Mapping Hidden Residual Structure within the Myc bHLH-LZ Domain Using Chemical Denaturant Titration

Intrinsically disordered proteins (IDPs) underpin biological regulation and hence are highly desirable drug-development targets. NMR is normally the tool of choice for studying the conformational preferences of IDPs, but the association of regions with residual structure into partially collapsed states can lead to poor spectral quality. The bHLH-LZ domain of the oncoprotein Myc is an archetypal example of such behavior. To circumvent spectral limitations, we apply chemical denaturant titration (CDT)-NMR, which exploits the predictable manner in which chemical denaturants disrupt residual structure and the rapid exchange between conformers in IDP ensembles. The secondary structure propensities and tertiary interactions of Myc are determined for all bHLH-LZ residues, including those with poor NMR properties under native conditions. This reveals conformations that are not predictable using existing crystal structures. The CDT-NMR method also maps sites perturbed by the prototype Myc inhibitor, 10058-F4, to areas of residual structure. [Display omitted] •Developed the chemical denaturant titration-NMR techniques•Secondary and tertiary structures are determined for residues with poor NMR properties•Sites perturbed by the inhibitor, 10058-F4, map to areas of Myc with residual structure We apply chemical denaturant titration (CDT)-NMR to the bHLH-LZ domain of the oncoprotein Myc to determine the secondary structure propensities and tertiary interactions for all residues in the domain, including those with poor NMR properties under native conditions, and define the regions perturbed by a small-molecule inhibitor.