Cooperative ordering in homeodomain-DNA recognition: Solution structure and dynamics of the MATa1 homeodomain

The mating type homeodomain proteins, MATa1 and MAT alpha 2, combine to form a heterodimer to bind DNA in diploid yeast cells. The a1-alpha 2 heterodimer tightly and specifically binds haploid-specific gene operators to repress transcription. On its own, however, the a1 homeodomain does not bind DNA in a sequence-specific manner. To help understand this interaction, we describe the solution structure and backbone dynamics of the free al homeodomain. Free al in solution is an ensemble of structures having flexible hinges at the two turns in the small protein fold. Conformational changes in the al homeodomain upon ternary complex formation are located in the loop between helix I and helix 2, where the C-terminal tail of alpha 2 binds to form the heterodimer, and at the C-terminus of helix 3, the DNA recognition helix. The observed differences, comparing the free and bound al structures, suggest a mechanism linking van der Waals stacking changes to the ordering of a final turn in the DNA-binding helix of a1. The tail of a2 induces changes in loop 1 of al that push it toward a properly folded DNA binding conformation.