Epitope mapping.
Epitope mapping can be used to identify areas of a protein that an antibody recognizes and binds to. Monoclonal antibodies are easier to characterize, but epitope maps can also be produced for polyclonal antisera.
Animals↗
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Glycoprotein B of Aujeszky's disease virus: topographical epitope mapping and epitope-specific antibody response.
A panel of 26 monoclonal antibodies (mAbs) against glycoprotein B (gB) of Aujeszky's disease (pseudorabies) virus (ADV), a glycoprotein complex consisting of three glycoproteins, gBa, gBb, and gBc, was produced by two research groups and was used for the topographical epitope mapping of gB. An epitope map was constructed in which the identified epitopes of gB were situated in 14 topologically distinct antigenic domains; ten antigenic domains represented by 22 mAbs were localized on gBc, while four antigenic domains represented by four mAbs resided on gBb of the gB complex. All the epitopes located on gBc appeared to be conformation-dependent, whereas all the epitopes on gBb were conformation-independent. The identified epitopes of gB were conserved among laboratory, vaccine and field ADV strains. Conformation-dependent epitopes were shown to contribute largely to the overall antibody response to gB in naturally infected swine and immunized mice. Moreover, it was found that most of the infected animals responded relatively weakly to the identified conformation-independent epitopes of gB, while a group of immunodominant epitopes that induced a strong antibody response was represented exclusively by conformation-dependent epitopes from different antigenic domains. The results clearly demonstrated that conformation-dependent epitopes of gBc play a crucial role in inducing the humoral immune response to gB of ADV during the natural infection of swine and immunization of mice. The application of mAbs of our panel as research and diagnostic tools is discussed.
Animals↗
[Epitope mapping of monoclonal antibodies to human plasma membrane Ca2-ATPase].
Overlapping fragments of the fourth isoform of human plasma membrane Ca(2+)-ATPase (hPMCA4) and several fragments of hPMCA1 were expressed in bacterial cells and purified by metal affinity chromatography. Enzyme immunoassays of the fragments helped map epitopes for 4 monoclonal antibodies (2D8, 8B8, 7C8 and 5E6). The epitope for 2D8 was localized within the 222-249 site (i.e., in the putative transduction domain), the epitopes for 8B8 and 7C8 were localized within the 330-353 site, in which phospholipids are presumably bound, and the 5E6 epitope was found within the 791-843 site, where the putative hinge region is situated. 2D8 recognizes hPMCA1 and hPMCA4 isoforms, while 8B8 and 7C8 are specific for hPMCA4. The amino acid sequences of these epitopes and phage-displayed mimotopes were compared.
Amino Acid Sequence↗
Epitope mapping using histidine-tagged protein fragments: application to Escherichia coli RNA polymerase sigma 70.
We present a simple, rapid, and inexpensive method for mapping epitopes of monoclonal antibodies using His-tagged protein fragments. In essence, four steps are involved: (i) purify overproduced His-tagged protein from inclusion body; (ii) fragment the protein by partial chemical or enzymatic hydrolysis and isolate the His-tagged peptides with a Ni(2+)-chelate column to generate a "ladder" containing a distribution of peptide fragment sizes; (iii) fractionate the isolated peptides by SDS-polyacrylamide gel electrophoresis and probe the ladder by immunoblot analysis; (iv) determine the size of the fragments that do and do not bind the monoclonal antibody using size markers specific to the His-tagged protein being studied. We have applied this method successfully to map the epitope positions of known and new monoclonal antibodies to Escherichia coli sigma 70. We believe this method will find broad application.
Antibodies, Monoclonal↗
The use of T bag synthesis with paper discs as the solid phase in epitope mapping studies.
Epitope mapping with synthetic peptides bound to derivatized paper discs has been investigated using the discs both as a solid-phase matrix for peptide synthesis as well as the solid phase in immunologic testing procedures without detachment of the peptides from the paper discs. Using the T bag (tea bag) method the simultaneous synthesis and subsequent immunologic testing of large numbers of peptides was demonstrated for the feline major allergen Fel d I. A total of 15,000 paper disc-bound peptides, comprising the 146 nonapeptides overlapping by eight amino acid residues on both chains, were synthesized simultaneously with 100 paper discs per T bag. Using these paper disc-bound peptides as the solid phase in radioimmunoassays the binding sites found coincided with those detected in the PEPSCAN with the commercially available epitope mapping kit and with the binding sites that had been found with Sepharose-coupled peptides. The signal to background-ratio in the paper disc-RIA was comparable to that in the PEPSCAN and the reproducibility was good. The bound antibodies could be eluted from the paper disc-bound peptides, permitting regeneration and repeated use of the paper discs for immunologic testing. This method was shown to be a useful alternative to the PEPSCAN and to have the major advantage that large numbers of antibodies could be tested with large numbers of peptides simultaneously.
