Mapping the Conformational Variability in Mutants of the Amyloid Precursor Protein Intracellular Domain

The amyloid precursor protein intracellular domain (AICD) is an intrinsically disordered regulatory segment whose conserved YENPTY motif mediates transient interactions with multiple adaptor and signaling proteins. How sequence perturbations within this motif modulate its accessibility and interaction potential within a disordered ensemble remains poorly understood. Here, we combine small-angle X-ray scattering (SAXS), synchrotron radiation circular dichroism (SRCD), and extensive atomistic molecular dynamics simulations to characterize conformational variability in three designed AICD variants (Y22G, T26A, and Y27A) that preserve overall charge while selectively altering local side-chain chemistry. All variants remain intrinsically disordered, yet each mutation induces a distinct redistribution of conformational populations. Y22G and T26A increase local flexibility and solvent exposure around the YENPTY motif and enhance motif-centered interaction propensities, whereas Y27A favors more compact conformations with reduced motif accessibility. Contact and network analyses reveal that these local perturbations propagate across the chain, reshaping long-range intramolecular coupling within the ensemble. Together, our results demonstrate that local changes in side-chain chemistry within YENPTY can tune motif accessibility and interaction potential through population shifts in a disordered ensemble, without stabilizing persistent secondary or tertiary structure. These findings highlight how intrinsic disorder enables sensitive regulation of signaling motifs through sequence-encoded modulation of conformational landscapes.