Mapping Of Conformational Epitopes Research Articles

Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping

Precise epitope determination of therapeutic antibodies is of great value as it allows for further comprehension of mechanism of action, therapeutic responsiveness prediction, avoidance of unwanted cross reactivity, and vaccine design. The golden standard for discontinuous epitope determination is the laborious X-ray crystallography method. Here, we present a combinatorial method for rapid mapping of discontinuous epitopes by mammalian antigen display, eliminating the need for protein expression and purification. The method is facilitated by automated workflows and tailored software for antigen analysis and oligonucleotide design. These oligos are used in automated mutagenesis to generate an antigen receptor library displayed on mammalian cells for direct binding analysis by flow cytometry. Through automated analysis of 33930 primers an optimized single condition cloning reaction was defined allowing for mutation of all surface-exposed residues of the receptor binding domain of SARS-CoV-2. All variants were functionally expressed, and two reference binders validated the method. Furthermore, epitopes of three novel therapeutic antibodies were successfully determined followed by evaluation of binding also towards SARS-CoV-2 Omicron BA.2. We find the method to be highly relevant for rapid construction of antigen libraries and determination of antibody epitopes, especially for the development of therapeutic interventions against novel pathogens.

053 Conformational epitope mapping of autoantibodies against BP180 in dipeptidyl peptidase-4 inhibitors-associated bullous pemphigoid

053 Conformational epitope mapping of autoantibodies against BP180 in dipeptidyl peptidase-4 inhibitors-associated bullous pemphigoid

Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti-NGF monoclonal antibodies.

Nerve growth factor (NGF) plays a central role in multiple chronic pain conditions. As such, anti-NGF monoclonal antibodies (mAbs) that function by antagonizing NGF downstream signaling are leading drug candidates for non-opioid pain relief. To evaluate anti-canine NGF (cNGF) mAbs we sought a yeast surface display platform of cNGF. Both mature cNGF and pro-cNGF displayed on the yeast surface but bound conformationally sensitive mAbs at most 2.5-fold in mean fluorescence intensity above background, suggesting that cNGF was mostly misfolded. To improve the amount of folded, displayed cNGF, we used comprehensive mutagenesis, FACS, and deep sequencing to identify point mutants in the pro-region of canine NGF that properly enhance the folded protein displayed on the yeast surface. Out of 1,737 tested single point mutants in the pro region, 49 increased the amount of NGF recognized by conformationally sensitive mAbs. These gain-of-function mutations cluster around residues A-61-P-26. Gain-of-function mutants were additive, and a construct containing three mutations increased amount of folded cNGF to 23-fold above background. Using this new cNGF construct, fine conformational epitopes for tanezumab and three anti-cNGF mAbs were evaluated. The epitope revealed by the yeast experiments largely overlapped with the tanezumab epitope previously determined by X-ray crystallography. The other mAbs showed site-specific differences with tanezumab. As the number of binding epitopes of functionally neutralizing anti-NGF mAbs on NGF are limited, subtle differences in the individual interacting residues on NGF that bind each mAb contribute to the understanding of each antibody and variations in its neutralizing activity. These results demonstrate the potential of deep sequencing-guided protein engineering to improve the production of folded surface-displayed protein, and the resulting cNGF construct provides a platform to map conformational epitopes for other anti-neurotrophin mAbs.

Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti-NGF monoclonal antibodies

Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti-NGF monoclonal antibodies

Reverse epitope mapping of the E2 glycoprotein in antibody associated hepatitis C virus.

The humoral immune system responds to chronic hepatitis C virus (HCV) infection by producing neutralising antibodies (nAb). In this study we generated three HCV pseudoparticles in which E1E2 glycoprotein sequence was targeted by the host humoral immune system. We used patient derived virus free Fabs (VF-Fabs) obtained from HCV genotype 1a (n = 3), genotype 1b (n = 7) and genotype 3a (n = 1) for neutralisation of HCVpp produced in this study both individually and in combination. Based on the available anti-HCV monoclonal nAb mapping information we selected amino acid region 384–619 for conformational epitope mapping. Amongst our notable findings, we observed significant reduction in HCVpp infectivity (p<0.05) when challenged with a combination of inter genotype and subtype VF-Fabs. We also identified five binding motifs targeted by patient derived VF-Fab upon peptide mapping, of which two shared the residues with previously reported epitopes. One epitope lies within an immunodominant HVR1 and two were novel. In summary, we used a reverse epitope mapping strategy to identify preferred epitopes by the host humoral immune system. Additionally, we have combined different VF-Fabs to further reduce the HCVpp infectivity. Our data indicates that combining the antigen specificity of antibodies may be a useful strategy to reduce (in-vitro) infectivity.

