Functional Specificity of a Protein-DNA Complex Mediated by Two Arginines Bound to the Minor Groove

Abstract

Bacteriophage Ø29 transcriptional regulator, protein p4, interacts with its DNA target employing two mechanisms: direct readout of the chemical signatures of only one DNA base, and inducing local modification on the topology of short A-tracts (indirect readout). P4 binds as a dimer to targets consisting of imperfect inverted repeats. Here, we use Molecular Dynamic simulation to define interactions of a cluster of 12 positive charged amino acids of p4 with DNA and biochemical assays with modified DNA targets and mutated proteins to quantify the contribution of residues in the nucleoprotein complex. Our results show the implication of Arg54, with base-unspecific interaction in the central A-tract, in p4 binding affinity. Despite being chemically equivalent and in identical protein monomers, the two Arg54 residues differed in their interactions with DNA. We discuss an indirect-readout mechanism for p4-DNA recognition mediated by dissimilar interaction of arginines penetrating the minor groove and the inherent properties of the A-tract. Our finding extent the current understanding of protein-DNA recognition and contributes to the relevance of the sequence-dependent conformational malleability of the DNA, enlightening the role of arginines in binding affinity. Characterization of mutant p4R54A shows that the residue is required for the activity of the protein as transcriptional regulator.