Protein–Nucleic Acid Interaction: Major Groove Recognition Determinants


Protein–nucleic acid interactions play a crucial role in central biological processes. It is known that the most common binding element of proteins is an α helix and the primary binding site on DNA is in the major groove. Some general rules of the α helix binding to the DNA major groove have been derived, but there is no general code (one‐to‐one correspondence) for recognition.

Keywords: protein–nucleic acid complexes; zinc finger; α helix binding; major groove interactions

Figure 1.

α Helix binding to the major groove of DNA. Two views (90° apart) of a helix–turn–helix (HTH) motif are shown. Reproduced from Matthews, .

Figure 2.

Docking of α helix in the major groove, the accessible area in the major groove is highlighted in red.

Figure 4.

Docking of the α helices in the major groove. The recognition helix of the i + 3 superfamily is shown in yellow and that of the i + 4 superfamily in red. Reproduced from Pabo and Nekludova .

Figure 3.

(a) The ββα folding of Cys2His2 zinc finger motif. Reproduced from Wolfe et al. (b) Binding of the zinc finger in the major groove of DNA.

Figure 5.

Interactions in Zif268 zinc finger–DNA complex. (a) Cartoon representation of the complex. (b). Schematic illustration of the contacts between the fingers and the DNA bases. Arrows indicate hydrogen‐bonding interactions and circles represent van der Waals contacts. (c) Side‐chains forming hydrogen‐bonding interaction to G•C base pairs. Reproduced from Pavletich and Pabo ; Wolfe et al..



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Further Reading

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Saenger W (1984) Principle of Nucleic Acid Structure. New York: Springer–Verlag.

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Xiong, Yong, and Sundaralingam, Muttaiya(Apr 2001) Protein–Nucleic Acid Interaction: Major Groove Recognition Determinants. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0003138]