X-ray crystallography and electron microscopy maps resolved to 3–8 Å are generally sufficient for tracing the path of the polypeptide chain in space, while often insufficient for unambiguously registering the sequence on the path (i.e., threading). Frequently, however, additional information is available from other biophysical experiments, physical principles, statistical analyses, and other prior models. Here, we formulate an integrative approach for sequence assignment to a partial backbone model as an optimization problem, which requires three main components: the representation of the system, the scoring function, and the optimization method. The method is implemented in the open source Integrative Modeling Platform (IMP) (https://integrativemodeling.org), allowing a number of different terms in the scoring function. We apply this method to localizing the sequence assignment within a 199-residue disordered region of three structured and sequence unassigned helices in the DNA-PKcs crystallographic structure, using chemical crosslinks, hydrogen deuterium exchange, and sequence connectivity. The resulting ensemble of threading models provides two major solutions, one of which suggests that the crucial ABCDE cluster of phosphorylation sites cannot undergo intra-molecular autophosphorylation without a conformational rearrangement. The ensemble of solutions embodies the most accurate and precise sequence threading given the available information.

通常，解析为3–8Å的X射线晶体学和电子显微镜图足以在空间中追踪多肽链的路径，而通常不足以在路径上明确记录序列（即穿线）。但是，经常可以从其他生物物理实验，物理原理，统计分析和其他现有模型中获得更多信息。在这里，我们提出了一种将序列分配给部分骨干模型作为优化问题的综合方法，该方法需要三个主要组件：系统表示，评分功能和优化方法。该方法在开源集成建模平台中实现（IMP）（https://integrativemodeling.org），在评分功能中允许使用许多不同的术语。我们将这种方法应用于使用化学交联，氢氘交换和序列连接性在DNA-PKcs晶体结构中三个结构化和序列未分配的螺旋结构的199个残基无序区域内的序列分配。由此产生的线程模型集成提供了两种主要解决方案，其中一种表明关键的ABCDE磷酸化位点簇不能在没有构象重排的情况下经历分子内自磷酸化。解决方案的集合体现了给定可用信息的最准确和最精确的序列线程。