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A HLA-DRB supertype chart with potential overlapping peptide binding function.

Mohanapriya A, Nandagond S, Shapshak P, Kangueane U, Kangueane P - Bioinformation (2010)

Bottom Line: HLA-DRB alleles are class II alleles that are associated with CD4+ T-cell immune response.Definition of DRB supertypes using binding data is limited to few (about 29) known alleles (< 5% of all known DRB alleles).Hence, we describe a strategy using structurally defined virtual pockets to group all known DRB alleles with regard to their overlapping peptide binding specificity.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Informatics, Pondicherry 607 402, India; VITU, Vellore, Tamil Nadu 632 014, India.

ABSTRACT
HLA-DRB alleles are class II alleles that are associated with CD4+ T-cell immune response. DRB alleles are polymorphic and currently there are about 622 named in the IMGT/HLA sequence database. Each allele binds short peptides with high sensitivity and specificity. However, it has been suggested that majority of HLA alleles can be covered within few HLA supertypes, where different members of a supertype bind similar peptides showing distinct repertoires. Definition of DRB supertypes using binding data is limited to few (about 29) known alleles (< 5% of all known DRB alleles). Hence, we describe a strategy using structurally defined virtual pockets to group all known DRB alleles with regard to their overlapping peptide binding specificity.

No MeSH data available.


The workflow for the identification of DRB alleles in IMGT/HLA with overlapping function is given.
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Figure 3: The workflow for the identification of DRB alleles in IMGT/HLA with overlapping function is given.

Mentions: We extracted the residues corresponding to the 25 HERP in 622 DRBalleles in IMGT/HLA. The sequence stretch formed by thediscontinuous HERP in 622 DRB alleles was compared amongthemselves to cluster those having similar sequence stretch. Thus, weobtained 395 groups by this procedure such that alleles within thesame group share the HERP sequence stretch. This proceduregenerated 73 groups (Table 2 supplementary material) containingtwo or more alleles and 322 groups with only one allele. Thehypothesis is that alleles within the group show functional overlapthereby exhibiting potential supertypes. It should be noted that allelesin 322 groups do not share HERP sequence stretch among them. Theworkflow for the identification of DRB alleles in IMGT/HLA withoverlapping function is given in Figure 3 and the grouping is shown inFigure 4.


A HLA-DRB supertype chart with potential overlapping peptide binding function.

Mohanapriya A, Nandagond S, Shapshak P, Kangueane U, Kangueane P - Bioinformation (2010)

The workflow for the identification of DRB alleles in IMGT/HLA with overlapping function is given.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2957767&req=5

Figure 3: The workflow for the identification of DRB alleles in IMGT/HLA with overlapping function is given.
Mentions: We extracted the residues corresponding to the 25 HERP in 622 DRBalleles in IMGT/HLA. The sequence stretch formed by thediscontinuous HERP in 622 DRB alleles was compared amongthemselves to cluster those having similar sequence stretch. Thus, weobtained 395 groups by this procedure such that alleles within thesame group share the HERP sequence stretch. This proceduregenerated 73 groups (Table 2 supplementary material) containingtwo or more alleles and 322 groups with only one allele. Thehypothesis is that alleles within the group show functional overlapthereby exhibiting potential supertypes. It should be noted that allelesin 322 groups do not share HERP sequence stretch among them. Theworkflow for the identification of DRB alleles in IMGT/HLA withoverlapping function is given in Figure 3 and the grouping is shown inFigure 4.

Bottom Line: HLA-DRB alleles are class II alleles that are associated with CD4+ T-cell immune response.Definition of DRB supertypes using binding data is limited to few (about 29) known alleles (< 5% of all known DRB alleles).Hence, we describe a strategy using structurally defined virtual pockets to group all known DRB alleles with regard to their overlapping peptide binding specificity.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Informatics, Pondicherry 607 402, India; VITU, Vellore, Tamil Nadu 632 014, India.

ABSTRACT
HLA-DRB alleles are class II alleles that are associated with CD4+ T-cell immune response. DRB alleles are polymorphic and currently there are about 622 named in the IMGT/HLA sequence database. Each allele binds short peptides with high sensitivity and specificity. However, it has been suggested that majority of HLA alleles can be covered within few HLA supertypes, where different members of a supertype bind similar peptides showing distinct repertoires. Definition of DRB supertypes using binding data is limited to few (about 29) known alleles (< 5% of all known DRB alleles). Hence, we describe a strategy using structurally defined virtual pockets to group all known DRB alleles with regard to their overlapping peptide binding specificity.

No MeSH data available.