Binding Analysis of 95 HIV gp120 Peptides to HLA-DR1101 and -DR0401 Evidenced Many HLA-Class II Binding Regions on gp120 and Suggested Several Promiscuous Regions

Abstract

To identify HLA-DR-binding peptides within the human immunodeficiency virus (HIV)-1 proteins. 95 overlapping synthetic peptides representing the entire sequence of gp120-LAI were screened for their capacity to bind to two HLA-DR molecules with distant sequences (DR0401 and DR1101). By using a cell surface competitive binding assay, 56 DR-binding peptides were identified, of which 35 bound to both DR1101 and DR0401. A highly significant concordance was evidenced by statistical analysis between binding of peptides to one and to the other DR molecule, suggesting a high proportion of promiscuity among gp120 peptides, even though no clear sequence pattern accounting for such promiscuity was found. DR-binding peptides were located along the entire gp120 sequence. Yet, the majority of them (42 among 56) were concentrated in seven multiagretopic regions that were arbitrarily defined as regions containing four or more overlapping continuous peptides binding to DR1011 and/or DR0401. A good correlation was found between DR-binding regions or DR-binding peptides defined in this study and promiscuous T helper gp120 epitopes previously described in seropositive individuals. All these results suggest that the identification of multiagretopic DR-binding regions may be a great help for the predicition of protein determinants that have the likelihood of being promiscuous T helper epitopes in humans.

Differences in self-peptide binding between T1D-related susceptible and protective DR4 subtypes

“…Biotinylated influenza hemagglutinin derived peptide HA306 (PKYVKQNTLKLAT) was used as a reference peptide for DR0401 (ED50 for HA306 to bind 0.05 µM DR0401=0.035 µM from a 16-hour direct binding assay) and DR0405 (ED50 for HA306 to bind 0.05 µM DR0405=0.271 µM) binding assays [20]. Since HA306 was unable to bind DR0403 (ED50 for HA306 to bind 0.05 µM DR0403≫15 µM), as an alternative, biotinylated GAD65-557I (NFIRMVISNPAAT) was used as a reference peptide for DR0403 binding assays (ED50 for 557I to bind 0.05 µM DR0403=0.01 µM).…”

Genomewide Conserved Epitope Profiles of HIV-1 Predicted by Biophysical Properties of MHC Binding Peptides

“…a Sequence numbering in the rst column is based on the NCBI reference genome NC_001802. b Independent identi cation: special symbols in the rst column indicate the following: ¤ proliferative response (Wilson et al, 2001); § intracellular IFN-°response (Altfeld et al, 2001); # binding (Altfeld et al, 2001); † raised T cells recognizing virion-pulsed APC (van der Burg et al, 1999); ‡ binding (van der Burg et al, 1999); ¶ proliferative response (Manca et al, 1995); † † binding (Gaudebout et al, 1997); ¤¤ cytotoxic response (Dupuis et al, 1995); § § proliferative response (Nehete et al, 1998) …”

Major Histocompatibility Complex Class II Molecule-Human Immunodeficiency Virus Peptide Analysis Using a Microarray Chip

“…The peptide repertoire presented by MHC class II molecules to CD4 ϩ T cells is edited by intracellular, nonclassical MHC molecules, i.e., HLA-DM and -DO (43). MHC class II alleles exhibit four major pockets (13) to accommodate and present a broad peptide repertoire to CD4 ϩ T cells: the same peptide can be presented by different MHC class II alleles due to highly degenerate peptide binding motifs (12,16,29,36). CD4…”

“…A number of assays are currently available to assess peptide binding to MHC class II alleles. These include computer-based algorithms (5,20,27,40,47), functional assays (enzyme-linked immunospot and intracellular cytokine staining), mass spectrometric sequencing of peptides eluted from purified HLA alleles (6,7,42), and peptide binding assays (12,25,34).…”