Connecting the αα-hubs: same fold, disordered ligands, new functions

Abstract

Background: Signal fidelity depends on protein-protein interaction-'hubs' integrating cues from large interactomes. Recently, and based on a common secondary structure motif, the αα-hubs were defined, which are small α-helical domains of large, modular proteins binding intrinsically disordered transcriptional regulators.

Methods: Comparative structural biology.

Results: We assign the harmonin-homology-domain (HHD, also named the harmonin N-terminal domain, NTD) present in large proteins such as harmonin, whirlin, cerebral cavernous malformation 2, and regulator of telomere elongation 1 to the αα-hubs. The new member of the αα-hubs expands functionality to include scaffolding of supra-modular complexes mediating sensory perception, neurovascular integrity and telomere regulation, and reveal novel features of the αα-hubs. As a common trait, the αα-hubs bind intrinsically disordered ligands of similar properties integrating similar cellular cues, but without cross-talk.

Conclusion: The inclusion of the HHD in the αα-hubs has uncovered new features, exemplifying the utility of identifying groups of hub domains, whereby discoveries in one member may cross-fertilize discoveries in others. These features make the αα-hubs unique models for decomposing signal specificity and fidelity. Using these as models, together with other suitable hub domain, we may advance the functional understanding of hub proteins and their role in cellular communication and signaling, as well as the role of intrinsically disordered proteins in signaling networks. Video Abstract.

Keywords: HHD; Hub proteins; IDP; Interactome; Intrinsically disordered protein; NCBD; PAH; RST; Signaling; TAFH.

Fig. 1

Connecting the αα-hubs. a Hub proteins are involved in diverse functions such as transcription, post-translational modification and organization of cell structure. Hub proteins are shown in the center of protein–protein interaction networks where they organize relevant molecular components. The drawings are based on αα-hub protein functions such as transcriptional regulation (Sin3a) and cell structure organization (harmonin). b Domain structure of αα-hub proteins. Representative parent protein (not drawn to scale) for each of the founding αα-hubs PAH, RST, TAFH and NCBD, as well as the new member HHD. Experimentally-based interactome sizes obtained from the STRING database are shown for each αα-hub. Hp: small hairpin extension of the HHD-PDZ supramodule. c Superimposition of the αα-hairpin super-secondary structure motif. Representatives of each domain type of the αα-hubs (pdb codes 2CZY (PAH1), 2LD7 (PAH3), 5ECJ (TAFH), 2L14 (NCBD), 2KBQ (HHD), 5N9Q (RST)). The zoom illustrates the α_L-β₄ link motif found in the prototypical αα-hubs [1], where the highlighted hydrophobic β₃-anchor residue forms stabilizing interactions between the two hairpin helices. d Cartoon structures comparing αα-hubs. The PAH1 domain of Sin3a (purple) is compared to the HHDs of CCM2 (red), whirlin (dark orange) and harmonin (bright orange). Top row illustrates the two domains in their free form whereas the second row shows overlays of free PAH1 with whirlin HHD (left) and CCM2 HHD (right) (pdb codes 2RMR (PAH1), 6FDD (whirlin-HHD), 4FQN (CCM2-HHD)). The third row illustrates complexes of the two domains: PAH1 in complex with SAP25 and CCM2 HHD in complex with MEKK3 (pdb codes 2RMS and 4Y5O, respectively). The ligands are shown in grey. The bottom panel displays the harmonin PDZ-HHD supramodule (PDZ in blue) in complex with sans (grey). The short hairpin extension responsible for tethering the PDZ and HHD is shown in light blue. e Disorder profiles of HHD binding ligands cadherin-23 intracellular domain (ICD) and MEKK3. The disorder propensity ranging from 0 to 1 was predicted using IUPred2A (black) [32] and PONDR VSL2 (blue) [33], whereas MoRFs were predicted by MoRFpred (red) [34]. The regions responsible for binding to HHD based on available structures (pdb codes 4Y5O, 2LSR and 2KBR) are highlighted with orange background, whereas the regions binding as α-helix in the hydrophobic cleft are highlighted with white boxes