Multidomain Relaxation Dispersion NMR Resolves an Intermediate-Gated Binding Pathway for Selective Recognition of...

Molecular recognition is governed not only by the structural complementarity of the final complex, but by the kinetic pathway through which it forms. Polyubiquitin chains, in which sequence-identical domains are covalently linked yet must be discriminated by dedicated receptors to encode distinct cellular signals, exemplify this challenge. For NMR relaxation dispersion studies of such systems, spectral overlap between identical domains prevents conventional uniform isotope labeling from resolving the per-domain exchange contributions. Here we show, using domain-selective 15N labeling combined with R2 relaxation dispersion, that the binding of linear (Met1-linked) diubiquitin to HOIL-1L NZF proceeds through an apparent three-state pathway as detected by relaxation dispersion, in which rapid ligand-dependent pre-equilibration populates a conformationally preorganized intermediate that is selectively captured by NZF in a slower, chain-type-selective step. This kinetic hierarchy offers a mechanistic basis for understanding the discrimination between linear and Lys63-linked ubiquitin chains that static structures alone cannot reveal. This strategy should be broadly applicable to multidomain recognition systems─including epigenetic reader complexes and multivalent signaling adaptors─where the pathway between known structural end points remains hidden.