Bioinformatics-based Analyses and B/Th Cell Epitope Prediction of Mugwort Pollen Allergen Art v 1 Protein

Summary

Here, we present a protocol to perform bioinformatics correlation analysis to predict the physicochemical properties, secondary structure, and B and T helper cell epitopes of mugwort pollen main allergen Art v 1 protein to provide a theoretical basis for the subsequent development of artemisia pollen allergic disease vaccine and disease treatment.

Abstract

To analyze the sequence characteristics of mugwort pollen allergen Art v 1 protein and predict its B cell and Th (helper T cell) cell epitopes, the gene sequence and amino acid sequence of Art v 1 protein were obtained by referring to Genebank. ExPASy's Prot Param, TMHMM, DNAstar Protean, Swiss-Model, UCLA-DOE LAB SAVES v6.0, and IEDB were used to analyze and predict physicochemical properties, transmembrane region, secondary structure, tertiary structure, and B cell and Th cell epitopes of the protein.

The Art v 1 protein is composed of 132 amino acid residues, the relative molecular weight is 13404.26, the molecular formula is C₅₈₄H₉₀₃N₁₅₇O₁₈₁S₁₂, pI value is 7.49, the lipid solubility index is 41.59, and the hydrophilic index is -0.454, which is considered as hydrophilic protein. The instability index (ii) is 78.11, which is classified as an unstable protein. The N-terminus of the protein has an α-helical transmembrane region, which is located in the 5-27 amino acid residue sequence, and the 1-24 position is the signal peptide sequence. There are random coil, β-turn, α-helix, and β-sheet, and it also contains hydrophilic region, flexible region, and surface accessibility region structures.

The prediction results of tertiary structure are consistent with the analysis results of secondary structure. Five dominant B cell epitopes were predicted, which were Art v 1 71-87, Art v 1 33-49, Art v 1 104-120, Art v 1 95-111, and Art v 1 86-102. There were five Th cell dominant epitopes, which were Art v 1 2-16, Art v 1 3-17, Art v 1 4-18, Art v 1 5-19, and Art v 1 6-20. The Art v 1 protein is predicted to have good antigenicity due to the presence of B cell and Th cell epitopes.

Introduction

Mugwort, a genus of Artemisia in Compositae, is widely distributed in Inner Mongolia, Gansu, and other regions of China¹. Various allergic diseases induced by mugwort pollen are usually type I allergies caused by the repeated exposure of atopic individuals to pollen allergens and the generation of bioactive mediators, resulting in catarrhal inflammation of nasal mucosa, conjunctiva, and bronchus and even asthma attacks². The WHO/IUIS Allergen Nomenclatory Subcommittee³ has officially recognized seven mugwort allergens at present, namely, Art v 1-Art v 6 and Art AN 7. Art v 1 protein is one of the ....

Protocol

1. Physical and chemical properties of Art v 1 protein

1. Input AF493943.1 in the GeneBank (Table of Materials) to obtain the amino acid sequence of Art v 1 protein (Supplemental File 1-Supplemental Figure S1).
   NOTE: The Art v 1 protein contains 132 amino acids, which are coded by 624 bp of gene sequences. Its amino acid sequence (AAO24900.1) is MAKCSYVFCAVLLIFIVAIGEMEAAGSKLCEKTSKTYSG
   KCDNKKCDKKCIEWEKAQHGACHKREAGKESCFCYF
   DCS.......

Discussion

Artemisia is one of the most important outdoor allergens in China, and its pollen particles are small, with a diameter of 19-25 µm, which are easily dispersed by wind and produce large amounts of powder. In addition, the severity of allergic symptoms of patients is correlated with the pollen content in the air⁵. Art v 1 is regarded as the landmark allergen of mugwort pollen allergy, and more than 95% of patients with mugwort allergy are sensitive to Art v 1. In China, ~81% of patients with mu.......

Materials

Name	Company	Catalog Number	Comments
ABCpred	Indraprastha Institute of Information Technology, India		https://webs.iiitd.edu.in/raghava/abcpred/ABC_submission.html
DNAstar Protean software	DNASTAR, Inc.	Version 7.1
Expasy ProtParam Tool	SIB Swiss Institute of Bioinformatics		https://web.expasy.org/protparam/
GeneBank	National Center for Biotechnology Information		https://www.ncbi.nlm.nih.gov/nuccore/
IEDB Analysis Resource	National Institute of Allergy and Infectious Diseases		http://www.iedb.org/
SignaIP-5.0 Server	DTU Health Tech		https://services.healthtech.dtu.dk/services/SignalP-5.0/
Swiss-Model online software	BIOZENTRUM		https://swissmodel.expasy.org/interactive
TMHMM Server	DTU Health Tech	Version 2.0	https://services.healthtech.dtu.dk/services/TMHMM-2.0/
UCLA - DOE LAB SAVES	US Department of Energy Office of Science	Version 6.0	https://saves.mbi.ucla.edu/