Allergens↗
Generation and epitope mapping of high-affinity scFv to eukaryotic elongation factor 1A by dual application of phage display.
To generate specific tools for, in particular, localization studies of the eukaryotic elongation factor 1A (eEF1A), we have applied phage display in various formats to affinity-improve and map epitopes of two previously isolated, low-affinity single-chain Fv (scFv) G3 and D1. The scFv differ in their reactivity toward the eEF1A isoforms, eEF1A-1 and eEF1A-2. By PCR-based randomization of six residues within the variable light chain CDR3 (LCDR3), and subsequent phage-based affinity-selection, two 'families' of affinity-improved scFv were obtained. The scFv of highest affinity, A8, has a Kd of 9 nM to eEF1A-1. Interestingly, two affinity-improved scFvs have abnormally short LCDR3 consisting of two and four residues compared to 11 in the parental scFv. Hence, the LCDR3 of the parental clones may play a modulating rather than a direct role in antigen-binding. Despite different preferences for the eEF1A isoforms, both families of scFv recognize antigenic determinant(s), which was mapped to residues 413-450 of eEF1A-1/2 by Western blot analysis of recombinant human eEF1A (hEF1A) fragments. Prior to the Western blotting analysis, the epitope location had been suggested using a novel approach where phage-antibody repertoire derived scFv were used to select phage-displayed peptides. Hereby, peptides containing a SFXD motif, matching the SFSD(414-418) sequence found in hEF1A-1 were isolated. The structure of eukaryotic EF1A from yeast indicates a discontinuous nature of the epitope with distal functional elements juxtaposed by the protein fold. Finally, the scFv A8 was applied for immunofluorescence studies of transformed human amnion cells and MCF-7 fibroblasts. In both cases a perinuclear localization of hEF1A was observed. No evidence for the reported nuclear localization of hEF1A was obtained.
Amino Acid Sequence↗
A new technique for mapping epitope specificities of monoclonal antibodies using quasi-elastic light scattering spectroscopy.
Quasi-elastic light scattering (QLS) was used to determine relative epitope specificities of a group of anti-bovine serum albumin (BSA) monoclonal antibodies (MAb). QLS is a non-invasive technique which can determine the mean size and size distributions of macromolecular scatterers by analysis of the fluctuations in the intensity of laser light scattering. When two MAbs are mixed together with antigen, QLS detects the complex formation which results from the Ag-Ab reaction, and can easily distinguish between the large complexes formed by interaction of non-competitive MAbs and the smaller complexes formed by competitive MAbs. In this report, the competitive or non-competitive behavior of six anti-BSA MAbs were assessed by radioimmunoassay (RIA) and QLS analysis. The results obtained by QLS analysis confirmed the RIA findings indicating that the six MAbs examined can be categorized into three distinct, non-interacting groups. QLS analysis represents a simple, and extremely rapid technique for epitope mapping studies.
Antibodies, Monoclonal↗
Binding of antithyrotropin receptor autoantibodies in Graves' disease serum to nascent, in vitro translated thyrotropin receptor: ability to map epitopes recognized by antibodies.
The binding of Graves' disease autoantibodies and xenogeneic antibodies to the human TSH receptor (TSH-R) has been studied using receptor preparations generated in an in vitro transcription and translation reaction. The complementary DNAs encoding for the full-length (764 amino acids) and the extracellular region of TSH-R (amino acids 20-414, lacking the signal sequence) were used to generate the translated receptor antigen. Stable [35S]methionine-labeled nascent protein for full-length and extracellular regions of TSH-R of approximate size 87 and 50 kDa, respectively, together with other smaller proteins were generated. The 87- and 50-kDa translated receptor proteins react by immunoprecipitation analysis with monoclonal antibodies, polyclonal antisera, and unfractionated Graves' disease serum containing autoantibody to TSH-R. The translated products of the extracellular TSH-R were examined in detail. Using three well characterized murine monoclonal antibodies whose epitopes encompass the amino-, central, and carboxyl-terminals of the extracellular region of the receptor led to immunochemical identification of the smaller translated products to derive from internal methionine start sites of TSH-R. These smaller, N-terminal-truncated translated proteins were also recognized by polyclonal antisera generated against recombinant TSH-R, thus allowing epitope mapping of some antibodies. A large proportion of Graves' disease autoantibodies (> 70%) bind to the translated extracellular region of TSH-R. This indicates that the majority of pathogenic anti-TSH-R autoantibody binds the nascent translated extracellular region of TSH-R, which is not influenced by the lack of glycosylation of the receptor.
