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Network Modeling Analysis in Health Informatics and Bioinformatics : Volume 4

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Network Modeling Analysis in Health Informatics and Bioinformatics : Volume 1

In silico vaccine design against type 1 diabetes based on molecular modeling of coxsackievirus B4 epitopes

Content Provider	Springer Nature Link
Author	Esmaeili, Abolghasem Taherzadeh, Mahsa Ganjalikhany, Mohamad Reza
Copyright Year	2016
Abstract	An in silico study was conducted to identify antigens with potential possibility of being a vaccine against type 1 diabetes mellitus (T1DM). A molecular mimicry between protein 2C of coxsackievirus B4 and autoantigen glutamic acid decarboxylase 65 is a significant factor in the pathogenesis of T1DM. The aim of this study was to predict the protein 2C of coxsackievirus B4 epitopes and design a vaccine against T1DM. Several web servers were used to predict continuous B cell epitopes and 8 peptides (P1–P8) were selected. Then the 3D structure of P2C was built by structural modeling using Robetta and the structure was subjected to 10 ns molecular dynamics simulation by Amber to obtain an average structure in an explicit water system. Molecular mimicry theory was confirmed by local structural alignment of modeled structure protein 2C with glutamic acid decarboxylase 65 using Swiss pdb viewer. Then conformational B cell epitope web servers were used to identify discontinuous B cells epitopes. PDBsum was used for the analysis of the protein 2C secondary structure. Finally, T cells epitopes have been predicted by the immune epitope database analysis resource (IEDB). In silico analysis of the sequence and structure retrieved by mentioned methods and web servers, revealed that two out of 8 peptides (P2 and P7 epitopes) are the best choices for the vaccine design. These results suggest that epitopes and structural features of the protein 2C of coxsackievirus B4 can be predicted and this information could be used to make novel vaccines for control of T1DM.
Starting Page	1
Ending Page	7
Page Count	7
File Format	PDF
ISSN	21926662
Journal	Network Modeling Analysis in Health Informatics and Bioinformatics
Volume Number	5
Issue Number	1
e-ISSN	21926670
Language	English
Publisher	Springer Vienna
Publisher Date	2016-01-29
Publisher Place	Vienna
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	B cell epitopes Computational Biology/Bioinformatics T cell epitopes Epitope prediction Coxsackievirus B4 Health Informatics Diabetes Molecular dynamics simulation Bioinformatics Applications of Graph Theory and Complex Networks
Content Type	Text
Resource Type	Article
Subject	Urology

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In silico vaccine design against type 1 diabetes based on molecular modeling of coxsackievirus B4 epitopes

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