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Mass spectrometric epitope mapping has become a versatile method to precisely determine a soluble antigen's partial structure that directly interacts with an antibody in solution. Typical lengths of investigated antigens have incr...
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Mass spectrometric epitope mapping has become a versatile method to precisely determine a soluble antigen's partial structure that directly interacts with an antibody in solution. Typical lengths of investigated antigens have increased up to several 100 amino acids while experimentally determined epitope peptides have decreased in length to on average 10-15 amino acids. Since the early 1990s more and more sophisticated methods have been developed and have forwarded a bouquet of suitable approaches for epitope mapping with immobilized, temporarily immobilized, and free-floating antibodies. While up to now monoclonal antibodies have been mostly used in epitope mapping experiments, the applicability of polyclonal antibodies has been proven. The antibody's resistance towards enzymatic proteolysis has been of key importance for the two mostly applied methods: epitope excision and epitope extraction. Sample consumption has dropped to low pmol amounts on both, the antigen and the antibody. While adequate in-solution sample handling has been most important for successful epitope mapping, mass spectrometric analysis has been found the most suitable read-out method from early on. The rapidity by which mass spectrometric epitope mapping nowadays is executed outperforms all alternative methods. Thus, it can be asserted that mass spectrometric epitope mapping has reached a state of maturity, which allows it to be used in any mass spectrometry laboratory. After 25 years of constant and steady improvements, its application to clinical samples, for example, for patient characterization and stratification, is anticipated in the near future. (c) 2016 Wiley Periodicals, Inc.
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Identification of B-cell epitopes in target antigens is one of the most crucial steps for epitope-based vaccine development, immunodiagnostic tests, antibody production, and disease diagnosis and therapy. Experimental methods for ...
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Identification of B-cell epitopes in target antigens is one of the most crucial steps for epitope-based vaccine development, immunodiagnostic tests, antibody production, and disease diagnosis and therapy. Experimental methods for B-cell epitope mapping are time consuming, costly and labor intensive; in the meantime, various in-silico methods are proposed to predict both linear and conformational B-cell epitopes. The accurate identification of B-cell epitopes presents major challenges for immunoinformaticians. In this paper, we have comprehensively reviewed in-silico methods for B-cell epitope identification. The aim of this review is to stimulate the development of better tools which could improve the identification of B-cell epitopes, and further for the development of therapeutic antibodies and diagnostic tools.
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Identification of B-cell epitopes in target antigens is one of the most crucial steps for epitope-based vaccine development, immunodiagnostic tests, antibody production, and disease diagnosis and therapy. Experimental methods for ...
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Identification of B-cell epitopes in target antigens is one of the most crucial steps for epitope-based vaccine development, immunodiagnostic tests, antibody production, and disease diagnosis and therapy. Experimental methods for B-cell epitope mapping are time consuming, costly and labor intensive; in the meantime, various in-silico methods are proposed to predict both linear and conformational B-cell epitopes. The accurate identification of B-cell epitopes presents major challenges for immunoinformaticians. In this paper, we have comprehensively reviewed in-silico methods for B-cell epitope identification. The aim of this review is to stimulate the development of better tools which could improve the identification of B-cell epitopes, and further for the development of therapeutic antibodies and diagnostic tools.
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Although it is widely acknowledged that most B-cell epitopes are discontinuous, the degree of discontinuity is poorly understood. For example, given that an antigen having a single epitope that has been chopped into peptides of a ...
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Although it is widely acknowledged that most B-cell epitopes are discontinuous, the degree of discontinuity is poorly understood. For example, given that an antigen having a single epitope that has been chopped into peptides of a specific length, what is the likelihood that one of the peptides will span all the residues belonging to that epitope? Or, alternatively, what is the largest proportion of the epitope's residues that any peptide is likely to contain? These and similar questions are of direct relevance both to computational methods that aim to predict the location of epitopes from sequence (linear B-cell epitope prediction methods) and window-based experimental methods that aim to locate epitopes by assessing the strength of antibody binding to synthetic peptides on a chip.In this paper we present an analysis of the degree of B-cell epitope discontinuity, both in terms of the structural epitopes defined by a set of antigen-antibody complexes in the Protein Data Bank, and with respect to the distribution of key residues that form functional epitopes. We show that, taking a strict definition of discontinuity, all the epitopes in our data set are discontinuous. More significantly, we provide explicit guidance about the choice of peptide length when using window-based B-cell epitope prediction and mapping techniques based on a detailed analysis of the likely effectiveness of different lengths.
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HLA matching at the epitope level offers new opportunities to identify suitable donors for transplant patients. The International HLA Epitope Registry (www.Epregistry.com.br) describes for the various HLA loci, repertoires of eple...
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HLA matching at the epitope level offers new opportunities to identify suitable donors for transplant patients. The International HLA Epitope Registry (www.Epregistry.com.br) describes for the various HLA loci, repertoires of eplets including those that correspond to epitopes experimentally verified with specific antibodies. There are also many eplets which have remained as theoretical entities because no informative antibodies have been found. Which of them have immunogenic potential or conversely, might be considered as non-epitopes that cannot elicit specific antibody responses? This question is important for the application of epitope-based HLA matching in clinical transplantation.
