Understanding the Function of a Pro-Angiogenic Polypeptide hFGF-1 with a Cancer Inhibitor Imatinib

Abstract

Polysaccharide lyases (PLs) are enzymes that our commonly used by microorganisms to degrade polyuronides. These enzymes are produced by bacteria to aid in reducing the high molecular weight of the host's extracellular matrix to enhance its virulence. PLs can also be used to degrade polysaccharides as a source of carbon for the pathogen. Our focus is on the alginate lyase of Stenotrophomonas maltophilia (Smlt1473), which has been shown recently to be active against alginate, hyaluronic acid (HA) and poly-D-glucuronic acid at varying pH values (J. Biol. Chem. 289: 312 ( 2014)). The active site appears to have regions specific to binding these three sugars and an active catalytic site. Our objective is to understand how pH influences binding of a HA and if this involves structural changes in the protein. Docking of HA to a homology-based structure of Smlt1473 (based on the crystal structure of alginate lyase A1-III) was used to provide initial starting conformations for our molecular dynamics (MD) simulations. ProPKa was used to determine the ionization state of residues at our three simulated pHs (5, 7 and 9). MD simulations at neutral pH confirm the binding residues seen in experiment. However, at the acidic and basic condtions, the homology-based model of the binding pocket opens. At ph¼5, there is an increase in the exposure of HA-specific residues in the vicinity of W171 suggesting this exposure is the cause for Smlt1473 increased activity (J. Biol. Chem. 289: 312 ( 2014)). Therefore, Smlt1473's structure appears to strongly depend on pH and is used to control its activity toward different sugars.