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Dynamic Investigation of Protein Metal Active Sites: Interplay of XANES and Molecular Dynamics Simulations

机译:蛋白质金属活性位点的动态研究:XANES和分子动力学模拟的相互作用

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The effect of structural disorder on the X-ray absorption near-edge structure (XANES) spectrum of a heme protein has been investigated using the dynamical description of the system derived from molecular dynamics (MD) simulations. The XANES spectra of neuroglobin (Ngb) and carbonmonoxy-neuroglobin (NgbCO) have been quantitatively reproduced, starting from the MD geometrical configurations, without carrying out any optimization in the structural parameter space. These results provide an important experimental validation of the reliability of the potentials used in the MD simulations and accordingly corroborate the consistency of the structural dynamic information on the metal center, related to its biological function. This analysis allowed us to demonstrate that the configurational disorder associated with the distortion of the heme plane and with the different orientations of the axial ligands can affect the XANES features at very low energy. Neglecting configurational disorder in the XANES quantitative analysis of heme proteins is a source of systematic errors in the determination of Fe coordination geometry. The combined use of XANES and MD is a novel strategy to enhance the resolution and reliability of the structural information obtained on metalloproteins, making the combination of these techniques powerful for metalloprotein investigations.
机译:使用从分子动力学(MD)模拟得出的系统动力学描述,研究了结构紊乱对血红素蛋白X射线吸收近边缘结构(XANES)光谱的影响。从MD的几何构型开始,已经定量再现了神经球蛋白(Ngb)和一氧化碳-神经球蛋白(NgbCO)的XANES光谱,而没有在结构参数空间中进行任何优化。这些结果为MD模拟中使用的电位的可靠性提供了重要的实验验证,并因此证实了金属中心上与其生物学功能相关的结构动态信息的一致性。该分析使我们能够证明,与血红素平面的变形以及轴向配体的不同取向相关的构型紊乱可以在非常低的能量下影响XANES特征。在XANES血红素蛋白定量分析中忽略构型紊乱是铁配位几何测定中系统错误的来源。 XANES和MD的组合使用是一种新颖的策略,可以提高在金属蛋白上获得的结构信息的分辨率和可靠性,从而使这些技术的结合对金属蛋白的研究非常有效。

著录项

  • 来源
    《Journal of the American Chemical Society》 |2010年第42期|p.14901-14909|共9页
  • 作者

    Paola D’Angelo;

  • 作者单位

    Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacr;

  • 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);
  • 原文格式 PDF
  • 正文语种 eng
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  • 入库时间 2022-08-18 00:50:25

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