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Analysis of inhibitory epitopes in the Plasmodium falciparum rhoptry protein RAP-1 including identification of a second inhibitory epitope.

Immune responses to Plasmodium falciparum rhoptry-associated protein 1 (RAP-1), RAP-2, and RAP-3 appear to contribute to protection against infection by this human malarial parasite. This conclusion is suggested by results of monkey immunization trials and of cell culture studies showing antibody-dependent inhibition of erythrocyte invasion. In the present study, splenectomized owl monkeys were infected with P. falciparum in order to monitor anti-RAP-1 antibody production as antiparasite immunity developed. The monkeys responded to a primary infection with the production of antibodies to a fragment of RAP-1 containing amino acids 1 to 294 (RAP-1(1-294)). After drug cure and reinfection, the monkeys had a prolonged prepatent period, indicating they had already developed partial immunity to the parasite. Sera from these animals showed major increases in anti-RAP-1(1-294) antibodies. In contrast, only low levels of antibodies to inhibitory B-cell epitope 1 (iB-1), an inhibitory epitope in RAP-1(1-294) with the sequence N200TLTPLEELYPT211, was observed after the initial parasite infection, and the anti-iB-1 antibodies were not readily boosted upon reinfection. These results suggest that iB-1 is an immunogenic but not immunodominant epitope and that anti-iB-1 antibodies do not substantially contribute to early stages of naturally acquired immunity in the owl monkey model. To identify additional epitopes bound by inhibitory antibodies, mouse monoclonal antibodies were produced with a recombinant fusion protein containing RAP-1(1-294). Monoclonal antibody 1D6 inhibited parasite invasion of erythrocytes in vitro. 1D6 did not bind peptide iB-1 but rather bound a second inhibitory epitope called iB-2. iB-2, like iB-1, is found near the amino terminus of p67, a RAP-1 processing product thought to be involved in merozoite invasion of erythrocytes. Since anti-iB-1 antibodies were not readily produced during parasite infection, it may be desirable to direct antibody responses to particular epitopes in RAP-1, such as iB-1 and iB-2.

Amino Acid Sequence↗

Solid-phase epitope recovery: a high throughput method for antigen identification and epitope optimization.

Self tolerance to MHC class I-restricted nonmutated self Ags is a significant hurdle to effective cancer immunotherapy. Compelling evidence is emerging that altered peptide ligands can be far more immunogenic than their corresponding native epitopes; however, there is no way to reliably predict which modifications will lead to enhanced native epitope-specific immune responses. We reasoned that this limitation could be overcome by devising an empirical screen in which the nearly complete combinatorial spectrum of peptides of optimal length can be rapidly assayed for reactivity with a MHC class I-restricted cytotoxic T cell clone. This method, solid-phase epitope recovery, quantitatively ranks all reactive peptides in the library and allows selection of altered peptide ligands having desirable immunogenic properties of interest. In contrast to rationally designed MHC anchor-modified peptides, peptides identified by the present method are highly substituted in predicted TCR contact residues and can reliably activate and expand effector cell populations in vitro which lyse target cells presenting the wild-type epitope. We demonstrate that solid-phase epitope recovery peptides corresponding to a poorly immunogenic epitope of the melanoma Ag, gp100, can reliably induce wild-type peptide-specific CTL using normal donor T cells in vitro. Furthermore, these peptides can complement one another to induce these responses in an overwhelming majority of normal individuals in vitro. These data provide a rationale for the design of superior vaccines comprising a mixture of structurally diverse yet functionally convergent peptides.

Antigen Presentation↗

3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins.

