A multistage approach to protein-protein docking

蛋白质之间的相互作用几乎是所有生物途径所不可或缺的。许多重要的交互作用发生在 弱的、瞬时的复合体将不能直接进行实验分析，即使当两种蛋白质 可以被分离并确定它们的结构。因此，发展计算对接非常重要。 从组分蛋白质的结构出发，确定其结构的方法 复合体。我们开发了一种多阶段对接算法，在最新的 几轮CAPRI(预测相互作用的关键评估)全球对接实验。此外, 我们的对接服务器ClusPro是自动化服务器中最好的。尽管卡普里的结果表明 在取得进展的同时，一些重大问题仍未得到解决。首先，对接同源模型是一项挑战，所有 在CAPRI中使用的方法在这些目标上表现不佳。在以下情况下，停靠未绑定的结构也很困难 结合伴随着实质性的骨架构象变化。其次，目前还不清楚一个 对接生成的模型代表着一种特定而稳定的情结。第三，界面可以包括区域 这些蛋白质在分离的蛋白质中是无序的，挑战了对接方法。我们通过以下方式解决这些问题 追求三个具体目标。首先，我们开发了一种新的算法来对接同源模型和蛋白质 具有相当大的主干灵活性。该方法是基于络合物中的界面是 在序列和结构上比其他蛋白质更保守。因为这样的地区经常 足以识别、识别和正确对接关键片段可以产生近乎原生对接 结构。对于同源模型，这意味着可以对接可以可靠建模的区域，并且 然后，使用固定结构作为约束，通过重新添加已移除的零件来展开模型。这个 对接具有实质性骨架构象变化的“疑难病例”的问题也可以得到解决 通过识别和对接结构上最保守的区域。一旦一簇簇停靠的刚性碎片 通过对更灵活的部分进行重构，对模型进行了扩展。其次，我们使用两步法 一种检查蛋白质复合体稳定性的方法，首先通过去除因此而不太可能的小簇 低能对接结构，然后通过随机路线图模拟计算解离速率。 该方法将在包括真实蛋白质复合体和诱饵模型的基准集上进行验证 通过对接非相互作用的蛋白质对产生。该方法还将用于确定是否 沉积在PDB上的复杂结构具有生物学意义。第三，我们考虑的是 当柔性环和/或无序区域成为蛋白质的一部分时，确定它们的结构- 蛋白质界面。而不是试图预测和停靠最有可能的柔性构象 我们将它们的结合结构直接构建到伙伴蛋白的结合热点上。弹性多肽 将使用对接方法通过添加更多残基来扩展对接的碎片。

Protein-protein interactions are integral to virtually all biological pathways. Many important interactions occur in weak, transient complexes that will not be amenable to direct experimental analysis, even when both proteins can be isolated and their structures determined. Thus, it is important to develop computational docking methods which, starting from the structures of component proteins, can determine the structure of their complexes. We have developed a multistage docking algorithm that provided the best results in the latest rounds of the CAPRI (Critical Assessment of Predicted Interactions) worldwide docking experiment. In addition, our docking server ClusPro was the best among automated servers. Although the CAPRI results demonstrate progress, a number of major problems remain unsolved. First, docking homology models is a challenge and all methods used in CAPRI performed poorly for such targets. Docking unbound structures is also difficult if binding is accompanied by substantial backbone conformational change. Second, it is not clear whether a model generated by docking represents a specific and stable complex. Third, the interface may include regions that are disordered in the separate proteins, challenging docking methods. We address these problems by pursuing three specific aims. First, we develop a novel algorithm for docking homology models and proteins with substantial backbone flexibility. The method is based on the hypothesis that the interface in complexes is sequentially and structurally more conserved than the rest of the proteins. Since such regions are frequently sufficient for recognition, identification and correct docking of the key segments can yield near-native docked structures. For homology models this implies that one can dock the regions that can be reliably modeled, and then expand the models by adding back the removed parts using the docked structures as constraints. The problem of docking "difficult cases" with substantial backbone conformational change can also be addressed by identifying and docking the structurally most conserved regions. Once clusters of the docked rigid fragments are obtained, the models are expanded by rebuilding the more flexible parts. Second, we use a two-step approach to examine the stability of protein complexes, first by removing small and hence unlikely clusters of low energy docked structures, and then by calculating dissociation rates by stochastic roadmap simulation. The method will be validated on a benchmark set that includes models of real protein complexes and decoys generated by docking non-interacting protein pairs. The approach will also be used to determine whether complex structures deposited to the PDB are biologically relevant. Third, we consider the problem of determining the structure of flexible loops and/or disordered regions when they become parts of a protein- protein interface. Rather than attempting to predict and to dock the most likely conformation of the flexible fragment, we build their bound structure directly into binding hot spots of the partner protein. Flexible peptide docking methods will be used to expand the docked fragments by adding further residues.