DNA fine structure and dynamics in crystals and in solution: The impact of BI/BII backbone conformations
DNA fine structure and dynamics in crystals and in solution: The impact of BI/BII backbone conformations
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DOI：
10.1002/bip.10528
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发表时间：
2004-02-15
期刊：
影响因子：
2.9
通讯作者：
Hartmann, B
中科院分区：
文献类型：
--
作者：
Djuranovic, D;Hartmann, B
糖-磷酸骨架构象是完整理解核酸-蛋白质相互作用中特异性识别的重要结构要素。它们既可以参与目标识别的早期阶段，也可以参与结合后的结构适应。在本研究的第一部分中，我们分析了高分辨率的结构的双链B-DNA分离或绑定到蛋白质，并探讨了标准的BI和不寻常的BII磷酸骨架构象对相邻的糖puckers和选定的螺旋参数的影响。相关性被发现是类似的自由和绑定的DNA，并在这两个类别中，可能面临的骨干构象（BI.BI，BI.BII，和BII.BII）定义良好的特征子状态在B-DNA构象空间。值得注意的是，BII.BII步骤的特征在于特异性的、序列独立的结构效应，其涉及几乎所有构象参数的降低的标准偏差。在这项工作的第二部分中，我们分析了四个10 ns的分子动力学模拟在明确的溶剂上的DNA靶的NF-κ B和牛乳头瘤病毒E2蛋白，突出了骨干动力学行为的多样性。这些结果表明，序列效应的百分比BI和BII构象，面对的骨干，发生耦合转换的优先状态。因此，骨架状态可以被视为将信息从碱基传递到磷酸基团的机制，从而调节靶DNA的整体结构特性。(C)2003 Wiley Periodicals，Inc.
Sugar-phosphate backbone conformations are an important structural element for a complete understanding of specific recognition in nucleic acid-protein interactions. They can be involved both in early stages of target discrimination and in structural adaptation upon binding. In the first part of this study, we have analyzed high-resolution structures of double-stranded B-DNA either isolated or bound to proteins, and explored the impact of both the standard BI and the unusual BII phosphate backbone conformations on neighboring sugar puckers and on selected helical parameters. Correlations are found to be similar for free and bound DNA, and in both categories, the possible facing backbone conformations (BI.BI, BI.BII, and BII.BII) define well-characterized substates in the B-DNA conformational space. Notably, BII.BII steps are characterized by specific, and sequence-independent, structural effects involving reduced standard deviations for almost all conformational parameters. In the second part of this work, we analyze four 10 ns molecular dynamics simulations in explicit solvent on the DNA targets of NF-kappaB and bovine papillomavirus E2 proteins, highlighting the multiplicity of backbone dynamical behavior. These results show sequence effects on the percentages of BI and BII conformers, the preferential state of facing backbones, the occurrence of coupled transitions. The backbone states can consequently be seen as a mechanism for transmitting information from the bases to the phosphate groups and thus for modulating the overall structural properties of the target DNA. (C) 2003 Wiley Periodicals, Inc.