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The International Registry of Antibody-Defined HLA Epitopes (http://www.epregistry.com.br) has been recently established as a tool to understand humoral responses to HLA mismatches. These epitopes can be structurally defined as ep...
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The International Registry of Antibody-Defined HLA Epitopes (http://www.epregistry.com.br) has been recently established as a tool to understand humoral responses to HLA mismatches. These epitopes can be structurally defined as eplets by three-dimensional molecular modeling and amino acid sequence differences between HLA antigens. A major goal is to identify HLA eplets that have been verified experimentally with informative antibodies. This report addresses class II epitopes encoded by genes in the HLA-D region. Our analysis included reviews of many publications about epitope specificity of class II reactive human and murine monoclonal antibodies and informative alloantibodies from HLA sensitized patients as well as our own antibody testing results. As of July 1, 2014, 24 HLA-DRB1/3/4/5, 15 DQB, 3 DQA and 8 DPB antibody-verified epitopes have been identified and recorded. The Registry is still a work-in-progress and will become a useful resource for HLA professionals interested in histocompatibility testing at the epitope level and investigating antibody responses to HLA mismatches in transplant patients. (C) 2014 Published by Elsevier Inc. on behalf of American Society for Histocompatibility and Immunogenetics.
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The International Registry of Antibody-Defined HLA Epitopes (http://www.epregistry.com.br) has been recently established as a tool to understand humoral responses to HLA mismatches. These epitopes can be structurally defined as ep...
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The International Registry of Antibody-Defined HLA Epitopes (http://www.epregistry.com.br) has been recently established as a tool to understand humoral responses to HLA mismatches. These epitopes can be structurally defined as eplets by three-dimensional molecular modeling and amino acid sequence differences between HLA antigens. A major goal is to identify HLA eplets that have been verified experimentally with informative antibodies. This report addresses class II epitopes encoded by genes in the HLA-D region. Our analysis included reviews of many publications about epitope specificity of class II reactive human and murine monoclonal antibodies and informative alloantibodies from HLA sensitized patients as well as our own antibody testing results. As of July 1, 2014, 24 HLA-DRB1/3/4/5, 15 DQB, 3 DQA and 8 DPB antibody-verified epitopes have been identified and recorded. The Registry is still a work-in-progress and will become a useful resource for HLA professionals interested in histocompatibility testing at the epitope level and investigating antibody responses to HLA mismatches in transplant patients. (C) 2014 Published by Elsevier Inc. on behalf of American Society for Histocompatibility and Immunogenetics.
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Chikungunya is a viral infection transmitted by Aedes mosquitoes in humans. Currently there is no drug available for the treatment of this infection. In absence of a proven therapeutic, vaccines provide an alternative preventive m...
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Chikungunya is a viral infection transmitted by Aedes mosquitoes in humans. Currently there is no drug available for the treatment of this infection. In absence of a proven therapeutic, vaccines provide an alternative preventive measure for the spread of viral infection in risk prone population. The identification of epitopes is an important step in designing vaccines for viral infections. Traditional methods for vaccine production can be augmented by incorporation of in silico methods at epitopes identification stage. Protein sequences were retrieved for three different viral strains from primary database. Multiple sequence alignment for the retrieved sequences was performed by using MEGA 6.06 to spot the conserved regions. Various immunological databases were utilized to determine the binding affinity with T cells and B cells from structural and non-structural proteins from three different isolates of Chikungunya virus. Five different epitopes were predicted for both structural and non-structural proteins. The epitopes "KKKPGRRERMCMKIE" and "DAE-KEAEEEREAELT" and "AEEEREAEL" were predicted as core sequences for class I and class II MHC molecules whereas "SSKYDLECAQ" and "QVLKAKNIGL" were predicted as probable B cell epitopes for structural and non-structural proteins respectively. The identified epitopes can be used for developing a broad spectrum vaccines having effectiveness against different strains of Chikungunya.
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Based on the hypothesis suggested by us that epitope-vaccine may be a new strategy against HIV mutation, we have studied several neutralizing epitopes on HIV envelope proteins. However we do not know whether a repeated epitope in ...
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Based on the hypothesis suggested by us that epitope-vaccine may be a new strategy against HIV mutation, we have studied several neutralizing epitopes on HIV envelope proteins. However we do not know whether a repeated epitope in a recombinant epitope-peptide can enhance epitope-specific antibody response or not. ELDKWA-epitope (aa669-674) on the C-domain of HIV-1 gp41 is a neutralizing epitope defined by the monoclonal antibody (mAb) 2F5 with broad neutralizing activity. In this study, we designed and pre-pared a series of the recombinant epitope-peptides bearing 1, 4 and 8 copies of ELDKWA-epitope respectively. In the comparison of the antisera induced by the three recombinant antigens, an obviously increased title of ELDKWA-epitope-specific antibody was observed in the case of four and eight repeated epitopes. In flow cytometry analysis, the epitope-specific antibodies in both antisera showed stronger activity to bind the transfected CHO-WT cells that stably express HIV-1 envelope glycoprotein on the cell surfaces. These experimental results indicated that repeated epitope in the recombinant epitope-peptide could enhance ELDKWA-epitope-specific antibody response, which could contribute to designing an effective recombinant epitope-vaccine.
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