scholarly journals Bioinformatics analysis of rhinovirus capsid proteins VP1-4 sequences for cross-serotype vaccine development

2021 ◽  
Vol 14 (11) ◽  
pp. 1603-1611
Author(s):  
Ahmed S. Alshrari ◽  
Shuaibu A. Hudu ◽  
Syed M.B. Asdaq ◽  
Alreshidi M. Ali ◽  
Chin V. Kin ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Vaccine Development ◽  
Capsid Proteins

scholarly journals Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

2020 ◽  
Author(s):  
Hongzhi Chen ◽  
Lingli Tang ◽  
Xinling Yu ◽  
Jie Zhou ◽  
Yunfeng Chang ◽  
...  
Keyword(s):  
B Cell ◽  
Nucleocapsid Protein ◽  
Bioinformatics Analysis ◽  
Vaccine Development ◽  
Wide Spectrum ◽  
Cell Epitope ◽  
Spike Protein ◽  
B Cell Epitopes ◽  
Surface Accessibility ◽  
Binding Peptides

Abstract Background: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. Methods: ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. Results: A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike315-324, Spike333-338, Spike648-663, Spike1064-1079) exhibited high antigenicity score and good surface accessibility. 10 residues within spike protein (Gly496, Glu498, Pro499, Thr500, Leu1141, Gln1142, Pro1143, Glu1144, Leu1145, Asp1146) are forecasted as components of discontinuous B-cell epitopes. The bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind class-I and class-II molecule respectively. The peptides (Nucleocapsid66-75, Nucleocapsid104-112) were predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. Conclusions: B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.

Architecture of African swine fever virus and implications for viral assembly

Science ◽  
2019 ◽  
Vol 366 (6465) ◽  
pp. 640-644 ◽  
Author(s):  
Nan Wang ◽  
Dongming Zhao ◽  
Jialing Wang ◽  
Yangling Zhang ◽  
Ming Wang ◽  
...  
Keyword(s):  
Vaccine Development ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Capsid Proteins ◽  
Dna Viruses ◽  
Capsid Shell ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Swine Disease ◽  
Capsid Stability

African swine fever virus (ASFV) is a giant and complex DNA virus that causes a highly contagious and often lethal swine disease for which no vaccine is available. Using an optimized image reconstruction strategy, we solved the ASFV capsid structure up to 4.1 angstroms, which is built from 17,280 proteins, including one major (p72) and four minor (M1249L, p17, p49, and H240R) capsid proteins organized into pentasymmetrons and trisymmetrons. The atomic structure of the p72 protein informs putative conformational epitopes, distinguishing ASFV from other nucleocytoplasmic large DNA viruses. The minor capsid proteins form a complicated network below the outer capsid shell, stabilizing the capsid by holding adjacent capsomers together. Acting as core organizers, 100-nanometer-long M1249L proteins run along each edge of the trisymmetrons that bridge two neighboring pentasymmetrons and form extensive intermolecular networks with other capsid proteins, driving the formation of the capsid framework. These structural details unveil the basis of capsid stability and assembly, opening up new avenues for African swine fever vaccine development.

scholarly journals Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

2020 ◽  
Author(s):  
Hongzhi Chen ◽  
Lingli Tang ◽  
Xinling Yu ◽  
Jie Zhou ◽  
Yunfeng Chang ◽  
...  
Keyword(s):  
B Cell ◽  
Mhc Class Ii ◽  
Nucleocapsid Protein ◽  
Bioinformatics Analysis ◽  
Vaccine Development ◽  
Cell Epitope ◽  
Spike Protein ◽  
B Cell Epitopes ◽  
Surface Accessibility ◽  
Binding Peptides

Abstract Background: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. Methods : ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. Results : A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike 315-324 , Spike 333-338 , Spike 648-663 , Spike 1064-1079 ) exhibited high antigenicity score and good surface accessibility. 10 residues within spike protein (Gly 496 , Glu 498 , Pro 499 , Thr 500 , Leu 1141 , Gln 1142 , Pro 1143 , Glu 1144 , Leu 1145 , Asp 1146 ) are forecasted as components of discontinuous B-cell epitopes. The bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind MHC class I and MHC class II molecule respectively. The peptides (Nucleocapsid 66-75 , Nucleocapsid 104-112 ) were predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. Conclusions : B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.

