Discontinuous conformational epitope. Medical search. Frequent questions

Anti-PvTRAMP antisera was obtained by inoculating rabbits with PvTRAMP B cell epitopes produced as synthetic peptides in order to assess its recognition in parasite lysates by Western blot and in intact parasites by indirect immunofluorescence. (biomedcentral.com)

The Pepitope Server is used to map epitopes using affinity-selected peptides. (wikipedia.org)

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)
Host-specific characteristics are important features and constraints for effective epitope prediction. (biomedcentral.com)
Within the SFB he wants to solve the three-dimensional structures of allergens and allergen-IgE immune complexes to develop tools for the prediction of conformational epitopes important for the evolution of allergens towards new vaccines. (allergy-research-program.at)
First, he will develop the methodology for the reliable prediction of conformational and/or discontinuous epitopes. (allergy-research-program.at)
Second, he will use experimentally determined IgE epitopes of clinically important allergens in this SFB for the modification of allergens towards hypoallergenic derivatives and as standard for the verification of the validity of his prediction methodology and for the improvement of the built in filter algorithms. (allergy-research-program.at)
NetCTL 1.2 algorithms enabled the prediction of probable T-cell epitopes which were structurally modeled and subjected to blind peptide-protein docking with HLA-A*02:01. (ojcius.net)

Conclusion This study implemented an integrative meta-analytical approach to model highly probable B-cell and T-cell epitopes as potential peptide-vaccine candidates for the treatment of EBV-related diseases. (ojcius.net)

Potential B-cell and T-cell epitopes were predicted for nine antigenic EBV proteins that mediate epithelial cell-attachment and spread, capsid self-assembly, DNA replication and processivity . (ojcius.net)
These were combined with a string-kernel method and an antigenicity predictive AlgPred tool to enhance accuracy in the end-point selection of highly potential antigenic EBV B-cell epitopes. (ojcius.net)
Results Computational predictions and sequence overlapping analysis yielded 18 linear (continuous) and discontinuous (conformational) subunit epitopes from the antigenic proteins with characteristic surface accessibility, flexibility and antigenicity, and predictive scores above the threshold value (1) set. (ojcius.net)
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)

This is the central theme of the project, because it should give access to all IgE epitopes on a particular allergen simultaneously, corresponding to the "polyclonal" situation as it occurs in vivo. (allergy-research-program.at)

Methods Predictive algorithms incorporated in the Immune Epitope Database (IEDB) resources were used to determine potential B-cell epitopes based on their physicochemical attributes. (ojcius.net)

Here, we compiled a detailed human antibody epitope map comprising epitope binning data and structures of multiple human monoclonal antibodies, including three new crystal structures of Pfs25 in complex with transmission-reducing antibodies from Malian volunteers immunized with Pfs25 conjugated to EPA and adjuvanted with AS01. (bvsalud.org)
This work informs immunogen design to focus the antibody response to transmission-reducing epitopes of Pfs25, enabling development of more potent transmission-blocking vaccines for malaria. (bvsalud.org)
We have previously described R1a-B6, an alpaca-derived single domain antibody (nanobody), that is capable of potent cross-subtype neutralization in vitro of H1N1, H5N1, H2N2, and H9N2 influenza viruses, through binding to a highly conserved epitope in the influenza hemagglutinin stem region. (frontiersin.org)
On the basis of its potential to block anti-collagen type II (CII) antibody-induced arthritis (CAIA) and to suppress the conformational activation of β 2 -integrins in leukocytes, the present study was undertaken to investigate its interference with leukocyte adherence to cytokine-activated endothelium. (biomedcentral.com)

Mutations that occur within the immunodominant epitopes of hepatitis B surface antigen (HBsAg) allow mutant virus to propagate in the presence of a neutralizing immune response, while wild-type virus is reduced to undetectable levels. (cdc.gov)

The mAb epitope comprises two closely spaced surfaces, I and II, connected by a sharp turn and bearing critical residues Asn46 and Lys47 on one surface, and Lys54 and Arg57 on the other. (ntnu.edu.tw)
Epitope surface II is further predicted to undergo conformational exchange in the millisecond to microsecond range. (ntnu.edu.tw)