Neutralizing antibodies often recognize conformational, discontinuous epitopes. Linear peptides mimicking such conformational epitopes can be selected from phage display peptide libraries by screening with the respective antibodies. However, it is difficult to localize these "mimotopes" within the three-dimensional (3D) structures of the target proteins. Knowledge of conformational epitopes of neutralizing antibodies would help to design antigens able to elicit protective immune responses. Therefore, we provide here a software that allows to localize linear peptide sequences within 3D structures of proteins. The 3D-Epitope-Explorer (3DEX) software allows to map conformational epitopes in 3D protein structures based on an algorithm that takes into account the physicochemical neighborhood of C(alpha)- or C(beta)-atoms of individual amino acids. A given amino acid of a peptide sequence is localized within the protein and the software searches within predefined distances for the amino acids neighboring that amino acid in the peptide. Surface exposure of the amino acids can also be taken into consideration. The procedure is then repeated for the remaining amino acids of the peptide. The introduction of a joker function allows to map peptide mimotopes, which do not necessarily have 100% sequence homology to the protein. Using this software we were able to localize mimotopes selected from phage displayed peptide libraries with polyclonal antibodies from HIV-positive patient plasma within the 3D structure of gp120, the exterior glycoprotein of HIV-1. We also analyzed two recently published peptide sequences corresponding to known conformational epitopes to further confirm the integrity of 3DEX.

Algorithms↗

Display of epitopes on the surface of tobacco mosaic virus: impact of charge and isoelectric point of the epitope on virus-host interactions.

The biophysical properties of the tobacco mosaic tobamovirus (TMV) coat protein (CP) make it possible to display foreign peptides on the surface of TMV. The immunogenic epitopes G5-24 from the rabies virus (RV) glycoprotein, and 5B19 from murine hepatitis virus (MHV) S-glycoprotein were successfully displayed on the surface of TMV, and viruses accumulated to high levels in infected leaves of Nicotiana tabacum Xanthi-nn. The peptide RB19, which contains an arginine residue plus the 5B19 epitope fused to the CP (TMV-RB19), resulted in the induction of necrotic local lesions on inoculated leaves of N. tabacum Xanthi-nn and cell death of infected BY2 protoplasts. RNA dot blot assays confirmed that expression of the acidic and basic pathogenesis-related PR2 genes were induced in infected Xanthi-nn leaf tissue. TMV that carried epitope 31D from the RV nucleoprotein did not accumulate in inoculated tobacco leaves. Analysis of hybrid CPs predicted that the isoelectric points (pI):charge value was 5.31:-2 for wild-type CP, 5.64:-1 for CP-RB19, and 9.14:+2 for CP-31D. When acidic amino acids were inserted in CP-RB19 and CP-31D to bring their pI:charge to near that of wild-type CP, the resulting viruses TMV-RB19E and TMV-4D:31D infected N. tabacum Xanthi-nn plants and BY2 protoplasts without causing cell death. These data show the importance of the pI of the epitope and its effects on the hybrid CP pI:charge value for successful epitope display as well as the lack of tolerance to positively charged epitopes on the surface of TMV.

Amino Acid Sequence↗

Binding patterns of 51 monoclonal antibodies to peptide and carbohydrate epitopes of the epithelial mucin (MUC1) on tissue sections of adenolymphomas of the parotid (Warthin's tumours): role of epitope masking by glycans.

Warthin's tumours provide a unique opportunity to distinguish and compare monoclonal antibodies (mAbs) to the epithelial mucin, MUC1. In this study, we have applied the range of anti-MUC1 antibodies submitted to the ISOBM TD-4 Workshop for this purpose. mAbs and lectins against MUC1-associated carbohydrate epitopes were also included. Among 39 mAbs to peptide epitopes of MUC1, eight distinct types of staining patterns towards the two epithelial cell layers of Warthin's tumours could be observed. A majority of 27 mAbs reacted preferentially (17) or exclusively (10) with columnar cells, whereas 10 mAbs favoured basal cells (1 of them almost exclusively). The observed staining patterns revealed no correlation with the epitopes. However, after carbohydrate-specific periodate oxidation, 33 of the mAbs stained columnar and basal cells equally well, indicating that epitope masking by glycan side chains was in most cases responsible for the different staining patterns. The results demonstrate the profound impact of glycosylation on immunohistochemistry. Among carbohydrate epitopes, sialyl-TF, sialyl-Le(x), sialyl-dimeric Le(x) and Tn were expressed on both columnar and basal cells (the s-TF3 isomer on columnar cells only). The carcinoma-associated Thomsen-Friedenreich epitope was absent.

Adenolymphoma↗

Nested sets of protein fragments and their use in epitope mapping: characterization of the epitope for the S4D5 monoclonal antibody binding to receptor associated protein.

