Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries.
Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries.
复制标题
DNA 结合蛋白和复合物与 ARCIMBOLDO 文库的结构解决方案。
DOI：
10.1107/s1399004714007603
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发表时间：
2014-06
期刊：
影响因子：
--
通讯作者：
Usón I
中科院分区：
文献类型：
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作者：
Pröpper K;Meindl K;Sammito M;Dittrich B;Sheldrick GM;Pohl E;Usón I
在多解框架下，结合DNA结合蛋白基序片段的定位和密度修正，描述了DNA结合蛋白结构和复合物的结构解。蛋白质-DNA相互作用在生物体内遗传活动的各个方面都起着重要作用，例如转录、包装、重排、复制和修复。蛋白质-DNA相互作用的分子细节可以通过晶体学最好地可视化，并且强调洞察结合和碱基序列识别原理的结构对于理解潜在机制的微妙之处至关重要。尽管核酸的晶体学特性往往对主要为蛋白质开发的方法提出特定挑战，但已经见证了越来越多的高质量DNA结合蛋白质结构测定。因此，蛋白质-DNA复合物的晶体结构解决方案仍然是一个具有挑战性的领域，需要优化的实验和计算方法。因此，对蛋白质-DNA复合物溶液的结构-溶液程序ARCIMBOLDO的潜力进行了评估。该方法的基础上定位小，非常准确的碎片使用程序相位和密度修改程序SHELXE的组合。对于典型的蛋白质，主链α-螺旋提供了理想的、几乎普遍存在的小片段来开始搜索，而对于DNA复合物，结合基序和DNA双螺旋构成了合适的搜索片段。这项工作的目的是提供一个有效的库的搜索片段，以及确定最佳的ARCIMBOLDO策略，这类结构的解决方案。
The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.