Percent of highly immunogenic amino acid residues forming B-cell epitopes is higher in homologous proteins encoded by GC-rich genes

2011 ◽  
Vol 282 (1) ◽  
pp. 71-79 ◽  
Author(s):  
Vladislav V. Khrustalev ◽  
Eugene V. Barkovsky
2006 ◽  
Vol 13 (2-4) ◽  
pp. 125-132 ◽  
Author(s):  
L. Guilherme ◽  
K. C. Faé ◽  
F. Higa ◽  
L. Chaves ◽  
S. E. Oshiro ◽  
...  

Rheumatic fever (RF) is an autoimmune disease which affects more than 20 million children in developing countries. It is triggered byStreptococcus pyogenesthroat infection in untreated susceptible individuals. Carditis, the most serious manifestation of the disease, leads to severe and permanent valvular lesions, causing chronic rheumatic heart disease (RHD). We have been studying the mechanisms leading to pathological autoimmunity in RF/RHD for the last 15 years. Our studies allowed us a better understanding of the cellular and molecular pathogenesis of RHD, paving the way for the development of a safe vaccine for a post-infection autoimmune disease. We have focused on the search for protective T and B cell epitopes by testing 620 human blood samples against overlapping peptides spanning 99 residues of the C-terminal portion of the M protein, differing by one amino acid residue. We identified T and B cell epitopes with 22 and 25 amino acid residues, respectively. Although these epitopes were from different regions of the C-terminal portion of the M protein, they showed an identical core of 16 amino acid residues. Antibodies against the B cell epitope inhibited bacterial invasion/adhesionin vitro. Our results strongly indicated that the selected T and B cell epitopes could potentially be protective againstS. pyogenes.


2001 ◽  
Vol 69 (5) ◽  
pp. 2909-2919 ◽  
Author(s):  
Angel Viudes ◽  
Sofia Perea ◽  
Jose L. Lopez-Ribot

ABSTRACT The 58-kiloDalton mannoprotein (mp58) on the surface ofCandida albicans is highly immunogenic, is expressed by allC. albicans isolates tested, and elicits strong antibody responses during candidiasis. It belongs to a family of immunodominant fungal antigens with representatives also in different species ofAspergillus. The amino acid sequence of the protein portion of mp58 as deduced from the DNA sequence of its encoding gene (FBP1/PRA1) was used to synthesize a complete set of overlapping dodecapeptides (overlap, 7; offset, 5) covalently attached to the surface of derivatized polyethylene pins. The pin-coupled peptides were used in a modified enzyme-linked immunosorbent assay (ELISA) to identify continuous epitopes recognized by a number of antiserum preparations containing anti-mp58 antibodies. This comprehensive epitope-scanning study revealed the presence of multiple immunoreactive continuous B-cell epitopes within the protein sequence. Regions of increased reactivity included both the amino and carboxy termini of the mature protein (encompassing amino acid residues 16 to 50 and 286 to 299, respectively) and four internal regions spanning amino acids at positions 66 to 92, 121 to 142, 148 to 192, and 211 to 232. Further delineation of epitopic regions and identification of the boundaries of the antigenic sites was performed upon ELISA testing with a second Pepset consisting of completely overlapping 8-mer peptides spanning these reactive regions in the protein moiety of mp58. The highly reactive epitopic region at the C terminus of the protein was further evaluated using both window net and replacement net analyses. A synthetic peptide corresponding to the last 10 amino acid residues at the C terminus of the protein was immunogenic when injected into mice after being coupled to a carrier protein. Moreover, antibodies in the resulting sera specifically recognized the homologus mp58 in ELISAs and immunoblot assays. Delineation of the antibody responses to mp58 could provide the basis for the development of novel immunity-based prophylactic, therapeutic, and diagnostic techniques for the management of candidiasis.


2004 ◽  
Vol 200 (4) ◽  
pp. 519-525 ◽  
Author(s):  
Bradley T. Messmer ◽  
Emilia Albesiano ◽  
Dimitar G. Efremov ◽  
Fabio Ghiotto ◽  
Steven L. Allen ◽  
...  

