Statistics of Unrelated Sequence Properties to Improve Prediction of B-Cell Based Linear Epitopes

Abstract Background Mycoplasma hyorhinis (Mhr) is the etiologic agent of lameness and polyserositis in swine. P37 is a membrane protein of Mhr that may be an important immunogen and is a potential target for diagnostic development. However, there is little information concerning Mhr P37 protein epitopes. A precise analysis of the P37 protein epitopes should extend our understanding of the antigenic composition of the P37 protein and the humoral immune responses to Mhr infection. Investigating the epitopes of Mhr P37 will help to establish a detection method for Mhr in tissue and provide an effective tool for detecting Mhr infection. Results Western blot and indirect immunofluorescence assays (IFA) confirmed that the expressed P37 protein was recognized by Mhr-positive porcine and mouse sera. Furthermore, the P37 protein was purified using affinity chromatography and used to immunize mice for hybridoma cell fusion. Four monoclonal antibodies (mAbs) found to be positive for Mhr were detected in infected lung tissue. A panel of truncated P37 proteins was used to identify the minimal B cell linear epitopes of the protein based on these mAbs. The core epitope was determined to be 206KIKKAWNDKDWNTFRNF222. Conclusions In this study, we identified 17 critical amino acids that determine the epitope of the P37 protein of Mhr. This study identified mAbs that could provide useful tools for investigating the Mhr P37 antigenic core epitope (amino acids 206–222) and detecting Mhr-specific antigens in infected tissue.

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In SilicoPrediction of T and B Cell Epitopes of Der f 25 inDermatophagoides farinae

International Journal of Genomics ◽

10.1155/2014/483905 ◽

2014 ◽

Vol 2014 ◽

pp. 1-10 ◽

Cited By ~ 14

Author(s):

Xiaohong Li ◽

Hai-Wei Yang ◽

Hao Chen ◽

Jing Wu ◽

Yehai Liu ◽

...

Keyword(s):

T Cell ◽

B Cell ◽

Triosephosphate Isomerase ◽

Allergic Diseases ◽

Major Allergen ◽

House Dust Mites ◽

T Cell Epitopes ◽

B Cell Epitopes ◽

Physiochemical Properties ◽

Linear Epitopes

The house dust mites are major sources of indoor allergens for humans, which induce asthma, rhinitis, dermatitis, and other allergic diseases. Der f 25 is a triosephosphate isomerase, representing the major allergen identified inDermatophagoides farinae. The objective of this study was to predict the B and T cell epitopes of Der f 25. In the present study, we analyzed the physiochemical properties, function motifs and domains, and structural-based detailed features of Der f 25 and predicted the B cell linear epitopes of Der f 25 by DNAStar protean system, BPAP, and BepiPred 1.0 server and the T cell epitopes by NetMHCIIpan-3.0 and NetMHCII-2.2. As a result, the sequence and structure analysis identified that Der f 25 belongs to the triosephosphate isomerase family and exhibited a triosephosphate isomerase pattern (PS001371). Eight B cell epitopes (11–18, 30–35, 71–77, 99–107, 132–138, 173–187, 193–197, and 211–224) and five T cell epitopes including 26–34, 38–54, 66–74, 142–151, and 239–247 were predicted in this study. These results can be used to benefit allergen immunotherapies and reduce the frequency of mite allergic reactions.

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Identification of Mycoplasma hyorhinis P37 protein-specific B cell linear epitopes using monoclonal antibodies against baculovirus-expressed P37 protein

10.21203/rs.2.9644/v1 ◽

2019 ◽

Author(s):

Hongzhen Zhu ◽

Yanwu Wei ◽

Liping Huang ◽

Dan Liu ◽

Yongxing Xie ◽

...

