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 main contributors to mugwort pollen allergies. It has a molecular weight of 24-28 kDa and can be recognized by 95% of individuals allergic to mugwort pollen4. It consists of an N-terminal beta-defensin-like domain that is connected to a C-terminal proline-rich tail. Defensins represent endogenous antimicrobial polypeptides that are expressed in several eukaryotes5.
Currently, allergen immunotherapy (AIT) is the only etiologic treatment that can change the natural course of allergic diseases in addition to avoiding exposure to allergens6. The increasing prevalence of allergic diseases over the recent decades underscores the importance of basic and clinical research on allergen molecules and their potential applications in allergy diagnosis and treatment. Many of the allergens used for AIT belong to recombinant proteins, whose physical, chemical, and immunological properties are suitable for the production of allergen vaccines with reduced allergenicity. Therefore, AIT is considered the primary means of effectively preventing and treating allergic diseases, as allergy vaccines are relatively easy to produce at a low cost7. However, vaccine development in the past depended exclusively on molecular biology and immunological experiments. In addition, epitome identification is essential for vaccine development, and the most reliable methods for identification of an epitope are X-ray crystallography and NMR techniques at present; however, they are time-consuming and expensive8. Hence, computational methods and tools, with the advantages of low cost and high speed, were employed to predict epitopes.
This paper describes a bioinformatics correlation analysis method for the prediction of the physicochemical properties, secondary structure, tertiary structure, and B/Th cell epitopes of mugwort pollen main allergen Art v 1 protein. This will provide a theoretical basis for the subsequent development of artemisia pollen allergic disease vaccine and disease treatment.
Protocol
Representative Results
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…
Offenlegungen
The authors have nothing to disclose.
Acknowledgements
This work was supported by the Natural Science Foundation of Ningxia (2022AAC03601 and 2023AAC02087) and the Research Foundation of Ningxia Medical University (XM2019052).
Materials
| 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/ |
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