Theoretical Aspects of DNA Supercoiling

描述(申请人提供)：这项研究将计算机模拟(能量优化/展开技术、蒙特卡罗计算和简正模式分析)与新的自然离散的DMA模型相结合，以检查超螺旋DMA的结构和性质，超螺旋DMA是一种受更高阶折叠和补偿性链扭曲的拓扑约束形式的双螺旋，以及DMA在活细胞中的存在方式。长的线状聚合物的碱基序列相关特征被纳入理论并通过数值模拟进行处理。通过将分析研究与计算机模拟相结合，我们获得了互补的信息，并有一系列内置的制衡机制来评估我们发现的重要性。计算结果促进了新的理论发展，这反过来又可以用来评估计算的有效性。从双螺旋DMA的高分辨率结构中提取的基于知识的势隐含地处理了糖-磷酸骨架和局部化学环境的影响，在典型情况下，还显式地处理了长程力。我们的近期目标是研究DMA小环和环的序列依赖的生物物理性质，并建立体内环的物理化学基础。拟议的研究旨在阐明主要化学特征(碱基序列)、配体结合(蛋白质)和超螺旋水平(对碱基对定位施加限制)对双螺旋整体折叠的作用。我们将扩展我们对与Lac抑制蛋白相连的DMA环的研究，目的是收集对分子组装在转录调控中的作用以及它作为真核绝缘体模型的潜在适用性的新见解。第二个目标是深入了解DMA序列和超螺旋对蛋白质结合和随后的细胞功能的影响。其他需要解决的问题包括：(1)局部序列依赖的结构和配体结合在空间受限双链的大规模构象转变中的作用；(2)多个蛋白质对超螺旋分子构型性质的竞争效应；以及(3)局部结构和全局结构在超螺旋动力学中的相互作用。

DESCRIPTION (provided by applicant): The research combines computer simulation (energy optimization/expansion techniques, Monte-Carlo calculations, and normal-mode analysis) with a new naturally discrete model of DMA to examine the configurations and properties of supercoiled DMA, a topologically constrained form of the double helix subject to higher-order folding and compensatory strand twisting and the way that DMA exists in living cells. Base sequence-dependent features of the long, threadlike polymer are incorporated in the theory and treated by numerical simulations. By combining analytical studies with computer simulations, we obtain complementary information and have a series of built-in checks and balances for assessing the significance of our findings. The computational results stimulate new theoretical developments, which in turn can be used to assess the validity of the calculations. The effects of the sugar-phosphate backbone and local chemical environment are treated implicitly with knowledge-based potentials extracted from high-resolution structures of double-helical DMA and, in representative cases, with explicit treatment of long-range forces. Our immediate goals are to study the sequence-dependent biophysical properties of DMA minicircles and loops and to establish the physico-chemical basis of in-vivo looping. The proposed studies aim to clarify the role of primary chemical features (base sequence), ligand binding (proteins), and levels of supercoiling (imposed constraints on base-pair positioning) on the overall folding of the double helix. We will extend our studies of DMA loops tethered to the Lac represser protein with the aim of gathering new insights into the role of the molecular assembly in the regulation of transcription and its potential applicability as a model of eukaryotic insulators. A second goal is to gain insight into the effect of DMA sequence and supercoiling on protein binding and consequent cellular function. Other issues to be addressed include: (1) the role of local sequence-dependent structure and ligand binding on large-scale configurational transitions of spatially constrained duplexes; (2) the competing effects of multiple proteins on the configurational properties of supercoiled molecules; and (3) the interplay of local and global structure in supercoiling dynamics.