Amairy, D.; Pekel, H.; Gul, S.; Sensoy, O.

Phosphorylation of the CLOCK/BMAL1 complex is a reversible post-translational modification that plays a central role in regulating circadian oscillations; however, its underlying mechanistic basis remains poorly understood. Although biochemical studies have shown that phosphorylation modulates CLOCK/BMAL1 binding to DNA, yet it remains unclear whether these effects are confined to local perturbation or also propagate through allosteric effects. Moreover, the influence of phosphorylation on histone dynamics and transcription factor-nucleosome interactions has not been systematically investigated. Here, we address these questions using atomistic trajectories obtained through backmapping of coarse-grained molecular dynamics simulations based on the recently resolved cryoEM structure of the CLOCK/BMAL1 and nucleosome complex. We investigated three experimentally identified phosphorylation states: CLOCK bHLHS38/42, BMAL1 bHLHS78, and simultaneous phosphorylation of both proteins. Our results demonstrate that phosphorylation regulates CLOCK and BMAL1 asymmetrically. Whereas phosphorylation weakens the interaction of the modified bHLH domain with the E-box, BMAL1 phosphorylation simultaneously enhances DNA engagement by the CLOCK bHLH domain, an effect that persists in the doubly phosphorylated complex and identifies BMAL1 phosphorylation as the dominant regulatory event. Steered pulling simulations further demonstrate that phosphorylation equalizes the mechanical stability of CLOCK and BMAL1 interactions with DNA. Beyond modulating DNA binding, phosphorylation remodels protein histone interactions by altering contacts between the CLOCK PASB domain and histone H3 and between the BMAL1 PASA domain and the H2A/H2B acidic patch, while simultaneously rewiring residue-correlation and allosteric communication networks throughout the heterodimer. Importantly, phosphorylation increases the separation between the CLOCK HI loop and the H31 L1 elbow, supporting a structural model in which phosphorylation acts as a priming event that provides a more permissive environment for CRY1 recruitment to the chromatin-bound CLOCK/BMAL1 complex, thereby facilitating transcriptional repression. Collectively, our findings reveal that phosphorylation regulates the CLOCK/BMAL1 complex through coordinated remodeling of DNA binding, nucleosome interactions, and long-range allosteric communication, providing a mechanistic framework for circadian transcriptional repression and a foundation for the rational design of therapeutics targeting the molecular circadian clock.