STRUCTURE, PROTEIN RECOGNITION AND ENERGETICS OF DAMAGED DNA

我们工作的总体目标是建立结构-功能 突变和DNA修复的关系，并开发计算 可以用来预测修复酶 识别受损的DNA我们建议确定解决方案的结构 几个DNA分子含有诱变加合物，锌指基序 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，苯基咪唑并吡啶-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）进行，这些加合物将被纳入DNA 作为受损DNA模型的双链体;作为模型的未对齐的凸出双链体 用于移码诱变;和引物模板作为 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 同位素标记以增强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，使用斯托尼布鲁克的600 MHz分光光度计。NMR数据 将用于推导二面角、距离和体积约束， 当结合到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上运行， 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水桥接到我们目前的，刚性的， 人体分子模型我们电脑程序的改进将被编码 并在应用科学院的超立方体并行计算机设备上运行 数学系。

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.