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 修复之间的关系并开发计算 可用于预测修复酶模式的方法 识别受损的 DNA。我们建议确定解决方案结构 几个含有诱变加合物（锌指基序）的 DNA 分子 Fpg 蛋白及其与 DNA 的 1:1 复合物。待研究的加合物 包括乙酰氨基芴-C(8)-和N2-鸟嘌呤、氨基芴-G(8)- 鸟嘌呤、苯咪唑并吡啶-C(8)-鸟嘌呤、8-氧代鸟嘌呤、8-氧代腺嘌呤、 8-氨基鸟嘌呤，以及脱碱基位点。基于诱变研究 在（项目2）中进行，这些加合物将被整合到DNA中 双链体作为受损 DNA 的模型；未对齐的凸出双工，如模型 用于移码诱变；和引物模板作为模型 复制叉中间体。这些加合物将在 Johnson 博士的实验室（项目 i）；将会有多个基地 同位素标记以提高 NMR 分辨率。一维和二维 将对加合的 DNA 进行高分辨率 NMR 实验 分子，使用石溪分校的 600 MHz 分光光度计。核磁共振数据 将用于导出二面角、距离和体积约束，其中， 当纳入分子力学和动力学计算时， 将建立上述加合物的溶液结构。 计算将在我们的 Silicon Graphics 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 包括动态灵活性和水桥到我们当前的刚性 身体分子模型。我们的计算机程序的增强功能将被编码 并在应用材料公司的超立方并行计算机设施上运行 数学系。