Hydroxyl radical mapping of protein interfaces

蛋白质界面的羟基自由基图谱

• 批准号: 6408335
• 负责人: Vernon E. Anderson
• 金额: $ 10万
• 依托单位: EXSAR CORPORATION
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-09-15 至 2003-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6408335
• 关键词: analytical chemistry; benzimidazoles; cesium; computer simulation; enzyme inhibitors; hirudins; hydroxyl radical; intermolecular interaction; liquid chromatography mass spectrometry; mathematical model; method development; model design /development; molecular dynamics; molecular site; peptides; physical model; protein structure function; proteomics; prothrombin; protonation; radiotracer; statistics /biometry; structural biology; surface property; thermolysin; thrombin

DESCRIPTION (provided by applicant): Identifying amino acid residues of a protein that form the binding site for a drug, or that are present at the interface in a protein-protein complex are difficult to identify from the crystal structures of the individual partner proteins. Carta Proteomics is committed to the premise that monitoring isotope exchange into proteins by mass spectrometry will permit the rapid identification of contact residues of proteins that form macromolecular complexes. Prior work and proprietary development has established amide-proton solvent exchange as one facet of Carta Proteomics. This proposal is to develop a complementary method of hydroxyl radical (-OH) induced 1I-TJ2H exchange into the aliphatic carbons of the amino acid side chains. This proposal takes advantage of the basic underlying chemistry that has been recently well characterized. The goal of this proposal is to demonstrate the capability of this chemistry to use the multiple binding sites present on thrombin to validate the ability of this methodology to correctly identify the active site in a BABIM thrombin complex and to identify the allosteric binding site for hirudin, an inhibitory oligopeptide. This demonstration will validate the application of the method to inhibitors identified from combinatorial chemistry screens. PROPOSED COMMERCIAL APPLICATION: Structure based drug design is severely hampered by the lack of a low-cost, rapid method of determining structure. Our technology of determining structures of a small molecule/protein target interaction can be easily adapted to high throughput and very fast turn-around at very low cost. Because of these unique features we expect the technology to be readily integrated into the small molecule drug discovery process. Carta Proteomics will participate by providing the proprietary expertise through research partnership agreements.

描述(申请人提供)：鉴定一种氨基酸残基 形成药物结合部位的蛋白质，或存在于 蛋白质-蛋白质复合体中的界面很难从 单个配对蛋白的晶体结构。Carta蛋白质组学是 致力于监测同位素通过质量交换成蛋白质的前提 光谱分析将使快速鉴定接触残留物成为可能 形成大分子复合体的蛋白质。以前的工作和专有 发展已将酰胺-质子溶剂交换确立为CATA的一个方面 蛋白质组学。这项建议是为了开发一种补充羟基的方法 自由基(-OH)诱导1I-TJ2H交换为氨基上的脂肪族碳 酸性侧链。这一提议利用了基本的基础 最近被很好地描述的化学。 这项提议的目标是展示这一能力 使用凝血酶上存在的多个结合位点来验证 此方法能够正确识别BABIM中的活动站点 凝血酶复合体和鉴定水飞蓟素的变构结合部位 抑制性寡肽。本演示将验证 该方法用于从组合化学筛选中鉴定出抑制剂。 建议的商业应用： 由于缺乏一种低成本、快速确定结构的方法，基于结构的药物设计受到严重阻碍。我们确定小分子/蛋白质靶相互作用的结构的技术可以很容易地适应高通量和非常低的成本非常快的周转。由于这些独特的特点，我们希望这项技术可以很容易地整合到小分子药物的发现过程中。Carta蛋白质组学公司将通过研究伙伴协议提供专有专业知识。