Topology of the thyroid transcription factor 1 homeodomain-DNA complex

The topology of the thyroid transcription factor 1 homeodomain (TTF-1HD)-DN A complex was investigated by a strategy which combines limited proteolysis and selective chemical modification experiments with mass spectrometry met hodologies. When limited proteolysis digestions were carried out with the p rotein in the absence or presence of its target oligonucleotide, differenti al peptide maps were obtained from which the amino acid residues involved i n the interaction could be inferred. Similarly, selective acetylation of ly sine residues in both the isolated and the complexed homeodomain allowed us to identify the amino acids protected by the interaction with DNA. Surface topology analysis of isolated TTF-1HD performed at neutral pH was in good agreement with the three-dimensional structure of the molecule as determine d by NMR studies under acidic conditions. Minor differences were detected i n the C-terminal region of the protein which, contrary to NMR data, showed no accessibility to proteases. Analysis of the complex provided an experime ntal validation of the model proposed on the basis of the homology with the homeodomain structures described so far. An increased accessibility of the C-terminal region was observed following the interaction, suggesting its d isplacement from the protein core by the oligonucleotide molecule. Comparat ive experiments with DNA fragments differing in sequence and binding capabi lities highlighted structural differences among the complexes, mainly locat ed in the N-terminal region of the homeodomain, thus accounting for their d ifferent dissociation constants.