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Epitope MappingEpitopesAntibodies, MonoclonalAmino Acid SequenceMolecular Sequence DataChromosome MappingAntibody SpecificityEpitopes, B-LymphocyteImmunodominant EpitopesPeptide LibraryBinding Sites, AntibodyEpitopes, T-LymphocyteEnzyme-Linked Immunosorbent AssayCross ReactionsPeptide FragmentsPeptide MappingPeptidesNeutralization TestsModels, MolecularBinding, CompetitiveMice, Inbred BALB CAutoantibodiesAutoantigensProtein ConformationBase SequenceAntibodies, NeutralizingProtein Structure, TertiaryRecombinant Fusion ProteinsAntibodies, ViralRecombinant ProteinsHybridomasAntigens, BacterialBinding SitesAntigens, ViralProtein BindingHIV AntibodiesBlotting, WesternImmunoglobulin GAntibody AffinityAntigen-Antibody ReactionsHIV AntigensAntibodies, BacterialSequence Homology, Amino AcidCloning, MolecularAntigen-Antibody ComplexSpecies SpecificitySurface Plasmon ResonanceCell LineAntibodiesViral Envelope ProteinsRestriction MappingAntigens, PlantMutagenesis, Site-DirectedAllergensImmunizationRabbitsImmunoblottingProtein Structure, SecondaryHIV Envelope Protein gp120
AntibodyAntibodiesPeptidesVaccineCharacterizationAntigenicAmino acidsPredictionConformationalRevealProteinProteinsComparableExperimentalCellAnalysisPotentialResiduesContinuousAntigenConformational epitopeImmunodominant epitopesAffinityComputationalSilicoVaccine DesignSpecificityAntigensCross-reactivePeptide vaccineGp120CombinatorialExperimentallyDissectionPhageVaccinesSegmentsMAbsExtracellularAlgorithmMolecularReplicationBioinformaticsApproachDependsAssaysInfectiousStrainsLinearBindRelevance
Antibody14
  • In immunology, epitope mapping is the process of experimentally identifying the binding site, or epitope, of an antibody on its target antigen (usually, on a protein). (wikipedia.org)
  • Epitope characterization can also help elucidate the binding mechanism of an antibody and can strengthen intellectual property (patent) protection. (wikipedia.org)
  • citation needed] By providing information on mechanism of action, epitope mapping is a critical component in therapeutic monoclonal antibody (mAb) development. (wikipedia.org)
  • In addition to verifying antibody patentability, epitope mapping data have been used to support broad antibody claims submitted to the United States Patent and Trademark Office. (wikipedia.org)
  • There are several methods available for mapping antibody epitopes on target antigens: X-ray co-crystallography and cryogenic electron microscopy (cryo-EM). (wikipedia.org)
  • X-ray co-crystallography has historically been regarded as the gold-standard approach for epitope mapping because it allows direct visualization of the interaction between the antigen and antibody. (wikipedia.org)
  • Cryo-EM can similarly provide high-resolution maps of antibody-antigen interactions. (wikipedia.org)
  • Mapping Discontinuous Antibody Epitopes to Reveal Protein Structure and Changes in Structure Related to Function. (dagstuhl.de)
  • Revealing protein structures: a new method for mapping antibody epitopes. (dagstuhl.de)
  • Linear antibody epitopes are readily mapped with PepSets. (mimotopes.com)
  • Antibody epitope mapping by ELISA is simple to perform using biotinylated peptides because the peptides can be captured onto Streptavidin™ or NeutrAvidin™ coated plates through the strong noncovalent avidin-biotin binding. (mimotopes.com)
  • Custom synthesized biotinylated PepSets for linear antibody mapping are designed by the research scientist with help from experienced Technical Consultants at Mimotopes, and are shipped either ready to redissolve and plate or as ready-to-use plates already coated with the peptide (Figure 2). (mimotopes.com)
  • Here we exploited a naïve human single chain antibody phage display library, to isolate binders against carefully chosen ORF3a recombinant epitopes located towards the extracellular N terminal and cytosolic C terminal domains of the protein using peptide antigens. (bvsalud.org)
