AbstractInvolvement of aquaporins in gas conduction across the membrane and the physiological significance of this process have attracted marked attention from both experimental and theoretical studies. Previous work demonstrated that AQP1 is permeable to both CO2 and O2. Here we employ various simulation techniques to examine the permeability of the brain aquaporin AQP4 to NO and O2 and to describe energetics and pathways associated with these phenomena. The energy barrier to NO and O2 permeation through AQP4 central pore is found to be only ∼3 kcal mol−1. The results suggest that the central pore of AQP4, similar to that of AQP1, can indeed conduct gas molecules. Interestingly, despite a longer and narrower central pore, AQP4 appears to provide an energetically more favorable permeation pathway for gas molecules than AQP1, mainly due to the different orientation of its charged residues near the pore entrance. Although the low barrier against gas permeation through AQP4 indicates that it can participate in gas conduction across the cellular membrane, physiological relevance of the phenomenon remains to be established experimentally, particularly since pure lipid bilayers appear to present a more favorable pathway for gas conduction across the membrane. With an energy well of −1.8 kcal mol−1, the central pore of AQP4 may also act as a reservoir for NO molecules to accumulate in the membrane. Proteins 2010. © 2009 Wiley‐Liss, Inc.