Aquaporins are trans-membrane channels that are responsible for the permeation of water across the cell boundary. Responding to environmental stresses such as osmolarity, voltage and pH is an important aspect of regulation of channel permeability. We demonstrate that aquaporin-4, a membrane water channel modulates water transport via pH sensing. Aquaporin-4 is expressed mostly on the cytoplasmic membrane of cells of the nervous system. It has been implicated in the formation of edema during stress caused to the brain and thus has medical relevance. In this work we combine a Molecular Dynamics based computational approach with empirical methods to identify the molecular mechanism involved in the regulation of the channel via pH. Using a Partial Least Squares (PLS) based machine learning algorithm, we perform Functional Mode Analysis (FMA) to elucidate collective motions in the protein that are responsible for opening and closing the channel pore. We find that the protonation of conserved histidine residue H95 opens the channel and locally increases the pore radius. We employ Essential Dynamics (ED) simulations to ascertain that the collective mode identified by the computational method can indeed switch the protein function on and off. This mechanism is then tested experimentally by expressing the protein on Xenopus oocytes. By controlling the pH on either side of the cell boundary the location of the pH sensor is identified with respect to the cell membrane. Finally using mutational analysis it is established that H95 is the residue responsible for the pH sensing.
