Very large datasets and new models to predict and design protein interactions

项目摘要 特定的蛋白质-蛋白质相互作用负责组织细胞，处理生物信号和信息，以及生命的化学。因此，理解生物学机制依赖于理解蛋白质之间发生的相互作用。一个重要的长期目标是开发可靠预测和合理修改蛋白质-蛋白质相互作用的方法。这种能力将 提供深入了解病理学的分子细节，并突出疾病治疗的机会。该提案描述了一个集成的实验/计算技术平台，将提供蛋白质相互作用特异性的预测模型。实验部分涉及构建蛋白质或肽的随机文库，所述文库将根据它们结合特定蛋白质或肽的亲和力进行分类。 受体的将使用高通量测序方法解码非常大量的文库成员的身份和结合亲和力。每个测序运行由多达107个{序列，亲和力}对组成的数据将用作计算机器学习方法的输入。将生成捕捉序列和相互作用之间关系的模型，以及这些模型的预测能力 将通过实验进行测试。本提案中描述的工作强调新平台的技术开发和应用，以研究两种一般类型的蛋白质复合物。首先是短螺旋配体与中等大小的球状蛋白的相互作用，在这里研究使用抗凋亡Bcl-2和Ca 2+结合EF-手蛋白。第二是短线性肽与模块相互作用的相互作用 域，这里是PDZ和SH 3域。这四个蛋白质家族在人类细胞中介导了大量重要的分子识别事件，由此产生的模型将为研究其生物学功能提供有价值的支持。这项工作还将对所提出的技术的能力进行严格的测试，然后可以将其应用于更广泛的分子复合物，例如，蛋白质-蛋白质、蛋白质-小分子和蛋白质-核酸组装。鉴于缺乏高- 准确测量蛋白质-蛋白质相互作用的通量方法，以及大多数计算模型预测蛋白质结合的原始能力，所提出的技术平台有可能极大地改变蛋白质相互作用特异性的研究。

PROJECT SUMMARY Specific protein-protein interactions are responsible for organizing the cell, for processing biological signals and information, and for the chemistry of life. Thus, understanding biological mechanism relies on understanding the interactions that occur between proteins. An important long-term goal is to develop methods for reliably predicting and rationally modifying protein-protein interactions. Such capabilities would provide insight into the molecular details of pathology and highlight opportunities for disease treatment. This proposal describes an integrated experimental/computational technology platform that will provide predictive models of protein interaction specificity. The experimental component involves constructing randomized libraries of proteins or peptides that will be sorted according to their affinities for binding a particular receptor. The identities and binding affinities for very large numbers of library members will be decoded using high-throughput sequencing methods. The data, consisting of up to 107 {sequence, affinity} pairs per sequencing run, will be used as input to computational machine learning methods. Models will be generated that capture the relationship between sequence and interactions, and the predictive power of these models will be tested experimentally. The work described in this proposal emphasizes technology development and application of the new platform to study two general types of protein complexes. First are interactions of short helical ligands with mid-sized globular proteins, here studied using anti-apoptotic Bcl-2 and Ca2+- binding EF-hand proteins. Second are interactions of short linear peptides with modular interaction domains, here PDZ and SH3 domains. These four protein families mediate an enormous number of important molecular recognition events in human cells, and the resulting models will provide valuable support to study of their biological functions. This work will also provide a stringent test of the capabilities of the proposed technology, which can then be applied to a much wider variety of molecular complexes, e.g., protein-protein, protein-small molecule and protein-nucleic acid assemblies. Given the paucity of high- throughput methods for accurately measuring protein-protein interactions, and the primitive capabilities of most computational models for predicting protein binding, the proposed technology platform has the potential to dramatically transform the study of protein interaction specificity.