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.

中文翻译：

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肾脏尿素转运蛋白结构特征的计算与模拟及尿素转运行为

尿素转运蛋白是一种膜蛋白家族，可在细胞膜上转运尿素分子，并在各种生理过程中发挥重要作用。尽管已经解决了细菌尿素通道dv UT的晶体结构，但仍缺乏对dv UT中尿素转运动力学的了解。在这项研究中，通过使用分子动力学模拟，蒙特卡洛方法和自适应偏压力方法，我们建立了dv UT的平衡结构，计算了尿素自由能的变化，确定了dv UT的尿素结合位点，深入了解尿素运输的微观过程，并研究了dv中的水渗透性UT包括对孔中水链的分析。这项工作中使用的策略可以应用于研究其他膜蛋白的运输行为。