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.

总结