  • The area in which the mutation occurs is an important epitope to which vaccine-induced neutralizing antibodies bind, however the mutant virus is not neutralized by antibody to this specificity. (ehd.org)
Antibodies9
  • B-cell epitope mapping studies suggest that most interactions between antigens and antibodies, particularly autoantibodies and protective antibodies (e.g., in vaccines), rely on binding to discontinuous epitopes. (wikipedia.org)
  • Epitope data have been central to several high-profile legal cases involving disputes over the specific protein regions targeted by therapeutic antibodies. (wikipedia.org)
  • This method is fast, relatively inexpensive, and specifically suited to profile epitopes for large numbers of candidate antibodies against a defined target. (wikipedia.org)
  • In a typical example, a library of monoclonal antibodies to a small protein, thought to recognize linear epitopes, was screened using a PepSet of biotinylated peptides (Figure 2). (mimotopes.com)
  • Using this approach, the linear epitopes of several monoclonal antibodies were quickly and clearly identified. (mimotopes.com)
  • Evaluation of the ability of AlphaFold to predict the three-dimensional structures of antibodies and epitopes. (tau.ac.il)
  • We find that each of the two antibodies has comparable, but nonidentical, discontinuous epitopes that include regions of subdomain 2 encompassing the dimerization interface. (imacst.com)
  • Both ORF3a N and C termini, epitope-specific monoclonal antibodies were identified in our study. (bvsalud.org)
  • Antigenic variation in a major discontinuous site (site D) of foot-and-mouth disease virus (FMDV) of serotype C has been evaluated with neutralizing monoclonal antibodies. (ox.ac.uk)
Peptides5
Vaccine1
  • Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. (biomedcentral.com)
Characterization3
  • Rodda, S.J. (2002) Peptide Libraries for T-Cell Epitope Screening and Characterization. (mimotopes.com)
  • Therefore, Y498 is a novel neutralizing human mAb targeting a conformation-dependent CD4bs-based epitope, and its isolation and characterization could provide helpful information for elucidating human immune response to HIV-1 infection and designing effective vaccines and immunotherapeutics. (oncotarget.com)
  • These binders were subjected to further characterization using enzyme-linked immunosorbent assays and surface plasmon resonance analysis to assess their binding affinities to the target epitopes. (bvsalud.org)
Antigenic3
  • Epitope mapping has been crucial to the development of vaccines against prevalent or deadly viral pathogens, such as chikungunya, dengue, Ebola, and Zika viruses, by determining the antigenic elements (epitopes) that confer long-lasting immunization effects. (wikipedia.org)
  • Membrane proteins frequently have short antigenic regions (epitopes) that fold correctly only when in the context of a lipid bilayer. (wikipedia.org)
  • By combining molecular docking and site-directed mutagenesis, the epitope of Y498 was characterized to contain three antigenic sites on gp120, including the CD4 binding loop in C3, the β23 in C4 and the β24-α5 in C5, which overlap the binding sites of CD4 and CD4bs-directed mAbs (b12, VRC01, A16). (oncotarget.com)
Amino acids3
  • Linear epitopes are formed by a continuous sequence of amino acids in a protein. (wikipedia.org)
  • Conformational epitopes epitopes are formed by amino acids that are nearby in the folded 3D structure but distant in the protein sequence. (wikipedia.org)
  • Finally, neither technique can distinguish key epitope residues (energetic "hot spots") for mAbs that bind to the same group of amino acids. (wikipedia.org)
Prediction3
  • Experimental epitope mapping data can be incorporated into robust algorithms to facilitate in silico prediction of B-cell epitopes based on sequence and/or structural data. (wikipedia.org)
  • Filtering Epitope Alignments to Improve Protein Surface Prediction. (dagstuhl.de)
  • Host-specific characteristics are important features and constraints for effective epitope prediction. (biomedcentral.com)