Previous studies suggest that the diversity of the expressed variable (V) region repertoire of the immunoglobulin (Ig)H chain of B-CLL cells is restricted. Although limited examples of marked constraint in the primary structure of the H and L chain V regions exist, the possibility that this level of restriction is a general principle in this disease has not been accepted. This report describes five sets of patients, mostly with unmutated or minimally mutated IgV genes, with strikingly similar B cell antigen receptors (BCRs) arising from the use of common H and L chain V region gene segments that share CDR3 structural features such as length, amino acid composition, and unique amino acid residues at recombination junctions. Thus, a much more striking degree of structural restriction of the entire BCR and a much higher frequency of receptor sharing exists among patients than appreciated previously. The data imply that either a significant fraction of B-CLL cells was selected by a limited set of antigenic epitopes at some point in their development and/or that they derive from a distinct B cell subpopulation with limited Ig V region diversity. These shared, stereotyped Ig molecules may be valuable probes for antigen identification and important targets for cross-reactive idiotypic therapy.


Amino Acids ◽  
2007 ◽  
Vol 33 (3) ◽  
pp. 423-428 ◽  
Author(s):  
J. Chen ◽  
H. Liu ◽  
J. Yang ◽  
K.-C. Chou

Biochimie ◽  
2014 ◽  
Vol 103 ◽  
pp. 1-6 ◽  
Author(s):  
Jian-Hua Huang ◽  
Ming Wen ◽  
Li-Juan Tang ◽  
Hua-Lin Xie ◽  
Liang Fu ◽  
...  

2015 ◽  
Vol 89 (10) ◽  
pp. 5491-5501 ◽  
Author(s):  
Xinjie Wang ◽  
Qin Zhao ◽  
Lu Dang ◽  
Yani Sun ◽  
Jiming Gao ◽  
...  

ABSTRACTAntisera raised against the avian hepatitis E virus (HEV) capsid protein are cross-reactive with human and swine HEV capsid proteins. In this study, two monoclonal antibodies (MAbs) against the avian HEV capsid protein, namely, 3E8 and 1B5, were shown to cross-react with the swine HEV capsid protein. The motifs involved in binding both MAbs were identified and characterized using phage display biopanning, peptide synthesis, and truncated or mutated protein expression, along with indirect enzyme-linked immunosorbent assay (ELISA) and Western blotting. The results showed that the I/VPHD motif is a necessary core sequence and that P and H are two key amino acids for recognition by MAb 3E8. The VKLYM/TS motif is the minimal amino acid sequence necessary for recognition by MAb 1B5. Cross-reactivity between the two epitopes and antibodies against avian, swine, and human HEVs in sera showed that both epitopes are common to avian, swine, and human HEVs. In addition, amino acid sequence alignment of the capsid proteins revealed that the key motifs of both novel epitopes are the same in HEVs from different animal species, predicting that they may be common to HEV isolates from boars, rabbits, rats, ferrets, mongooses, deer, and camels as well. Protein modeling analysis showed that both epitopes are at least partially exposed on the surface of the HEV capsid protein. Protective capacity analysis demonstrated that the two epitopes are nonprotective against avian HEV infection in chickens. Collectively, these studies characterize two novel linear B-cell epitopes common to avian, swine, and human HEVs, which furthers the understanding of HEV capsid protein antigenic structure.IMPORTANCEMore and more evidence indicates that the host range diversity of hepatitis E virus (HEV) is a global public health concern. A better understanding of the antigenic structure of the HEV capsid protein may improve disease diagnosis and prevention. In this study, binding site mapping and localization as well as the antigenic biology of two novel linear B-cell epitopes common to several different species of HEV were characterized. These findings partially reveal the antigenic structure of the HEV capsid protein and provide potential applications for the development of diagnostics and interventions for HEV infection.


Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1657
Author(s):  
Lana Bitencourt Chaves ◽  
Glaucia de Oliveira Guimarães ◽  
Daiana de Souza Perce-da-Silva ◽  
Dalma Maria Banic ◽  
Paulo Renato Rivas Totino ◽  
...  

