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Charge-density analysis of an iron-sulfur protein at an ultra-high resolution of 0.48 angstrom

机译：铁硫蛋白在0.48埃的超高分辨率下的电荷密度分析

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摘要

The fine structures of proteins, such as the positions of hydrogen atoms, distributions of valence electrons and orientations of bound waters, are critical factors for determining the dynamic and chemical properties of proteins. Such information cannot be obtained by conventional protein X-ray analyses at 3.0-1.5 angstrom resolution, in which amino acids are fitted into atomically unresolved electron-density maps and refinement calculations are performed under strong restraints(1,2). Therefore, we usually supplement the information on hydrogen atoms and valence electrons in proteins with preexisting common knowledge obtained by chemistry in small molecules. However, even now, computational calculation of such information with quantum chemistry also tends to be difficult, especially for polynuclear metalloproteins(3). Here we report a charge-density analysis of the high-potential iron-sulfur protein from the thermophilic purple bacterium Thermochromatium tepidum using X-ray data at an ultra-high resolution of 0.48 angstrom. Residual electron densities in the conventional refinement are assigned as valence electrons in the multipolar refinement. Iron 3d and sulfur 3p electron densities of the Fe4S4 cluster are visualized around the atoms. Such information provides the most detailed view of the valence electrons of the metal complex in the protein. The asymmetry of the iron-sulfur cluster and the protein environment suggests the structural basis of charge storing on electron transfer. Our charge-density analysis reveals many fine features around the metal complex for the first time, and will enable further theoretical and experimental studies of metalloproteins.
机译：蛋白质的精细结构，例如氢原子的位置，价电子的分布和结合水的方向，是决定蛋白质动态和化学性质的关键因素。这种信息不能通过传统的蛋白质X射线分析以3.0-1.5埃的分辨率获得，其中将氨基酸拟合到原子上未解析的电子密度图上，并且在强约束条件下进行精制计算（1,2）。因此，我们通常利用小分子化学过程中获得的常识来补充蛋白质中氢原子和价电子的信息。但是，即使是现在，利用量子化学方法对此类信息进行计算也仍然很困难，尤其是对于多核金属蛋白而言（3）。在这里，我们报告了使用X射线数据以0.48埃的超高分辨率对嗜热紫色细菌温色嗜铬菌（Thermochromatium tepidum）产生的高潜力铁硫蛋白进行的电荷密度分析。常规精制中的残余电子密度在多极精制中被指定为价电子。 Fe4S4团簇的铁3d和硫3p电子密度在原子周围可见。此类信息提供了蛋白质中金属络合物的价电子的最详细视图。铁-硫簇和蛋白质环境的不对称性表明电子转移中电荷存储的结构基础。我们的电荷密度分析首次揭示了金属配合物周围的许多精细特征，并将使金属蛋白的进一步理论和实验研究成为可能。

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  • 来源
    《Nature》 |2016年第7606期|281-284|共4页
  • 作者

    Hirano Yu; Takeda Kazuki; Miki Kunio;

  • 作者单位

    Kyoto Univ, Grad Sch Sci, Dept Chem, Sakyo Ku, Kyoto 6068502, Japan|Natl Inst Quantum & Radiol Sci & Technol, Quantum Beam Sci Res Directorate, Tokai, Ibaraki 3191195, Japan;

    Kyoto Univ, Grad Sch Sci, Dept Chem, Sakyo Ku, Kyoto 6068502, Japan;

    Kyoto Univ, Grad Sch Sci, Dept Chem, Sakyo Ku, Kyoto 6068502, Japan;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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