Concerted dynamics link allosteric sites in the PBX homeodomain

The PBX1 homeodomain (PBX-HD) cooperatively binds DNA with Hox transcription factors and helps to regulate gene expression during vertebrate development. Allostery plays an important role in these interactions. DNA binding on one surface of PBX-HD enhances interactions with Hox proteins at a different interface. In addition, DNA binding causes a 15-residue extension at the C-terminus of PBX-HD to undergo a disorder-to-helix transition, although this region does not directly contact the DNA. Deletion of the C-terminal extension reduces both the DNA affinity of PBX-HD and the cooperativity of forming the DNA/Hox/PBX-HD ternary complex. To better understand the mechanism underlying these allosteric interactions, we used NMR relaxation dispersion dynamics experiments to characterize millisecond-timescale motions in PBX-HD over a range of temperatures. The data show that the C-terminal extension folds to form a fourth α-helix to a level of 5-10%, even in the absence of binding partners. This suggests that PBX-HD transiently preorganizes prior to binding DNA, reminiscent of the "conformational selection" model of molecular recognition. Folding of the C-terminal extension in the unbound protein is accompanied by structural rearrangements in both the DNA binding site and the Hox binding site, suggesting a possible role for these dynamics in the allosteric mechanism of PBX-HD.