He is interested in understanding conformational IgE epitopes on allergens and works on the development of computational programs for their analysis. (allergy-research-program.at)

This discontinuous epitope overlaps with the human IgE epitope(s) of Blo t 5. (ntnu.edu.tw)
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)
Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein. (cusabio.com)

A novel site was identified on HLA-A*02:01 with preferential affinity binding for modeled BMRF2, BXLF1 and BGLF4 T-cell epitopes. (ojcius.net)
1] Ansari, H. R., Raghava, G. P., Identification of conformational B-cell Epitopes in an antigen from its primary sequence. (degruyter.com)

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)

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)
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)
We applied this paradigm to successfully predict the epitope of the Trastuzumab antibody on the surface of the Her-2/neu receptor in a third model system. (tau.ac.il)
The IgE immunoglobulin (antibody) class binds to specific regions on the allergen proteins (termed epitopes) leading to allergic symptoms in patients. (usda.gov)
1997. Helical epitopes determined by low-stringency antibody screening of a combinatorial peptide library. (gershonilab.com)
2001. Dissection of the humoral immune response toward an immunodominant epitope of HIV: a model for the analysis of antibody diversity in HIV+ individuals. (gershonilab.com)
2006. Computational prediction of the cross-reactive neutralizing epitope corresponding to the monclonal antibody b12 specific for HIV-1 gp120. (gershonilab.com)
2011. Conformational and structural features of HIV-1 gp120 underlying the dual receptor antagonism by cross-reactive neutralizing antibody m18. (gershonilab.com)
However, we find that stable antibody domains with improved affinity are reliably identified by replacing the display antibody that recognizes an epitope tag at the terminus of both folded and unfolded antibody domains with a conformational ligand (Protein A) that recognizes a discontinuous epitope on the framework of folded antibody domains. (confex.com)
This study focused on identification of immunodominant epitopes in the Trop2 extracellular domain (ECD) that can mount an efficient anti-Trop2 antibody response. (bvsalud.org)
The vaccine candidate protein (Domains-gB) was recognized by a monoclonal antibody from a commercial ELISA kit used for IBR diagnostic, which may suggest that the epitopes are conserved of the entire infectious virus. (biomedcentral.com)

Antibodies are raised either against structural/conformational (discontinuous) or linear (continuous) epitopes. (medscape.com)
After this initial step, subsequent rigorous downselection procedures, such as the use of affinity-purified human specific antibodies to demonstrate expression of the epitope in parasites, in vitro determination of biological activity, and determination of the polymorphism of the selected fragments and immunogenicity in animal models, are reasonably rapid. (medscape.com)
To determine the ratio of patients' IgE antibodies recognizing the two forms of epitopes, we will use affinity chromatography to separate the two forms of antibodies and will test them by ELISA and western blot assays. (usda.gov)
Numerous broadly neutralizing antibodies (Abs) target epitopes that are formed or enhanced during mature HIV envelope formation ( i . e . quaternary epitopes). (plos.org)
Because epitope specificity may be a key factor determining anti-MOG reactivity we aimed at identifying a priori immunodominant MOG epitopes by monoclonal antibodies (mAbs) and at assessing clinical relevance of these epitopes in MS. (biomedcentral.com)
Thus high-titer reactivity likely represents high-affinity antibodies against pathologically relevant MOG epitopes, that are only present in a small proportion of patients with MS. Our study provides valuable information about requirements of anti-MOG reactivity for being regarded as a prognostic biomarker in a subtype of MS. (biomedcentral.com)
Three isoforms of recombinant MOG were generated and the differential exposure of immunodominant epitopes characterized by a panel of monoclonal anti-MOG antibodies. (biomedcentral.com)
Despite the potential clinical application of this finding, the epitopes of the three human P-gp-specific monoclonal antibodies MRK-16, UIC2 and 4E3, which bind to the extracellular loops (ECLs) have not yet been mapped. (nih.gov)
By generating human-mouse P-gp chimeras, we mapped the epitopes of these antibodies to ECLs 1 and 4. (nih.gov)
Computational modeling from the sequences from the immunoaffinity-selected mimotopes continues to be used in combination with great achievement for the elucidation of focus on epitopes of monoclonal antibodies. (academiaperuanadepsicologia.org)
An IgE epitope is a part of an allergen that is capable of binding to IgE antibodies and eliciting an immune response. (bvsalud.org)

mAbs defined unique immunodominant epitopes distinct to each of the isoforms. (biomedcentral.com)
Mutations that occur within the immunodominant epitopes of hepatitis B surface antigen (HBsAg) allow mutant virus to propagate in the presence of a neutralizing immune response, while wild-type virus is reduced to undetectable levels. (cdc.gov)

