In silico analysis of peroxidase from Luffa acutangula

Abstract

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.

Keywords: Enzyme functions; Gene ontology; Homology modelling; Molecular docking; Peroxidase; Phylogenesis.

Fig. 1

3 D structure of horseradish peroxidase (Berglund et al. 2002) and active site of heme b

Fig. 2

(a) Amino acid sequence of the secondary structure of LP. (Hh) represents alpha helix, (Ee) extended strand, (Tt) beta turn, and (Cc) random coil. (b) graphical representation of the amino acid sequence. The red line represents the extended strand, the blue line is the alpha helix, the green line is the beta turn, and the violet line is the random coil

Fig. 3

Quality estimate: (A) QMEAN Z-scores, (B) Comparison with a non-redundant set of PDB structures, (C) Local quality estimation of luffa peroxidase, and (D) Residual quality. The figures were generated on the Swiss server

Fig. 4

Predicted structure of luffa peroxidase: (A) Cartoon, and (B) Molecular Surface, and (C) Ramachandran plot of the predicted protein structure obtained from MolProbity server

Fig. 5

Neighbor-joining livelihood phylogenetic tree of plant peroxidases. The amino acid sequences were aligned, and the tree was constructed in MEGA 11 tool using the bootstrap method of 1000 replicates

Fig. 6

Ancestor chart for GO:0004601. The black lines represent 'is a', and the blue lines represent 'part of ' (http://amigo.geneontology.org/amigo/term/GO:0004601)

Fig. 7

Ancestor chart for GO:0020037. The black lines represent 'is a', and the blue lines represent 'part of ' (http://amigo.geneontology.org/amigo/term/GO:0020037)

Fig. 8

Ancestor chart for GO:0005576. The black lines represent 'is a', and the blue lines represent 'part of ' (http://amigo.geneontology.org/amigo/term/GO:0005576)

Fig. 9

General catalytic mechanism of peroxidases in the presence of electron mediator H₂O₂ (Flohé et al. 2022)

Fig. 10

Homology model of (A) heme binding and (B) Ca²⁺ binding sites deduced by COFACTOR on I-TASSER server