Computation and simulation of the structural characteristics of the kidney urea transporter and behaviors of urea transport

The Journal of Physical Chemistry. B
Zhe WangXiaoqin Zou

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.

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Citations

Aug 31, 2016·Journal of Chemical Theory and Computation·Siladitya Padhi, U Deva Priyakumar
Jun 8, 2018·Physical Chemistry Chemical Physics : PCCP·Seongjin ParkYun Hee Jang
Feb 19, 2020·Biophysics Reviews·Shampa RaghunathanU Deva Priyakumar
Jul 2, 2016·Current Opinion in Nephrology and Hypertension·Janet D Klein, Jeff M Sands
Aug 10, 2017·The Journal of Chemical Physics·Xi ZhangZhi-Jie Tan
May 17, 2017·Journal of Molecular Graphics & Modelling·Hai-Tian ZhangXiaoqin Zou

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