Paper Citing NAMD - Abstract
Wang, Zhe; Yu, Tao; Sang, Jian-Ping; Zou, Xian-Wu; Yan, Chengfei; Zou, Xiaoqin
Computation and Simulation of the Structural Characteristics of the Kidney Urea Transporter and Behaviors of Urea Transport
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5124-5131, APR 23 2015
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 dvUT has been solved; there lacks an understanding cif the dynamics of urea transport in dvUT. In this Study, by using Molecular dynamics simulations, Monte Carlo methods, and the adaptive biasing force approach, we built the equilibrium structure of dvUT, calculated the variation hi the free energy of urea, determined the urea-binding sites of dvUT, gained insight into the microscopic process of urea transport, and studied the Water permeability in dvUT 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.