Epitope Mapping of Mono- and Polyclonal Antibodies by Screening Phage-displayed Random Peptide Libraries.

Detailed knowledge of antigenic determinants is crucial when characterizing therapeutic and diagnostic antibodies, assessing vaccine effectiveness and developing epitope-based vaccines. Most epitope mapping approaches are labor intensive and costly. In this study, we evaluated panning of phage-displayed random peptide libraries against antibodies as a tool for cognate epitope identification. We used six antibodies directed to three model protein antigens as targets to show that the approach is applicable to both mono- and polyclonal antibodies. The technique is well-suited especially for identification of linear epitopes. Mapping of conformational epitopes is more challenging, tends to be more subjective and requires use of computational tools. Nevertheless, when combined with functional data such as structure-activity relationship of antigen muteins, one can make reliable conformational epitope predictions based on phage display experiment data. As the described approach is fast and relatively inexpensive, we suggest it is employed early in antibody characterization and later validated by complementary methods.

Epitope Mapping of Neutralizing Monoclonal Antibodies to Human Interferon-γ Using Human-Bovine Interferon-γ Chimeras.

Our aim was to identify conformational epitopes, recognized by monoclonal antibodies (mAbs) made against human (h) interferon (IFN)-γ. Based on the mAbs' (n = 12) ability to simultaneously bind hIFN-γ in ELISA, 2 epitope clusters with 5 mAbs in each were defined; 2 mAbs recognized unique epitopes. Utilizing the mAbs' lack of reactivity with bovine (b) IFN-γ, epitopes were identified using 7 h/bIFN-γ chimeras where the helical regions (A-F) or the C terminus were substituted with bIFN-γ residues. Chimeras had a N-terminal peptide tag enabling the analysis of mAb recognition of chimeras in ELISA. The 2 mAb clusters mapped to region A and E, respectively; the epitopes of several mAbs also involved additional regions. MAbs in cluster A neutralized, to various degrees, IFN-γ-mediated activation of human cells, in line with the involvement of region A in the IFN-γ receptor interaction. MAbs mapping to region E displayed a stronger neutralizing capacity although this region has not been directly implicated in the receptor interaction. The results corroborate earlier studies and provide a detailed picture of the link between the epitope specificity and neutralizing capacity of mAbs. They further demonstrate the general use of peptide-tagged chimeric proteins as a powerful and straightforward method for efficient mapping of conformational epitopes.

Rapid Fine Conformational Epitope Mapping Using Comprehensive Mutagenesis and Deep Sequencing

Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day.

Mechanisms Mediating Enhanced Neutralization Efficacy of Staphylococcal Enterotoxin B by Combinations of Monoclonal Antibodies

Staphylococcal enterotoxin B (SEB) is a superantigen that cross-links the major histocompatibility complex class II and specific V-β chains of the T-cell receptor, thus forming a ternary complex. Developing neutralizing mAb to disrupt the ternary complex and abrogate the resulting toxicity is a major therapeutic challenge because SEB is effective at very low concentrations. We show that combining two SEB-specific mAbs enhances their efficacy, even though one of the two mAbs by itself has no effect on neutralization. Crystallography was employed for fine-mapping conformational epitopes in binary and ternary complexes between SEB and Fab fragments. NMR spectroscopy was used to validate and identify subtle allosteric changes induced by mAbs binding to SEB. The mapping of epitopes established that a combination of different mAbs can enhance efficacy of mAb-mediated protection from SEB induced lethal shock by two different mechanisms: one mAb mixture promoted clearance of the toxin both in vitro and in vivo by FcR-mediated cross-linking and clearance, whereas the other mAb mixture induced subtle allosteric conformational changes in SEB that perturbed formation of the SEB·T-cell receptor·major histocompatibility complex class II trimer. Finally structural information accurately predicted mAb binding to other superantigens that share conformational epitopes with SEB. Fine mapping of conformational epitopes is a powerful tool to establish the mechanism and optimize the action of synergistic mAb combinations.

