Conformational Analyses of the AHD1-UBAN Region of TNIP1 Highlight Key Amino Acids for Interaction with Ubiquitin

Tumor necrosis factor ɑ (TNFɑ)-induced protein 3 (TNFAIP3)-interacting protein 1 (TNIP1) is genetically and functionally linked to limiting auto-immune and inflammatory responses. We have shown that TNIP1 (alias A20-binding inhibitor of NF-κB 1, ABIN1), functioning as a hub location to coordinate other proteins in repressing inflammatory signaling, aligns with biophysical traits indicative of its being an intrinsically disordered protein (IDP). IDPs move through a repertoire of three-dimensional structures rather than being in one set conformation. Here we employed bioinformatic analysis and biophysical interventions via amino acid mutations to assess and alter, respectively, conformational flexibility along a crucial region of TNIP1, encompassing the ABIN homology domain 1 and ubiquitin-binding domain in ABIN proteins and NEMO (AHD1-UBAN), by purposeful replacement of key residues. In vitro secondary structure measurements were mostly in line with, but not necessarily to the same degree as, expected results from in silico assessments. Notably, changes in single amino acids outside of the ubiquitin-binding region for gain-of-order effects had consequences along the length of the AHD1-UBAN propagating to that region. This is evidenced by differences in recognition of the partner protein polyubiquitin ≥ 28 residues away, depending on the mutation site, from the previously identified key binding site. These findings serve to demonstrate the role of conformational flexibility in protein partner recognition by TNIP1, thus identifying key amino acids likely to impact the molecular dynamics involved in TNIP1 repression of inflammatory signaling at large.