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.

总结 在后基因组学时代，对遗传变异引起的“蛋白形式”的全面分析， 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，并考虑个体差异，以实现精准医疗。顶部- 基于质谱（MS）的蛋白质组学分析完整的蛋白质是最有效的方法， 全面表征蛋白质型，以破译PTM代码以及序列变异。 尽管最近在MS硬件和软件方面都取得了重大进展， MS更接近主流，自上而下的蛋白质组学仍面临重大挑战。特别是蛋白质组， 非常复杂，除了许多蛋白质的低溶解度外，还具有高动态范围， 这对于高通量蛋白质组学研究是非常具有挑战性。在上一个供资期取得成功的基础上， 多PI更新应用程序，我们将继续开发由纳米技术授权的创新策略 和材料/有机化学，以进一步解决自上而下的蛋白质组学的挑战。具体 本提案的目标是：1）为了解决蛋白质溶解性的挑战，我们将开发一种新的策略 通过用于细胞外基质（ECM）蛋白质组学的光可裂解表面活性剂实现;并设计，合成， 评估一类新型的可光裂解的非离子表面活性剂，其可以保留蛋白质的天然结构， 基于MS的自上而下蛋白质组学。2)为了应对高动态范围的挑战，我们将开发新的 表面功能化的磁性纳米颗粒（NP），以模拟抗体，用于捕获和富集低 大量蛋白质，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，一种主要的药物靶标），用于 通过自上而下的蛋白质组学对所有蛋白质组进行下游综合分析。我们高度跨学科的 这种方法将材料化学/纳米技术与自上而下的基于MS的蛋白质组学相结合，并基于 两个PI之间现有的富有成效的合作，导致了重大进展和出版物， 过去的融资期。我们所提议的研究的成功将提供创新工具， 蛋白质组学的研究，将为蛋白质组学研究奠定重要的技术基础。 了解ECM在癌症和心脏病疾病进展中的关键作用， 天然膜复合物的结构-功能关系，开发一种全面的cTnI检测方法， 心脏疾病的高准确性诊断，并了解GPCR信号的重要作用 在许多人类疾病包括癌症、糖尿病和心血管疾病的发病期间。