Keyword(s):

Monoclonal Antibodies ◽

B Cell ◽

Critical Role ◽

Diagnostic Techniques ◽

Etiologic Agent ◽

Antigenic Structure ◽

Mycoplasma Hyorhinis ◽

Linear Epitopes ◽

Baculovirus System ◽

And Function

Abstract Background Mycoplasma hyorhinis (Mhr) is the etiologic agent of lameness and polyserositis in swine. Mhr P37 is a membrane protein that may play a critical role in immunity. It is a potential target for diagnostic development, but there is little information concerning its B cell epitopes. To investigate the epitopes of Mhr P37, a recombinant protein was developed in a baculovirus system using monoclonal antibodies (mAbs) prepared against P37 protein. Results Western blot and indirect immunofluorescence assays (IFA) confirmed that the expressed P37 protein was recognized by Mhr-positive porcine and mouse sera. Furthermore, the P37 protein was purified using affinity chromatography and used to immunize mice for hybridoma cell fusion. Four mAbs were found to be positive for Mhr. A panel of truncated P37 proteins was used to identify the minimal B cell linear epitopes of the protein based on these mAbs. The core epitope was determined to be 206KIKKAWNDKDWNTFRNF222. Conclusions This study identified mAbs that could provide useful tools for investigating the antigenic structure and function of the Mhr P37 protein as well as its application to diagnostic techniques.

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Prediction and Evolution of B Cell Epitopes of Surface Protein in SARS-CoV-2

10.1101/2020.04.03.022723 ◽

2020 ◽

Cited By ~ 2

Author(s):

Jerome R Lon ◽

Yunmeng Bai ◽

Bingxu Zhong ◽

Fuqaing Cai ◽

Hongli Du

Keyword(s):

B Cell ◽

Vaccine Development ◽

Surface Protein ◽

The Other ◽

Reference Sequence ◽

Prediction Methods ◽

Whole Genome ◽

B Cell Epitopes ◽

Conformational Epitopes ◽

Linear Epitopes

AbstractThe discovery of epitopes is helpful to the development of SARS-CoV-2 vaccine. The sequences of the surface protein of SARS-CoV-2 and its proximal sequences were obtained by BLAST, the sequences of the whole genome of SARS-CoV-2 were obtained from the GenBank. Based on the NCBI Reference Sequence: NC_045512.2, the conformational and linear B cell epitopes of the surface protein were predicted separately by various prediction methods. Furthermore, the conservation of the epitopes, the adaptability and other evolutionary characteristics were also analyzed. 7 epitopes were predicted, including 5 linear epitopes and 2 conformational epitopes, one of the linear and one of the conformational were coincide. The epitope D mutated easily, but the other epitopes were very conservative and the epitope C was the most conservative. It is worth mentioning that all of the 6 dominated epitopes were absolutely conservative in nearly 1000 SARS-CoV-2 genomes, and they deserved further study. The findings would facilitate the vaccine development, had the potential to be directly applied on the treatment in this disease, but also have the potential to prevent the possible threats caused by other types of coronavirus.

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Identification of specific B cell linear epitopes of Mycoplasma hyorhinis P37 protein using monoclonal antibodies against baculovirus-expressed P37 protein

10.21203/rs.2.9644/v3 ◽

2019 ◽

Author(s):

Hongzhen Zhu ◽

Yanwu Wei ◽

Liping Huang ◽

Dan Liu ◽

Yongxing Xie ◽

...

Keyword(s):

Amino Acids ◽

Monoclonal Antibodies ◽

B Cell ◽

Etiologic Agent ◽

Mycoplasma Hyorhinis ◽

Humoral Immune ◽

Humoral Immune Responses ◽

Precise Analysis ◽

Linear Epitopes ◽

Specific Antigens

Abstract Background Mycoplasma hyorhinis (Mhr) is the etiologic agent of lameness and polyserositis in swine. P37 is a membrane protein of Mhr that may be an important immunogen and is a potential target for diagnostic development. However, there is little information concerning Mhr P37 protein epitopes. A precise analysis of the P37 protein epitopes should extend our understanding of the antigenic composition of the P37 protein and the humoral immune responses to Mhr infection. Investigating the epitopes of Mhr P37 will help to establish a detection method for Mhr in tissue and provide an effective tool for detecting Mhr infection. Results Western blot and indirect immunofluorescence assays (IFA) confirmed that the expressed P37 protein was recognized by Mhr-positive porcine and mouse sera. Furthermore, the P37 protein was purified using affinity chromatography and used to immunize mice for hybridoma cell fusion. Four monoclonal antibodies (mAbs) found to be positive for Mhr were detected in infected lung tissue. A panel of truncated P37 proteins was used to identify the minimal B cell linear epitopes of the protein based on these mAbs. The core epitope was determined to be 206 KIKKAWNDKDWNTFRNF 222 . Conclusions In this study, we identified 17 critical amino acids that determine the epitope of the P37 protein of Mhr. This study identified mAbs that could provide useful tools for investigating the Mhr P37 antigenic core epitope (amino acids 206-222) and detecting Mhr-specific antigens in infected tissue.

