Fig. 3

Structure–function prediction of SUOX protein and its mutants

(A) RMSD plot for the backbone of SUOX wild-type (in violet), p.A69P (in pink), and p.Y400* (in grey) for 30 ns of simulation. Conformation of wild-type protein equilibrated at a level of 6.0 Å after 5 ns and the two mutants equilibrated after 10 ns at higher RMSD. The larger RMSD and later equilibration of the mutants indicate a more unstable structure than that of the wild-type proteins

(A’) RMSF graphs for the backbone of SUOX wild-type (in violet), p.A69P (in pink), and p.Y400* (in grey) during the simulation. Both mutants manifested higher levels of flexibility, especially at the N-terminal, than the wild-type. The p.A69P mutant displayed significantly higher RMSF around the mutated residue, indicating more movement than in the wild-type (arrowhead). Plot of p.Y400* terminated at residue 400, consistent with its truncation effects

(A’’) RoG plot for the backbone of SUOX wild-type (in violet), p.A69P (in pink), and p.Y400* (in grey) over 30 ns of simulation. The higher RoG indicated more loose conformation in p.A69P, while the p.Y400* is more compact, probably as a result of the reduced size

(B-B’’’) Conformation alignment (B) of the wild-type (B’, in violet), p.A69P (B’’, in pink), and p.Y400* (B’’’, in grey) after molecular dynamics simulation. More coil and fewer helix structures (arrows) were found in the two mutants

(C-C’’) Molecular docking of the wild-type (C, in violet), p.A69P (C’, in pink), and p.Y400* (C’’, in grey) with sulfite (SO₃²⁻ ) after molecular dynamics simulation. Wild-type SUOX binds sulfite with Arg366 and Arg217 through a hydrogen bond and salt bridge. p.A69P interacts with additional Phe215. The interaction sites changed to Arg 192, Ser190, Val142, and Phe215 in p.Y400*

RMSD, root mean square deviation; RMSF, residue-based root mean square deviation; RoG, radius of gyration