Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.28.316596v1?rss=1 Authors: Santra, M., Seal, A., Bhattacharjee, K., Chakrabarty, S. Abstract: Photoisomerisation in retinal leads to a channel opening in the rhodopsins that triggers translocation of an ion/proton. Crystal structures of rhodopsins contain several structurally conserved water molecules. It has been suggested that water plays an active role in facilitating the ion pumping/translocation process by acting as a lubricant in these systems. In this work, we investigate the localisation, local structure and dynamics of water molecules along the channel for the resting/dark state of KR2 rhodopsin. Employing 1.5 s long atomistic molecular dynamics (MD) simulations of this trans-membrane protein system, we demonstrate the presence of five distinct water containing pockets/cavities separated by gateways controlled by the protein side-chains. We present evidence of significant structural and dynamical heterogeneity in the water molecules present in these cavities. The exchange time-scale of these buried water with bulk ranges from tens of nanoseconds to >1.5 s. The translational and rotational dynamics of buried water are found to be strongly dependent on protein cavity size and local interactions with possible functional significance. Copy rights belong to original authors. Visit the link for more info