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. 2008 Oct 30;12(5b):1915–1935. doi: 10.1111/j.1582-4934.2008.00174.x

Fig 7.

Fig 7

(A) Ribbon representation of the HLA-DRβ1*0401 [103] (PDB accession number 2SEB) molecule showing the A chain in pink and the β chain in light blue. Localization of residues forming Pocket 1 are shown in fuchsia, Pocket 4 in blue, Pocket 6 in light brown and Pocket 9 in green. (B) HLA-DRβ1*0401 surface [103], showing the deep localization of Pockets 1 (fuchsia) and Pocket 9 (green) and the superficial localization of Pockets 4 (dark blue) and 6 (light brown) on the PBR platform of this HLA-DRβ1*0401 molecule. The TCR contacting residues on this molecule are displayed in yellow and show the elevated prominence above this molecule's peptide-binding residue (PBR) groove. (C) Docking and molecular modelling of malarial immunogenic, protection-inducing, modified HABP 24112 residues (12YNMVIRRSM20) fitting into the HLA-DRβ1*0401 molecule's PBR based on this peptide's binding activity, binding motifs and reading registers for this Class II molecule. Van der Waals surface amino acid colour code is displayed at the bottom of this figure in panel c. Note the fit of residues Y12 (fuchsia), V15 (dark blue), R17 (light brown) and M20 (green) into the corresponding pockets P1, P4, P6 and P9, including R18 (grey) in P7, confirming the suggested existence of this pocket in the HLA-DRβ1*0401 molecule. (D) This shows the H bonds spontaneously established between amino acids Qα9, Nα62, Nα69, Nβ82, Kβ71 and Wβ61 of HLA-DRβ1*0401 (code 2SEB in PDB) [103] and the backbone of modified HABP 24112. Seven out of nine residues showed a distance <3.5 Å, characteristic of the H bonds with which the peptide is anchored into the PBR of these Class II molecules to conform a stable MHCII–peptide–TCR complex. It has also to be stressed that both structures were determined by very different methods: X-ray crystallography for HLA-DRβ1*0401 and 1H NMR in solution for HABP 24112. In spite of these methodological differences, RMSD between Col II peptide with which HLA-DRβ1*0401 was crystallized and modified HABP 24112 was only 1.82 Å. (E) Diagrammatic representation of 24112 residues orientation fitting into HLA-DRβ1*0401 pockets (downwardly oriented) and TCR (upwardly oriented). Colour code as previously described.