2008. Computational characterization of B-cell epitopes. (gershonilab.com)
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 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)
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)

1993. HIV binding to its receptor creates specific epitopes for the CD4/gp120 complex. (gershonilab.com)
[6] Schreiber M, Wachsmuth C, M?ller H, Odemuyiwa S, Schmitz H, Meyer S, Meyer B, Schneider-Mergener J. The V3-directed immune response in natural human immunodeficiency virus type 1 infection is predominantly directed against a variable, discontinuous epitope presented by the gp120 V3 domain. (org.ua)

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)
2007. Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. (gershonilab.com)
This study opened a fresh method of vaccine and diagnostics development predicated on phage screen epitope library screening. (academiaperuanadepsicologia.org)

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)
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)

2. Immunogenicity and antitumor efficacy of a novel human PD-1 B-cell vaccine (PD1-Vaxx) and combination immunotherapy with dual trastuzumab/pertuzumab-like HER-2 B-cell epitope vaccines (B-Vaxx) in a syngeneic mouse model. (nih.gov)
11. Novel engineered trastuzumab conformational epitopes demonstrate in vitro and in vivo antitumor properties against HER-2/neu. (nih.gov)

Many tree nut allergens have been subjected to linear epitope characterization but far less is known about conformational epitopes. (usda.gov)
To address these issues, we propose to 1) identify and map conformational epitopes on the otherwise well characterized allergens from cashew and almond nuts for comparison to previously mapped linear epitopes from these nut proteins. (usda.gov)

1. B-cell epitope peptide cancer vaccines: a new paradigm for combination immunotherapies with novel checkpoint peptide vaccine. (nih.gov)
3. A newly discovered PD-L1 B-cell epitope peptide vaccine (PDL1-Vaxx) exhibits potent immune responses and effective anti-tumor immunity in multiple syngeneic mice models and (synergizes) in combination with a dual HER-2 B-cell vaccine (B-Vaxx). (nih.gov)
10. A chimeric multi-human epidermal growth factor receptor-2 B cell epitope peptide vaccine mediates superior antitumor responses. (nih.gov)
12. [Epitope peptide vaccine with oncoantigen for cancer and its biomarker]. (nih.gov)
16. A novel multi-epitope peptide vaccine against cancer: an in silico approach. (nih.gov)

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)
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)

The ABCpred and BepiPred software were used to discover linear B-cell epitopes on envelope protein. (nih.gov)
Conformational B-cell epitopes on envelope protein were identified using SEPPA 3.0 and Ellipro tools. (nih.gov)
SEPPA 3.0 and Elliprotools predicted consensus conformational envelope 98-110 (DRGWGNGCGLFGK) and envelope 248-251 (AHAK) epitopes and one residue ( 75 PRO) within envelope protein as a component of B-cell epitopes. (nih.gov)
Generally, it is thought that Env epitopes that induce broadly neutralizing Abs are difficult to access and poorly immunogenic because of the characteristic oligomerization, conformational flexibility, sequence diversity and extensive glycosylation of Env protein. (plos.org)
Conformational epitopes within mature Env can be found within a single protomer, and distant patches of amino acid sequences that are brought together by protein folding. (plos.org)
isolated against the Western world Nile virus envelope protein (E) which acknowledge distinct epitopes inside the protein. (academiaperuanadepsicologia.org)
Genetic and antigenic characterization of IVI-1173 revealed the importance of amino acid 90 of the nucleocapsid protein N as part of a conformational epitope. (biomedcentral.com)
The extraordinary biology and transmissibility of these disorders stems from the protean conformational properties of the prion protein (PrP). (cdc.gov)

