Amino acid sequence of anionic peroxidase from the windmill palm tree Trachycarpus fortunei

In silico analysis of peroxidase from Luffa acutangula

Peroxidases are oxidoreductase enzymes that widely gained attention as biocatalysts for their robust catalytic activity, specificity, and regioselective functionality for phenolic compounds. The study of molecular aspects of peroxidases is as crucial as that of the physicochemical aspects. A bioinformatics approach is utilized in this study to investigate the structural aspects and functions of luffa peroxidase (LPrx) from Luffa acutangula. The evolutionary relationship of LPrx with other class III peroxidases was studied by constructing a neighbour-joining phylogenetic tree. An analysis of the phylogenetic tree revealed that plant peroxidases share a common ancestor. The gene ontology term showed that LPrx had a molecular functionality of the oxidation-reduction process, heme binding and peroxidase-like activity, and the biological function of hydrogen peroxide scavenging activity. The enzyme-ligand interactions were studied from a catalytic point of view using the molecular docking technique. The molecular docking was carried out with LPrx as a receptor and guaiacol, m-cresol, p-cresol, catechol, quinol, pyrogallol, 2,4-dimethoxyphenol, gallic acid, aniline, and o-phenylenediamine as ligands. The results presented in the current communication will have a significant implication in proteomics, biochemistry, biotechnology, and the potential applications of peroxidases in the biotransformations of organic compounds.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03432-8.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014

This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.

Effect of N-Linked Glycosylation of Recombinant Windmill Palm Tree Peroxidase on Its Activity and Stability

Plant secretory peroxidases are valuable commercial enzymes. The windmill palm tree Trachycarpus fortunei produces one of the most stable and fastest peroxidases (WPTP) characterized to date; however, an economical source is needed. Pichia pastoris has been used as an expression system for WPTP and other peroxidases. However, yeast and plants synthesize different types of N-linked glycan structures and may differ the level of glycosylation at each site. Such non-native glycosylation can have unwanted consequences. Glycosylation site N256 was under-glycosylated in the wild-type (1.5%) compared to the native enzyme (55%); therefore, we mutated WPTP to promote glycosylation at this site (WPTP E254G). Glycosylation increased four-fold, as measured by liquid chromatography-tandem mass spectrometry. The mutation did not change the substrate specificity and optimal pH- and thermo-stability ranges, but it increased the catalytic activity 2-3-fold. In comparison with wild-type WPTP, WPTP E254G showed a shift of the most stable pH from 7 to 9, making it suitable for applications under alkaline conditions.

Characterization of Plant Glycoproteins: Analysis of Plant Glycopeptide Mass Spectrometry Data with plantGlycoMS, a Package in the R Statistical Computing Environment

plantGlycoMS is a set of tools, implemented in R, which is used to assess and validate glycopeptide spectrum matches (gPSMs). Validity of gPSMs is based on characteristic fragmentation patterns of glycopeptides (gPSMvalidator), adherence of the glycan moiety to the known N-glycan biosynthesis pathway in plants (pGlycoFilter), and elution of the glycopeptide within the observed retention time window of other glycopeptides sharing the same peptide backbone (rt.Restrict). plantGlycoMS also contains a tool for relative quantitation of glycoforms based on selected ion chromatograms of glycopeptide ion precursors in the mass spectrometry level 1 data (glycoRQ). This protocol walks the user through this workflow with example mass spectrometry data obtained for a plant glycoprotein.

Expression and Characterization of Windmill Palm Tree (Trachycarpus fortunei) Peroxidase by Pichia pastoris

Currently, commercial plant peroxidases are all native and are isolated from plants such as horseradish and soybean. No recombinant plant peroxidase products have been available on the commercial market. The gene encoding peroxidase was cloned from windmill palm tree leaves. The codon-optimized gene was transformed into Pichia pastoris for expression. The recombinant windmill palm tree peroxidase (rWPTP) expressed by P. pastoris showed high stability under pH 2-10 and temperatures up to 70 °C to many metallic salts and organic solvents. The substrate specificity of WPTP was determined, and among the substrates tested, 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) was most suitable for WPTP. The Michaelis constants with the substrates H₂O₂ and ABTS were 4.6 × 10^-4 and 1.6 × 10^-4 M, respectively. The rWPTP expressed in P. pastoris may be a suitable enzyme for the biosynthesis of polymers because of its high stability and activity under acidic conditions.

Rapid Sample Preparation Methodology for Plant N-Glycan Analysis Using Acid-Stable PNGase H+

The quantification of potentially allergenic carbohydrate motifs of plant and insect glycoproteins is increasingly important in biotechnological and agricultural applications as a result of the use of insect cell-based expression systems and transgenic plants. The need to analyze N-glycan moieties in a highly parallel manner inspired us to develop a quick N-glycan analysis method based on a recently discovered bacterial protein N-glycanase (PNGase H(+)). In contrast to the traditionally used PNGase A, which is isolated from almond seeds and only releases N-glycans from proteolytically derived glycopeptides, the herein implemented PNGase H(+) allows for the release of N-glycans directly from the glycoprotein samples. Because PNGase H(+) is highly active under acidic conditions, the consecutive fluorescence labeling step using 2-aminobenzamide (2AB) can be directly performed in the same mixture used for the enzymatic deglycosylation step. All sample handling and incubation steps can be performed in less than 4 h and are compatible with microwell-plate sampling, without the need for tedious centrifugation, precipitation, or sample-transfer steps. The versatility of this methodology was evaluated by analyzing glycoproteins derived from various plant sources using ultra-performance liquid chromatography (UPLC) analysis and further demonstrated through the activity analysis of four PNGase H(+) mutant variants.