CLONING, EXPRESSION AND PRELIMINARY ANTIGENICITY ANALYSIS OF STRUCTURAL PROTEINS OF A KOI HERPESVIRUS ISOLATE FROM KOI, CYPRINUS CARPIO IN TAIWAN

2014 ◽  
Vol 40 (02) ◽  
pp. 69-75 ◽  
Author(s):  
Chien Tu ◽  
Ruey-Yu Chiou ◽  
Meei-Mei Chen
Keyword(s):  
Vaccine Development ◽  
Immunological Response ◽  
Capsid Proteins ◽  
Structural Proteins ◽  
Wild Type ◽  
Serological Tests ◽  
General Applicability ◽  
Japanese Strain ◽  
Koi Herpesvirus ◽  
Clone And Express

The aim of this study was to clone and express the ORF72 and ORF92 genes of koi herpesvirus (KHV) in a prokaryotic system and to examine the antigenicity of recombinant proteins. Phylogenetic analysis revealed that both ORF72 and ORF92 had 100% homology with KHV-J, and 99% homology with those from KHV-U and KHV-I in nucleotides. This suggests that the KHV isolate in Taiwan is more closely related to the Japanese strain (Asian genotype). In the antigenicity analysis, the crude recombinant ORF72 and ORF92 capsid proteins reacted with the positive sera of the survival fish after a KHV outbreak, indicating that these recombinant capsid proteins might mimic antigens of the wild type KHV to induce an immunological response in the infected host. Our results demonstrated potential for general applicability to serological tests and vaccine development.

scholarly journals Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Hong-Zhi Chen ◽  
Ling-Li Tang ◽  
Xin-Ling Yu ◽  
Jie Zhou ◽  
Yun-Feng Chang ◽  
...  
Keyword(s):  
B Cell ◽  
Mhc Class Ii ◽  
Nucleocapsid Protein ◽  
Bioinformatics Analysis ◽  
Vaccine Development ◽  
Cell Epitope ◽  
Spike Protein ◽  
B Cell Epitopes ◽  
Surface Accessibility ◽  
Binding Peptides

Abstract Background An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. Methods The genome sequence and protein sequences of SARS-CoV-2 were retrieved from the National Center for Biotechnology Information (NCBI) database. ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. Results A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike315–324, Spike333–338, Spike648–663, Spike1064–1079) exhibited high antigenicity score and good surface accessibility. Ten residues within spike protein (Gly496, Glu498, Pro499, Thr500, Leu1141, Gln1142, Pro1143, Glu1144, Leu1145, Asp1146) are forecasted as components of discontinuous B-cell epitopes. The bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind MHC class I and MHC class II molecules respectively. The peptides (Nucleocapsid66–75, Nucleocapsid104–112) were predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. Conclusions B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.

Alphavirus capsid proteins self-assemble into core-like particles in insect cells: A promising platform for nanoparticle vaccine development

2015 ◽  
Vol 11 (2) ◽  
pp. 266-273 ◽  
Author(s):  
Mia C. Hikke ◽  
Corinne Geertsema ◽  
Vincen Wu ◽  
Stefan W. Metz ◽  
Jan W. van Lent ◽  
...  
Keyword(s):  
Insect Cells ◽  
Vaccine Development ◽  
Capsid Proteins

scholarly journals Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

2020 ◽  
Author(s):  
hongzhi chen ◽  
Lingli Tang ◽  
Xinling Yu ◽  
Jie Zhou ◽  
Yunfeng Chang ◽  
...  
Keyword(s):  
B Cell ◽  
Nucleocapsid Protein ◽  
Bioinformatics Analysis ◽  
Vaccine Development ◽  
Wide Spectrum ◽  
Cell Epitope ◽  
Spike Protein ◽  
B Cell Epitopes ◽  
Surface Accessibility ◽  
Binding Peptides

Abstract Background: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. Methods : The genome sequence and protein sequences of SARS-CoV-2 were retrieved from the National Center for Biotechnology Information (NCBI) database. ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. Results : A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike 315-324 , Spike 333-338 , Spike 648-663 , Spike 1064-1079 ) exhibited high antigenicity score and good surface accessibility. Ten residues within spike protein (Gly 496 , Glu 498 , Pro 499 , Thr 500 , Leu 1141 , Gln 1142 , Pro 1143 , Glu 1144 , Leu 1145 , Asp 1146 ) are forecasted as components of discontinuous B-cell epitopes. The bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind MHC classⅠand MHC classⅡ molecules respectively. The peptides (Nucleocapsid 66-75 , Nucleocapsid 104-112 ) were predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. Conclusions : B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.

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