Effect of Mutations on Smlt1473 Binding to Various Substrates Using Molecular Dynamics Simulations

Smlt1473 is a polysaccharide lyase from Stenotrophomonas maltophilia whose crystal structure was solved recently using X-ray crystallography. There was an effort to study the effect of mutations on the activity of Smlt1473 binding to various substrates like hyaluronic acid(HA), mannuronic acid(ManA), and alginate. In this study, we use molecular docking and molecular dynamics simulations to investigate the effect of binding of various substrates (HA and ManA) to Smlt1473 and two of its mutants H221F and R312L. We further studied the stability in the binding of Smlt1473 to its various substrates as well as the role of fluctuations. Machine-Learning based clustering algorithms were used to group the entire simulation trajectory into various stable states. The molecular interactions Smlt1473 to the substrates were calculated and the importance of specific residues were tested with observed activity assays due to residue mutations. Overall, we find that the R218 plays an important role in substrate binding and thus impacting the activity due to the H221F mutant and R/L312 itself plays an important role in the R312 mutation. In addition, we have also found three more residues K56, R107, and R164 important for substrate binding which we further proceed to confirm using wet lab mutagenesis studies.