Bioinformatic prediction of epitopes in the Emy162 antigen of Echinococcus multilocularis

Lǐ, Yànhuá; Liu, Xianfei; Zhu, Yuejie; Zhou, Xinping; ChunBao, Cao; Hu, Xiaoan; Ma, Hongwei; Wen, Hao; Ma, Xiumin; Ding, Jianbing

doi:10.3892/etm.2013.1142

Cited by 31 publications

(20 citation statements)

References 26 publications

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“…Furthermore, plant allergens exhibited more random coils in secondary structure analysis by the GOR IV server. Since the random coils in a protein structure is mainly located in the surface domains, these random coiled parts have more likelihood ratio to include B-cell epitopes [43, 44]. This matter is also confirmed through our epitope prediction results, in which the numbers of plant B-cell epitopes were significantly more than animal ones.…”

Section: Discussionsupporting

confidence: 78%

A Comparative Analysis of Allergen Proteins between Plants and Animals Using Several Computational Tools and Chou’s PseAAC Concept

Behbahani¹,

Rabiei²,

Mohabatkar³

2020

Int Arch Allergy Immunol

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Background: A large number of allergens are derived from plant and animal proteins. A major challenge for researchers is to study the possible allergenic properties of proteins. The aim of this study was in silico analysis and comparison of several physiochemical and structural features of plant- and animal-derived allergen proteins, as well as classifying these proteins based on Chou’s pseudo-amino acid composition (PseAAC) concept combined with bioinformatics algorithms. Methods: The physiochemical properties and secondary structure of plant and animal allergens were studied. The classification of the sequences was done using the PseAAC concept incorporated with the deep learning algorithm. Conserved motifs of plant and animal proteins were discovered using the MEME tool. B-cell and T-cell epitopes of the proteins were predicted in conserved motifs. Allergenicity and amino acid composition of epitopes were also analyzed via bioinformatics servers. Results: In comparison of physiochemical features of animal and plant allergens, extinction coefficient was different significantly. Secondary structure prediction showed more random coiled structure in plant allergen proteins compared with animal proteins. Classification of proteins based on PseAAC achieved 88.24% accuracy. The amino acid composition study of predicted B- and T-cell epitopes revealed more aliphatic index in plant-derived epitopes. Conclusions: The results indicated that bioinformatics-based studies could be useful in comparing plant and animal allergens.

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Section: Discussionsupporting

confidence: 78%

A Comparative Analysis of Allergen Proteins between Plants and Animals Using Several Computational Tools and Chou’s PseAAC Concept

Behbahani¹,

Rabiei²,

Mohabatkar³

2020

Int Arch Allergy Immunol

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“…The α-helices and extended strands accounted for 84.82 % and 6.60 % in EgPmy, indicating a good stability of the protein. On the contrary, the random coils and β-turns often appear on the protein surface and have the potential to form epitopes (Li et al, 2013). The proportions of the random coils and β-turns were 5.56 % and 3.01 % in EgPmy, respectively.…”

Section: Discussionmentioning

confidence: 98%

“…These regions are likely to form epitopes. A key process of epi t ope vaccine preparation is to obtain useful epitopes (Li et al, 2013). Epitopes can be divided into B-and T-cell epitopes.…”

Section: Discussionmentioning

confidence: 99%

In silicocharacterization ofEchinococcus granulosusparamyosin nucleotide sequence for the development of epitope vaccine against cystic echinococcosis

Chen

Hao

et al. 2017

Helminthologia

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SummaryThe paramyosin (Pmy) protein has been presented as a potential vaccine candidate against Schistosoma spp. However, it remains elusive whether it works in controlling cystic echinococcosis (CE), which is caused by the larval stages of Echinococcus granulosus (E. granulosus). This study investigated the characteristics of E. granulosus Pmy (EgPmy) using in silico analysis and evaluated its potential as an epitope vaccine. The secondary structure was predicted by SOPMA software and linear B-cell epitopes were screened by the Kolaskar and Tongaonkar's method on IEBD while conformational B-cell epitopes were predicted by the Ellipro. Additionally, the epitopes of cytotoxic T lymphocyte (CTL) were analyzed by the NetCTL-1.2 server. The results showed that α-helices, extended strands, random coils and β-turns accounted for 84.82 %, 6.60 %, 5.56 % and 3.01 % in EgPmy's secondary structure, respectively. A total of 29 linear B-cell epitopes and 6 conformational epitopes were identifi ed together with 25 CTL epitopes. The CTL epitope 709 KLEEAEAFA 717 showed a high potential to elicit CTL response. These results suggested that EgPmy has a strong immunogenicity, which could serve as a reference for the development of EgPmy-based epitope vaccine against CE.

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“…Based on the Gamier‐Robson and Chou‐Fasman methods, a prediction on the ChIFN‐γ structure was obtained (Li et al ). The hydrophobicity of the protein was analyzed by Kyte‐Doolittle method (Kastritis et al ).…”

Section: Methodsmentioning

confidence: 99%

Prokaryotic expression of chicken interferon‐γ fusion protein and its effect on expression of poultry heat shock protein 70 under heat stress

Sun

Chen

et al. 2016

Animal Science Journal

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Interferons have attracted considerable attention due to their vital roles in the host immune response and low induction of antibiotic resistance. In this study, total RNA was extracted from spleen cells of chicken embryos inoculated with Newcastle disease vaccine, and the full-length chicken interferon-γ (ChIFN-γ) gene was amplified by RT-PCR. The full complementary DNA sequence of the ChIFN-γ gene was 495 bp long and was cloned into the prokaryotic expression vector pProEX™HT . The plasmid was transformed into Escherichia coli DH5α and the expression of ChIFN-γ was induced by isopropyl β-D-1-thiogalactopyranoside. Sodium dodecyl sulfate - polyacrylamide gel electrophoresis and Western blot results showed the expressed fusion protein had a molecular weight of approximately 18 kDa and was recognized by an anti-His mAb. Moreover, ChIFN-γ was found to demonstrate anti-viral activity in vitro. To test the in vivo function of ChIFN-γ in broilers under heat stress, a total of 100 broilers were randomly assigned to either a control group or a treated group, in which they were hypodermically injected with recombinant ChIFN-γ. Results demonstrated ChIFN-γ affects the messenger RNA expression levels of heat shock protein 70 (HSP70) in the heart and lung tissues, and decreases the concentration of HSP70 in serum. Therefore, we conclude recombinant ChIFN-γ can reduce heat stress to some extent in vivo.

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Bioinformatic prediction of epitopes in the Emy162 antigen of Echinococcus multilocularis

Cited by 31 publications

References 26 publications

A Comparative Analysis of Allergen Proteins between Plants and Animals Using Several Computational Tools and Chou’s PseAAC Concept

A Comparative Analysis of Allergen Proteins between Plants and Animals Using Several Computational Tools and Chou’s PseAAC Concept

In silicocharacterization ofEchinococcus granulosusparamyosin nucleotide sequence for the development of epitope vaccine against cystic echinococcosis

Prokaryotic expression of chicken interferon‐γ fusion protein and its effect on expression of poultry heat shock protein 70 under heat stress

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