N-Glycosidase Rudaea cellulosilytica (PNGase Rc) Column for the Characterization of Glycoprotein Conformational Epitopes by Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS)

Abstract

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a sensitive technique used to study the conformational dynamics of proteins in solution. However, performing HDX-MS with N-linked glycoproteins is challenging. Analyzing glycoproteins through HDX-MS requires the use of N-glycoprotein deglycosylation enzyme (peptide: N-glycanase, abbreviated as PNGase) to deglycosylate glycoproteins. Traditional PNGases are inactive or have low activity under HDX-MS operating conditions. Here, we recommend the use of ultra-acidic N-glycopeptidase from PNGase Rc, which exhibits optimal enzymatic activity compared to other PNGases at pH 2.2. We covalently fixed PNGase Rc onto POROS resin for HDX-MS online deglycosylation. The results show that the immobilized PNGase Rc combined with pepsin column has good stability under various quenching conditions. Its online deglycosylation efficiency is better than other PNGases. Meanwhile, we used AlphaFold 2 and molecular dynamics (MD) to characterize the structure and stability of PNGase Rc and other PNGases, and demonstrated that PNGase Rc is the most stable.