All-Atom Molecular Dynamics Simulation of Photosystem II Embedded in Thylakoid Membrane
All-Atom Molecular Dynamics Simulation of Photosystem II Embedded in Thylakoid Membrane
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DOI：
10.1021/ja404317d
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发表时间：
2013-10-23
影响因子：
15
通讯作者：
Nakamura, Shinichiro
中科院分区：
文献类型：
--
作者：
Ogata, Koji;Yuki, Taichi;Nakamura, Shinichiro
报告了分子动力学模拟。使用光系统II结构的最新数据，类囊体膜模型，其脂质类别分布和脂肪酸组成与天然类囊体膜相同。结果表明，水、氧和质子的传递具有不同的途径。轨迹的均方根（rms）波动分析表明，氧演化中心（OEC）周围的残基显示出较小的波动，并且那里的大多数水分子显示出较大的波动，并且位于水和氧转移的拟议路径上。 OEC附近波动较小的水分子可能参与质子转移。我们假设本研究中描述的每种途径都在光合作用中发挥作用。
The molecular dynamics simulation is reported. The latest data on photosystem II structure, a thylakoid membrane model with the same lipid class distribution and fatty acid composition as the native thylakoid membrane, are used. The results indicate that the transfer of water, oxygen and protons has different pathways. The root mean square (rms)-fluctuation analysis of trajectory revealed that the residues surrounding the oxygen-evolving center (OEC) show small fluctuations and that most of the water molecules there show large fluctuation and are on proposed pathways for water and oxygen transfer. The water molecules near the OEC having small fluctuation could be involved in proton transfer. We assume that each kind of pathway characterized in this study plays a role in photosynthesis.