Advancing Proteomics Technologies to Decipher the Ubiquitin-Proteasome System

推进蛋白质组学技术破译泛素-蛋白酶体系统

• 批准号: 10405969
• 负责人: Lan Huang
• 金额: $ 26.63万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-01 至 2027-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10405969
• 关键词: Address; Biological; Biological Process; Biology; Cell physiology; Cells; Clinical; Cullin Proteins; Degradation Pathway; Development; Disease; Environment; Eukaryota; Five-Year Plans; Health; Human; Human Pathology; Lead; Ligase; Link; Malignant Neoplasms; Mass Spectrum Analysis; Mediating; Medicine; Molecular; Neurodegenerative Disorders; Pathway interactions; Physiological; Proteasome Inhibitor; Proteins; Proteome; Proteomics; Regulation; Research; Resolution; System; Systems Biology; Technology; Therapeutic; Ubiquitin; Ubiquitination; advanced system; crosslink; drug discovery; human disease; improved; in vivo; multicatalytic endopeptidase complex; novel; preservation; protein complex; protein degradation; protein protein interaction; structural biology; success; therapeutic development

Protein-protein interactions (PPIs) are key to the formation of protein complexes, the active components responsible for a multitude of cellular functions. Aberrant PPIs can have detrimental effects on essential biological processes and lead to various human diseases. Elucidating PPI networks and their structural features within cells is central to understanding fundamental biology and molecular alterations associated with human pathologies, and ultimately facilitating therapeutic development. However, delineation of proteome networks to define the cell’s functional states at the systems-level is challenging due to limitations in existing approaches. Cross-linking mass spectrometry (XL-MS) has emerged as a powerful technology for PPI studies, owing to its unique capability of preserving and capturing protein interactions in their native environments, as well as uncovering PPI identities with structural details. Although current XL-MS technologies are successful in global PPI analysis, unmet challenges still remain especially for complete illustration and quantitative assessment of cellular networks, and spatial PPI mapping. This necessitates new developments to enhance technical capabilities for advancing systems structural biology. The ubiquitin-proteasome system (UPS) is the major degradation pathway in eukaryotes, whose network is remarkably dynamic and made of a large number of compositionally and structurally dynamic machines that orchestrate protein ubiquitination and degradation. Dysregulation of the UPS has been linked to many human diseases including cancer and neurodegenerative disorders. Given the clinical success of proteasome inhibitors, the UPS has become an effective platform for drug discovery. Although basic functions of the UPS are understood, molecular details underlying its multi-layer regulation and mechanistic action remain elusive. Therefore, elucidating the interaction and structural dynamics of the UPS network in its physiological context is essential not only for advancing the understanding of UPS biology, but also for augmenting their therapeutic potential in human health and medicine. In the next five years, we plan to address several outstanding technological challenges in PPI studies to better decipher the UPS pathways, by pursuing the following two research directions: 1) Advancing XL-MS technologies for interactomics and structural proteomics at the systems-level; 2) Mapping the UPS network to uncover molecular details underlying protein ubiquitination and degradation. Specifically, we will center our efforts on developing novel XL- MS technologies to enable in-depth and quantitative analysis of proteome networks with structural details and enhanced spatial resolution to define cellular functional states. In addition, we will employ the newly established technologies to delineate action mechanisms of proteasome regulators in protein degradation, investigate Cullin- RING Ligase mediated protein ubiquitination and dissect the organization of the UPS network. Together, these studies will result in an exciting technological advancement in proteomics research, and facilitate answering important but unresolved biological questions associated with UPS biology.

蛋白质 - 蛋白质相互作用（PPI）是形成蛋白质复合物，活性成分的关键 负责多种细胞功能。异常PPI可能对必需品产生不利影响 生物过程并导致各种人类疾病。阐明PPI网络及其结构特征 细胞内的核心是了解与人相关的基本生物学和分子改变 病理，并最终支持治疗性发育。但是，将蛋白质组网络描述为 由于现有方法的局限性，在系统级别上定义单元格的功能状态具有挑战性。 交联质谱（XL-MS）已成为PPI研究的强大技术，因此 在其本地环境中保存和捕获蛋白质相互作用的独特能力以及 发现具有结构细节的PPI身份。尽管当前的XL-MS技术在全球范围内还是成功的 PPI分析，未满足的挑战仍然特别是为了完整的例证和定量评估 蜂窝网络和空间PPI映射。这需要新的发展来增强技术 推进系统结构生物学的能力。泛素 - 蛋白酶体系统（UPS）是主要的 真核生物中的退化途径，其网络非常动态，由大量 在整理蛋白质泛素化和降解的构图和结构动态机器上。 UPS的失调与许多人类疾病有关，包括癌症和神经退行性疾病 疾病。鉴于蛋白酶体抑制剂的临床成功，UPS已成为有效的平台 毒品发现。尽管已理解UP的基本功能，但其多层的分子细节是分子细节 监管和机械作用仍然难以捉摸。因此，阐明相互作用和结构动力学 UPS网络在其物理环境中的了解不仅对于推进对UPS的理解至关重要 生物学，但也用于增强其在人类健康和医学方面的治疗潜力。在接下来的五年中， 我们计划解决PPI研究中的几个杰出技术挑战，以更好地破译UPS 途径，通过追求以下两个研究方向：1）推进XL-MS Interactomics的XL-MS技术 和系统级的结构蛋白质组学； 2）映射UPS网络以发现分子细节 潜在的蛋白质泛素化和降解。具体而言，我们将集中精力开发新颖的XL- MS技术能够深入和定量分析蛋白质组网络，并具有结构细节和 增强的空间分辨率以定义细胞功能状态。此外，我们将采用新成立的 描述蛋白质调节剂蛋白质降解中蛋白质调节剂的作用机理的技术，研究cullin- 环连接酶介导的蛋白质泛素化并剖析UPS网络的组织。在一起，这些 研究将导致蛋白质组学研究的激动人心的技术进步，并促进回答 重要但尚未解决的生物学问题与UPS生物学相关。