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TLR X-ray structures

TLR X-ray structures. Harma Brondijk Bio-informatics course 2009. TIR domain structures. Protein-protein interaction surfaces: Oligomerizationn interface Interaction surface(s) with TIR domains of adapter molecules: MAL/MyD88 TRAM/TRIF SARM. TIR-domain structures. TLR-TIR domains:

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TLR X-ray structures

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  1. TLR X-ray structures Harma Brondijk Bio-informatics course 2009

  2. TIR domain structures Protein-protein interaction surfaces: Oligomerizationn interface Interaction surface(s) with TIR domains of adapter molecules: MAL/MyD88 TRAM/TRIF SARM

  3. TIR-domain structures • TLR-TIR domains: • hTLR1 2.90 Å 1fyv (2000) • hTLR2 3.00 Å 1fyw (2000) • hTLR2-P681H 2.80 Å 1fyx (2000) • hTLR2-C713S 3.20 Å 1o77 (2002) • hTLR10 2.20 Å 2j67 (2006) • Other TIR-domains • hMyD88 (NMR) 2js7/2z5v (2008) • IL1RAPL 2.30 Å 1t3g (2005)

  4. TIR domains: similar structure, flexible regions hTLR1 hTLR2 hTLR2_P681H hTLR10 IL1RAPL hTLR2_C713S

  5. TIR domains: similar structure, flexible regions BB-loop

  6. Dimer interfaces: which is the ‘true’ interface? hTLR1: - 1 molecule in the asymetric unit - protein-protein contacts -> two possible dimer interfaces hTLR1 807 Å2, 2 saltbridges hTLR1 725 Å2, 2 disulfide

  7. Dimer interfaces: which is the ‘true’ interface? hTLR1 hTLR10 hTLR2 hTLR2-P681H hTLR2-C713S

  8. TLR1-TLR2 TIR domain docking: putative dimer GAUTAM et al. JBC 2006

  9. hTLR10 TIR dimer: most likely ‘real’ signaling dimer Molecule B Molecule A Nyman et al. JBC 2008

  10. Conserved surface patches: possible interaction surfaces In general surface residues are much less conserved than core residues Interaction surfaces need to change concerted in both interaction partners -> Interaction surfaces are relatively higly conserved Xu et al. Nature 2000

  11. Modelling + Information driven docking programs -> Putative TLR4-Mal/TRAM interactions Miguel et al. PLoS ONE 2007

  12. LRR domain structures Issues: Overall structure Interaction with ligands (agonist/antagonist) Ligand induced dimerization? Conformational changes Interfaces Interactions with co-factors

  13. LRR-domain structures • TLR ectodomains: • hTLR1/hTLR2 dimer + PAM3CSK4 (TLR1 aa 25-475/TLR2 aa 27-506) 2.10 Å 2z7x (2007) • hTLR2aa 1-284 1.80 Å 2z80 (2007) • mTLR2aa 27-506 1.80 Å/2.60 Å 2z81/2z82 (2007) • hTLR3 2.10 Å 1ziw (2005) • hTLR3 2.40 Å 1aoz (2005) • mTLR3 2.66 Å 3cig (2008) • mTLR3 + dsRNA 3.41 Å 3ciy (2008) • hTLR4 aa27-228 1.70 Å 2z62 (2007) • hTLR4aa 27-527 2.00 Å 2z63 (2007) • hTLR4/MD2/Eritoran 2.70 Å 2z65 (2007) - hTLR4/MD2/LPS 3.10 Å 3FXI (2009) • mTLR4/MD2 2.84 Å 2z64 (2007) • CD14 2.50 Å 1wwl (2005)

  14. convex lateral concave TLR ecto-domains consist ofleucine-rich-repeats hTLR3 hTLR3 Curvature may vary along the ectodomain: TLR1/2/4: divided in 3 distinct regions Choe et al. Science 2005 Bell et al. PNAS 2005

  15. LRR domain architecture • LRR: • 20-30 residues (extensions possible) • defining motif: LxxLxLxxNxL L=Leu/Val/Ile/Phe N=Asn/Thr/Ser/Cys • Repeat -> curved solenoid structure • Concave side: continuous parallel ß-sheet • Convex side: variable • Cavity of solenoid structure filled with hydrophobic residues

  16. The Leucine-rich repeat structure: diversity rules! Always ß-sheet on concave side, convex side varaible: Polyproline II helix α-helix Extensions possible on convex and lateral sides (examples from TLR3 structure) 310-helix 2 Polyproline II helices Other combinations of helices and strands

  17. (TLR3) (TLR3) Pam2CSK4 (TLR6/TLR2 heterodimer) Flagellin (TLR5) Ligand binding: TLRs recognize chemically diverse compounds

  18. How do TLR’s recognize/bind their ligands? How does ligand binding induce TLR oligomerization?

  19. mTLR3-dsRNA complex 2 TLR3 molecules bind adjacently to the dsRNA C-termini 25 Å apart Liu et al. Science, 2008

  20. dsRNA-mTRL3 interactions • Two interaction sites close to N and C terminus • Interactions with sugar-phosphate backbones only explains lack of sequence specificity • Histidine involvement explains pH dependence N C N C Liu et al. Science, 2008

  21. mTRL3-mTLR3 interactions • Direct TLR3-TLR3 contacts near C-terminal interaction site explains concerted binding C N N C Liu et al. Science, 2008

  22. hTLR1-hTLR2 Pam3CSK4 complex C-termini <42 Å apart Jin et al. Cell 2007

  23. hTLR1-hTLR2 Pam3CSK4 complex Ligand binds to both TLR1 and TLR2 -> heterodimerization Top view Question: How does the hTLR2-hTLR6 dimer form?? (ligand lacks the 3rd lipid chain) Jin et al. Cell 2007

  24. mTLR4-mMD2 complex MD2 binds on the edge of the central and N-terminal region, at the lateral side of the molecule Kim et al. Cell 2007

  25. hTLR4/VLR-hMD2 Eritoran Kim et al. Cell 2007

  26. hTLR4-MD2-LPS homodimer Park et al. Nature 2009

  27. Dimerization through LPS and MD2 interactions MD2 TLR4* MD2* TLR4

  28. What makes LPS an agonist? Lipid Iva and Eritoran have fewer lipid tails -> bind deeper in the MD2 binding pocket -> Phosphates not available for interactions Park et al. Nature 2009

  29. TLR4 dimerization appears to induce a conformational change Central domains of TLR1/2/4 less rigid compared to standard LRR structures; needed to accommodate conformational changes??? Park et al. Nature 2009

  30. Central theme: ligand interactions induce dimerization -> C-termini in close approximation Park et al. Nature 2009

  31. Thanks for your attention

  32. Dimerization through LPS and MD2 interactions

  33. TLR4-MD2-LPS dimerization interactions

  34. TIR domain plasticity TLR2-TLR2 comparison TLR1-TLR2 comparison Xu et al. Nature 2000 Tao et al. BBRC 2002

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