Integrated tools for higher order structure determination by cross-link analysis

通过交联分析确定高阶结构的集成工具

• 批准号: 9347159
• 负责人: Beatrix Magdalena Ueberheide
• 金额: $ 22.49万
• 依托单位: PROTEIN METRICS, LLC
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2019-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9347159
• 关键词: Address; Adopted; Adoption; Affinity; Algorithmic Software; Algorithms; Amination; Amines; Antibodies; Antigen-Antibody Complex; Antigens; Area; Benchmarking; Biological; Biological Products; Biology; CCNE1 gene; Carboxylic Acids; Cell Membrane Permeability; Chemicals; Chemistry; Complex; Computer software; Crosslinker; Cullin Proteins; DNA-Directed RNA Polymerase; Data; Data Set; Deuterium; Development; Epitopes; Escherichia coli; Glycopeptides; Goals; Health; Higher Order Chromatin Structure; Histone H3; Human; Hydrogen; In Vitro; Individual; Industrialization; Industry; Ions; Laboratories; Length; Lysine; Maps; Mass Spectrum Analysis; Medical Research; Methods; Modification; Peptides; Pharmaceutical Preparations; Phase; Protein-Protein Interaction Map; Proteins; Proteomics; Reagent; Research; Sales; Sampling; Sensitivity and Specificity; Small Business Technology Transfer Research; Solvents; Standardization; Structure; Techniques; Testing; Time; Training; Visualization software; Water; blind; crosslink; data acquisition; drug development; improved; in vivo; instrumentation; novel; protein complex; protein protein interaction; search engine; therapeutic protein; three dimensional structure; tool; translational medicine; vaccine development

Summary The use of mass spectrometry (MS) for quantitative protein characterization has increased dramatically; identifying and quantifying thousands of proteins is no longer a heroic task nor is characterizing therapeutic proteins in detail. Due to widely available software, quantitative mass spectrometry has become routine and widely used for addressing questions in basic biology, translational medicine and drug development. MS Methods are now poised to have similar impact on the study of protein-protein interaction and higher order structure (HOS) determination. In particular, crosslinking mass spectrometry, which obtains distance and accessibility constraints from two-ended chemical modifications, is emerging as a powerful tool to map protein-protein interaction interfaces. Recent years have seen large improvements in crosslink mass spectrometry. Yet despite these advances, crosslink analysis is not yet a technique that has found widespread use, due to a range of problems such as the low abundance of crosslinked peptides, unavailability of proprietary reagents, the need for different search algorithms adopted to specific cross-linkers, and the difficulty of reliably characterizing crosslinked peptide spectra. To alleviate these problems and democratize the use of crosslinking, we propose to develop standardized and effective methods for crosslinking in conjunction with sensitive and accurate search algorithms, incorporated into our well-established Byonic search engine. Our algorithms will support almost all commercially available crosslinking chemistries and most major peptide fragmentation methods (ETD, CAD/HCD, EthcD), as well as cleavable and non-cleavable crosslinkers. The near universal applicability and ease-of-use of the software will promote rapid adoption of crosslinking mass spectrometry in academic research and biopharmaceutical development.

摘要 越来越多地使用质谱学(MS)对蛋白质进行定量表征 戏剧性地；鉴定和量化数以千计的蛋白质不再是一项英勇的任务，也不是 详细描述治疗性蛋白质。由于广泛使用的软件，定量质量 光谱学已经成为解决基础生物学问题的常规和广泛使用的方法， 转化医学与药物开发。MS方法现在已经准备好有类似的 对蛋白质相互作用和高阶结构研究的影响 决心。 尤其是交联质谱学，它可以获得距离和可及性 来自两端化学修饰的限制，正在成为一种强大的作图工具 蛋白质-蛋白质相互作用界面。近年来，交联剂有了很大的改进 质谱学。然而，尽管有这些进步，交联度分析还不是一种 由于一系列问题，如低丰度，已被广泛使用 交联肽，没有专利试剂，需要不同的搜索 算法适用于特定的交联剂，以及可靠表征的难度 交联肽光谱。 为了缓解这些问题并普及使用交联剂，我们建议开发 规范有效的交联法与灵敏准确的联用 搜索算法，整合到我们久负盛名的Byonic搜索引擎中。我们的算法 将支持几乎所有商业上可用的交联剂和大多数主要多肽 碎裂方法(ETD、CAD/HCD、ethcD)以及可切割和不可切割 交联剂。该软件的近乎普遍的适用性和易用性将促进快速 交联质谱在学术研究和生物制药中的应用 发展。