Structural classification of HTH DNA-binding domains and protein-DNA interaction modes

This paper constitutes an attempt to rationalize the structural similarities and differences that are observed among the HTH DNA-binding domains, and the various modes of protein-DNA interactions. It consists of classifying all the domains of known structure into families on the basis of the spatial arrangement of their helices, irrespective of the type of loops and the presence of beta-strands, and examining the interaction patterns between amino acids and DNA within each family. It is found that the recognition helix and the preceding helix along the chain have always the same relative orientation. Structural differences arise when considering three helices, corresponding usually to the recognition helix and the two preceding ones, but sometimes to the recognition helix and the two flanking helices. Using an automatic classification procedure, seven main families are obtained, whose members have in common the spatial arrangement of their three key helices, but have sometimes different topology and belong to different species. The structural divergence among these families and the existence of structural intermediates are analyzed. Searching these families systematically for recurrent motifs, leads to identify two specific turns, besides the HTH turn. They both link the two helices preceding the recognition helix and are each characteristic of a given family. Furthermore, the conservation of protein-DNA interaction patterns is examined with respect to the structural alignments. These patterns are found to be relatively well conserved within each family and to be different between the different families. The agreement of the structural classification and the patterns of protein-DNA contacts justify our approach, and suggests its applicability, in particular for modelling protein-DNA interactions.