OAF: a new member of the BRICHOS family

Abstract

Summary: The 10 known BRICHOS domain-containing proteins in humans have been linked to an unusually long list of pathologies, including cancer, obesity and two amyloid-like diseases. BRICHOS domains themselves have been described as intramolecular chaperones that act to prevent amyloid-like aggregation of their proteins' mature polypeptides. Using structural comparison of coevolution-based AlphaFold models and sequence conservation, we identified the Out at First (OAF) protein as a new member of the BRICHOS family in humans. OAF is an experimentally uncharacterized protein that has been proposed as a candidate biomarker for clinical management of coronavirus disease 2019 infections. Our analysis revealed how structural comparison of AlphaFold models can discover remote homology relationships and lead to a better understanding of BRICHOS domain molecular mechanism.

Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Fig. 1.

Structural and sequence analysis of BRICHOS. (A) Structural comparison of proSP-C and BRI2. Top: Secondary structure topology diagrams of proSP-C and BRI2. We adopt the nomenclature of secondary structural elements initially defined by Willander et al. (2012) for the proSP-C BRICHOS domain. Three additional β-strands can be found in the BRI2 AlphaFold model (labeled in pink: β-strands 1', 2' and 4'). Bottom: proSP-C and BRI2 BRICHOS domains AlphaFold models are shown, corresponding to positions 88–197 and 83–234, respectively. Cartoons of proSP-C and BRI2 were coloured in blue and light violet, respectively. (B) Z-Scores arising from Dali structural comparison searches against all human AlphaFold models, using as query a core BRICHOS domain AlphaFold structure for each human BRICHOS subfamily: ITM2B_HUMAN, residues 83–234 for ITMB/BRI2 (label BRI); PSPC_HUMAN residues 88–197 for SP-C; GKN2_HUMAN residues 20–151 for Gastrokine-2 (label GKN); BRID5_HUMAN residues 62–195 for BRICD5 (label BC5); TNMD_HUMAN residues 59–191 for Tenomodulin/Chondromodulin (label TNM); and OAF_HUMAN residues 27–172 for OAF. (C) The significance of profile-to-profile matches was evaluated in terms of an E-value, which estimates the number of observations of better sequence matches expected in a database by chance alone (Zimmermann et al., 2018). The E-values correspond to HHpred searches against all Pfam profile database (including profiles independently generated for each human BRICHOS subfamily), using profiles of each human BRICHOS subfamily as query. For example, in an HHpred profile versus profile comparison search, the OAF profile matched the GKN (Gastrokine subfamily), BRI (ITM subfamily) and SPC (proSP-C subfamily) profiles with E-values 1.6 × 10⁻⁴, 0.008 and 0.015, respectively

Fig. 2.

Structural superposition of BRI2 and OAF. Structural similarity of BRI2 and OAF AlphaFold model is shown. Top: BRI2 and OAF BRICHOS domains, corresponding to positions 84–233 and 29–172, respectively. Cartoons of BRI2 and OAF were coloured in violet and red, respectively. The BRI2 and OAF BRICHOS domains’ structural superposition (top row and middle column) was generated using Dali (Holm, 2022); other models in this figure are shown in this orientation. Middle: BRICHOS domains including their respective mature polypeptides. BRI2 and OAF mature polypeptide cartoons were coloured in a violet and dark red, respectively. Bottom: BRI2 and OAF mature polypeptides, corresponding to positions 244–266 and 204–273, respectively. Disulphide bridges in the mature polypeptides (one in BRI2 and four in OAF) are shown in yellow sticks. AlphaFold structural models were rendered using Pymol (http://www.pymol.org)