Animals↗
Epitope mapping of the human surface suppressor/cytotoxic T cell molecule Tp32.
The complexity of the suppressor/cytotoxic subset marker of human T lymphocytes was demonstrated by biochemical analysis, cross-blocking experiments, phylogenetic comparisons, and functional studies. At the biochemical level, the antigen was shown to be a heteromultimer of at least three polypeptide chains covalently associated into four different higher m.w. species. Sixteen different murine monoclonal antibodies were used to map epitopes of this heteromultimeric complex. Cross-blocking experiments undertaken with six directly labeled reference antibodies identified at least seven spacially distinct epitopes. Flow microfluorometric analysis of peripheral blood lymphocytes showed two distinct subpopulations of bright and dull-stained cells that differed approximately 10-fold in antigen density. The distribution of epitopes on bright and dull cells was not uniform because in several combinations, blocking was observed on bright cells only. Studies with nonhuman primate T cells demonstrated a high degree of phylogenetic heterogeneity in the antigen. The combined cross-blocking and primate data divided the 17 antibodies into 15 groups. Each of the antibodies was capable of blocking lysis by alloreactive cytotoxic T lymphocytes, indicating that the mechanism of inhibition may not necessarily involve hindrance of an active site.
Adolescent↗
Characterization of naturally occurring autoantibodies against tumour necrosis factor-alpha (TNF-alpha): in vitro function and precise epitope mapping by phage epitope library.
Naturally occurring autoantibodies against cytokines exist in the sera of patients with autoimmune diseases as well as in the sera of normal individuals. We report here that affinity-purified autoantibodies against human TNF-alpha from one rheumatoid arthritis (RA) patient inhibited the cytotoxic effect of TNF-alpha on the mouse fibrosarcoma cell line WEHI 164, by 50%. In an attempt to predict the autoantibodies' recognition site on TNF-alpha protein we screened a random nanopeptide phage library with the affinity-purified TNF-alpha autoantibodies. Among 63 random selected clones, 46 clones carried the sequence ASSLLASSP, NSSPYLNTK or PQSPGSSFP. Frequency analysis of the relative occurrence of the 20 amino acids in the nanopeptides displayed by 50 random bacteriophages picked before selection and 63 after selection to bind to TNF-alpha autoantibodies indicated that proline (P < 0.0003) and serine (P < 0.04) are involved in the binding of the autoantibodies to the phages. Furthermore, we demonstrated that three synthetic peptides (ASSLLASSP, NSSPYLNTK and PPLKPVIDE) displayed by the selected phages reduced the binding of the autoantibodies to TNF-alpha protein by 50%. Interestingly, the sera of mice (BALB/c) immunized with phages displaying ASSLLASSP and NSSPYLNTK peptide showed an anti-TNF-alpha response as detected by ELISA. This response was not found in mice immunized with the wild type phage. Thus, the recombinant phages selected from the phage libraries could be used as carrier for immunization, and therefore as a tool for vaccine development. This work sets the stage for experiments designed to isolate ligands for protective antibodies.
Antibody Specificity↗
B-Cell epitope mapping of DNA topoisomerase I defines epitopes strongly associated with pulmonary fibrosis in systemic sclerosis.