Conformational5
  • Epitopes are generally divided into two classes: linear and conformational/discontinuous. (wikipedia.org)
  • Note that conformational epitopes can include some linear segments. (wikipedia.org)
  • Many therapeutic mAbs target conformational epitopes that are only present when the protein is in its native (properly folded) state, which can make epitope mapping challenging. (wikipedia.org)
  • As a result, mAb epitopes on these membrane proteins are often conformational and, therefore, are more difficult to map. (wikipedia.org)
  • 1] Ansari, H. R., Raghava, G. P., Identification of conformational B-cell Epitopes in an antigen from its primary sequence. (degruyter.com)
Reveal1
  • Epitope mapping can reveal how a mAb exerts its functional effects - for instance, by blocking the binding of a ligand or by trapping a protein in a non-functional state. (wikipedia.org)
Protein2
  • ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels. (dagstuhl.de)
  • Human thyroid peroxidase: complete protein sequence, chromosome mapping, and identification two alternately spliced mRNAs. (rusmedserv.com)
Proteins2
  • Mapping epitopes on these targets can be challenging because of the difficulty in expressing and purifying these complex proteins. (wikipedia.org)
  • Epitope tagged CDPK1 and MyoE are enriched at the cell periphery, and both proteins co-immunoprecipitate multiple glideosome or IMC components. (pberghei.eu)
Comparable1
  • Extensive variation, comparable to that of continuous epitopes within the hypervariable immunodominant site A (the VP1 G-H loop), was found. (ox.ac.uk)
Experimental1
  • The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. (biomedcentral.com)
Cell1
  • This application is summarized in a separate article entitled Truncated Peptide Libraries for Cytotoxic T-Cell Epitope Mapping, available on the Mimotopes website. (mimotopes.com)
Analysis1
  • T. Zhang, J. Singh, T. Litfin, J. Zhan, K. Paliwal, and Y. Zhou, "RNAcmap: A fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis. (sparks-lab.org)
Potential1
  • paratuberculosis (MAP) represents a good example of the potential of this discovery-phase. (degruyter.com)
Residues5
  • Nearly all neutralizing Abs recognize discontinuous determinants formed by residues present on different stretches of the HA primary structure. (nih.gov)
  • Finally, neither technique can distinguish key epitope residues (energetic "hot spots") for mAbs that bind to the same group of amino acids. (wikipedia.org)
  • The reactive sequence was further narrowed down to nine discontinuous amino acid residues. (lu.se)
  • In fact, most natural epitopes are discontinuous consisting of residues that are not adjacent in the sequence but instead brought into proximity due to the conformation of the cognate, intact protein. (proteogenix.science)
  • The IgE-defined dominant epitope is discontinuous and formed by 21 residues located mostly within the beta strands. (rcsb.org)
Continuous6
  • Linear epitopes are formed by a continuous sequence of amino acids in a protein. (wikipedia.org)
  • The relative ratio of linear (sequential, continuous) to conformational (discontinuous, 3-D) epitopes probably varies significantly between allergens and may correlate with patient symptom severity. (usda.gov)
  • Three high scoring continuous and two discontinuous B cell epitopes were found in EDIII. (springer.com)
  • Most, if not all, eukaryotic origins initiate replication in both directions, resulting in a transition from discontinuous to continuous DNA synthesis on each template strand "origin of bi-directional replication" (OBR), Fig. 2B. (nih.gov)
  • Fourthly, we have systematically reviewed the in silico methods developed in the last four decades for predicting linear or continuous B-cell epitopes. (bvsalud.org)
  • Finally, we have discussed the overall challenge of identifying continuous or conformational B-cell epitopes. (bvsalud.org)
Antigen8
