Energetics and Molecular Mechanisms of Permeation and Selectivity of Transport in the Urea Transporter

Abstract

Urea, ubiquitously used as a nitrogen source by bacteria and a safe end product of protein catabolism, depends on a specialized facilitator, urea transporter (UT) for its selective transport across the plasma membrane. Despite the name “transporter”, UT has been suggested to operate by a channel like mechanism owing to its high transport rate. The crystal structure of a bacterial UT was reported recently as a homotrimer in the apo and substrate (dimethylurea; DMU)-bound states. However, important transport characteristics, such as urea binding sites and water permeability, have not been identified. To understand these transport properties of UT, we have performed extended equilibrium molecular dynamics simulations of the UT trimer with each monomer in one of the apo, DMU-bound, and urea-bound (modeled by Ming Zhou group) states, as well as umbrella sampling simulations of urea. These simulations allowed us to characterize expulsion pathways of the DMU and urea from the substrate-bound channels along with water permeation properties through the apo channel. Although the three urea molecules sampled almost every point along the channel during our equilibrium simulations, we also carried out umbrella sampling simulations of urea to better characterize the energetics associated with urea transport. The absence of a gating mechanism and the stability of the protein structure supports that UT operates via a non-gated channel-like mechanism by providing a hydrated passageway for urea across the membrane. Our results also suggest that urea is co-transported with water as indicated by water permeability of UT obtained from equilibrium simulations and that urea maintains its hydration in the pore in umbrella sampling simulations. Interestingly, UT manifests peak energy barriers of similar height to that of many aquaporins not only for water but also for urea.