Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, M1-B514, Seattle, Washington 98109, USA.
Protein Sci. 2012 Apr;21(4):471-4. doi: 10.1002/pro.2034. Epub 2012 Feb 14.
TAL (transcriptional activator-like) effectors are DNA-binding repeat proteins recently shown to recognize their target sites by an unprecedented, 1:1 mapping between repeat residues and DNA bases. The structural basis for this recognition is not known; in particular, it is not clear whether such 1:1 recognition can be accommodated by standard major-groove readout of B-form DNA. Here we describe a structure prediction protocol tailored to the TAL-DNA system, and report simulation results that shed light on observed repeat-base associations and overall TAL structure. Our models demonstrate that TAL-DNA interactions can be explained by a model in which the TAL repeat domain forms a superhelical repeat structure that wraps around undistorted B-form DNA, paralleling the geometry of the major groove, with contacts between position 13 of each repeat and its associated base pair on the sense strand determining the specificity of DNA recognition.
TAL（转录激活样）效应子是 DNA 结合重复蛋白，最近的研究表明，它们通过重复残基与 DNA 碱基之间前所未有的 1:1 映射来识别其靶位。这种识别的结构基础尚不清楚；特别是，尚不清楚这种 1:1 识别是否可以通过 B 型 DNA 的标准主沟读出来适应。在这里，我们描述了一种专门针对 TAL-DNA 系统的结构预测方案，并报告了模拟结果，这些结果阐明了观察到的重复-碱基关联和整体 TAL 结构。我们的模型表明，TAL-DNA 相互作用可以用一种模型来解释，在这种模型中，TAL 重复结构域形成一个超螺旋重复结构，围绕未扭曲的 B 型 DNA 缠绕，与主沟的几何形状平行，每个重复的第 13 位与有义链上与其相关的碱基对之间的接触决定了 DNA 识别的特异性。
