Occupancies in the DNA-Binding Pathways of Intrinsically Disordered Helix-Loop-Helix Leucine-Zipper Proteins

Quantifying the stability of intermediates along parallel molecular pathways is often hampered by the limited experimental resolution of ensemble methods. In biology, however, such intermediates may represent important regulatory targets, thus calling for strategies to map their abundance directly. Here, we use single-molecule Förster resonance energy transfer (FRET) to quantify the occupancies of intermediates along two parallel DNA-binding pathways of the basic helix-loop-helix leucine-zipper (bHLH-LZ) domains of the transcription factors c-Myc and Max. We find that both proteins are intrinsically disordered with sub-microsecond end-to-end distance dynamics. In mixtures of the proteins with their promoter DNA, our experiments identify the disordered conformers, the folded Myc-Max dimer, and ternary Myc-Max-DNA complexes. However, signatures of the intermediate along the alternative pathway, i.e., one domain bound to DNA, remained undetectable. This implies that disordered Max-DNA and Myc-DNA complexes are by at least 6 k_B T higher in free energy than folded dimers of Myc and Max. The disordered monomer-DNA complex is therefore unlikely to be of importance for the regulation of transcriptional processes.