The present report describes a new general procedure by which linear and some structure-dependent epitopes may be mapped in a protein antigen using a nested set of protein fragments prepared from partial proteolysis products of a recombinant protein. Briefly, the antigen, fused to an affinity tag, is partially fragmented and affinity sorted under denaturing conditions to produce a nested set of polypeptides, consisting of N- (or C-)terminal fragments. Immunoblots of SDS-PAGE fractionated sets of fragments are therefore directly readable in terms of molecular mass--i.e., approximate sequence positions--that identify sequence segments harbouring an epitope and any additional structural elements, required to maintain epitope conformation. Blots of N- and C-terminal nested sets of polypeptide fragments representing the human receptor associated protein (RAP) were prepared and probed with mAb S4D5 (Moestrup and Gliemann, 1991). Fragments 1-177 and 94-323 were the shortest fragments detected by the antibody, suggesting the presence of an epitope within the 94-177 segment. Independent mapping based on recombinant fragments of the RAP homologue, rat Heymann nephritis antigen, confirmed that the epitope resides in the Pro115-Asp177 segment. The model study demonstrates the utility of nested sets of protein fragments as fast and inexpensive tools for epitope mapping.

Amino Acid Sequence↗

Epitope specificity and V gene expression of cerebrospinal fluid T cells specific for intact versus cryptic epitopes of myelin basic protein.

Recent evidence supports the possible involvement of myelin basic protein (BP) as one of the target autoantigens in multiple sclerosis (MS), including elevated frequencies of MS blood and cerebrospinal fluid (CSF) T cells, and the presence in MS plaque tissue of V beta gene sequences and CDR3 motifs characteristic of BP-reactive T cells. Because of its proximity to the target organ, the CSF has long been thought to harbor T cells involved in the pathogenic process. In order to evaluate their frequency and response characteristics, BP-reactive T cells were isolated by limiting dilution from the CSF of patients with MS and other neurological diseases (OND) for quantitation and determination of epitope specificity and V alpha and V beta gene expression. In addition to isolates responsive to intact BP epitopes that were present at a significantly higher frequency in MS versus OND CSF, we here describe a second clonotype responsive to 'cryptic' BP epitopes that is present at approximately equal frequencies in MS and OND patients. In spite of their difference in recognition of intact versus 'cryptic' BP determinants, both clonotypes predominantly recognized epitopes in the N terminal half of human BP, using a similar V gene repertoire that included biased use of V alpha 2 and to a lesser degree V beta 7 and V beta 18. These V gene biases were not related to the epitope specificity of the T cells, indicating that V gene selection is not epitope-driven. These data suggest that there is differential recognition of intact versus 'cryptic' BP determinants in MS versus OND patients that may be related to the processing and presentation of BP to the immune system.

Adult↗

Humanization and epitope mapping of the H23 anti-MUC1 monoclonal antibody reveals a dual epitope specificity.

The tumor-associated antigen MUC1 is a cell surface mucin that is expressed on the apical surface of most glandular epithelial cells, including the ducts of the breast, ovary, pancrease, lung and colon. During malignancy, epithelial tissues regularly display elevated levels of MUC1 in a non-polar fashion and in an underglycosylated form, exposing cryptic peptide and carbohydrate epitopes. As such, MUC1 is regarded a potential target for immunotherapeutical intervention. Murine monoclonal H23 antibody specifically recognizes a MUC1 epitope on the surface of human breast cancer cells. We describe the cloning of the variable domains of H23 and their expression in (Escherichia coli) E. coli as maltose-binding protein-scFv (MBP-scFv) fusions. We humanized H23 and evaluated the binding properties of the murine and the humanized recombinant forms, which were similar in affinity and specificity, but lower in apparent affinity in comparison to the original monoclonal IgG. We mapped the epitope of humanized H23 by affinity-selecting a phage-displayed random peptide library on humanized H23 scFv-displaying bacteria. Our results show that humanized H23 binds an epitope corresponding to the MUC1 tandem repeat and an additional epitope not related to MUC1. These epitopes are competitive, bound with similar affinities and are recognized by the original murine H23 monoclonal antibody as well.

