Enabling Top-Down Proteomics through Material Chemistry and Nanotechnology

通过材料化学和纳米技术实现自上而下的蛋白质组学

• 批准号: 10246801
• 负责人: Ying Ge
• 金额: $ 29.83万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-25 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10246801
• 关键词: Achievement; Address; Affinity; Alprenolol; Amides; Antibodies; Binding; Biological; Biological Assay; Biological Markers; Blood; Blood Proteins; Blood specimen; Canes; Carbohydrates; Cardiac; Cardiovascular Diseases; Cells; Chemistry; Code; Collaborations; Complex; Computer software; Detection; Diabetes Mellitus; Diagnosis; Disease; Disease Progression; Drug Targeting; Extracellular Matrix; Extracellular Matrix Proteins; Face; Foundations; Funding; G Protein-Coupled Receptor Signaling; G-Protein-Coupled Receptors; Genetic Variation; Genomics; Gold; Heart Diseases; Human; Ligands; Magnetic nanoparticles; Magnetism; Mainstreaming; Malignant Neoplasms; Mass Spectrum Analysis; Membrane; Membrane Proteins; Methods; Molecular; Nanotechnology; Organic Chemistry; Performance; Play; Post-Translational Protein Processing; Progress Reports; Protein Denaturation; Proteins; Proteome; Proteomics; Publications; Reagent; Receptor Cell; Research; Role; Series; Solubility; Structural Protein; Structure-Activity Relationship; Surface; System; Techniques; Tissues; Troponin I; Variant; analog; base; beta-adrenergic receptor; biological systems; complex biological systems; design; diagnostic assay; empowered; human disease; individual variation; innovation; insight; interdisciplinary approach; nanoparticle; nanoproteomic; new therapeutic target; novel; novel strategies; polypeptide; precision medicine; preservation; protein complex; protein structure; success; surfactant; tool; tumor; ultraviolet irradiation

Summary In the post-genomics era, a comprehensive analysis of “proteoforms” that arise from genetic variations and post-translational modifications (PTMs) is essential for understanding biological systems at a functional level and for dissecting complex molecular systems with consideration of individual variability for precision medicine. Top- down mass spectrometry (MS)-based proteomics that analyzes intact proteins is the most powerful method to comprehensively characterize proteoforms to decipher the PTM codes together with sequence variations. Although significant strides have been made recently in both MS hardware and software to advance top-down MS closer to the mainstream, top-down proteomics still faces major challenges. In particular, the proteome is extremely complex and has a high dynamic range in addition to the low solubility of many proteins, making it highly challenging for high-throughput proteomic study. Building on the success in the last funding period, in this multiple-PI renewal application, we will continue to develop innovative strategies empowered by nanotechnology and materials/organic chemistry to further address the challenges in top-down proteomics. The specific objectives of this proposal are: 1) To address the protein solubility challenge, we will develop a novel strategy enabled by a photocleavable surfactant for extracellular matrix (ECM) proteomics; and design, synthesize, and evaluate a novel class of photocleavable nonionic surfactants that can retain the native structures of proteins for native MS-based top-down proteomics. 2) To address the high dynamic range challenge, we will develop novel surface functionalized magnetic nanoparticles (NPs) to mimic antibodies for capturing and enriching low abundance proteins, such as cardiac troponin I (cTnI, a gold-standard biomarker for heart diseases) from tissues/blood and G-protein coupled receptors (GPCRs, a major class of drug targets) from cells/tissues, for downstream comprehensive analysis of all proteoforms by top-down proteomics. Our highly interdisciplinary approach integrates materials chemistry/nanotechnology with top-down MS-based proteomics, and is based on an existing productive collaboration between two PIs that has led to significant progress and publications from the past funding period. Success in our proposed research will provide innovative tools to enable top-down proteomics of poorly soluble and low abundance proteins, which will lay important technological foundation for understanding the critical role that ECM plays in disease progression in cancer and cardiac diseases, defining the structure-function relationship of native membrane complexes, developing a comprehensive cTnI assay for the diagnosis of cardiac diseases with high accuracy, and understanding the important roles of GPCR signaling during the onset of numerous human diseases including cancer, diabetes, and cardiovascular diseases.

概括 在后代后时代，对遗传变异和 翻译后修饰（PTMS）对于了解功能层面的生物系统和 用于剖析复杂的分子系统，以考虑精确医学的个体变异性。顶部- 下质谱（MS）的蛋白质组学，分析完整蛋白质是最强大的方法 全面地表征蛋白质成型，以解读PTM代码以及序列变化。 尽管最近在MS硬件和软件中都取得了重大进展，以推动自上而下 MS更接近主流，自上而下的蛋白质组学仍然面临重大挑战。特别是，蛋白质组是 极其复杂，除了许多蛋白质的低可溶性外，还具有高动态范围 高通量蛋白质组学研究的挑战。在最后的资金期间建立成功的基础 多次续签应用程序，我们将继续制定纳米技术增强的创新策略 以及材料/有机化学，以进一步解决自上而下蛋白质组学的挑战。具体 该提案的目标是：1）解决蛋白质溶解度挑战，我们将制定一种新颖的策略 由可光透明表面活性剂启用，用于细胞外基质（ECM）蛋白质组学；和设计，合成以及 评估一类新的可光透明的非离子表面活性剂，可以保留蛋白质的天然结构 基于天然MS的自上而下蛋白质组学。 2）解决高动态范围挑战，我们将开发新颖 表面功能化磁性纳米颗粒（NP），以模拟捕获和富集低的抗体 抽象蛋白，例如心脏肌钙蛋白I（CTNI，一种金标准的心脏病标准生物标志物） 来自细胞/组织的组织/血液和G蛋白偶联受体（GPCR，主要类药物） 自上而下的蛋白质组学对所有蛋白质成型的下游综合分析。我们的跨学科 与自上而下的MS蛋白质组学相结合的材料化学/纳米技术，并基于 两个PI之间的现有产品合作导致 过去的资金期。我们拟议的研究的成功将提供创新的工具，以实现自上而下 固体和低丰度蛋白质的蛋白质组学，这将奠定重要的技术基础 了解ECM在疾病进展中在癌症和心脏疾病中发挥的关键作用，定义 天然膜络合物的结构功能关系，开发了一种全面的CTNI分析 具有高精度的心脏疾病的诊断，并了解GPCR信号的重要作用 在许多人类疾病发作期间，包括癌症，糖尿病和心血管疾病。