Conformational Heterogeneity and DNA Recognition by the Morphogen Bicoid

The morphogenic activity of the Drosophila transcription factor bicoid (Bcd), the first morphogenic protein identified, is controlled by its DNA binding homeodomain. Homeodomains mediate developmental processes in all multicellular organisms, but the Bcd homeodomain appears to be unique as it can bind multiple DNA sequences and even RNA. All homeodomain proteins adopt a three-helix fold, with residues of the third helix mediating recognition of the nucleic acid target via interactions with the major groove. Interestingly, previous studies have revealed that conformational heterogeneity is present in the Bcd residues that interact with bound DNA, suggesting that it may underlie the morphogen’s unique polyspecificity. To begin to directly characterize the conformational heterogeneity in the homeodomain, we have introduced C–D bonds within each structural element and characterized their absorptions in the free and bound states, as well as during thermal denaturation. The data reveal that while residues withi...