Antigenic regions within gp41 present unexpectedly diverse structural epitopes, including these QtAb epitopes, which may be targeted by the naturally occurring Ab response to HIV infection. (plos.org)
Although CWD prions from Finland and Norway moose had comparable responses to primary structural differences at residue 226, other distinctive criteria, including transmission kinetics, patterns of neuronal degeneration, and conformational features of prions generated in the brains of diseased mice, demonstrated that the strain properties of Finland moose CWD prions are different from those previously characterized in Norway CWD. (cdc.gov)

The output is usually 1-3 epitope candidates on the surface of the atomic structure of the antigen. (tau.ac.il)

Here we present Mapitope, a computer algorithm for epitope mapping. (tau.ac.il)
Detailed epitope mapping studies revealed that two of the four epitopes were located in the gp41 subunit of Env. (plos.org)
2003. The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1. (gershonilab.com)
2007. Epitope mapping: the first step in developing epitope-based vaccines. (gershonilab.com)

These predicted linear and conformational B-cell epitopes will help in designing peptide vaccines that will activate the humoral response. (nih.gov)

Generally, it is thought that the broadly neutralizing epitopes may be relatively weakly immunogenic and structurally difficult to access [ 1 ]. (plos.org)

The identification of B-cell epitopes in antigens is a crucial step in developing recombinant vaccines or immunotherapies for various diseases. (bvsalud.org)

Over the past four decades, numerous in silico methods have been developed for predicting B-cell epitopes. (bvsalud.org)

The specificity of these biological effects is supported by the lack of any significant change, either on neuronal activity or on cellular integrity, shown by administration of its reverse sequence counterpart which behaves as an inactive control, likely due to a poor conformational flexibility which makes it unable to dynamically perturb biomembrane-like environments. (oncotarget.com)

The IgE-defined dominant epitope is discontinuous and formed by 21 residues located mostly within the beta strands. (rcsb.org)

Two consensus linear B-cell epitopes, envelope 165-180 (AKVEITPNSPRAEATL) and envelope 224-238 (PWHAGADTGTPHWNN) were identified using ABCpred and BepiPredtools. (nih.gov)

Previous attempts were focused on engineering artificial mini proteins that are able to mimic the conformational epitopes of native proteins. (medscape.com)
Aim 2) is to assess the relative contribution of conformational and linear epitopes to the IgE-reactivity of these proteins. (usda.gov)
Our final aim, 3), is to assess the relative stability of the conformational epitopes when these almond and cashew proteins are subjected to conditions comparable to those that would be encountered during food processing to see if food processing can be used to lessen allergenic potential. (usda.gov)
The stability (durability) of the identified epitopes will be assessed by subjected the nut allergen proteins to various chemical and physical denaturing conditions. (usda.gov)

2013. The use of epitope arrays in immunodiagnosis of infectious disease: hepatitis C virus, a case study. (gershonilab.com)

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)

[ 19 ] The natively unstructured regions, in contrast to the a-helical coiled coil motifs, do not fold in any particular unique structure [ 20 ] and, as previously mentioned, are the most suitable for mimicking native linear epitopes. (medscape.com)
However, existing reviews have only covered specific aspects, such as the progress in predicting conformational or linear B-cell epitopes. (bvsalud.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)

The first step was to select potential conformational epitopes by using a genome-wide, bioinformatics-based approach. (medscape.com)
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)

5. A paradigm shift: Cancer therapy with peptide-based B-cell epitopes and peptide immunotherapeutics targeting multiple solid tumor types: Emerging concepts and validation of combination immunotherapy. (nih.gov)

This study was thus designed to assess the MOG epitope usage in humans employing a novel quantitative high-throughput ELISA. (biomedcentral.com)

N(A 90 ) totally disrupted or severely affected the epitope in 7 out of 8 strains tested. (biomedcentral.com)

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)

they also failed to compete for binding by Abs to known major neutralizing epitopes. (plos.org)

In contrast to anti-MOG reactivity observed in a mouse model of MS, in patients with MS these never reacted with ubiquitously exposed epitopes. (biomedcentral.com)

Identifying and characterizing human-allergy-relevant epitopes are important for diagnosis and prognosis of food allergy and development of immunotherapy treatments. (bvsalud.org)

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