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: 9982021
• 负责人: Ying Ge
• 金额: $ 29.74万
• 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/9982021
• 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 后基因组时代，对遗传变异产生的“蛋白质形态”进行全面分析 翻译后修饰（PTM）对于在功能水平上理解生物系统至关重要 用于解剖复杂的分子系统，同时考虑精准医学的个体差异。顶部- 基于质谱 (MS) 的蛋白质组学分析完整蛋白质是最强大的方法 全面表征蛋白质组，以破译 PTM 代码和序列变异。 尽管最近在 MS 硬件和软件方面都取得了重大进展，以推进自上而下的发展 MS 已接近主流，自上而下的蛋白质组学仍面临重大挑战。特别是，蛋白质组是 除了许多蛋白质的低溶解度之外，它极其复杂并且具有高动态范围，使其 高通量蛋白质组学研究极具挑战性。在上一个融资期取得成功的基础上，本次融资 多PI更新应用，我们将持续开发纳米技术赋能的创新策略 和材料/有机化学，以进一步应对自上而下蛋白质组学的挑战。具体的 该提案的目标是：1）为了解决蛋白质溶解度挑战，我们将制定一种新策略 由可光裂解的表面活性剂实现细胞外基质 (ECM) 蛋白质组学；以及设计、合成和 评估一类新型可光裂解非离子表面活性剂，该表面活性剂可以保留蛋白质的天然结构 基于原生 MS 的自上而下蛋白质组学。 2）为了应对高动态范围挑战，我们将开发新颖的 表面功能化磁性纳米颗粒（NP）可模拟抗体，用于捕获和富集低浓度 丰富的蛋白质，例如心肌肌钙蛋白 I（cTnI，心脏病的金标准生物标志物） 组织/血液和来自细胞/组织的 G 蛋白偶联受体（GPCR，一类主要的药物靶点）， 通过自上而下的蛋白质组学对所有蛋白质形式进行下游综合分析。我们的高度跨学科 方法将材料化学/纳米技术与自上而下的基于 MS 的蛋白质组学相结合，并且基于 两位 PI 之间现有的富有成效的合作带来了重大进展并发表了论文 过去的资助期。我们提议的研究的成功将提供创新工具，以实现自上而下的 难溶性、低丰度蛋白质的蛋白质组学研究，将为研究奠定重要的技术基础 了解 ECM 在癌症和心脏病的疾病进展中发挥的关键作用，定义 天然膜复合物的结构-功能关系，开发了一种全面的 cTnI 检测方法 高精度诊断心脏病，并了解 GPCR 信号传导的重要作用 包括癌症、糖尿病和心血管疾病在内的许多人类疾病的发作期间。