Rearrangement of side-chains in a zif268 mutant highlights the complexities of zinc finger-DNA recognition

Structural and biochemical studies of Cys(2)His(2) zinc finger proteins ini tially led several groups to propose a "recognition code" involving a simpl e set of rules relating key amino acid residues in the zinc finger protein to bases in its DNA site. One recent study from our group, involving geomet ric analysis of protein-DNA interactions, has discussed limitations of this idea and has shown how the spatial relationship between the polypeptide ba ckbone and the DNA helps to determine what contacts are possible at any giv en position in a protein-DNA complex. Here we report a study of a zinc fing er variant that highlights yet another source of complexity inherent in pro tein-DNA recognition. In particular, we find that mutations can cause key s ide-chains to rearrange at the protein-DNA interface without fundamental ch anges in the spatial relationship between the polypeptide backbone and the DNA. This is clear from a simple analysis of the binding site preferences a nd co-crystal structures for the Asp20 --> Ala point mutant of Zif268. This point mutation in finger one changes the specificity of the protein from G CG TGG GCG to GCG TGG GC(G/T), and we have solved crystal structures of the D20A mutant bound to both types of sites. The structure of the D20A mutant bound to the GCG site reveals that contacts from key residues in the recog nition helix are coupled in complex ways. The structure of the complex with the GCT site also shows an important new water molecule at the protein-DNA interface. These side-chain/side-chain interactions, and resultant changes in hydration at the interface, affect binding specificity in ways that can not be predicted either from a simple recognition code or from analysis of spatial relationships at the protein-DNA interface. Accurate computer model ing of protein-DNA interfaces remains a challenging problem and will requir e systematic strategies for modeling sidechain rearrangements and change in hydration. (C) 2001 Academic Press.