Prediction of the self-association of the nuclear inhibitor of DNA binding and differentiation proteins

The inhibitor of DNA binding and differentiation (ID) proteins (ID1–ID4) are members of the helix-loop-helix (HLH) family of transcriptional regulators that play a critical role in regulating cell cycle progression and cell differentiation. Their overexpression in various cancer types makes them promising therapeutic targets. It has been reported that ID4 acts as a tumor suppressor as ID4 heterodimerizes with ID-1, -2, and − 3 and promotes bHLH DNA binding, essentially acting as an inhibitor of inhibitors of differentiation proteins. In this work, we utilize advanced computational biophysics and bioinformatics tools to map the structural foundations of ID protein self-association. High-resolution models were generated and subjected to 100 ns Molecular Dynamics (MD) simulations to capture their conformational dynamics in physiological environments. Through protein-protein docking (HADDOCK) and interface analysis, aiming to characterize the binding hotspots of both homodimers and heterodimers, facilitating the development of inhibitors that can disrupt its pathological interactions. Results revealed that ID1 can self-dimerize and form a stable dimer with ID4. The dimerization is exerted by the HLH domain, and the dimers are stable compared to the monomeric isoforms. The ID1-ID4 dimer formation has an important role in lowering their concentration in the nucleus and hence affecting their function. Hence, the identified interaction pattern may have important implications for regulating their activity.