scholarly journals Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study

2021 ◽  
Vol 31 (2) ◽  
Author(s):  
Hadi Sedigh Ebrahim-Saraie ◽  
Behzad Dehghani ◽  
Ali Mojtahedi ◽  
Mohammad Shenagari ◽  
Meysam Hasannejad-Bibalan
Keyword(s):  
B Cell ◽  
In Silico ◽  
Disulfide Bonds ◽  
Deep Understanding ◽  
Structural Features ◽  
Spike Protein ◽  
Tertiary Structures ◽  
In Silico Study ◽  
High Prevalence

BACKGROUND፡ Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the global outbreak of coronavirus disease 2019 (Covid-19), which has been considered as a pandemic by WHO. SARS-CoV-2 encodes four major structural proteins, among which spike protein has always been a main target for new vaccine studies. This in silico study aimed to investigate some physicochemical, functional, immunological, and structural features of spike protein using several bioinformatics tools.METHOD: We retrieved all SARS-CoV-2 spike protein sequences from different countries registered in NCBI GenBank. CLC Sequence Viewer was employed to translate and align the sequences, and several programs were utilized to predict B-cell epitopes. Modification sites such as phosphorylation, glycosylation, and disulfide bonds were defined. Secondary and tertiary structures of all sequences were further computed.RESULTS: Some mutations were determined, where only one (D614G) had a high prevalence. The mutations did not impact the B-cell and physicochemical properties of the spike protein. Seven disulfide bonds were specified and also predicted in several N-link glycosylation and phosphorylation sites. The results also indicated that spike protein is a non-allergen.CONCLUSION: In summary, our findings provided a deep understanding of spike protein, which can be valuable for future studies on SARS CoV-2 infections and design of new vaccines.

Simultaneous characterization of nine isolated flavonoids in Iranian Dracocephalum species and in silico study of their inhibitory properties against MTH1 enzyme

2022 ◽  
Vol 146 ◽  
pp. 254-261
Author(s):  
Shahrbanou Ashrafian ◽  
Mahdi Moridi Farimani ◽  
Ali Sonboli ◽  
Hossein Ashrafian ◽  
Maryam Kabiri ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Study

Characterization of Tannase Protein Sequences of Bacteria and Fungi: An In Silico Study

2012 ◽  
Vol 31 (4) ◽  
pp. 306-327 ◽  
Author(s):  
Amrita Banerjee ◽  
Arijit Jana ◽  
Bikash R. Pati ◽  
Keshab C. Mondal ◽  
Pradeep K. Das Mohapatra
Keyword(s):  
In Silico ◽  
Protein Sequences ◽  
In Silico Study ◽  
Bacteria And Fungi

scholarly journals Immuno-informatics Design of a Multimeric Epitope Peptide Based Vaccine Targeting SARS-CoV-2 Spike Glycoprotein

2020 ◽  
Author(s):  
Onyeka S. Chukwudozie ◽  
Clive M. Gray ◽  
Tawakalt A. Fagbayi ◽  
Rebecca C. Chukwuanukwu ◽  
Victor O. Oyebanji ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Peptide Vaccine ◽  
Spike Protein ◽  
Cell Mediated Immunity ◽  
Epitope Peptide ◽  
Mhc I ◽  
B Cell Epitopes ◽  
Antibody Recognition

ABSTRACTDeveloping an efficacious vaccine to SARS-CoV-2 infection is critical to stem COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in the design of an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers along with 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC-I and II alleles respectively. We used this information to construct an in silico chimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. The vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, with triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Upon in silico challenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We therefore propose that potential vaccine designs consider this approach.

scholarly journals Molecular cloning, expression, purification and in silico epitope prediction of cobalamin-independent methionine synthase (Mor a 2), as a novel allergen from Morus alba pollen

2021 ◽  
Author(s):  
Yunus AKSÜT
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Allergic Diseases ◽  
Structural Features ◽  
Morus Alba ◽  
Methionine Synthase ◽  
Antigenic Peptides ◽  
T Cell Epitopes ◽  
B Cell Epitopes

IntroductionMorus alba (white mulberry) pollen is an aero-allergen source that can trigger allergic diseases. Cobalamin-independent methionine synthase (MetE) in M. alba pollen has been proved to be one of the major allergens for some patients living in Istanbul (Turkey). The aim of the present study was the recombinant production and identification of MetE (Mor a 2), a novel allergen from M. alba pollen. The IgE binding reactivity of rMor a 2 produced for the first time was evaluated and some structural features were investigated by in silico methods to better understand its immunogenicity.Material and methodsThe gene encoding Mor a 2 was cloned in fission yeast, Schizosaccharomyces pombe ura4-D18h- strain, using pSLF1073 vector. This is the first report of the production of recombinant pollen allergen in S. pombe. After the purification, immunoreactivity of rMor a 2 was confirmed by immunoblotting using sera of patient allergic to M. alba pollen. Besides, B-cell epitopes of rMor a 2 were predicted using various bioinformatic tools, namely Bioinformatics Predicted Antigenic Peptides, BepiPred 2.0 and Immune Epitope Database whereas T-cell epitopes were estimated using NetMHCIIpan-3.2 and NetMHCII 2.3 servers.ResultsThe immunoblotting analysis yielded 11 of 11 positive reactions to rMor a 2. In silico predictions exerted seven B-cell epitopes (22-33, 384-394, 407-423, 547-553, 571-577, 671-678, 736-741) and seven T-cell epitopes (54-62, 161-170, 197-205, 347-358, 622-630, 657-665, 756-764).ConclusionsThese findings may help the use of rMor a 2 in the diagnosis and treatment of allergic diseases associated with M. alba and/or MetE.

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