lipid membrane. The results reported in this investigation demonstrate that MD simulations of human AQP5 provide valuable insights into the gas permeation mechanism for both the equilibrium self-diffusion, and quasi-equilibrium condition.