Electron microscopy (EM) continues to provide near-atomic resolution structures for well-behaved proteins and protein complexes. Unfortunately, structures of some complexes are limited to low- to medium-resolution due to biochemical or conformational heterogeneity. Thus, the application of unbiased systematic methods for fitting individual structures into EM maps is important. A method that employs co-evolutionary information obtained solely from sequence data could prove invaluable for quick, confident localization of subunits within these structures. Here, we incorporate the co-evolution of intermolecular amino acids as a new type of distance restraint in the Integrative Modeling Platform (IMP) in order to build three-dimensional models of atomic structures into EM maps ranging from 10-14 Å in resolution. We validate this method using four complexes of known structure, where we highlight the conservation of intermolecular couplings despite dynamic conformational changes using the BAM complex. Finally, we use this method to assemble the subunits of the bacterial holo-translocon into a model that agrees with previous biochemical data. The use of evolutionary couplings in integrative modeling improves systematic, unbiased fitting of atomic models into medium- to low-resolution EM maps, providing additional information to integrative models lacking in spatial data.

中文翻译：

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通过演化耦合将集成3D建模改进为低至中分辨率EM结构

电子显微镜（EM）继续为行为良好的蛋白质和蛋白质复合物提供近原子的拆分结构。不幸的是，由于生化或构象异质性，某些复合物的结构仅限于中低分辨率。因此，将单个结构拟合到EM映射中的无偏系统方法的应用很重要。使用仅从序列数据中获得的共同进化信息的方法对于在这些结构中快速，可靠地定位亚基可能是无价的。在这里，我们将分子间氨基酸的协同进化作为一种​​新型的距离约束机制纳入了集成建模平台（IMP）中，以便将原子结构的三维模型建立到分辨率为10-14Å的EM图中。我们使用四种已知结构的复合物验证了该方法，尽管使用BAM复合物进行了动态构象变化，但我们着重指出了分子间偶联的保守性。最后，我们使用这种方法将细菌完整的亚单位组装成一个模型，该模型与以前的生化数据相符。在集成建模中使用演化耦合可改善原子模型到中低分辨率EM映射的系统，无偏拟合，从而为缺乏空间数据的集成模型提供更多信息。