Animals↗

Linkage of Ii-Key segment to gp100(46-58) epitope enhances the production of epitope-specific antibodies.

Linkage of the Ii-Key segment of the Ii protein to MHC class II epitope gp100(46-58) using a polymethylene linker significantly enhances the production of epitope-specific antibodies in HLA-DR4-IE transgenic mice. This enhancement is not restricted by the spacer length in between the Ii-Key and epitope. The use of either IFA or CFA induced only epitope-specific IgG1. In contrast, CpG adjuvant induced both IgG1 and IgG2a isotypes. These results indicate that the Ii-Key hybrid technology is a novel and potent method to increase the immunogenicity of a MHC class II epitope. It can also be used to more efficiently generate epitope-specific antibodies.

Amino Acid Sequence↗

Spying the neutralizing epitopes on E2 N-terminal by candidate epitope-vaccines against classical swine fever virus.

Our previous study proved that the N-terminal (aa693-711) of glycoprotein E2 contained sequential neutralizing epitopes. In this study, four candidate epitope-vaccines (EVs) were separately prepared and evaluated. Among them, epitope-vaccine EV-BC1a (BC1a: aa693-699) induced high level of epitope-specific neutralizing antibodies and exhibited similar protective capability with that induced by Chinese vaccine strain (C-strain). These results confirmed CKEDYRY (aa693-699) as a principal sequential neutralizing epitope on E2 N-terminal. Moreover, these findings also indicate that epitope-vaccine is a potent candidate strategy for marker vaccine against classical swine fever virus (CSFV).

Amino Acid Sequence↗

Selection of SARS-coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice.

Antibodies to SARS-Coronavirus (SARS-CoV)-specific B cell epitopes might recognize the pathogen and interrupt its adherence to and penetration of host cells. Hence, these epitopes could be useful for diagnosis and as vaccine constituents. Using the phage-displayed peptide library screening method and purified Fab fragments of immunoglobulin G (IgG Fab) from normal human sera and convalescent sera from SARS-CoV-infected patients as targets, 11 B cell epitopes of SARS-CoV spike glycoprotein (S protein) and membrane protein (M protein) were screened. After a bioinformatics tool was used to analyze these epitopes, four epitope-based S protein dodecapeptides corresponding to the predominant epitopes were chosen for synthesis. Their antigenic specificities and immunogenicities were studied in vitro and in vivo. Flow cytometry and ELISPOT analysis of lymphocytes as well as a serologic analysis of antibody showed that these peptides could trigger a rapid, highly effective, and relatively safe immune response in BALB/c mice. These findings might aid development of SARS diagnostics and vaccines. Moreover, the role of S and M proteins as important surface antigens is confirmed.

Amino Acid Sequence↗

Assembly of synthetic peptide vaccines by chemoselective ligation of epitopes: influence of different chemical linkages and epitope orientations on biological activity.

In this paper, we describe the assembly of synthetic peptide vaccines composed of a T helper cell epitope and a B cell epitope that were synthesized separately and then attached using three different chemoselective ligation methods: oxime bond formation, thioether bond formation and disulfide bond formation. The resulting vaccines were tested in animals to investigate their efficacy. We found that thioether bond formation gave the highest yield of material and that the chemistry involved did not adversely affect immunogenicity and biological activity of the peptide vaccine. Ligation of epitopes by oxime bond formation did not diminish biological activity either, but the yields of peptide vaccine were lower than when thioether bond formation was used. The vaccines in which a disulfide bond was used to attach the two epitopes resulted in the lowest yield and produced vaccines that also generated a weaker immune response with sub-optimal biological activity. Connecting the T helper epitope via its N-terminus or its C-terminus to the N-terminus of the B cell epitope had little influence on resulting immunogenicity and biological activity.

Amino Acid Sequence↗

B-cell epitopes of the allergen Chi t 1.01: peptide mapping of epitopes recognized by rabbit, murine, and human antibodies.

