Biochemistry/BIMS 503

Protein-DNA Interactions: Zinc finger proteins

David Auble

Zinc finger domains are very common, with many thousands identified in many hundreds of proteins. The domain is typically ~25-30 residues long and possesses two cysteine and two histidine residues that coordinate a zinc atom. The stably folded structure consists of a beta strand-turn-beta strand-turn-alpha helix and is shown below (1zfn). Extensive studies have shown that the while the zinc finger structure depends on the zinc-coordinating residues as well as 3 conserved hydrophobic residues, the structure of the domain is surprisingly tolerant of a wide range of amino acid substitutions. This flexibility has made it an especially good scaffold for design of DNA binding proteins with new specificities. Zinc finger DNA binding proteins typically contain two or more zinc fingers. The alpha helices in each finger interact with 3 base pairs of DNA, typically interacting with contiguous 3 base pair recognition sites. Specific residues in the domain interact with specific bases. For example, it was noticed that arginine in the first position preceding the alpha helix (position -1) can specify interaction with G in a particular position whereas histidine in position 3 specifies a preference for G or A at a particular position. "Rules" for these interactions have been discerned through many studies involving both rational design and selection of interactions from pools of random variants. Below you can see several variants of the Zif268 zinc finger protein bound to different DNA sequences. Although there is considerable complexity in these interactions, the modularity of the domain has led to a code of sorts for protein-DNA interaction.

Zif268 has 3 fingers. In the variants shown here, residues in the first finger were randomized and selection was performed to identify new DNA binding specificities. The variant Zif268 molecules are 90 residues long and are named by the amino acids that occupy positions in the first finger that contact DNA. For example, DSNR is a variant with D at position -1, S at position 2, N at position 3 and R at position 6. The numbering refers to standard nomenclature for residue position near or within the alpha helix that provides the DNA recognition. The sequence recognized by the finger is shown in shorthand. For example, the DSNR protein is shown bound to a DNA variant with the sequence GACC. Protein is blue; DNA is cyan. Some of the specific contacts are highlighted in the same color so you can get a feel for how the specificity is determined. In some cases, specificity involves alternate amino acid side chain conformations and indirect or water-mediated hydrogen bonds.

Back to Index of Macromolecular Structures

Auble Lectures Home Page