STRUCTURE, PROTEIN RECOGNITION AND ENERGETICS OF DAMAGED DNA

受损 DNA 的结构、蛋白质识别和能量

• 批准号: 6106126
• 负责人: MOSHE EISENBERG
• 金额: $ 19.84万
• 依托单位: STATE UNIVERSITY NEW YORK STONY BROOK
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-03-01 至 2000-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6106126
• 关键词: DNA damage; DNA repair; acetylaminofluorene; adduct; adenine analog; chemical models; chemical structure function; computer simulation; environmental toxicology; guanine analog; molecular dynamics; nuclear magnetic resonance spectroscopy; nucleic acid sequence; nucleic acid structure

The overall goal of our work is to establish structure-function relationships in mutagenesis and DNA repair and to develop computational methods that can be used to predict patterns by which repair enzymes recognize damaged DNA. We propose to determine solution structures of several DNA molecules containing mutagenic adducts, the zinc finger motif of Fpg protein, and its 1:1 complex with DNA. Adducts to be studied include acetylaminofluorene-C(8)- and N2-guanine, aminofluorene-G(8)- guanine, phenilimidazopyridine-C(8)-guanine, 8-oxoguanine, 8-oxoadenine, 8-aminoguanine, as well as abasic sites. Based on mutagenesis studies conducted in (Project 2), these adducts will be incorporated into DNA duplexes as models for damaged DNA; misaligned bulged duplexes, as models for frameshift mutagenesis; and primer-templates as models for replication fork intermediates. These adducts will be synthesized in the laboratories of Dr. Johnson (Project i); several bases will be isotopically labeled to enhance NMR resolution. One- and two-dimensional high resolution NMR experiments will be performed on the adducted DNA molecules, using the 600 MHz spectrophotometer at Stony Brook. NMR data will be used to derive dihedral-, distance- and volume-restraints which, when incorporated into molecular mechanics and dynamics calculations, will establish the solution structure of the above-mentioned adducts. Calculations will run on our Silicon Graphics computers, as well as on NSF supercomputers. We propose to expand our computational methods for macromolecular docking based on hydrogen bond pattern recognition by including dynamic flexibility and water bridging to our current, rigid- body molecular model. Enhancements of our computer programs will be coded and run on the hypercube parallel computer facility at the Applied Mathematics Department.

我们工作的总体目标是建立结构功能 诱变和DNA修复的关系并发展计算 可用于预测修复酶的模式的方法 识别受损的DNA。我们建议确定的解决方案结构 几个含有诱变加合物的DNA分子，锌指基序 FPG蛋白的及其1：1复合物与DNA。要研究的加合物 包括乙酰氨基氟烯-C（8）和N2-瓜氨酸，氨基氟烯烯-G（8） - 鸟嘌呤，苯胺甲酰咪酸吡啶-C（8） - 鸟嘌呤，8-氧气甘氨酸，8-氧化丙氨酸，， 8-氨基瓜氨酸以及无碱性地点。基于诱变研究 在（项目2）进行的，这些加合物将纳入DNA 双链体作为损坏的DNA的模型；作为模型 用于移除诱变；和底漆 - 用作模型 复制叉中间体。这些加合物将在 约翰逊博士的实验室（项目I）；几个基地将是 同位素标记以增强NMR分辨率。一维和二维 高分辨率NMR实验将在加合的DNA上进行 分子，使用Stony Brook的600 MHz分光光度计。 NMR数据 将用于得出二面，距离和体积重模具，这些束缚 当纳入分子力学和动力学计算中时 将建立上述加合物的溶液结构。 计算将在我们的硅图形计算机以及 NSF超级计算机。我们建议扩展我们的计算方法 基于氢键模式识别的大分子对接 包括动态的灵活性和桥接到我们当前的刚性 - 身体分子模型。计算机程序的增强功能将被编码 并在应用的HyperCube平行计算机设施上运行 数学系。