BACKGROUND: Chi t 1.01, a hemoglobin of the midge Chironomus thummi thummi, is a widespread environmental and occupational allergen. The aim of the present investigation was to identify and compare peptides involved in B-cell epitopes of Chi t 1.01 recognized by 15 human IgE sera, six murine monoclonal antibodies (mAbs), and a polyclonal rabbit antiserum. METHODS: Synthetic peptides 19-21 amino acids long covering the whole Chi t 1.01-sequence were covalently coupled to activated paper disks as well as adsorbed to wells of immunoplates and used for enzyme-linked immunosorbent assay. For fine epitope mapping, we used overlapping synthetic octapeptides with one amino-acid offset. RESULTS: Peptides containing the amino acids 13-17, 23-29, and 40-50 were recognized by three of the mAbs, while three other mAbs reacting with none of the peptides obviously recognized conformational epitopes. Binding sites for rabbit antibodies and for human IgE antibodies were scattered over the whole molecule. The peptide 80-100 seemed to comprise at least one important IgE epitope. Depending on the method of antigen binding to the solid phase, differing results were obtained. CONCLUSIONS: Several linear epitopes in Chi t 1.01 are recognized by human IgE antibodies, by mAbs, and by polyclonal rabbit antibodies. In addition, the results indicate the presence of conformational epitopes.

Amino Acid Sequence↗

Synthetic peptide epitope-based polymers: controlling size and determining the efficiency of epitope incorporation.

The assembly of synthetic peptide-based vaccines that incorporate multiple epitopes is a major goal of vaccine development, because such vaccines will potentially allow the immunization of outbred populations against a number of different pathogens. We have shown that free radical-induced polymerization of individual peptide epitopes results in the incorporation of multiple copies of the same or different epitopes into high molecular weight immunogens (O'Brien-Simpson, N.M., Ede, N.J., Brown, L.E., Swan, J. & Jackson, D.C. (1997) Polymerization of unprotected synthetic peptides: a view toward synthetic peptide vaccines. J. Am. Chem. Soc.119, 1183-1188; Jackson, D.C., O'Brien-Simpson, N., Ede, N.J. & Brown, L.E. (1997) Free radical induced polymerization of synthetic peptides into polymeric immunogens. Vaccine 15, 1697-1705). The ability to control the size of these polymers, to determine the physical and chemical properties of the backbone material and also to know the extent to which individual peptide epitopes are incorporated are important manufacturing considerations and form the subject of this study. We show here that the polymerization process is highly efficient with at least 70% of peptides incorporated into the resulting polymer, that acrylamide and acryloylated amino acids can be used as comonomers with peptide epitopes in the polymerization reaction and that the choice of the comonomer can influence the properties of the resulting polymer. We also show that the size of chain growth polymers is restricted in the presence of chain transfer agents, that the resulting polymer size can be predicted and that there is little or no difference in the immunogenicity of polymers that range in apparent molecular size between 18 kDa and 335 kDa. The successful polymerization of peptide epitopes with an acryloyl-amino acid creates the potential for introducing different physical and chemical properties into artificial protein immunogens.

Acrylamide↗

The Fya, Fy6 and Fy3 epitopes of the Duffy blood group system recognized by new monoclonal antibodies: identification of a linear Fy3 epitope.

Four new anti-Duffy murine monoclonal antibodies (MAbs): two anti-Fy6 (MIMA-107 and MIMA-108), one anti-Fya (MIMA-19) and one anti-Fy3 (MIMA-29) were characterized. Identification of epitopes by means of synthetic peptides (Pepscan) showed that the anti-Fy6 reacted most strongly with peptides containing the sequence 19QLDFEDV25 of the Duffy glycoprotein, and less strongly with peptides containing LDFEDV (MIMA-107) or LDF only (MIMA-108). The anti-Fya recognized epitope 38DGDYGA43 containing the Gly42 residue, which defines the Fya blood group antigen. MIMA-29 is the first anti-Fy3 reactive with a linear epitope 281ALDLL285 located in the fourth extracellular domain (ECD4, loop 3) of the Duffy glycoprotein. The four new antibodies extend the list of six anti-Fy MAbs formerly characterized by Pepscan analysis that allow some general conclusions. Fine specificities of various anti-Fya, or anti-Fy6 are not identical, but all of them recognize linear epitopes located around, respectively, Gly42 or between two potential N-glycosylation sites at Asn16 and Asn27. Anti-Fy3 recognize either a linear epitope located in ECD4, or a conformational epitope that includes amino acid residues of ECD4 and of other ECDs.

