Computation and Simulation of the Structural Characteristics of the Kidney Urea Transporter and Behaviors of Urea Transport

Abstract

Urea transporters are a family of membrane proteins that transport urea molecules across cell membranes and play important roles in a variety of physiological processes. Although the crystal structure of bacterial urea channel <i>dv</i>UT has been solved, there lacks an understanding of the dynamics of urea transport in <i>dv</i>UT. In this study, by using molecular dynamics simulations, Monte Carlo methods, and the adaptive biasing force approach, we built the equilibrium structure of <i>dv</i>UT, calculated the variation in the free energy of urea, determined the urea-binding sites of <i>dv</i>UT, gained insight into the microscopic process of urea transport, and studied the water permeability in <i>dv</i>UT including the analysis of a water chain in the pore. The strategy used in this work can be applied to studying transport behaviors of other membrane proteins