A novel approach for characterisation of conformational allergen epitopes combining phage display and high-throughput sequencing

Background Characterization of allergen epitopes is an essential task in unraveling the molecular mechanisms of allergy. At present, the procedures to characterize conformational epitopes are relatively laborious and, consequently, knowledge of conformational allergen epitopes is limited. The aim of this study was to couple an established epitope mapping approach, based on phage-displayed peptide libraries, with high-throughput sequencing in order to make conformational epitope mapping less laborious and increase data output.

Structure of allergens and structure based epitope predictions

The structure determination of major allergens is a prerequisite for analyzing surface exposed areas of the allergen and for mapping conformational epitopes. These may be determined by experimental methods including crystallographic and NMR-based approaches or predicted by computational methods. In this review we summarize the existing structural information on allergens and their classification in protein fold families. The currently available allergen-antibody complexes are described and the experimentally obtained epitopes compared. Furthermore we discuss established methods for linear and conformational epitope mapping, putting special emphasis on a recently developed approach, which uses the structural similarity of proteins in combination with the experimental cross-reactivity data for epitope prediction.

Conformational epitope mapping of Pru du 6, a major allergen from almond nut

Tree nuts are a widely consumed food. Although enjoyed safely by most individuals, allergic reactions to tree nuts, including almond, are not uncommon. Almond prunin (Pru du 6), an 11S globulin (legumin), is an abundant nut seed protein and a major allergen. Conformational epitope mapping studies of prunin have been performed with a murine monoclonal antibody (mAb) 4C10. This mAb reacts with non-reduced but not reduced prunin in immunoblotting assays, indicating the recognition of a conformational epitope. 4C10 competes with patient IgE, as assessed by ELISA, indicating clinical significance of the epitope. To characterize the 4C10 epitope, hydrogen/deuterium exchange (HDX) monitored by 14.5T Fourier transform ion cyclotron resonance mass spectrometry (MS) was performed on the native prunin–4C10 complex and on uncomplexed native prunin. Several epitope candidate peptides that differ in deuterium uptake between the complexed and uncomplexed forms were identified. The epitope was further mapped by analyzing chimeric molecules incorporating segments of the homologous soybean allergen, Gly m 6, in immunoassays. These data indicate that the 4C10 epitope overlaps with a subset of patient IgE binding epitopes on almond prunin and further supports HDX-MS as a valid technique for mapping conformational epitopes.

Rapid conformational epitope mapping of anti-gp120 antibodies with a designed mutant panel displayed on yeast.

gp120 is a substrate for protein engineering both for human immunodeficiency virus (HIV) immunogen design and as a bait for isolating anti-HIV antibodies from patient samples. In this work, we describe the display of a stripped core gp120 on the yeast cell surface. Validation against a panel of neutralizing antibodies confirms that yeast-displayed gp120 presents the CD4 binding site in the correct conformation. We map the epitope of the broadly neutralizing anti-gp120 antibody VRC01 using both a random mutagenesis library and a defined mutant panel and find that the resultant epitope maps are consistent with one another and with the crystallographically identified contact residues. Mapping the VRC01-competitive antibodies b12 and b13 reveals energetic differences in their epitopes that are not obvious from existing crystal structures. These data suggest mutation sets that abrogate binding to broadly neutralizing antibodies with greater specificity than the canonical mutation D368R, useful in rapidly assessing the nature of a vaccine response.

