Fig. 4: Comparison of ALX4 and PRD S50Q structures reveals asymmetric N-terminal ARM interactions in ALX4 but not PRD.

A, B Protein-protein interactions of the ALX4 and PRD S50Q structure with the canonical HD numbering for comparison. Van der waals interactions are shown in the bar graphs and are measured by the residue’s accessible surface area buried by the other chain. Polar bond contacts are shown as dashed lines between contacting residues with hydrogen bonds in black and salt bridges in red. A, C In Chain A, K -1 forms bonds with T23 and Y25, K1 contacts V28, and R3 contacts E42. R2 inserts into the minor groove. B, D This interface is quite similar to the PRD S50Q structure as Q1 interfaces with I28 and Y29 in the turn between helix 1 and 2, and R3 interfaces with E32 and E42 in helix 2 and 3. A, E K −1, K1 and R3 of Chain B have limited involvement in the protein-protein interface as R3 inserts into the minor groove. Instead, R2 contacts the main chains of Y25 and V28 in the turn between helix 1 and 2, and N4 interfaces with E32 in the second helix. B, F This interface is not consistent with the PRD structure as Q1 and R3 are again the primary facilitators of the protein-protein interactions between the N-terminal ARM and the turn between helix 1 and 2 as well as the beginning of helix 3. Created in BioRender. Cain, B. (2025) https://BioRender.com/s80m002. Source Data are provided on Figshare⁶⁹.