Fitting Multimeric Protein Complexes into Electron Microscopy Maps Using 3D Zernike Descriptors
Fitting Multimeric Protein Complexes into Electron Microscopy Maps Using 3D Zernike Descriptors
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DOI：
10.1021/jp212612t
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发表时间：
2012-06-14
影响因子：
3.3
通讯作者：
Kihara, Daisuke
中科院分区：
文献类型：
--
作者：
Esquivel-Rodriguez, Juan;Kihara, Daisuke
提出了一种将多种蛋白质的高分辨率结构拟合到冷冻电子显微镜图上的新颖计算方法。名为 EMLZerD 的方法生成了一组候选蛋白质的多个蛋白质对接构象，随后将其与提供的电子显微镜 (EM) 密度图进行比较，以选择与 EM 图非常吻合的构象。使用 3D Zernike 描述符 (3DZD)（三维函数的数学级数展开）进行对接构象和 EM 图的比较。 3DZD提供了多聚蛋白复合物模型和EM图表面形状的统一表示，可以方便、快速地定量比较三维结构数据。在测试的 19 种多聚体复合物中，有 14 种情况获得了均方根偏差小于 2.5 埃的近天然复合物结构，而另外 5 种情况则计算了具有正确拓扑的中等分辨率结构。
A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The method named EMLZerD generates a pool of candidate multiple protein docking conformations of component proteins, which are later compared with a provided electron microscopy (EM) density map to select the ones that fit well into the EM map. The comparison of docking conformations and the EM map is performed using the 3D Zernike descriptor (3DZD), a mathematical series expansion of three-dimensional functions. The 3DZD provides a unified representation of the surface shape of multimeric protein complex models and EM maps, which allows a convenient, fast quantitative comparison of the three-dimensional structural data. Out of 19 multimeric complexes tested, near native complex structures with a root-mean-square deviation of less than 2.5 angstrom were obtained for 14 cases while medium range resolution structures with correct topology were computed for the additional 5 cases.