In silico analysis of cross reactivity among phospholipases from Hymenoptera species

Abstract

Background: Phospholipases are enzymes with the capacity to hydrolyze membrane lipids and have been characterized in several allergenic sources, such as hymenoptera species. However, cross-reactivity among phospholipases allergens are little understood. The objective of this study was to determine potential antigenic regions involved in cross-reactivity among allergens of phospholipases using an in silico approach. Methods: In total, 18 amino acids sequences belonging to phospholipase family derived from species of the order hymenoptera were retrieved from the UniProt database to perform phylogenetic analysis to determine the closest molecular relationship. Multialignment was done to identify conserved regions and matched with antigenic regions predicted by ElliPro server. 3D models were obtained from modeling by homology and were used to locate cross-reactive antigenic regions. Results: Phylogenetic analysis showed that the 18 phospholipases split into four monophyletic clades (named here as A, B, C and D). Phospholipases from A clade shared an amino acid sequences’ identity of 79%. Antigenic patches predicted by Ellipro were located in highly conserved regions, suggesting that they could be involved in cross-reactivity in this group (Ves v 1, Ves a 1 and Ves m 1). Conclusions: At this point, we advanced to the characterization of potential antigenic sites involved in cross-reactivity among phospholipases. Inhibition assays are needed to confirm our finding.

Potential honey bee (Apis mellifera) allergens associated with IgE-mediated allergy- An In-silico study

“…Despite the several reported successful prediction story of allergenic proteins, there is some limitation associated (selection of scoring function, issue in considering the flexibility of ligand and receptor molecules, solvation effect) with computational docking and simulations algorithm and it is strongly recommended to validate the prediction using in vitro and/or in vivo assays (31). To date, no In-silico studies exploring IgEmediated honey bee allergies have been reported so far in the world and the Ha'il region of Saudi Arabia (32). There have already been some studies related to the molecular genetics of honey bees (33)(34)(35).…”

In silico analysis of molecular mimicry between human aquaporin 3, Aspergillus fumigatus aquaporin and aquaporins from allergic sources

“…When carrying out the alignment, it was considered that the sequences were different and came from different sources; therefore, the alignment parameters were set to utilize the BLOSUM62 matrix, which primarily assesses evolutionary divergence, along with adjustments to the conditional scoring matrix. 15,16 Phylogenetic analysis To construct the phylogenetic tree, we conducted a study using "Molecular Evolutionary Genetic Analysis" (MEGA) version 11 program. We employed the neighbor-joining (R) reconstruction method, supported by 100 bootstrap repetitions, to ensure the reliability and robustness of the analysis.…”

“…Branch length summation (SBL) was presented as a measure of overall comparison and homologies, providing insights into the number of nodes, their positions, and the formation of the evolutionarily closest sequence "clusters. 15,17 3D models of proteins Aquaporin models were acquired from the Protein Data Bank and AlphaFold (Homo sapiens, Felis catus, Equus caballus, Bos taurus, Mus musculus, Malassezia sympodialis, Saccharomyces cerevisiae, Penicillium chrysogenum, Escherichia coli). For A. fumigatus and Cannis lupus familiaris aquaporin 3D structures were modeled by homology using the Swiss Model server (https://swissmodel.expasy.org/), and these models were refined in ModRefiner.…”

“…The potential epitopes were selected under the criteria of a score ≥ 7, as this value evaluates how exposed the residue is and the binding capacity of the epitope with the paratope. 15,17…”