Animals↗

Analysis of a conformation-independent epitope and a conformational epitope in a protein: a study on cobrotoxin from Taiwan cobra venom.

The antibodies against cobrotoxin were separated into two antibody preparations by successive affinity chromatographies on reduced and S-carboxymethylated (RCM)-cobrotoxin-Sepharose, and cobrotoxin-Sepharose columns. The antibodies (abbreviated as Abcf-i) that bound with the RCM-cobrotoxin-Sepharose were verified to specifically recognize the continuous epitopes of cobrotoxin, which were insensitive to conformational changes. Whilst the antibodies (abbreviated as Abcf-d) that did not bind with the RCM-cobrotoxin-Sepharose column recognized the conformational epitopes in cobrotoxin. The two antibody preparations were employed to screen the antigenic peptides derived from the proteolytic hydrolysate of cobrotoxin and RCM-cobrotoxin. Five antigenic peptides (AP-4, AP-5, AP-10, AP-11, and AP-12) were obtained from the acid protease A-digested hydrolysate of cobrotoxin, and two antigenic peptides (V8-2 and V8-4) were found in the hydrolysate of RCM-cobrotoxin after hydrolysis with Saccharomyces aureus V8 protease. The segments at positions 1-21 and 22-38 encompassed the peptide fractions, AP-4, AP-5, V8-2, and V8-4, that reacted with Abcf-i, indicating that the two segments bore the continuous epitopes of cobrotoxin. Alternatively, AP-10, AP-11, and AP-12 reacted with both Abcf-i and Abcf-d. The structures of the three peptides had a common segment at positions 43-62, suggesting that this region comprised the conformation-independent epitopes as well as conformational epitopes in cobrotoxin. These results reflected that the conformation-independent and conformational epitopes in a protein can be separately identified.

Amino Acid Sequence↗

Immunogenic and antigenic epitopes of immunoglobulins. X: Monoclonal antibodies specific for human IgA, the IgA1 and IgA2 subclasses and an nA2m(2) iso-allotypic epitope.

Monoclonal antibodies (McAb) specific for human IgA, the IgA1 and IgA2 subclasses and the iso-allotypic epitope nA2m(2) have been produced. Three distinct McAb recognize an IgA1-specific epitope expressed in the C alpha 2 domain or the hinge region whilst a further McAb is directed possibly to an IgA1 hinge region epitope. The McAb having nA2m(2) specificity recognizes an iso-allotypic epitope expressed within the Fab region. IgA1 and IgA2 epitopes were detected in gorilla but not rhesus or baboon sera suggesting that the IgA subclasses represent a recent gene duplication even. However, these epitopes were also detected in some non-primate sera.

Animals↗

Cell-invasive activity of epitope-tagged adenylate cyclase of Bordetella pertussis allows in vitro presentation of a foreign epitope to CD8+ cytotoxic T cells.

The adenylate cyclase (AC) toxin (CyaA) of Bordetella pertussis has an invasive catalytic domain (AC domain) which penetrates the cytoplasmic membrane of a variety of eukaryotic cells and intoxicates them by unregulated synthesis of cyclic AMP. Previous work led to identification of five permissive sites in the AC domain at which heterologous peptides are accommodated without affecting its enzymatic properties. We have constructed a set of CyaA toxins tagged at these permissive sites by insertion of a CD8+ T-cell epitope, RPQASGVYMGNLTAQ, from the nucleoprotein of lymphocytic choriomeningitis virus. Introduction of the epitope at any of the five sites did not affect the capacity of the toxin to deliver its AC domain into target cells. Moreover, the toxin with the inserted epitope was shown to sensitize target cells for lysis by epitope-specific CD8+ cytotoxic T lymphocytes in vitro, showing that the tagged AC was processed for presentation of the lymphocytic choriomeningitis virus epitope in association with the major histocompatibility complex class I molecules. This finding indicates that by virtue of delivery of foreign epitopes into the antigen-presenting cells, purpose-designed recombinant CyaAs may be useful for induction of specific major histocompatibility complex class I-restricted cell-mediated immunity also in vivo.

Adenylyl Cyclases↗