The Plasmodium vivax Cysteine-Rich Protective Antigen (PvCyRPA) has an important role in erythrocyte invasion and has been considered a target for vivax malaria vaccine development. Nonetheless, its genetic diversity remains uncharted in Brazilian malaria-endemic areas. Therefore, we investigated the pvcyrpa genetic polymorphism in 98 field isolates from the Brazilian Amazon and its impact on the antigenicity of predicted B-cell epitopes. Genetic diversity parameters, population genetic analysis, neutrality test and the median-joining network were analyzed, and the potential amino acid polymorphism participation in B-cell epitopes was investigated. One synonymous and 26 non-synonymous substitutions defined fifty haplotypes. The nucleotide diversity and Tajima’s D values varied across the coding gene. The exon-1 sequence had greater diversity than those of exon-2. Concerning the prediction analysis, seven sequences were predicted as linear B cell epitopes, the majority contained in conformational epitopes. Moreover, important amino acid polymorphism was detected in regions predicted to contain residues participating in B-cell epitopes. Our data suggest that the pvcyrpa gene presents a moderate polymorphism in the studied isolates and such polymorphisms alter amino acid sequences contained in potential B cell epitopes, an important observation considering the antigen potentiality as a vaccine candidate to cover distinct P. vivax endemic areas worldwide.


2017 ◽  
Author(s):  
Victor H. Salinas ◽  
Rama Ranganathan

Protein function arises from a poorly defined pattern of cooperative energetic interactions between amino acid residues. Strategies for deducing this pattern have been proposed, but lack of benchmark data has limited experimental verification. Here, we extend deep-mutation technologies to enable measurement of many thousands of pairwise amino acid couplings in members of a protein family. The data show that despite great evolutionary divergence, homologous proteins conserve a sparse, spatially distributed network of cooperative interactions between amino acids that underlies function. This pattern is quantitatively captured in the coevolution of amino acid positions, especially as indicated by the statistical coupling analysis (SCA), providing experimental confirmation of the key tenets of this method. This work establishes a clear link between physical constraints on protein function and sequence analysis, enabling a general practical approach for understanding the structural basis for protein function.


1999 ◽  
Vol 67 (5) ◽  
pp. 2284-2291 ◽  
Author(s):  
Banani Banerjee ◽  
Paul A. Greenberger ◽  
Jordan N. Fink ◽  
Viswanath P. Kurup

ABSTRACT Asp f 2 is a major Aspergillus fumigatus allergen involved in allergic bronchopulmonary aspergillosis. Knowledge of the B-cell epitopes may contribute to the understanding of immunoregulation and immunodiagnosis. To elucidate the immunoglobulin E (IgE) binding epitopes in the linear sequence of Asp f 2, we synthesized decamer peptides spanning the whole molecule of Asp f 2 on derivatized cellulose membranes and evaluated IgE binding in ABPA patient and control sera. Peptides three to five amino acids long were synthesized based on amino acid sequences within the IgE binding regions and evaluated for the specificity of epitope antibody interactions. Nine IgE binding regions were recognized in this protein of 268 amino acid residues. Of the nine epitopes, seven (ATQRRQI, RKYFG, HWR, YTTRR, DHFAD, ALEAYA, and THEGGQ) are present in the hydrophilic regions of Asp f 2. Immunologic evaluation of the three recombinant fragments, Asp f 2A encompassing the N-terminal epitope region, Asp f 2B without N- and C-terminal regions of the protein, and Asp f 2C representing C-terminal epitopes, revealed that either the N- or C-terminal region of the protein is essential for the correct folding and conformation for IgE antibody binding.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1101-1101
Author(s):  
Philip M Zakas ◽  
Kristine Vanijcharoenkarn ◽  
Rebecca Markovitz ◽  
Shannon L. Meeks ◽  
Christopher B Doering

