Cation-pi/H-bond stair motifs at protein-DNA interfaces

H-bonds and cation-π interactions between nucleic acid bases and amino acid side-chains are known to occur often concomitantly at the interface between protein and double-stranded DNA. Here we define and analyze stair-shaped motifs, which simultaneously involve base stacking, H-bond and cation-π interactions. They consist of two successive bases along the DNA stack, one in cation-π interaction with an amino acid side-chain that carries a total or partial positive charge, and the other H-bonded with the same side-chain. A survey of 52 high-resolution structures of protein/DNA complexes reveals the occurrence of such motifs in the majority of the complexes, the most frequent of these motifs involving Arg side-chains and G bases. These stair motifs are sometimes part of larger motifs, called multiple stair motifs, which contain several successive stairs; zinc finger proteins for example exhibit up to quadruple stairs. In another kind of stair motif extension, termed cation-π chain motif, an amino acid side-chain or a nucleic acid base forms simultaneously two cation-π interactions. Such a motif is observed in several homeodomains, where it involves a DNA base in cation-π interactions with an Arg in the minor groove and an Asn in the major groove. A different cation-π chain motif contains an Arg in cation-π with a G and a Tyr, and is found in ets transcription factors. Still another chain motif is encountered in proteins that expulse a base from the DNA stack and replace it by an amino acid side-chain carrying a net or partial positive charge, which forms cation-π interactions with the two neighboring bases along the DNA strand. The striking conservation of typical stair and cation-π chain motifs within families of protein/DNA complexes suggests that they might play a structural and/or functional role and might moreover influence electron migration through the DNA double helix. © 2002 Elsevier Science Ltd. All rights reserved.SCOPUS: ar.j