Monday, April 30, 2012
Napoleon Ballroom C-D, 3rd fl (Sheraton New Orleans)
Processive enzymes conduct much of the cellulose and chitin turnover in the biosphere, and are thus important contributors to the global carbon and nitrogen cycles and the major components in industrial cocktails in biomass conversion. Processive enzymes are typically multi-modular with a carbohydrate-binding module (CBM) connected via a flexible linker to a large catalytic domain (CD) with a tunnel or cleft in which a single carbohydrate chain can be threaded and hydrolyzed to a soluble product. Processive enzymes are believed to acquire single carbohydrate chains from polymer crystals and cleave chains without detaching for multiple monomeric units. The nature of this processive action is still not understood at the molecular level. To that end, here we investigate two well-characterized processive chitinases from the bacterium Serratia marcescens, namely the Glycoside Hydrolase (GH) Family 18 ChiA and ChiB enzymes, which act from the reducing end and non-reducing end of chitin, respectively. Both enzymes contain Family 2 CBMs connected by a short linker to GH18 CDs. Here we present the results from long molecular dynamics (MD) simulations of the whole enzymes, the CDs alone, and the CBMs alone in solution and catalytically engaged on the hydrophobic face of a chitin crystal to understand the interaction of the sub-domains and the role of the linkers. In addition, we present the results of MD simulations and thermodynamic integration to investigate the role of the CD-ligand interactions, which are known from previous mutational biochemistry studies to be important for processivity.