A Charge-Encoded Rheostat Permits Helix Nucleation but Limits Propagation in Skp1

Abstract

Molecular recognition by intrinsically disordered regions (IDRs) is widely thought to involve coupled folding and binding, yet the sequence features that regulate this transition remain underexplored. Here we show that helix 8 (H8), a disordered C-terminal segment of the SCF ubiquitin ligase adaptor Skp1, is intrinsically prevented from forming a stable helix by its own sequence grammar. Using an integrative approach to dissect its conformational dynamics, we find that H8 frequently nucleates helical structure but rarely propagates into a fully formed stable helix, populating instead a shallow metastable basin of helical intermediates. Contrary to conventional models of helix-coil exchange, where nucleation is rate limiting, helix initiation in H8 is readily accessible, while propagation is selectively suppressed by a glutamate-rich acidic patch. This acidic segment acts as a charge-sensitive conformational rheostat that limits helix extension and maintains H8 in a predominantly disordered state. As a result, H8 transiently samples partially helical conformations on the microsecond timescale without committing to a stable fold. We propose that this propagation-limited mechanism preserves conformational flexibility while maintaining recognition competence across a structurally diverse family of F-box binding partners. More broadly, our findings suggest that charged- hydrophobic-charged sequence patterning can encode conditional, context-dependent structure as a general organisational principle in intrinsically disordered proteomes.