A HOMOLOGY MODEL OF THE ID-3 HELIX-LOOP-HELIX DOMAIN AS A BASIS FOR STRUCTURE-FUNCTION PREDICTIONS

The function of the dominant negative Id (inhibitor of differentiation ) helix-loop-helix (HLH) proteins is to dimerize with, and prevent the DNA binding of basic HLH (bHLH) transcription factors. A three-dimens ional homology model was constructed for the HLH domain of human Id3 b ased on the X-ray crystal structures of the E47, MyoD, and Max bHLH pr oteins. The model showed that, in contrast to bHLH proteins, Id protei ns appear able to dimerize without DNA stabilization because of better packing of the hydrophobic core, and the absence of destabilizing pol ar loop residues and of repulsive positive charges in the monomer inte rface at the base of the four a-helix bundle. This prediction was test ed by in vitro protein-binding experiments, which showed that Id3 did indeed self-associate. It also showed that the inability of Id protein s to bind DNA arises from the non-basic, poorly defined, random coil s tructure of the region corresponding to that responsible for bHLH DNA- binding. A model of the Idl protein was constructed and revealed a pot ential site of charge-charge repulsion in the hypothetical homodimer i nterface that may explain its observed inability to form homodimers.