NEW TOOLS FOR EXPLORING THE DYNAMIC INTERACTOME

探索动态交互组的新工具

• 批准号: 8359911
• 负责人: MICHAEL P ROUT
• 金额: $ 323.5万
• 依托单位: ROCKEFELLER UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-01 至 2012-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8359911
• 关键词: Area; Biological; Cell Nucleus; Cell physiology; Cells; Cellular biology; Chromatin; Communities; Complex; Computational Biology; Coupling; Cytomegalovirus; Dancing; Data; Eukaryota; Freezing; Funding; Genetic; Genetic Transcription; Genome; Genomics; Grant; HIV; Hand; Human Virus; Laboratories; Macromolecular Complexes; Mass Spectrum Analysis; Methods; National Center for Research Resources; Nucleic Acids; Pathway interactions; Positioning Attribute; Principal Investigator; Process; Production; Property; Proteins; Proteomics; RNA; Research; Research Infrastructure; Resources; Source; Staging; Stretching; Structural Protein; Structure; System; Systems Biology; Techniques; Technology; Testing; Time; United States National Institutes of Health; Walking; cost; empowered; functional genomics; macromolecule; novel strategies; rapid technique; software development; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. DESCRIPTION (provided by applicant): The genomic revolution has been empowered by technologies that have determined a vast pool of genetic information. While nucleic acids encode this information, it is the proteins that act on it. Proteins are incredibly diverse in their abundance & their properties, making them highly versatile for the dynamic tasks at hand but at the same time exceptionally difficult to analyze. It is for these reasons that the proteomic revolution still lags behind the genomic revolution. Indeed, the comprehensive analysis of the dynamic properties of proteins in cells is still largely beyond current capabilities. Here, we seek to revolutionize proteomics by synergistically combining improvements in established techniques with new approaches. We will overcome major bottlenecks in 3 key areas of proteomics technology. First, we will reform the production stage for generating intact macromolecular complexes, so that we will be able to freeze a tagged macromolecular complex in place, within moments of visualizing its position in the cell, & then isolate it together with all its components & neighbors. Second, we will optimize the analysis of each complex such that its macromolecular composition, structure, & dynamics will be quantified & analyzed. Third, we will develop software to integrate our data & represent in unprecedented detail the actions of the macromolecular players in many dynamic subcellular assemblies. We will seek to make these techniques rapid, robust & routine by beta testing them in 4 experimental systems. These systems focus on aspects of the genetic information pathway, because (i) this is core to eukaryotes, & (ii) it will allow us to develop techniques to analyze the interactions of all 3 information-carrying biological macromolecules (DMA, RNA & proteins). First, we will walk along great stretches of chromatin, determining the normal flux of structural proteins & regulatory factors that together comprise dynamic segments of the genome. Second, we will follow the course of RNA after transcription, as it is processed, packaged & exported from the nucleus; we will enumerate the proteins that dance attendance on each kind of RNA molecule during its maturation. Finally, we will expose how 2 pathogenic human viruses, HIV & CMV, subvert their host's genetic information pathway & supplant it with their own. By creating a National Center for Dynamic Interactome Research, we will be coupling an established mass spectrometry resource, cell biology laboratories, a systems biology resource, & a computational biology center. As part of the larger NIH roadmap, the center's aim will be to create new & useful tools to elucidate the dynamics of macromolecular interactions. In summary, the present proposal seeks the support to advance our methods into totally new areas, & to spread these methods amongst the biomedical community. The Center will enable the community to assemble the kinds of detailed, dynamic representations of the interactions in the cell that will help elucidate the principles underlying all cellular processes, thus bridging the gaps between functional genomics, proteomics, & systems biology.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 描述（由申请人提供）：基因组革命已被确定了大量遗传信息的技术所赋予的能力。核酸编码此信息时，是蛋白质作用于其上的。蛋白质的丰富性和特性非常多样，使其在手头的动态任务方面具有极高的用途，但同时也很难分析。正是由于这些原因，蛋白质组学革命仍然落后于基因组革命。实际上，对细胞中蛋白质的动态特性的全面分析仍然超出了当前功能。在这里，我们试图通过协同结合既定技术的改进和新方法来彻底改变蛋白质组学。我们将在蛋白质组学技术的3个关键领域中克服主要的瓶颈。首先，我们将改革生成完整的大分子复合物的生产阶段，以便在可视化其在细胞中的位置的时刻，并将其与所有成分和邻居隔离，并在可视化其在细胞中的位置，并将其冻结为标记的大分子复合物。其次，我们将优化每个复合物的分析，以便将其大分子组成，结构和动力学进行量化和分析。第三，我们将开发软件以整合我们的数据并以前所未有的详细说明大分子球员在许多动态的亚细胞组件中的动作。我们将通过在4个实验系统中测试beta测试来使这些技术快速，鲁棒和常规。这些系统着重于遗传信息途径的各个方面，因为（i）这是真核生物的核心，＆（ii）它将使我们能够开发技术来分析所有3种信息携带生物学大分子（DMA，RNA和蛋白质）的相互作用。首先，我们将沿着大量的染色质延伸，确定结构蛋白和调节因子的正常通量，这些蛋白质和调节因子共同构成了基因组的动态段。其次，我们将遵循转录后的RNA过程，因为它是从核中处理，包装和导出的。我们将列举在成熟过程中每种RNA分子上舞蹈的蛋白质。最后，我们将揭露2种致病性人类病毒HIV和CMV如何颠覆宿主的遗传信息途径并自行取代。通过创建国家动态互动研究中心，我们将耦合已建立的质谱资源，细胞生物学实验室，系统生物学资源和计算生物学中心。作为较大的NIH路线图的一部分，该中心的目的是创建新的和有用的工具来阐明大分子相互作用的动态。总而言之，本提案寻求支持将我们的方法推向全新领域，并将这些方法传播到生物医学界。该中心将使社区能够组装细胞中相互作用的详细，动态表示，这将有助于阐明所有细胞过程的原理，从而弥合功能基因组学，蛋白质组学和系统生物学之间的差距。