Epitope Spreading Is Rarely Found in Pemphigus Vulgaris by Large-Scale Longitudinal Study Using Desmoglein 2–Based Swapped Molecules

Epitope spreading is involved in inducing and maintaining self-reactivity. Epitope spreading in pemphigus vulgaris (PV), caused by IgG autoantibodies to desmoglein 3 (Dsg3) and Dsg1, was previously analyzed using Dsg3/Dsg1 extracellular domain-swapped molecules. However, precise identification of the responsible epitopes in each molecule by using only this method was problematic. In this study, we studied epitope spreading in PV by a novel immunoprecipitation-immunoblot method using Dsg3 (or Dsg1)/Dsg2 domain-swapped molecules, which overcomes the problems associated with the previous approaches. We analyzed the antigenic epitopes recognized by 212 sera collected from 53 PV patients at multiple disease stages. The major epitopes were present at the N-terminal region of Dsgs and were unchanged over the course of the disease in both anti-Dsg3 mucosal dominant-type PV and anti-Dsg3/Dsg1 mucocutaneous-type PV. These N-terminal epitopes were calcium dependent. Circulating antibodies in paraneoplastic pemphigus and pemphigus herpetiformis had unique epitope distributions, although the Dsg N-termini still contained the major epitopes. These results suggest that, after onset, intramolecular and intermolecular epitope spreading among extracellular domains on Dsg3 and Dsg1 is rare in PV and has no correlation with disease course.

Mapping of B cell epitopes on desmoglein 3 in pemphigus vulgaris patients by the use of overlapping peptides

Pemphigus vulgaris (PV) is a severe autoimmune blistering disease associated with autoantibodies to desmoglein 3 (Dsg 3), a transmembrane glycoprotein of the cadherin family. Previous studies mainly focused on the mapping of conformational epitopes of Dsg 3 using recombinant fragments of Dsg 3 and competition ELISA. Here, we performed a mapping of linear B cell epitopes on Dsg 3 in PV patients by the use of overlapping synthetic peptides. A set of 254 overlapping synthetic peptides of 14 amino acids length covering the entire Dsg 3 extracellular domain was generated. Sera of patients with active PV (n=10) and healthy volunteers (n=10) were tested for IgG reactivity with the 254 peptides by ELISA. Testing each peptide separately, 7 major antigenic sites were identified. In order to validate these reactivities, 7 corresponding peptides of 13-33 amino acids in length were generated and employed by ELISA. Additional sera of active PV patients (n=17) and healthy volunteers (n=20) were tested and the most reactive peptide was used to specifically purify anti-Dsg 3 antibodies from PV sera (n=3). The major autoantibody reactivity in PV sera was mapped to amino acids 333-356 within the EC3 domain. Purifying patients IgG using the identified peptide, however, failed to induce acantholysis in keratinocyte dissociation assay. We conclude that linear epitopes do not play a major pathogenic role in human PV.

Mapping of Conformational Epitopes, and Analyze of the Distribution of Ig Isotypes and Subclasses Using a Semi-Quantitative Multiplex Assay in 6 Cases of Postpartum Acquired Hemophilia.

Background and objectives: Acquired hemophilia (AH) is a severe life-threatening autoimmune disease due to the development of polyclonal autoantibodies (autoAbs) which neutralize the procoagulant activity of coagulation factor VIII (FVIII). The most common epitopes for autoAbs to FVIII are located in the A2, A3 and C2 domains of FVIII. We have recently developed a multiplex assay based on the Luminex technology that allows simultaneously the detection and epitope mapping of anti-FVIII antibodies (Lavigne-Lissalde et al, Thromb; Haemost. 2008). This technology is fast and requires only 100 μl of plasma and we showed that most autoAbs to FVIII are monospecific and preferentially bind to the light chain (LC) of FVIII. The aim of the present study was to evaluate the epitope specificity and IgG isotype/subclasses of autoAbs to FVIII detected in the post partum period.Methods: Acquired hemophilia was diagnosed in six women (median age: 28 years) included in a French cohort (SACHA) and who exhibited prolonged activated partial thromboplastin time, low FVIII levels (range = 0.5–21 IU/dL) and inhibitor titers between 1.5 and 40 Bethesda units (BU). The epitope mapping was studied in each patient by testing 5 plasma samples collected (at inclusion and after 1, 3, 6 and 12 months of follow up) using a multiplex assay as previously described (Lavigne-Lissalde et al, Thromb; Haemost. 2008). A panel of monoclonal antibodies that bind to LC, heavy chain (HC) and the C2 domain of FVIII was employed and the use of specific immunoconjugates also allowed to define the isotype (IgG, A, M) and subclass (IgG1 to IgG4) distributions of autoAbs to FVIII. Results were expressed in mean fluorescence intensity (MFI).Results: The autoAbs detected in the post partum in the six women studied recognized both and simultaneously HC and LC with predominant epitopes located in the LC and the C2 domain in 5 cases. At the inclusion, the autoAbs were mixtures of IgG1 and IgG4 in all patients, but the latter subclass was predominant in most cases. In addition, IgM Abs were also present in 3 women. No correlation between the titer of inhibitor (in BU) and the level of autoAbs binding (in MFI) could be evidenced. The evolution was good in all patients but one case for whom an increase in IgG4 binding to the FVIII C2 domain was demonstrated whereas inhibitor titer decreased (from 40 to 2.6 BU). Importantly, no modification in the epitope specificity between inclusion and 12 months of follow-up was found.Conclusion: The study shows that autoAbs to FVIII developed in the context of pregnancy are mainly IgG4 specific to the C2 domain. In addition, the epitope mapping of anti-FVIII antibodies by multiplex approach could contribute to a better understanding of the pathophysiology of acquired hemophilia.

