Novel Structural and Dynamical Features of Water Permeation through an Aquaporin Crystallized at Sub-Angstrom Resolution

Abstract

Aquaporins are ubiquitous trans-membrane channels that maintain water homeostasis of the cell by facilitating selective diffusion of water across the membrane while preventing proton diffusion. The selectivity has been suggested to be achieved by two conserved regions located along the pore: the dual asparagine, proline, alanine (NPA) aquaporin signature motif, and the aromatic/arginine (ar/R) selectivity filter. Recently, our collaborators have crystallized a yeast aquaporin at sub-angstrom resolution, the highest resolution achieved to date for a membrane protein. The structure reveals a great deal of novel information on the structure of hydrogen-bonded network of water and protein side chains. In order to complement the experimental results by determining the dynamics and energetics of water diffusion along the channel, we performed molecular dynamics simulations of this impressively high quality crystal structure. The results show disruption of the water chain in both NPA and ar/R regions in this aquaporin, due to characteristic hydrogen-bonding patterns that dictate specific orientations to water molecules. The motion of water molecules is highly correlated on either side of the NPA region. On the other hand, the correlation is reduced at the NPA region, attesting yet another possible mechanism for this region to contribute to a barrier against proton transport. Besides, the NPA region appears as a barrier region with low occupancy for water, a feature not seen in other aquaporins. The correlated motion of adjacent water molecules along with their binary co-occupancies in the ar/R selectivity filter show that water molecules move in pairs in this region. Specific hydrogen-bonding patterns in the ar/R region may also play a role in exclusion of hydronium and/or hydroxide ions. These simulations have helped elucidate the dynamical basis of many intricate features revealed by this new structure.