Abstract Approximately 20-30% of severe hemophilia A patients develop inhibitors (anti-fVIII antibodies) to human fVIII (hfVIII) with the primary targets being the A2 and C2 domains. Studies of A2 domain-specific murine monoclonal antibodies (MAbs) targeting hfVIII identified 8 distinct groups of inhibitory MAbs displaying varying inhibitor titers and kinetics, with groups A, D, and E possessing the greatest inhibitory activity. Furthermore within the C2 domain, we previously characterized 5 distinct groups, whereby group BC antibodies were the most common and displayed the highest specific inhibitory activity. At present, a recombinant porcine fVIII (pfVIII) product (OBI-1, Baxter International) is being investigated within a pivotal clinical trial for persons with acquired hemophilia A. The rational for a recombinant pfVIII product stems from the limited cross reactivity of pfVIII, and potentially other fVIII orthologs, with antibodies developed against hfVIII and the prior clinical success of plasma-derived pfVIII. We have described the biochemical characterization of both pfVIII and, more recently, ovine fVIII (ofVIII) and now investigate their antigenic properties to define/refine key inhibitory epitopes and determine the amino acid differences that confer reduced antigenicity. Using an ELISA-based assay, 15 A2 and 12 C2 MAbs spanning all inhibitory groups were screened against B-domain deleted (BDD) pfVIII and ofVIII. Only 4 A2 domain targeting MAbs representing groups B, C, DE, and E were found to bind pfVIII and all displayed reduced cross-reactivity (Figure 1). Additionally, 3 MAbs within groups B, C, or E also bound ofVIII. No group A or D MAbs screened bound either ortholog. Of the C2 domain targeting MAbs tested, 3 MAbs (I109, D102, and ESH-8) from groups AB, B and C, respectively, bound pfVIII to lesser degrees. Nine of the 12 C2 targeting MAbs bound ofVIII, albeit at reduced signal strength, suggesting divergence in C2 epitopes between pfVIII and hfVIII as well as between pfVIII and ofVIII. Using these data and previous literature defining the specific epitopes of these MAbs, we suggest that species-specific amino acid sequence differences may be responsible for the differential binding. MAb413, a well characterized A2 group A inhibitor, was found not to bind either ortholog. Alanine scanning mutagenesis within the 484 – 508 epitope demonstrated that single point mutations at R484, Y487, R489, or P492 could each inhibit binding of MAb413 to below 10%. In addition, P485 or S488 mutations each reduced binding to approximately 40% (Lubin et al J Biol Chem 272:48). Both pfVIII and ofVIII share substitutions R484S, Y487H, R489G, and pfVIII contains unique substitutions P485A, S488P, and P492L. Since all but two A2 group A MAbs have been mapped to residues 484-508, and because all group A MAbs compete with each other for their epitope, we hypothesize that these substitutions are responsible for diminished binding of group A MAbs. Group D inhibitory antibodies have been mapped to residues 604-740. Within this region, there are 12 shared amino acid substitutions and 7 amino acids altered in either ortholog but not both. As it was demonstrated that the orthologs display differential cross reactivity, this suggests disparate amino acids alter inhibitor-epitope recognition. Walter et al. (J Biol Chem 2013 288:14) used small angle x-ray scattering (SAXS) to isolate the epitope of MAb 3E6, a C2 MAb group A inhibitor, to exposed loops R2209-S2216 and L2178-D2187. Our data show that this MAb is not cross reactive and both orthologs contain S2216T and S2182N substitutions. Finally, ESH-8, a well-studied C2 group C MAb, binds ofVIII and pfVIII equivalently at 29% of the hfVIII level. The epitope for ESH-8 contains amino acids 2248-2285 and within this region there is only one conserved substitution, F2275L. Therefore, we predict that substitution of this residue could restore or further diminish ESH-8 binding. These data provide evidence that the lack of A2 group A and D epitopes, as well as the C2 domain group BC epitopes within these orthologs may be responsible for the residual procoagulant activity in the context of inhibitor plasma. Furthermore, these data also suggest that 1) B-cell epitopes can be defined or refined through this approach, 2) less antigenic residues can be identified and 3) the information obtained can be utilized to rationally design recombinant fVIII products with reduced antigenicity. Disclosures: No relevant conflicts of interest to declare.


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