We hypothesized that B-cell epitope mapping of DNA Topoisomerase I (type-I topoisomerase, or Topo I) may define epitopes strongly associated with pulmonary interstitial fibrosis (PIF) in systemic sclerosis (SSc). B-cell epitope mapping of Topo I was performed using 63 20-mer peptides overlapping by eight residues and spanning the entire length of the Topo I sequence. These peptides, coupled to polystyrene pins, were tested for antibody binding by enzyme-linked immunosorbent assays (ELISAs) using immunoglobulin G fractions from anti-Topo I, anticentromere, anti-U3RNP-positive, and normal sera. Four major epitopes were recognized by anti-Topo I sera, but not from the control sera: WWEEERYPEGIKWKFLEHKG (205-224, epitope I), RIANFKIEPPGLFRGRGNHP (349-368, epitope II), PGHKWKEVRHDNKVTWLVSW (397-416, epitope III), and ELDGQEYVVEFDFLGKDSIR (517-536, epitope IV). Peptide-epitopes were then synthesized in their soluble forms and ELISA systems were developed. Epitopes II to IV are localized at highly exposed sites of the Topo I tertiary structure, whereas epitope I is localized at a less accessible site. In a cohort of 81 patients with SSc with clinical data on the evolution of their disease, patients with antibodies in their sera recognizing at least three of the four epitopes had 3.1 times (P = 0.02) the hazard of developing PIF compared with patients whose sera recognized no epitopes or only one or two of the four epitopes. The discrimination was much stronger than that achieved by the simple determination of Topo I antibodies by counterimmunoelectrophoresis and immunoblot (hazard ratio 1.7, P = 0.30) in the same patients. B-cell epitope mapping of the anti-Topo I response has identified four major epitopes which cumulatively show a strong association with the development of PIF in SSc.
Amino Acid Sequence↗
Epitope mapping and features of the epitope for monoclonal antibodies inhibiting enzymatic activity of Helicobacter pylori urease.
Two characteristic monoclonal antibodies (HpU-2 and -18) out of 26 monoclonal antibodies (HpU-1 approximately 26) produced against Helicobacter pylori (H. pylori) urease showed a strong inhibitory effect against the enzymatic activity of the urease. Epitope mapping about some monoclonal antibodies of the HpU-series inhibiting enzymatic activity was performed by using a surface plasmon resonance apparatus and by digesting H. pylori urease with trypsin, followed by mass spectroscopy. The sequences of the epitopes recognized by HpU-2 and -18 were SVELIDIGGNRRIFGFNALVDR (22 mer) and IFGFNALVDR (10 mer), respectively. The former sequence is present as a part of a loop structure at a position close to the C-terminal of the alpha-subunit of H. pylori urease, although it has been suggested that the active site of the urease resides in the beta-subunit. The above peptide (22 mer) was chemically synthesized in a linear and cyclic form, and its conjugate with BSA was immunized in rabbits. The resultant serum induced by the linear form could specifically bind to H. pylori infecting human gastric mucosa. These results suggest that the above sequence (22 mer) must be an important epitope, although it locates in the alpha-subunit but not in the beta-subunit.
Amino Acid Sequence↗
Epitope mapping for four monoclonal antibodies against human plasminogen activator inhibitor type-1: implications for antibody-mediated PAI-1-neutralization and vitronectin-binding.
The inhibitory mechanism of serine proteinase inhibitors of the serpin family is based on their unique conformational flexibility. The formation of a stable proteinase-serpin complex implies insertion of the reactive centre loop of the serpin into the large central beta-sheet A and a shift in the relative positions of two groups of secondary structure elements, the smaller one including alpha-helix F. In order to elucidate this mechanism, we have used phage-display and alanine scanning mutagenesis to map the epitopes for four monoclonal antibodies against alpha-helix F and its flanking region in the serpin plasminogen activator inhibitor-1 (PAI-1). One of these is known to inhibit the reaction between PAI-1 and its target proteinases, an effect that is potentiated by vitronectin, a physiological carrier protein for PAI-1. When combined with the effects these antibodies have on PAI-1 activity, our epitope mapping points to the mobility of amino-acid residues in alpha-helix F and the loop connecting alpha-helix F and beta-strand 3A as being important for the inhibitory function of PAI-1. Although all antibodies reduced the affinity of PAI-1 for vitronectin, the potentiating effect of vitronectin on antibody-induced PAI-1 neutralization is based on formation of a ternary complex between antibody, PAI-1 and vitronectin, in which PAI-1 is maintained in a state behaving as a substrate for plasminogen activators. These results thus provide new details about serpin conformational changes and the regulation of PAI-1 by vitronectin and contribute to the necessary basis for rational design of drugs neutralizing PAI-1 in cancer and cardiovascular diseases.
Alanine↗
[Epitope mapping of anti-glomerular basement membrane antibodies].
