Multivalency, autoinhibition, and protein disorder in the regulation of interactions of dynein intermediate chain with dynactin and the nuclear distribution protein

Cytoplasmic dynein plays crucial roles in the intracellular transport of organelles and other cargoes. Central to dynein function is the intrinsically disordered N-terminal domain of dynein intermediate chain (IC), which binds the three dimeric dynein light chains at multivalent sites, and dynactin p150^Glued and nuclear distribution protein (NudE) at overlapping sites. The disorder in IC has hindered cryo-electron microscopy and X-ray crystallography studies of its structure and interactions. Here we use a suite of biophysical methods to reveal how multivalent binding of the three light chains regulate IC interactions with p150^Glued and NudE. Using the N-terminal domain or the full-length IC from Chaetomium thermophilum, a tractable species to interrogate IC interactions, we identify a significant reduction in IC’s binding affinity for p150^Glued and a loss of binding to NudE in contrast to the tight binding observed with small IC constructs. We attribute this difference to autoinhibition caused by strong long-range intramolecular interactions that cover IC’s N-terminal single α-helix, the site for p150^Glued and NudE binding. Reconstitution of IC subcomplexes demonstrate that autoinhibition is differentially regulated by light chains binding underscoring their importance both in assembly and organization of IC, and in selection between multiple binding partners at the same site.