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Prediction and Evolution of B Cell Epitopes of Surface Protein in SARS-CoV-2

10.21203/rs.3.rs-26822/v2 ◽

2020 ◽

Author(s):

Jerome Rumdon Lon ◽

Yunmeng Bai ◽

Bingxu Zhong ◽

Fuqiang Cai ◽

Hongli Du

Keyword(s):

B Cell ◽

Vaccine Development ◽

Surface Protein ◽

Conformational Epitope ◽

Reference Sequence ◽

Effective Vaccine ◽

Antigenic Determinants ◽

B Cell Epitopes ◽

Linear Epitopes ◽

Long Acting

Abstract Background In order to obtain antibodies that recognize natural proteins, it is possible to predict the antigenic determinants of natural proteins, which are eventually embodied as polypeptides. The polypeptides can be coupled with corresponding vectors to stimulate the immune system to produce corresponding antibodies, which is also a simple and effective vaccine development method. The discovery of epitopes is helpful to the development of SARS-CoV-2 vaccine. Methods The analyses were related to epitopes on 3 proteins, including spike(S), envelope(E) and membrane(M) proteins, which were associated with the lipid envelope of the SARS-CoV-2. Based on the NCBI Reference Sequence: NC_045512.2, the conformational and linear B cell epitopes of the surface protein were predicted separately by various prediction methods. Furthermore, the conservation of the epitopes, the adaptability and other evolutionary characteristics were also analyzed, the sequences of the whole genome of SARS-CoV-2 were obtained from the GISAID. Results 7 epitopes were predicted, including 6 linear epitopes and 1 conformational epitope. One of the linear and one of the conformational consist of identical sequence, but represent different forms of epitopes. It is worth mentioning that all of the 6 dominated epitopes were conservative in nearly 3500 SARS-CoV-2 genomes, and they showed a phenomenon which is helpful to obtain stable and long-acting epitopes under the condition of high frequency of amino acid mutation, and deserved further study at the experiment level. Conclusion The findings would facilitate the vaccine development, had the potential to be directly applied on the prevention in this disease, but also have the potential to prevent the possible threats caused by other types of coronavirus.

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Experimental Identification of Immuno- dominant B-cell Epitopes from SARS-CoV-2

CHIMIA International Journal for Chemistry ◽

10.2533/chimia.2021.276 ◽

2021 ◽

Vol 75 (4) ◽

pp. 276-284

Author(s):

Lluc Farrera-Soler ◽

Jean-Pierre Daguer ◽

Sofia Barluenga ◽

Nicolas Winssinger

Keyword(s):

Public Health ◽

B Cell ◽

Neutralizing Antibodies ◽

Social Impact ◽

Adaptive Immune Response ◽

Diagnostic Tools ◽

Global Public Health ◽

Health Crisis ◽

Experimental Identification ◽

Linear Epitopes

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current public health crisis with devastating consequences to our societies. This COVID-19 pandemic has become the most serious threat to global public health in recent history. Given the unprecedented economic and social impact that it is causing, identification of immunodominant epitopes from SARS-CoV-2 is of great interest, not only to gain better insight into the adaptive immune response, but also for the development of vaccines, treatments and diagnostic tools. In this review, we summarize the already published or preprinted reports on the experimental identification of B-cell linear epitopes of SARS-CoV-2 proteins. Six different epitopes leading to neutralizing antibodies have been identified. Moreover, a summary of peptide candidates to be used for diagnostic tools is also included.

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