Novel recognition sign of DNA-binding alpha-helix in complexes of transcription factors from different families with...

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.