Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex
Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex
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DOI：
10.1021/acs.jpcb.5b00809
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发表时间：
2015-06-25
影响因子：
3.3
通讯作者：
Marrink, Siewert J.
中科院分区：
文献类型：
--
作者：
de Jong, Djurre H.;Liguori, Nicoletta;Marrink, Siewert J.
蛋白质复合物内部和之间的电子传递是类囊体（叶绿体）、线粒体和细菌膜中电子传递链的核心过程。这些电子转移涉及许多辅因子。在这里，我们描述了与光系统II核心复合物的功能相关的辅因子的分子力学参数的推导：质体醌，质体醌醇，血红素B，叶绿素A，脱镁叶绿素和β-胡萝卜素。还获得了泛醇和泛醌的参数，呼吸链中涉及的相关辅因子参数在原子和粗粒（CG）分辨率下推导，分别与GROMOS联合原子和Martini CG力场的构建块兼容。结构和热力学性质的辅因子进行了比较，实验值时可用。在辅因子在其生理环境中的分子动力学模拟中进一步测试拓扑结构，例如，在脂膜环境中或与血红素结合蛋白细菌铁蛋白复合。
Electron transfers within and between protein complexes are core processes of the electron transport chains occurring in thylakoid (chloroplast), mitochondrial, and bacterial membranes. These electron transfers involve a number of cofactors. Here we describe the derivation of molecular Mechanics parameters for the cofactors associated with the function of the photosystem II core complex: plastoquinone, plastoquinol, heme b, chlorophyll A, pheophytin, and beta-carotene. Parameters were also obtained for ubiquinol and ubiquinone, related cofactors involved in the respiratory chain Parameters were derived at both atomistic and coarse grain (CG) resolutions, compatible with the building blocks of the GROMOS united-atom and Martini CG force fields, respectively. Structural and thermodynamic properties of the cofactors were compared to experimental values when available. The topologies were further tested in molecular dynamics simulations of the cofactors in their physiological environment, e.g., either in a lipid membrane environment or in complex with the heme binding protein bacterioferritin.