Analysis and design of protein interactions that regulate cell death

蛋白质之间的相互作用控制着对人类健康至关重要的无数生物过程。工具用于 发现、预测和设计这种相互作用可以提供对生物机制的洞察 并强调治疗干预的可能途径。该项目将整合计算和 推进我们对序列和序列之间关系的理解的实验方法 Bcl2家族蛋白之间相互作用的功能。Bcl2家族调节细胞凋亡和 通过形成特定的复合体实现自噬，有些复合体抑制细胞死亡，有些复合体促进细胞死亡。 促凋亡和抗凋亡的Bcl-2家族蛋白与短螺旋结合的竞争 由BH3(BH3)基序编码的BH3控制着关键的细胞生存决定。它现在已经很成熟了 多肽和小分子可以模仿或抑制BH3的相互作用。这样的分子提供了一种方法 使用外源试剂控制信号结果，如批准的第一种药物所证明的那样 通过靶向Bcl-2治疗癌症。尽管取得了令人兴奋的进展，但关于Bcl-2蛋白的悬而未决的问题 与BH3基序的相互作用提供了更多的发现机会。特别是：到目前为止还在做 人类蛋白质组中未发现的含BH3基序的蛋白质通过Bcl-2影响信号转导 家族蛋白质？为什么一些含有BH3基序的蛋白质通过 促凋亡的BAK和BAX，而其他的不是？BH3结合诱导的机制是什么 导致线粒体膜孔形成和细胞死亡的构象变化？什么 是否存在使用设计的多肽或蛋白质来促进或阻止这种过程的机会？ 这些问题的答案将影响对多人重要的Bc l-2通路的分析 提供新的试剂，并指导癌症和其他疾病的治疗方法的发展。 在我们在上一次筹资期间取得重大成功的基础上，我们将推动 通过应用将互动筛选与结构分析相结合的新方法，在这些领域取得进展 建模和预测。我们将应用新的计算方法来预测新的Bcl-2结合 合作伙伴，测试我们的模型的预测，并突出候选的新的生物交互伙伴 意义。我们将提出BAK和BAX激活的分子机制，并用 BH3基序变体文库。我们将应用新的计算设计方法来制造多肽和 激活或抑制BAK和Bax介导的细胞死亡的微型蛋白质。总体而言，我们的贡献将 提供BH3基序的序列-功能景观图，这些基序是控制BH3基序的关键因素 细胞存活。这项工作中开发的方法和工具也将有助于发现和 抑制其他蛋白质之间的相互作用。 好了！

Protein-protein interactions control myriad biological processes important for human health. Tools for discovering, predicting and designing such interactions can provide insights into biological mechanisms and highlight possible routes to therapeutic intervention. This project will integrate computational and experimental approaches to advance our understanding of the relationships between sequence and function for protein interactions among Bcl-2 family proteins. The Bcl-2 family regulates apoptosis and autophagy by forming specific complexes, some of which inhibit and some of which promote cell death. Competition between pro- and anti-apoptotic Bcl-2 family proteins for binding to short alpha helices encoded by a Bcl-2 homology 3 (BH3) motif controls key cell survival decisions. It is now well established that peptides and small molecules can mimic or inhibit BH3 interactions. Such molecules provide a way to control signaling outcomes using exogenous reagents, as demonstrated by the first drug approved for treating cancer by targeting Bcl-2. Despite exciting progress, open questions about Bcl-2 protein interactions with BH3 motifs provide additional opportunities for discovery. In particular: Do as-yet undiscovered BH3 motif-containing proteins in the human proteome influence signaling through Bcl-2 family proteins? Why do some proteins that contain BH3 motifs trigger mitochondrial pore formation by pro-apoptotic BAK and BAX whereas others do not? What are the mechanisms of BH3 binding-induced conformational changes that lead to mitochondrial membrane pore formation and cell death? What opportunities exist for promoting or blocking such processes using designed peptides or proteins? Answers to these questions will impact analysis of Bcl-2 pathways important for multiple human diseases, provide new reagents, and guide development of therapies for cancer and other diseases. Building on the substantial successes that we realized in the previous funding period, we will drive progress in these areas by applying new methodology that integrates interaction screening with structural modeling and prediction. We will apply novel computational methods for predicting new Bcl-2 binding partners, test predictions of our models, and highlight candidate new interaction partners of biological significance. We will propose molecular mechanisms of BAK and BAX activation and test them using libraries of BH3 motif variants. We will apply new computational design methods to make peptides and mini-proteins that activate or inhibit BAK and BAX-mediated cell death. Collectively, our contributions will provide a map of the sequence-function landscape of BH3 motifs, which are critical factors controlling cell survival. The methods and tools developed in this work will also be useful for discovering and inhibiting other protein-protein interactions. !