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运用加速算法研究岩藻糖转运蛋白FucP的转运机理

发表时间:2014-03-15  浏览量:1454  下载量:563
全部作者: 刘裕峰,孙林峰,龚海鹏
作者单位: 清华大学生命学院
摘 要: 运用加速模拟方法,以岩藻糖转运蛋白(L-fucose/proton symporter, FucP)为对象,试图揭示主要协同转运蛋白超家族(major facilitator superfamily,MFS)的转运机理。结果表明:除了典型的胞外开口和胞内开口构象之外,FucP还存在一个两端都闭合的构象。这些构象之间的转变并非通过刚体运动,其结构域内部,特别是N端结构域发生了较大的结构重排。实验还证明了135位残基谷氨酸(E135)在底物转运和构象变化中的重要作用,并发现了312位精氨酸(R312)、159位谷氨酰胺(Q159)和365位酪氨酸(Y365)对构象变化的影响,提出了FucP中底物转运和构象变化之间耦合的可能机理。
关 键 词: 生物物理学;主要转运蛋白超家族;自我指导的Langevin动力学;岩藻糖转运蛋白;分子动力学模拟
Title: Research on the transport mechanism of the fucose transporter FucP using accelerated algorithm
Author: LIU Yufeng, SUN Linfeng, GONG Haipeng
Organization: School of Life Science, Tsinghua University
Abstract: In this paper, we employ an accelerated algorithm to simulate L-fucose/proton symporter (FucP) to reveal the transport mechanism of major facilitator superfamily (MFS). Preliminary results indicate that there is an occluded conformation existed in FucP besides the canonical outward-open and inward-open conformations. The transitions between these conformations do not follow the rigid body movement exactly. Instead, there are considerable structural rearrangements within domains, especially for the N domain. In addition, the simulations identify the indispensable role of the 135 residues to glutamic acid (E135) in both substrate transport and conformational change, and outline the influence of the 312 residues to arginine (R312), the 159 residues to glutamine (Q159) and the 365 residues to tyrosine (Y365) on the structural transition. Finally, we propose a possible mechanism to elucidate the coupling between substrate delivering and conformational change in FucP.
Key words: biophysics; major facilitator superfamily; self-guided Langevin dynamics; L-fucose/proton symporter; molecular dynamics simulation
发表期数: 2014年3月第5期
引用格式: 刘裕峰,孙林峰,龚海鹏. 运用加速算法研究岩藻糖转运蛋白FucP的转运机理[J]. 中国科技论文在线精品论文,2014,7(5):469-475.
 
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