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) 是蛋白质复合物形成的关键，蛋白质复合物是活性成分 异常的 PPI 可能会对重要的细胞功能产生不良影响。 阐明 PPI 网络及其结构特征。 细胞内的研究对于理解与人类相关的基础生物学和分子改变至关重要 病理学，并最终促进治疗的发展然而，蛋白质组网络的描绘。 由于现有方法的局限性，在系统级别定义细胞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，因为它具有以下特点： 在其天然环境中保存和捕获蛋白质相互作用的独特能力，以及 尽管当前的 XL-MS 技术在全球范围内取得了成功，但通过结构细节揭示 PPI 特性。 PPI 分析，尚未解决的挑战仍然存在，特别是在完整​​说明和定量评估方面 蜂窝网络和空间 PPI 测绘需要新的发展来增强技术。 泛素蛋白酶体系统（UPS）是推进系统结构生物学的主要能力。 真核生物中的降解途径，其网络异常动态并由大量组成 协调蛋白质泛素化和降解的组成和结构动态机器。 UPS 失调与许多人类疾病有关，包括癌症和神经退行性疾病 鉴于蛋白酶体抑制剂的临床成功，UPS 已成为治疗疾病的有效平台。 虽然 UPS 的基本功能已被了解，但其多层结构背后的分子细节。 因此，阐明相互作用和结构动力学仍然难以捉摸。 从生理角度了解 UPS 网络不仅对于增进对 UPS 的理解至关重要 生物学，而且还可以在未来五年内增强其在人类健康和医学方面的治疗潜力， 我们计划解决 PPI 研究中的几个突出技术挑战，以更好地解读 UPS 途径，通过追求以下两个研究方向：1）推进交互式组学的 XL-MS 技术 和系统水平的结构蛋白质组学；2) 绘制 UPS 网络以揭示分子细节 具体来说，我们将集中精力开发新型 XL-。 MS 技术能够对具有结构细节和结构细节的蛋白质组网络进行深入和定量分析 此外，我们将采用新建立的空间分辨率来定义细胞功能状态。 描述蛋白酶体调节剂在蛋白质降解中的作用机制的技术，研究 Cullin- RING 连接酶介导的蛋白质泛素化并剖析了 UPS 网络的组织。 研究将导致蛋白质组学研究中令人兴奋的技术进步，并促进回答 与 UPS 生物学相关的重要但尚未解决的生物学问题。