DYNAMICS OF DNA DAMAGE RECOGNITION BY REPAIR ENZYMES

描述：这项提议的长期目标是开发一种分子 理解，源于理论和实验的结合 协作性方法，认识的特殊性原则 修复酶对DNA损伤的修复及酶-DNA的稳定性 很复杂。几种修复体结构的最新X射线测定 酶提供了一个研究分子细节的机会 DNA损伤的选择性识别机制。研究人员将 研究胸腺嘧啶二聚体损伤对DNA的识别作用 被T4内切酶识别的V.X射线的可用性 酶的结构和与受损DNA的复合体是推动 特异性和致病性的分子机制研究进展 络合物的稳定性。工作假设是四个因素 有助于选择性识别受损的DNA。这些代码在1)中进行编码 损伤区域周围DNA结构的变化，2) DNA发生自发或蛋白质诱导的碱基翻转 损伤部位进入螺旋外位置，3)不对称分布 在受损的DNA周围凝聚的反离子会产生静电 定向场；4)节点处DNA水合作用的变化 影响相互作用的热力学的损伤 修复酶和受损的DNA。这些原则似乎是大体 适用于识别受损DNA的多种修复酶。这样做的目的是 建议对这些因素进行详细调查，不能全面 要么是纯理论的，要么是纯实验的 因此，他们提出了一种互补的协作方法 它们将计算模拟与时间依赖相结合 荧光测量，以调查决定的因素 修复酶识别受损DNA的特异性。解读 实验结果将由真实的表示支持 分子模型及其振动性质和水溶液离子 来自分子模拟的环境。以一种互补的方式， 来自分子模拟的机械论解释和预测将 通过实验测量进行严格的测试。这种互补性 研究将使我们更好地理解这些因素 对修复酶的特异性和在特异性中发挥重要作用 蛋白质-DNA的相互作用。

DESCRIPTION: The long term goal of this proposal is to develop a molecular understanding, derived from a combined theoretical-experimental collaborative approach, of the principles of specificity of the recognition of damaged DNA by repair enzymes and the stability of the enzyme-DNA complex. Recent x-ray determination of the structure of several repair enzymes presents an opportunity to investigate in molecular details the mechanisms of selective recognition of DNA damage. The researchers will investigate the recognition of DNA with a thymine dimer lesion that is recognized by the enzyme T4 endonuclease V. The availability of the x-ray structure of the enzyme and the complex with damaged DNA is the impetus for the investigation of the molecular principles of the specificity and stability of the complex. The working hypothesis is that four factors contribute to selective recognition of damaged DNA. These are encoded in 1) changes in the structure of DNA around the damaged area, 2) the ability of DNA to undergo a spontaneous or protein-induced flipping of a base near the damaged site into an extrahelical position, 3) asymmetric distribution of condensed counterions around damaged DNA that produces an electrostatic orientational field, and 4) changes in DNA hydration around the point of damage that influences the thermodynamics of the interaction between the repair enzyme and the damaged DNA. These principles appear to be generally applicable to many repair enzymes recognizing damaged DNA. The aims of this proposal to investigate in detail these factors, cannot be fully accomplished by either an exclusively theoretical or a purely experimental approach and they, therefore, propose a complementary collaborative approach in which they combine computational simulations with time-dependent fluorescence measurements to investigate the factors that determine the specificity of damaged DNA recognition by repair enzymes. Interpretation of experimental results will be supported by the realistic representation of molecular models, their vibrational properties and the aqueous ionic environment derived from molecular simulations. In a complementary way, mechanistic interpretations and predictions from molecular simulations will be tested rigorously by experimental measurements. Such complementary research will lead to a better understanding of the factors that contribute to specificity of repair enzymes and play an important role in specific protein-DNA interactions in general.