Limits...
Identification of B cell epitopes of alcohol dehydrogenase allergen of Curvularia lunata.

Nair S, Kukreja N, Singh BP, Arora N - PLoS ONE (2011)

Bottom Line: All T cell epitopes showed lower IgE binding.Four B cell epitopes of C. lunata ADH were identified.Peptide P2 can serve as a potential candidate for diagnosis of allergic diseases.

View Article: PubMed Central - PubMed

Affiliation: Allergy and Immunology Laboratory, Institute of Genomics and Integrative Biology (CSIR), Delhi, India.

ABSTRACT

Background/objective: Epitope identification assists in developing molecules for clinical applications and is useful in defining molecular features of allergens for understanding structure/function relationship. The present study was aimed to identify the B cell epitopes of alcohol dehydrogenase (ADH) allergen from Curvularia lunata using in-silico methods and immunoassay.

Method: B cell epitopes of ADH were predicted by sequence and structure based methods and protein-protein interaction tools while T cell epitopes by inhibitory concentration and binding score methods. The epitopes were superimposed on a three dimensional model of ADH generated by homology modeling and analyzed for antigenic characteristics. Peptides corresponding to predicted epitopes were synthesized and immunoreactivity assessed by ELISA using individual and pooled patients' sera.

Result: The homology model showed GroES like catalytic domain joined to Rossmann superfamily domain by an alpha helix. Stereochemical quality was confirmed by Procheck which showed 90% residues in most favorable region of Ramachandran plot while Errat gave a quality score of 92.733%. Six B cell (P1-P6) and four T cell (P7-P10) epitopes were predicted by a combination of methods. Peptide P2 (epitope P2) showed E(X)(2)GGP(X)(3)KKI conserved pattern among allergens of pathogenesis related family. It was predicted as high affinity binder based on electronegativity and low hydrophobicity. The computational methods employed were validated using Bet v 1 and Der p 2 allergens where 67% and 60% of the epitope residues were predicted correctly. Among B cell epitopes, Peptide P2 showed maximum IgE binding with individual and pooled patients' sera (mean OD 0.604±0.059 and 0.506±0.0035, respectively) followed by P1, P4 and P3 epitopes. All T cell epitopes showed lower IgE binding.

Conclusion: Four B cell epitopes of C. lunata ADH were identified. Peptide P2 can serve as a potential candidate for diagnosis of allergic diseases.

Show MeSH

Related in: MedlinePlus

ERRAT plot for CADH structure.Error values for residues as predicted by ERRAT for CADH structure. Y axis presents the error value and X axis presents the amino acid sequences of SADH (top) and CADH (bottom), respectively. An error value exceeding 99% confidence level indicates poorly modelled regions. The overall quality factor assigned to template and CADH structures are 94.232% and 92.733%, respectively.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3102081&req=5

pone-0020020-g002: ERRAT plot for CADH structure.Error values for residues as predicted by ERRAT for CADH structure. Y axis presents the error value and X axis presents the amino acid sequences of SADH (top) and CADH (bottom), respectively. An error value exceeding 99% confidence level indicates poorly modelled regions. The overall quality factor assigned to template and CADH structures are 94.232% and 92.733%, respectively.

Mentions: An overall quality factor of 94.232% was assigned by Errat for SADH structure while a quality factor of 92.733% was assigned to CADH structure (Figure 2).


Identification of B cell epitopes of alcohol dehydrogenase allergen of Curvularia lunata.

Nair S, Kukreja N, Singh BP, Arora N - PLoS ONE (2011)

ERRAT plot for CADH structure.Error values for residues as predicted by ERRAT for CADH structure. Y axis presents the error value and X axis presents the amino acid sequences of SADH (top) and CADH (bottom), respectively. An error value exceeding 99% confidence level indicates poorly modelled regions. The overall quality factor assigned to template and CADH structures are 94.232% and 92.733%, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102081&req=5

pone-0020020-g002: ERRAT plot for CADH structure.Error values for residues as predicted by ERRAT for CADH structure. Y axis presents the error value and X axis presents the amino acid sequences of SADH (top) and CADH (bottom), respectively. An error value exceeding 99% confidence level indicates poorly modelled regions. The overall quality factor assigned to template and CADH structures are 94.232% and 92.733%, respectively.
Mentions: An overall quality factor of 94.232% was assigned by Errat for SADH structure while a quality factor of 92.733% was assigned to CADH structure (Figure 2).

Bottom Line: All T cell epitopes showed lower IgE binding.Four B cell epitopes of C. lunata ADH were identified.Peptide P2 can serve as a potential candidate for diagnosis of allergic diseases.

View Article: PubMed Central - PubMed

Affiliation: Allergy and Immunology Laboratory, Institute of Genomics and Integrative Biology (CSIR), Delhi, India.

ABSTRACT

Background/objective: Epitope identification assists in developing molecules for clinical applications and is useful in defining molecular features of allergens for understanding structure/function relationship. The present study was aimed to identify the B cell epitopes of alcohol dehydrogenase (ADH) allergen from Curvularia lunata using in-silico methods and immunoassay.

Method: B cell epitopes of ADH were predicted by sequence and structure based methods and protein-protein interaction tools while T cell epitopes by inhibitory concentration and binding score methods. The epitopes were superimposed on a three dimensional model of ADH generated by homology modeling and analyzed for antigenic characteristics. Peptides corresponding to predicted epitopes were synthesized and immunoreactivity assessed by ELISA using individual and pooled patients' sera.

Result: The homology model showed GroES like catalytic domain joined to Rossmann superfamily domain by an alpha helix. Stereochemical quality was confirmed by Procheck which showed 90% residues in most favorable region of Ramachandran plot while Errat gave a quality score of 92.733%. Six B cell (P1-P6) and four T cell (P7-P10) epitopes were predicted by a combination of methods. Peptide P2 (epitope P2) showed E(X)(2)GGP(X)(3)KKI conserved pattern among allergens of pathogenesis related family. It was predicted as high affinity binder based on electronegativity and low hydrophobicity. The computational methods employed were validated using Bet v 1 and Der p 2 allergens where 67% and 60% of the epitope residues were predicted correctly. Among B cell epitopes, Peptide P2 showed maximum IgE binding with individual and pooled patients' sera (mean OD 0.604±0.059 and 0.506±0.0035, respectively) followed by P1, P4 and P3 epitopes. All T cell epitopes showed lower IgE binding.

Conclusion: Four B cell epitopes of C. lunata ADH were identified. Peptide P2 can serve as a potential candidate for diagnosis of allergic diseases.

Show MeSH
Related in: MedlinePlus