Results

Part 1: AlphaFold2 predicts the first third of scospondin structure with high confidence

AlphaFold2 was used to predict three approximately equal segments of the Danio rerio scospondin protein (Uniprot: B3LF39). Out of the three folded segments, the first segment (M-1 to F-1664) folded with the highest confidence. This is reflected by an average pLDDT score of 77.5, while the second (T-1665 to D-3320) and third (W-3321 to G-4990) segments folded with lower average scores of 60.9 and 66.7, respectively.

Within the first segment, the von-Willebrand factor type D (vWF, orange), cysteine-8 (C8, blue), and trypsin-inhibitor-like (TIL, green) domains formed a repeating modular structure that folded with high confidence and comprised the core of the structure. The vWF domains were predicted to form beta-pleated sheets, while the C8 domains formed alpha-helices. The LDL-receptor-type-a domains were folded with lower confidence and tended to decorate the surface of the structure. Within the middle segment, only the coagulation factor domain (S-2060 to G-2025) folded with high confidence. AlphaFold2 predicted this domain to fold into a series of beta-pleated sheets. The remaining domains were primarily thrombospondin-type-1 repeat (TSR) domains that folded with low confidence. The last segment contained one region that folded with high confidence (W-4461 to C-4570). This region included a TSR (pink) and a TIL (green) domain. The remaining domains were primarily TSR domains that folded with low confidence.

A closer look at the three vwF-C8-TIL modules.

AlphaFold2 predictions of last two segments of Scospondin fold with lower confidence