Chirgadze Yu N, Larionova E A, Ivanov V V
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
J Biomol Struct Dyn. 2009 Aug;27(1):83-96. doi: 10.1080/07391102.2009.10507298.
Binding sites of 75 protein domains from 65 complexes of transcription factors with fragments of double-chained operator B-DNA in the major groove region were considered for known spatial structures at a resolution higher than 2.5 A. The DNA-binding protein domains belong to various structural families and differ greatly in the molecular structure and size. However, in all cases mainly polar residues of the only recognizing alpha-helix of protein factor ensured the binding. We have shown that binding helical residues have a very clear novel recognition sign. For 95.8% of total protein domains the binding polar residues of the recognizing alpha-helix were localized within one of the two largest clusters of polar side groups on the protein surface. In fact, we have seen a unique recognition sign of the DNA-binding alpha-helix of transcription factors to be inherent to different structural families. This enables determining the binding helical residues of transcription factor due to its known spatial structure. The observed regularity on the localization of contact polar residues is general both in DNA and RNA-binding proteins as shown earlier. It contributes seriously to further understanding of a complex formation on the way to exact identification of binding helical residues of transcription factors.
对于分辨率高于2.5埃的已知空间结构，研究了来自65种转录因子与双链操纵子B - DNA片段在大沟区域形成的复合物中的75个蛋白质结构域的结合位点。DNA结合蛋白结构域属于不同的结构家族，在分子结构和大小上差异很大。然而，在所有情况下，蛋白质因子唯一识别的α - 螺旋的主要极性残基确保了结合。我们已经表明，结合螺旋残基具有非常清晰的新型识别标志。对于95.8%的总蛋白质结构域，识别α - 螺旋的结合极性残基位于蛋白质表面两个最大的极性侧链基团簇之一内。事实上，我们已经看到转录因子的DNA结合α - 螺旋的独特识别标志是不同结构家族所固有的。这使得能够根据转录因子已知的空间结构确定其结合螺旋残基。如前所示，观察到的接触极性残基定位规律在DNA和RNA结合蛋白中都是普遍存在的。这对于进一步理解在准确鉴定转录因子结合螺旋残基过程中的复合物形成有很大帮助。
