Interface-resolution domain-domain interactome map of the yeast complexome

酵母复合体的界面分辨率域-域相互作用图

• 批准号: 9918431
• 负责人: Marc Vidal
• 金额: $ 67万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-04-20 至 2023-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9918431
• 关键词: Animal Model; Applications Grants; Architecture; Biochemical; Biological Assay; Biological Process; Biology; Cell model; Cell physiology; Cells; Cellular biology; Communities; Complex; Computer Models; Cryoelectron Microscopy; DNA; Data; Data Set; Generations; Genes; Genotype; Goals; Human; Individual; Laboratories; Literature; Luciferases; Maps; Modeling; Molecular; Molecular Machines; Nature; Open Reading Frames; Organism; Organizational Models; Phenotype; Physiological; Protein Interaction Mapping; Proteins; Proteome; RNA-Protein Interaction; Reaction; Reporter; Resolution; Role; Saccharomyces cerevisiae; Set protein; Structure; Surveys; System; Technology; Testing; Time; Translating; Vision; Work; X-Ray Crystallography; Yeasts; base; improved; innovation; interest; macromolecule; novel; predictive modeling; protein complex; protein function; protein protein interaction; reconstitution; transcriptome

Project Summary/Abstract The physical interactome of an organism, which is the network formed by all physical interactions that can occur in a physiologically relevant dynamic range between all its macromolecules, including protein-protein, DNA- protein, and RNA-protein interactions, is a critical layer to allow us to understand cells from a global point-view. In this grant application, we will focus on a particular aspect of global interactome networks: the formation of all molecular machines or complexes needed to execute all major molecular reactions. While protein complexes are responsible for most biological processes, global models of the organization and architecture of complete sets of protein complexes, or “complexomes”, are still vastly incomplete for most species, including human. We propose to precisely map direct domain-domain interactions between subunits of the yeast complexome with a resolution approaching interface-level resolution. We will systematically fragment all open reading frames corresponding to all ~1,200 genes encoding the ~300 complexes of the yeast complexome and test for direct physical interactions between the corresponding encoded domains using four complementary protein-protein interaction (PPI) assays, one based on the reconstitution of the Gal4 protein in yeast (Gal4-Y2H) and the other three based on the reconstitution of a luciferase protein called NanoLuc in three different expression systems. We will then characterize the sequence requirements of the identified domain-domain interactions and first- generation models of complexes will be generated using interface prediction modeling. The long-term vision of this proposal is to generate binary protein interaction information inside each complex, which, eventually, will be extremely valuable to establish the complete architecture of the yeast complexome. This in turn will allow incorporating dynamic aspects of protein complexes in time and space and generating improving predictive models of genotype-phenotype relationships.

项目摘要/摘要 有机体的物理互动组，这是所有可能发生的物理互动形成的网络 在其所有大分子之间的物理相关动态范围内，包括蛋白质 - 蛋白质，DNA- 蛋白质和RNA - 蛋白质相互作用是一个关键层，可让我们从全局点视图中理解细胞。 在本赠款应用程序中，我们将重点关注全球Interactome网络的特定方面：所有人的形成 执行所有主要分子反应所需的分子机或复合物。而蛋白质复合物 负责大多数生物过程，组织的全球模型和完整的体系结构 对于包括人类在内的大多数物种，一组蛋白质复合物或“复合体”仍然非常不完整。我们 提案以精确绘制酵母复合体的亚基之间的直接域障碍相互作用 解决接口级分辨率的分辨率。我们将系统地片段片段所有开放式阅读框架 对应于所有〜1,200个基因编码酵母复合体的〜300络合物并进行直接测试 使用四个完整的蛋白质蛋白 相互作用（PPI）测定，一个基于酵母中GAL4蛋白的重构（GAL4-Y2H），另一个基于重构 三个基于三种不同表达系统中称为Nanoluc的荧光素酶蛋白的重建。 然后，我们将表征已识别的域域相互作用和首先的序列要求 复合物的生成模型将使用接口预测建模生成。长期的愿景 该建议是在每个复合物中生成二元蛋白质相互作用信息，最终将是 对于建立酵母复合体的完整体系结构非常有价值。反过来将允许 在时间和空间中结合蛋白质复合物的动态方面，并产生改善的预测性 基因型 - 表型关系的模型。