Detailed analysis of the effects of Glu/Lys β69 human leukocyte antigen‐DP polymorphism on peptide‐binding specificity

Abstract

The polymorphism at position beta69 of the human leukocyte antigen (HLA)-DP molecule has been associated with susceptibility to several immune disorders and alloreactivity. Using molecular modeling, we have predicted a detailed structure of the HLA-DP2 molecule (carrying Glubeta69) complexed with class II associated invariant chain derived peptide (CLIP) and compared it with the form carrying Lys at beta69 (HLA-DP2K69). Major changes between the two models were observed in the shape and charge distribution of pocket 4 and of the nearby pocket 6. Consequently, we analyzed in detail the peptide-binding specificities of both HLA-DP molecules expressed as recombinant proteins. We first determined that the minimum peptide-binding core of CLIP for both HLA-DP2 and DP2K69 is represented by nine aminoacids corresponding to the sequence 91-99 of invariant chain (Ii). We then assessed the peptide-binding specificities of the two pockets and determined the role of position beta69, using competition tests with the Ii-derived peptide CLIP and its mutated forms carrying all the aminoacidic substitutions in P4 and P6. Pocket 4 of HLA-DP2 showed high affinity for positively charged, aromatic, and polar residues, whereas aliphatic residues were disfavored. Pocket 4 of the DP2K69 variant showed a reduced aminoacid selectivity with aromatic residues most preferred. Pocket 6 of HLA-DP2 showed high affinity for aromatic residues, which was increased in DP2K69 and extended to arginine. Finally, we used the experimental data to determine the best molecular-modeling approach for assessing aminoacid selectivity of the two pockets. The results with best predictive value were obtained when single aminoacids were evaluated inside each single pocket, thus, reducing the influence of the overall peptide/ major histocompatibility complex interaction. In conclusion, the HLA-DPbeta69 polymorphism plays a fundamental role in the peptide-binding selectivity of HLA-DP. Furthermore, as this polymorphism is the main change in the pocket 4 area of HLA-DP, it could represent a supertype among HLA-DP molecules significantly contributing to the selection of epitopes presented in the context of this HLA isotype.

HLA-associated susceptibility to childhood B-cell precursor ALL: definition and role of HLA-DPB1 supertypes

“…Pocket 4 of DP2 is deeper, more negatively charged than DP4 , giving it a greater affinity for positively charged nonpolar aromatic residues, such as glutamine (Q), arginine (R), and lysine (K). Furthermore, glycine (G) makes pocket 1 (b84) and pocket 6 (b11) deep and hydrophilic, preferentially-binding hydrophobic and aromatic amino acids, notably phenylalanine (F), and tyrosine (Y) (Berretta et al, 2003;Diaz et al, 2003Diaz et al, , 2005. This predicts that infectious peptides with an 1 FXXKXFXXA/V 9 motif (where X is unknown, and P9 can be A or V) are likely to bind to DP2.…”

“…Using a similar approach, Castelli et al (2002) defined three DP supertype clusters with shared amino acid residues in the P1 (b84) and P6 (b11) PBP. However, the P4 peptide-binding pocket, at position b69, also makes an important contribution to antibody and peptide-binding (Arroyo et al, 1995;Chicz et al, 1997), T-cell responses (Berretta et al, 2003;Diaz et al, 2003) and disease susceptibility (Potolicchio et al, 1999;Wang et al, 1999). For this reason we clustered 430 DPB1 alleles into six supertypes based on polymorphisms in three PBP, at positions 11, 69, and 84 of the b1 domain (i.e., pockets 6, 4, and 1).…”

Beryllium Presentation to CD4+ T Cells Is Dependent on a Single Amino Acid Residue of the MHC Class II β-Chain

“…In addition, how does the beryllium moiety interact with this amino acid? To date, no crystal structure for HLA-DP2 or DR13 exists, but HLA-DP2 modeling based on the known crystal structure of HLA-DR1 suggests that the Glu 69 is located on the ␣-helix of the ␤-chain with side groups pointing into the peptide-binding cleft (19,27). Based on HLA-DP2 modeling studies, the Glu 69 appears to be involved in the formation of the P4 pocket (27).…”

“…To date, no crystal structure for HLA-DP2 or DR13 exists, but HLA-DP2 modeling based on the known crystal structure of HLA-DR1 suggests that the Glu 69 is located on the ␣-helix of the ␤-chain with side groups pointing into the peptide-binding cleft (19,27). Based on HLA-DP2 modeling studies, the Glu 69 appears to be involved in the formation of the P4 pocket (27). Berretta et al (27) suggested that the altering of the HLA-DP2 molecule with a lysine at position 69 (Lys 69 ) as opposed to a glutamic acid induced significant changes in both the shape and charge distribution of the P4 pocket, as well as the neighboring P6 pocket.…”

HLA‐DP2 binding prediction by molecular dynamics simulations

“…Combination of both types of interaction using the linear interaction energy method 36 did not improve the binding prediction (data not shown). Berretta et al 37 arrived at a similar conclusion after using the intermolecular Coulombic and van der Waals energies to predict binding in pockets 4 and 6 of HLA-DP2. They found the most significant contribution to the total energy came from the van der Waals interactions.…”