Analysis and design of interaction specifically in proteins regulating apoptosis

描述（由申请人提供）：Bcl-2家族蛋白对调节细胞凋亡至关重要，是治疗多种癌症的有希望的治疗靶点。重要的是，已知亲凋亡和抗凋亡家族成员之间的相互作用特异性对它们如何发挥作用至关重要。虽然高分辨率结构已经解决了几个Bcl-2家族复合体，但这些并不能解释为什么一些家族成员之间会发生相互作用，或者如何通过序列和结构的变化来实现一系列的结合亲和力。如果我们希望用合理的方法预测、设计或破坏这些和其他蛋白质相互作用，那么更好地理解相互作用特异性的分子基础是必要的。本提案的目标是使用计算和实验方法的集成程序来破译Bcl-2蛋白家族的相互作用，并探索其生物物理起源。具体目标是：(1)对天然、突变和设计的Bcl-2蛋白进行系统的实验相互作用研究，将其序列与其结合特性联系起来，为测试和改进计算模型提供数据；(2)利用计算蛋白设计鉴定多种与Bcl-2家族成员结合的新肽；(3)开发将计算设计与实验选择相结合的方法，以设计具有所需相互作用特异性的肽（即与某些Bcl-2家族蛋白相互作用的能力，而不是与其他蛋白相互作用的能力）；(4)利用Aims 1-3中对序列要求的见解，识别可能在细胞凋亡中起作用的新的哺乳动物和病毒Bcl-2家族成员。从这项工作中设计或选择的肽可以用作解剖调节细胞凋亡的复杂信号网络的试剂，或者作为开发更有针对性的治疗方法的先导。长期目标是将这些方法应用于其他具有有趣相互作用特征和在细胞凋亡中起重要作用的蛋白质。这项工作的一个持久成果将是对蛋白质序列、结构和相互作用特异性之间关系的更全面的理解，这将有助于塑造我们在蛋白质组学背景下思考分子识别的方式。促生和促死Bcl-2家族蛋白之间的失衡在癌症中很重要，这些蛋白之间的相互作用提供了有希望的治疗靶点。本研究的目的是在高水平上详细了解Bcl-2家族相互作用特异性的分子基础。这将有助于我们理解调控细胞死亡的生物学，支持治疗性抑制剂的开发，并为蛋白质-蛋白质识别的生物物理学提供见解。

DESCRIPTION (provided by applicant): Proteins of the Bcl-2 family are critical for regulating apoptosis and are promising therapeutic targets for treating a wide variety of cancers. Importantly, interaction specificity among pro- and anti-apoptotic family members is known to be critical to how they function. Although high-resolution structures have been solved for several Bcl-2 family complexes, these do not explain why interactions occur between some family members and not others, or how a range of binding affinities is achieved through variations in sequence and structure. A better understanding of the molecular basis for interaction specificity is necessary if we wish to predict, design or disrupt these and other protein interactions using rational methods. The goal of this proposal is to use an integrated program of computational and experimental methods to decipher the interactions of the Bcl-2 family of proteins and to probe their biophysical origins. The specific aims are to: (1) Carry out systematic experimental interaction studies of native, mutant and designed Bcl-2 proteins in order to relate their sequences to their binding properties and provide data for testing and improving computational models, (2) Use computational protein design to identify a wide variety of new peptides that bind to Bcl-2 family members, (3) Develop approaches for combining computational design with experimental selection to engineer peptides with desired interaction specificities (i.e. the ability to interact with some Bcl-2 family proteins but not others) and (4) Use insights into sequence requirements from Aims 1-3 to identify new mammalian and viral Bcl-2 family members that may play a role in apoptosis. Designed or selected peptides from this work could be used as reagents for the dissection of the complex signaling networks that regulate apoptosis, or as leads for the development of more targeted therapies. A longer-term goal is to apply these methods to other proteins with interesting interaction characteristics and an important role in apoptosis. A lasting outcome of this work will be a more comprehensive understanding of the relationship between protein sequence, structure and interaction specificity that will help shape the way we think about molecular recognition in the context of the proteome. PUBLIC HEALTH RELEVANCE Imbalances between pro-life and pro-death Bcl-2 family proteins are important in cancer, and interactions among these proteins provide promising therapeutic targets. The objective of this study is to understand at a high level of detail the molecular basis for the interaction specificity of the Bcl-2 family. This will contribute to our understanding of the biology of regulated cell death, support the development of therapeutic inhibitors and provide insights into the biophysics of protein-protein recognition.