Response to Anti CD20 Monoclonal Antibody Rituximab® and Epitope Mapping of Inhibitory Antibodies in Patients with Acquired Haemophilia.

Introduction: Acquired haemophilia (AcH) is associated with the development of polyclonal autoantibodies against FVIII, which affect directly the A2 or C2 domain of the FVIII molecule. Immunomodulatory therapy regimes to normalize FVIII levels and to eliminate the inhibitor are essential options in the treatment of patients (pts) with AcH. The aims of the present study were to investigate the response to Rituximab® and to localize the inhibitor epitopes on the FVIII domains.Patients and Methods: In 5 pts with AcH (2 females,3 males; age: 64–81 yrs) the inhibitor titers ranged from 9 to 156 BU and the FVIII activities from <1 % to 6 %. Rituximab® was administered once weekly for 4 weeks (dosage: 375 mg/m2) in combination with a prednisone therapy (1–1.5 mg/kg).Random peptide phage display libraries were used to identify peptide sequences specific for inhibitors. The short peptide sequences allow the mapping of conformational epitopes on the surface of the FVIII molecule.Results: In all pts (median follow up of 24 months, range: 2–49 months) we documented complete remission (CR). The median time to achieve CR was 13 weeks (range: 2–32 weeks). The time to CR was much longer (23/32 weeks) in two pts, who showed high inhibitor titers (50/188 BU) compared to pts (2/4/5 weeks) with low inhibitor titers (9/22/29 BU). One pt with a high inhibitor titer (50 BU) relapsed 19 months after CR, an other pt died in septic shock 8 weeks after the initiation of therapy with Rituximab®. No other relevant side effects were observed. In the pt with a relapse we identified target epitopes in the A1 and A2 domain of FVIII, and in the other pts (n=3) the peptide sequences mapped to epitopes on the C2 domain of FVIII.Conclusion: The therapy with Rituximab®shows high response rates and seems to be effective in the elimination of high and low inhibitors against FVIII in pts with AcH. Limited by the small number of pts, further studies are needed to confirm whether the different target epitopes found in patients with (A1/A2) or without a relapse (C2) might have a relevance in the specific immunomodulatory therapy.

Conformational epitope mapping of antibodies against desmoglein 3 in experimental murine pemphigus vulgaris

