Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining ?-l-Arabinofuranosidases.

ABSTRACT: Identifying and characterizing the enzymes responsible for an observed activity within a complex eukaryotic catabolic system remains one of the most significant challenges in the study of biomass-degrading systems. The debranching of both complex hemicellulosic and pectinaceous polysaccharides requires the production of ?-l-arabinofuranosidases among a wide variety of coexpressed carbohydrate-active enzymes. To selectively detect and identify ?-l-arabinofuranosidases produced by fungi grown on complex biomass, potential covalent inhibitors and probes which mimic ?-l-arabinofuranosides were sought. The conformational free energy landscapes of free ?-l-arabinofuranose and several rationally designed covalent ?-l-arabinofuranosidase inhibitors were analyzed. A synthetic route to these inhibitors was subsequently developed based on a key Wittig-Still rearrangement. Through a combination of kinetic measurements, intact mass spectrometry, and structural experiments, the designed inhibitors were shown to efficiently label the catalytic nucleophiles of retaining GH51 and GH54 ?-l-arabinofuranosidases. Activity-based probes elaborated from an inhibitor with an aziridine warhead were applied to the identification and characterization of ?-l-arabinofuranosidases within the secretome of A. niger grown on arabinan. This method was extended to the detection and identification of ?-l-arabinofuranosidases produced by eight biomass-degrading basidiomycete fungi grown on complex biomass. The broad applicability of the cyclophellitol-derived activity-based probes and inhibitors presented here make them a valuable new tool in the characterization of complex eukaryotic carbohydrate-degrading systems and in the high-throughput discovery of ?-l-arabinofuranosidases.

SUBMITTER: McGregor NGS 

PROVIDER: S-EPMC7068720 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature