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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images
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Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images

机译：通过满足电子显微镜图像的空间约束条件来组装大分子复合物

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摘要

To obtain a structural model of a macromolecular assembly by single-particle EM, a large number of particle images need to be collected, aligned, clustered, averaged, and finally assembled via reconstruction into a 3D density map. This process is limited by the number and quality of the particle images, the accuracy of the initial model, and the compositional and conformational heterogeneity. Here, we describe a structure determination method that avoids the reconstruction procedure. The atomic structures of the individual complex components are assembled by optimizing a match against 2D EM class-average images, an excluded volume criterion, geometric complementarity, and optional restraints from proteomics and chemical cross-linking experiments. The optimization relies on a simulated annealing Monte Carlo search and a divide-and-conquer message-passing algorithm. Using simulated and experimentally determined EM class averages for 12 and 4 protein assemblies, respectively, we show that a few class averages can indeed result in accurate models for complexes of as many as five subunits. Thus, integrative structural biology can now benefit from the relative ease with which the EM class averages are determined.
机译：为了通过单粒子EM获得大分子组装体的结构模型，需要收集，对齐，聚类，平均并最终通过重构将大量粒子图像组装成3D密度图。该过程受到粒子图像的数量和质量，初始模型的准确性以及组成和构象异质性的限制。在这里，我们描述了一种避免重建过程的结构确定方法。通过优化与2D EM类平均图像的匹配，排除的体积标准，几何互补性以及蛋白质组学和化学交联实验的可选约束条件，可以组装单个复杂组件的原子结构。该优化依赖于模拟退火蒙特卡洛搜索和分而治之的消息传递算法。分别使用模拟和实验确定的EM类平均数，分别针对12个和4个蛋白质装配，我们显示了几个类平均数确实可以为多达5个亚基的复合物建立准确的模型。因此，整合结构生物学现在可以从确定EM类平均值的相对简便性中受益。

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  • 作者

    Javier Velazquez-Muriel; Keren Lasker; Daniel Russel; Jeremy Phillips; Benjamin M. Webb; Dina Schneidman-Duhovny; Andrej Sali;

  • 作者单位

    Departments of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158-2552,Departments of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2552,Departments of California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158-2552;

    Departments of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158-2552,Departments of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2552,Departments of California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158-2552,Department of Developmental Biology, Stanford University, Stanford, CA 94305;

    Departments of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158-2552,Departments of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2552,Departments of California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158-2552;

    Departments of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158-2552,Departments of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2552,Departments of California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158-2552;

    Departments of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158-2552,Departments of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2552,Departments of California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158-2552;

    Departments of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158-2552,Departments of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2552,Departments of California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158-2552;

    Departments of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158-2552,Departments of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2552,Departments of California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158-2552;

  • 收录信息 美国《科学引文索引》(SCI);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
  • 中图分类
  • 关键词

    integrative modeling; structural determination; computational biology;

    机译：集成建模;结构确定;计算生物学;

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