Background: Pemphigus vulgaris (PV) is a blistering skin disease caused by IgG autoantibodies against desmoglein 3 (Dsg3). We have recently developed an active disease mouse model for PV by adoptive transfer of splenocytes from immunized or naive Dsg3−/− mice into Rag2−/− recipient mice. Objective: In this study, we characterized the conformational epitopes of anti-Dsg3 IgG antibodies and their pathogenic activities in the PV model mice. Methods: The binding regions of anti-Dsg3 IgG antibodies were assessed by competition ELISAs with domain-swapped mouse Dsg1/Dsg3 molecules in PV model mice receiving immunized ( n = 53) or naive ( n = 56) splenocytes. To compare the pathogenic activity of antibodies against N-terminal versus C-terminal extracellular domains, Dsg3−/− mice were immunized with the residues 1–162 or the residues 403–565 of mouse Dsg3, and the splenocytes were adoptively transferred into Rag2−/− mice. Results: The middle to C-terminal extracellular domains of Dsg3 (residues 195–565) showed >50% competition in 51/53 (96.2%) and 45/56 (80.4%) while the N-terminal domain (residues 1–162) showed >50% competition only in 3/53 (5.7%) and 8/56 (14.3%) in mice receiving immunized and naive splenocytes, respectively. The mice receiving Dsg3−/− splenocytes immunized with the residues 403–565 developed the PV phenotype as early as and as severely as the mice receiving splenocytes immunized with the residues 1–162. Conclusions: In PV model mice the antibodies were dominantly raised against the middle to C-terminal extracellular domains of mouse Dsg3 where amino acid sequences are less conserved among desmoglein isoforms and that those antibodies may also be involved in the blister formation.

Mapping of conformational epitopes on capsid protein VP2 of infectious bursal disease virus by fd-tet phage display

Conformational epitopes on VP2 protein of infectious bursal disease virus (IBDV) were mapped using fd-tet phage display. A gene-targeted phage display library was made using DNA fragments ranging approximately from 80 to 400 bp of the hypervariable region of the VP2 gene of IBDV strain 002-73, as neutralizing monoclonal antibodies against the VP2 protein recognize VP2 conformation-dependent epitopes within the hypervariable region. The phages were selected using immobilized monoclonal antibodies. Epitopes on five phages selected with monoclonal antibody 17–82 were located between amino acids 211 and 344. A constructed phage containing amino acids from 204 to 344 strongly reacted with monoclonal antibodies. Compared to that of the constructed phage, the binding of monoclonal antibodies to the five selected phages was dramatically reduced when several amino acids at either terminus or both termini were absent. The binding of a phage, with conversion of the first hydrophilic region into a hydrophobic region as a result of a chance frameshift mutation from amino acids 214 to 225, dropped sharply. It indicates that conformational epitopes may be up to 423 bp long and the commonly suggested fragments of 50–300 bp for making gene-targeted phage display libraries are not long enough to cover the conformational epitopes. This technique can be used to identify the minimum length of the conformational epitopes for developing recombinant vaccines and specific diagnostic tests.

Use of Domain-Swapped Molecules for Conformational Epitope Mapping of Desmoglein 3 in Pemphigus Vulgaris

Pemphigus vulgaris is an autoimmune blistering disease caused by autoantibodies against desmoglein 3, a member of the desmosomal cadherin family. These autoantibodies recognize conformation-dependent epitopes on desmoglein 3. In this study we attempted to map the conformational epitopes of desmoglein 3 in pemphigus vulgaris using recombinant desmoglein 3 produced by the baculovirus expression system. We developed a series of domain-swapped molecules between desmoglein 3 and desmoglein 1, which have similar structures but distinct epitopes. These were developed by substituting deleted segmental regions of desmoglein 3 by the corresponding desmoglein 1. Thus domain-swapped molecules containing desmoglein 3 residues 1-403, 1-161, 163-566, and 405-566 were constructed and used as competitors for competition enzyme-linked immunosorbent assay against the entire extracellular domain of desmoglein 3 with 25 pemphigus vulgaris sera. Considering more than 50% absorption as significant, residues 1-403 and 1-161 showed significant absorption in 24 out of 25 (96%) and 18 out of 25 (72%) pemphigus vulgaris sera, respectively, whereas only one serum and no sera showed significant absorption by residues 163-566 and 405-566, respectively. Furthermore, no apparent change in their major epitopes was seen during the time course in four pemphigus vulgaris cases tested. These findings indicate that the domain-swapping approach is useful for conformational epitope mapping in pemphigus and that amino-terminal residues 1-161, which are considered to include a region essential for cell-cell adhesion in cadherins, contain the critical residues of the conformational epitope of desmoglein 3 recognized by the autoantibodies in pemphigus vulgaris sera.