Probing the pH Effects on Sugar Binding to a Polysaccharide Lyase

Polysaccharide lyases (PLs) are an important class of proteins that are excreted from bacteria to degrade sugars in the extracellular matrix of the host. The PL from S. maltophilia (Smlt1473) was found to have pH-specific degradation of three varying polysaccharides: alginate, celluronic acid, and hyaluronic acid (J. Biol. Chem. 2014, 289, 18022–18032). In this work, we aim to further understand the effect of pH on sugar binding and cleavage using molecular dynamics (MD) simulations and activity assay experiments. The structure of Smlt1437 was modeled with crystal structure of alginate lyase A1-III (PDB 1QAZ) from Sphingomonas Sp. Ionizable resides were adjusted based on their predicted pKa’s at pH of 5, 7, and 9 and simulated in solution with predicted docked structures of hyaluronic acid (HA) and poly-β-d-glucuronic acid (poly-GlcUA). These docked structures were simulated for 125 ns using all-atom MD. The simulations with monomers of HA and poly-GlcUA revealed the importance of loop1 of the protein to ...