disease and infectious diseases
Kapoerchan, V.V.
Citation
Kapoerchan, V. V. (2009, December 22). Towards peptide based
therapeutics-applications in celiac disease and infectious diseases. Retrieved from https://hdl.handle.net/1887/14542
Version: Corrected Publisher’s Version
License: Licence agreement concerning inclusion of doctoral thesis in the Institutional Repository of the University of Leiden
Downloaded from: https://hdl.handle.net/1887/14542
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applicable).
Appendix
Figure 1Schematic representation of the HLA-DQ2 protein. The α en β chains are indicated in red and blue, with a bound gluten peptide indicated in yellow. Left: side view. Right: the binding pocket made up by two helices of each subunit and a β-sheet on the bottom. Pictures taken from the crystal structure provided in ref. 1.
Figure 2 Schematic representation of the pathogenesis of CD.
a) Digestion of gluten to small peptide fragments rich in proline and glutamine. b) Internalization of peptide fragments by the APC and weak binding of some peptides to HLA-DQ2 (APC = antigen presenting cell). c) Recognition by gluten-positive CD4+ T cell (TCR = T cell receptor). d) Conversion of selected glutamine residues to glutamates in the peptides by tTG. e) Enhanced binding of deamidated peptides and enhanced T cell recognition.
e c gluten TCR
peptides CD4
+
T cel a
gluten
HLA-DQ2
Immune response with tissue damage and release of tTG as a result
b
Amplified immune response
d tTG deamidated gluten peptides
Figure 3The crystal structure of HLA-DQ2 with peptide QLQPFPQPELPY (epitope shown in bold), shown in red. The prolines at positions p3 and p5 are both highlighted in yellow and clearly do not show any interaction with the HLA-DQ2 binding pocket. This picture was taken from the crystal structure provided in ref. 1.
Figure 4 a) Close view of the HLA-DQ2 p1 binding pocket occupied by a proline residue. The bound α- 9 peptide is indicated in yellow, the proline at p1 in red, the negatively charged Glu at the bottom of the pocket in purple and the positively charged His residue halfway the pocket in blue. Water molecules and some amino acid residues are omitted for clarity. b) Schematic representation of the p1 pocket of the HLA-DQ2 binding pocket, showing the hydrogen bond network formed by the three water molecules.
a b
O O HN NH
HOH HOH
H OH
Figure 5 Top view (left) and side view (right)of the GS molecule. Side chains are partially omitted for clarity.2 In top view, hydrogen bonds (stabilizing the secondary structure) are indicated by thin green lines. The side view clearly shows the separation of hydrophobic and charged residues.
Side view Top view
Figure 6The crystal structure of peptide 9. a) Top view of 9, with side chains partly omitted for clarity.
Dotted lines indicate hydrogen bonds stabilizing the secondary structure. b) Side view of 9. Arrows indicate the presence of additional methyl groups as compared to GS.
a b
Figure 7 a) X-ray analysis of peptide 7. Side (left) and top view (right) of the peptide monomer. In top view, side chains are omitted for clarity. Intramolecular hydrogen bonds are indicated with dotted lines.
The arrow indicates the ‘amide flip’. b) Side and top view of the monomer of 8. c) Side (left) and top (right) view of the GS molecule.2 In top view, hydrogen bonds (stabilizing the secondary structure) are depicted by thin green lines.
amide flip a
7
less amide flip b
8
c
Figure 8Structural characteristics of 8 according to X-ray analysis. a) Side and top view of the channel with each monomer highlighted in a different color. b) Side view with the MAA residues highlighted in red, and the ornithine side chain in yellow. c) Hydrogen bonding of the MAA residue to the ornithine of another monomer, indicated by a cyan dotted line. The ornithine side chain is highlighted in yellow, the MAA in red. Side chains are partially omitted for clarity.
a
c
b
Figure 9 Comparison of β-turn structures. All six-membered morpholine rings assume a chair conformation. Hydrogen bonds are depicted as dashed lines. Of peptide 9, the conformation of the MAA-Leu9 amide bond is uncertain and therefore depicted as CONH. The crystal structures, if available, of the turn regions are depicted next to the corresponding structural formulas, hydrogens and side chains are omitted for clarity. Hydrogen bonds are depicted as dotted lines.
N O
6 7
8 9
GS N
HN O O
HN O
NH O
HN HN
O
NH O
N O
HN HN
O
O O
N O
HN HN
O
NH O
O
N O
HN
NH O
O O
NH H
H
H H
H H
H H
CONH
7
8
