The collection of proteins that primarily drive circadian rhythms is known as the “core clock”; these proteins support a negative transcription-translation feedback loop through a cycle of gene activation and repression according to the subjective time of day. The transcription factor BMAL1 and its heterodimer partner CLOCK are the critical drivers of circadian gene activation. Both proteins harbor long intrinsically disordered regions (IDRs) that serve as signaling and interaction modules to control clock output. The BMAL1 C-terminal IDR (BMAL1-C) contains a ∼50-residue canonical transactivation domain (TAD), which interacts with at least five unique binding partners toward different functional outcomes (i.e., activation vs. repression). To date, TAD interactions with both co-activators and repressor proteins have been rigorously described in vitro. However, because these experiments focused on the isolated TAD, we lack a “structure”-function model for how the remaining residues in BMAL1-C contribute to protein-protein interactions. To investigate this, we generated full-length BMAL1-C (∼180 residues) and assessed its affinity for known TAD binders by fluorescence polarization measurements. Intriguingly, the presence of the full IDR increased the apparent affinity to the KIX domain of co-activator p300 by approximately five-fold. By integrating all-atom simulations, other biophysical methods, and NMR spectroscopy we interrogate atomistic details of the BMAL1-C conformational ensemble and its interactions. Summarily, these findings uncover new details about the contributions of local sequence context to IDR-mediated interactions and inform potential mechanisms of the core circadian clock.
Usher et al. (Sun,) studied this question.