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: 10670369
• 负责人: Lan Huang
• 金额: $ 58.88万
• 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/10670369
• 关键词: Address; Biological; Biological Process; Biology; Cell physiology; Cells; Clinical; Cullin Proteins; Degradation Pathway; Development; Disease; Environment; Eukaryota; Health; Human; Human Pathology; Ligase; Link; Malignant Neoplasms; Maps; Mass Spectrum Analysis; Mediating; Medicine; Molecular; Neurodegenerative Disorders; Pathway interactions; Physiological; Proteasome Inhibitor; Protein-Protein Interaction Map; 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的关键， 负责多种细胞功能。异常PPI可能对基本的 生物过程，导致各种人类疾病。解析PPI网络及其结构特征 在细胞内是理解与人类相关的基本生物学和分子改变的核心。 病理学，并最终促进治疗发展。然而，蛋白质组网络的描绘， 由于现有方法的限制，在系统级定义细胞的功能状态是具有挑战性的。 交联质谱（XL-MS）已成为PPI研究的强大技术，这是由于其 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 用结构细节揭示PPI身份。尽管目前的XL-MS技术在全球范围内取得了成功， 生产者价格指数分析，尚未满足的挑战仍然存在，特别是在全面说明和定量评估 蜂窝网络和空间PPI映射。这需要新的发展，以加强技术 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 真核生物中的降解途径，其网络是显着动态的，由大量的 在组成上和结构上动态的机器，协调蛋白质的泛素化和降解。 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。 紊乱鉴于蛋白酶体抑制剂的临床成功，UPS已成为一个有效的平台， 药物发现虽然UPS的基本功能已经被理解，但其多层结构的分子细节仍然是未知的。 监管和机械行动仍然难以捉摸。因此，阐明相互作用和结构动力学 在其生理背景下的UPS网络是必不可少的，不仅是为了促进对UPS的理解 生物学，而且还用于增强其在人类健康和医学中的治疗潜力。在接下来的五年里， 我们计划在PPI研究中解决几个突出的技术挑战，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技术的相互作用 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 潜在的蛋白质泛素化和降解。具体来说，我们将集中精力开发新型XL- MS技术能够对蛋白质组网络进行深入和定量分析，包括结构细节， 增强的空间分辨率以定义细胞功能状态。此外，我们会聘请新成立的 技术来描述蛋白酶体调节剂在蛋白质降解中的作用机制，研究Cullin- RING连接酶介导的蛋白质泛素化和剖析UPS网络的组织。所有这些 研究将导致蛋白质组学研究的令人兴奋的技术进步，并有助于回答 与UPS生物学相关的重要但尚未解决的生物学问题。