title: 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 dvUT has been solved, there lacks an understanding of 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 in 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.
authors.affiliation: †Department of Physics, Wuhan University, Wuhan 430072, China.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Wang
authors.affiliation: †Department of Physics, Wuhan University, Wuhan 430072, China.|‡Department of Physics, Jianghan University, Wuhan 430056, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Yu
authors.affiliation: †Department of Physics, Wuhan University, Wuhan 430072, China.|‡Department of Physics, Jianghan University, Wuhan 430056, China.
authors.forename: Jian-Ping
authors.initials: JP
authors.lastname: Sang
authors.affiliation: †Department of Physics, Wuhan University, Wuhan 430072, China.
authors.forename: Xian-Wu
authors.initials: XW
authors.lastname: Zou
authors.affiliation: §Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States.
authors.forename: Chengfei
authors.initials: C
authors.lastname: Yan
authors.affiliation: §Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States.
authors.forename: Xiaoqin
authors.initials: X
authors.lastname: Zou
mesh_terms: D001692:Biological Transport; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D011487:Protein Conformation; D013816:Thermodynamics; D014508:Urea / Q000378:metabolism*; D000096982:Urea Transporters
chemical_list: D026901:Membrane Transport Proteins; D014508:Urea; D000096982:Urea Transporters