  • In immunology, epitope mapping is the process of experimentally identifying the binding site, or epitope, of an antibody on its target antigen (usually, on a protein). (wikipedia.org)
  • X-ray co-crystallography has historically been regarded as the gold-standard approach for epitope mapping because it allows direct visualization of the interaction between the antigen and antibody. (wikipedia.org)
  • Cryo-EM can similarly provide high-resolution maps of antibody-antigen interactions. (wikipedia.org)
  • The output is usually 1-3 epitope candidates on the surface of the atomic structure of the antigen. (tau.ac.il)
  • Two model systems were analyzed in which the antibody of interest had previously been co-crystallized with the antigen and thus the epitope is a given. (tau.ac.il)
  • 10. Identification of a novel HLA-A2-restricted cytotoxic T lymphocyte epitope from cancer-testis antigen PLAC1 in breast cancer. (nih.gov)
  • Thirdly, we have extensively reviewed the computational methods developed for predicting conformational B-cell epitopes from the structure of the antigen, as well as the methods for predicting conformational epitopes from the sequence. (bvsalud.org)
  • The interaction between paratope (antibody) and epitope (antigen) is the fundamental driving force of both immunogenicity and antigenicity. (proteogenix.science)
Conformational epitope1
  • The structure of the Phl p 2/IgE Fab complex was determined by x-ray crystallography to 1.9 A resolution revealing a conformational epitope (876 A(2)) comprised of the planar surface of the four-stranded anti-parallel beta-sheet of Phl p 2. (rcsb.org)
Immunodominant epitopes2
Affinity2
  • We selected 13 CD8 + and 12 CD4 + T cell epitopes considering parameters such as binding affinity to HLA class I and II molecules, promiscuity based on the number of different HLA alleles that bind to the epitopes, and immunogenicity. (springer.com)
  • Our results indicate that IgE Abs recognize conformational epitopes with high affinity and provide a structural basis for the highly efficient effector cell activation by allergen/IgE immune complexes. (rcsb.org)
Computational1
Silico5
  • The identification and mapping of B-cell epitopes on therapeutic proteins in silico is difficult owing to the conformational nature of the B-cell epitope, which is often composed of discontinuous stretches of amino acids that are brought together spatially by protein folding rather than a single linear contiguous sequence. (medscape.com)
  • 4. A novel multi-epitope peptide vaccine against cancer: an in silico approach. (nih.gov)
  • 9. In Silico-Guided Sequence Modification of Epitopes in Cancer Vaccine Development. (nih.gov)
  • 11. In Silico Approach in Designing a Novel Multi-Epitope Vaccine Candidate against Non-Small Cell Lung Cancer with Overexpressed G Protein-Coupled Receptor 56. (nih.gov)
  • Over the past four decades, numerous in silico methods have been developed for predicting B-cell epitopes. (bvsalud.org)
Vaccine Design1
  • Mapping the epitope of an antibody is of great interest, since it contributes much to our understanding of the mechanisms of molecular recognition and provides the basis for rational vaccine design. (tau.ac.il)
Specificity1
  • Furthermore, the epitope specificity seems to be limited, as shown by monoclonal antibody inhibition. (lu.se)
Antigens2
  • There are several methods available for mapping antibody epitopes on target antigens: X-ray co-crystallography and cryogenic electron microscopy (cryo-EM). (wikipedia.org)
  • The identification of B-cell epitopes in antigens is a crucial step in developing recombinant vaccines or immunotherapies for various diseases. (bvsalud.org)
Cross-reactive1
Peptide vaccine2
  • We then attempted to exploit this cross-reactivity to develop a peptide vaccine against against VAR2CSA based on the epitope that generated 3D10. (ualberta.ca)
  • 7. Identification of B and T cell epitope based peptide vaccine from IGF-1 receptor in breast cancer. (nih.gov)
Gp1201
Combinatorial1
Experimentally2