OBJECTIVE: To map the epitopes of anti-glomerular basement membrane (GBM) antibodies and to study their clinical relevance. METHODS: 33 sera from patients with anti-GBM antibody mediated diseases were applied to inhibit monoclonal antibody against alpha 3 (IV) NC1 (Mab3), monoclonal antibody against alpha 5 (IV) NC1 (Mab5) and affinity purified, horseradish peroxidase conjugated, human anti-GBM antibodies (APab-HRP) in competitive inhibitory ELISA system using soluble human GBM proteins as solid phase ligands. The inhibition rates were evaluated in epitope mapping and used in comparison for patients with different clinical manifestations. RESULTS: All 33 sera inhibited Mab3, 30/33 sera inhibited APab-HRP, and 11/33 inhibited Mab5. However, the inhibition rates were not parallel. The mean inhibition rate for APab-HRP was 55% in 27 patients with anti-GBM antibody only and was 32% in 6 patients with both anti-GBM antibody and ANCA with a significant difference (P = 0.01). For patients with or without pulmonary hemorrhage, no significant differences could be found in the mean inhibition rates for Mab3, Mab5 or APab-HRP (P < 0.05). CONCLUSION: The anti-GBM antibodies from all patients in the present study recognize the common major epitopes on alpha 3 (IV) NC1, however, the epitopes recognized by different anti-GBM antibodies were not exactly the same. Only a small number of anti-GBM antibody positive sera recognizes alpha 5 (IV) NC1. The epitopes recognized by sera from patients with or without ANCA might be different.
Antibodies↗
Chimeric swine vesicular disease viruses produced by fusion PCR: a new method for epitope mapping.
A new method of epitope mapping based on chimeric swine vesicular disease (SVD) viruses produced by fusion PCR (polymerase chain reaction). Seven out of 16 neutralising and non-neutralising newly produced monoclonal antibodies (MAbs) discriminated between SVD isolate ITL/1/66 and NET/1/92. Using fusion PCR eight chimeric viruses were produced containing different supplementary pieces of the P1 region of both parent strains. Using these chimeric viruses we were able to map the epitope regions recognised by these seven neutralising and non-neutralising Mabs. This new method, using chimeric viruses produced by fusion PCR, is particularly valuable for the epitope mapping of non-neutralising MAbs.
Animals↗
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↗
Structure-function study of the p55 subunit of murine IL-2 receptor by epitope mapping.
Using a cell-free translation system we have expressed the Mr 55,000 subunit of the murine IL-2R (p55 IL-2R), which binds IL-2 with low affinity (Kd = 10 nM). Mutants and truncated forms of p55 IL-2R have been used to map the epitopes recognized by three anti-p55 IL-2R mAb: 135D5, 7D4, and 2E4. The mAb 135D5 inhibits IL-2 binding to p55 IL-2R and recognizes an epitope located between amino acids 64 to 125. This epitope can be mimicked by a synthetic peptide corresponding to the region defined by residues 72 to 88. However, the mAb 7D4 and 2E4 do not affect the IL-2 binding to p55 IL-2R. These mAb recognize an epitope of p55 IL-2R lying between residues 125 to 212 that can be mimicked with a peptide corresponding to amino acids 188 to 208. A strong correlation emerged between the experimental results on epitope mapping and predictions of potential antigenicity of murine p55 IL-2R. In addition, we described two internal initiation sites of p55 IL-2R mRNA under the in vitro conditions used leading to the production of significant amounts of N-terminal truncated p55 IL-2R proteins.
Amino Acid Sequence↗
Epitope mapping from real time kinetic studies - role of crosslinked disulphides and incidental interacting regions in affinity measurements: study with human chorionic gonadotropin and monoclonal antibodies.
Real time kinetic studies were used to map conformational epitopes in human chorionic gonadotropin (hCG) for two monoclonal antibodies (MAbs). The epitopes were identified in the regions (alpha 5--14 and alpha 55--62). The association rate constant (k+1) was found to be altered by chemical modification of hCG, and the ionic strength of the reaction medium. Based on these changes, we propose the presence of additional interactions away from the epitope- paratope region in the hCG-MAb reaction. We have identified such incidental interacting regions (IIRs) in hCG to be the loop region alpha 35--47 and alpha 60--84. The IIRs contribute significantly towards the KA of the interaction. Therefore, in a macromolecular interaction of hCG and its MAb, KA is determined not only by epitopeparatope interaction but also by the interaction of the nonepitopic-nonparatopic IIRs. However, the specificity of the interaction resides exclusively with the epitope-paratope pair.
Antibodies, Monoclonal↗