  • In addition, hCoronavirusesDB contains curated, experimentally validated B cell and T cell epitope data for these viruses. (oup.com)
  • Secondly, we have briefly described the historical perspectives and resources that maintain experimentally validated information on B-cell epitopes. (bvsalud.org)
Dissection1
  • They are also used as tools for the systematic dissection and mapping of chromosomes , in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. (lookformedical.com)
Phage1
  • Approach: Allergen epitope mapping will be accomplished by applying molecular genetic mutational analyses of recombinant allergen molecules, and state-of-the-art phage peptide-display mimotope and hydrogen/deuterium exchange (HDX) epitope mapping techniques. (usda.gov)
Vaccines1
  • 2007. Epitope mapping: the first step in developing epitope-based vaccines. (gershonilab.com)
Segments3
  • Note that conformational epitopes can include some linear segments. (wikipedia.org)
  • When we tested 3D10 against a broader, overlapping peptide array spanning SD1, we found that it recognized a discontinuous epitope consisting of three segments of SD1. (ualberta.ca)
  • Use of restriction endonucleases to analyze and generate a physical map of genomes, genes , or other segments of DNA . (lookformedical.com)
MAbs2
  • Epitope mapping has become prevalent in protecting the intellectual property (IP) of therapeutic mAbs. (wikipedia.org)
  • An increasing number of broadly neutralizing monoclonal Abs (mAbs) against HIV have been identified in recent years and have illuminated new neutralizing epitopes on the envelope (Env) glycoprotein complex. (plos.org)
Extracellular1
  • 3. Immunization with a novel chimeric peptide representing B and T cell epitopes from HER2 extracellular domain (HER2 ECD) for breast cancer. (nih.gov)
Algorithm2
Molecular1
  • Integral Molecular offers proprietary eptiope mapping services similar to those shown in this paper on a commercial basis. (plos.org)
Replication1
  • We and others have mapped replication origins to specific genomic loci in differentiated cells of flies, frogs and mammals (1,2) , but the nature of these loci, however, remains elusive. (nih.gov)
Bioinformatics1
  • 19. Predicted B-cell epitopes of HER-2 oncoprotein by a bioinformatics method: a clue for breast cancer vaccine development. (nih.gov)
Approach1
  • Therefore, in this paper, we have undertaken a systematic approach to provide a comprehensive review covering all aspects associated with the identification of B-cell epitopes. (bvsalud.org)
Depends1
  • In contrast, quaternary epitopes are conformational epitopes whose structure depends upon the arrangement of multiple protomers, or is enhanced by them, or may depend on the arrangement of multiple protomers ( i . e ., quaternary epitopes). (plos.org)
Assays1
  • AMMO1 recognizes a discontinuous epitope at the Domain-I/Domain-II interface between gH and gL and blocks membrane fusion and viral entry, as supported by cell-cell fusion assays. (nih.gov)
Infectious1
  • 2013. The use of epitope arrays in immunodiagnosis of infectious disease: hepatitis C virus, a case study. (gershonilab.com)
Strains1
  • N(A 90 ) totally disrupted or severely affected the epitope in 7 out of 8 strains tested. (biomedcentral.com)
Linear2
  • Epitopes are generally divided into two classes: linear and conformational/discontinuous. (wikipedia.org)
  • Firstly, we have covered the experimental techniques developed over the years for identifying linear and conformational epitopes, including the limitations and challenges associated with these techniques. (bvsalud.org)
Bind1
  • To enhance for isolation of quaternary epitope-targeting Abs (QtAbs), we previously used HIV virus-like particles (VLPs) to bind B cells from long-term non-progressor subjects to identify a panel of monoclonal Abs. (plos.org)
Relevance1
  • The relevance of this amino acid for the conformational SDOW17 epitope of PRRSV N was further confirmed by the opposite substitution in a functional cDNA clone of the genotype 2 isolate RVB-581. (biomedcentral.com)