Toll-like receptor 9 interaction with CpG ODN – An in silico analysis approach

Abstract

BackgroundToll-like receptor 9 (TLR9) recognises unmethylated CpG DNA and activates a signalling cascade, leading to the production of inflammatory cytokines such as TNF-α, IL-1, IL-6 and IL-12 via the adaptor protein MyD88. However, the specific sequence and structural requirements of the CpG DNA for the recognition of and binding to TLR9 are unknown. Moreover, the 3D structures of TLR9 and the TLR9-ODN complex have not been determined. In this study, we propose a reliable model of the interaction of the TLR9 ECD with CpG ODN using bioinformatics tools.ResultsThe three-dimensional structures of two TLR9 ECD-CpG ODN complexes were constructed using a homology modelling and docking strategy. Based on the models of these complexes, the TLR9 ECD-CpG ODN interaction patterns were calculated. The results showed that the interface between the human TLR9 and the CpG ODN molecule is geometrically complementary. The computed molecular interactions indicated that LRR11 is the main region of TLR9 that binds to CpG ODN and that five positively charged residues within LRR11 are involved in the binding of the TLR9 ECD to the CpG ODN. Observations in the close-up view of these interactions indicated that these five positively charged residues contribute differently to the binding region within the TLR9 ECD-CpG ODN complex. 337Arg and 338Lys reside in the binding sites of ODN, forming hydrogen bonds and direct contacts with the CpG ODN, whereas 347Lys, 348Arg, and 353His do not directly contact the CpG ODN. These results are in agreement with previously reported experimental data.ConclusionIn this study, we present two structural models for the human and mouse TLR9 ECD in a complex with CpG ODN. Some features predicted by this model are consistent with previously reported experimental data. This complex model may lead to a better understanding of the function of TLR9 and its interaction with CpG ODN and will improve our understanding of TLR9-ligand interaction in general.

In silico analysis of human Toll‐like receptor 7 ligand binding domain

“…All rights reserved. 8 with recently published structure of the TLR8 homodimer possessed significant structural similarity with RMSD value (5.473 Å) as shown in Figure 2. The constructed homodimer model was refined by energy minimization ( Figure 3A) and the critical residues involved in the homodimerization of hTLR7 ECD were analyzed by the protein-protein interactions (Table S2).…”

Cross talk between Leishmania donovani CpG DNA and Toll-like receptor 9: An immunoinformatics approach

“…Recent reports on TLR9-CpG DNA interactions suggest that the helical B-conformation of ssDNA binds the TLR9 catalytic site [9,33]. Therefore we modeled the 3D structure of ODN and identified CpG DNA sequences as a single stranded molecule in the B-helical conformation for docking.…”

“…The ECD of TLR9 comprises 25 LRRs contributing to the binding of ligand. However, it is still unknown which LRR and their specific amino acids are involved in interaction with the pathogenic fragment [9].…”

A Proteomics Perspective on Viral DNA Sensors in Host Defense and Viral Immune Evasion Mechanisms

“…TLR9 was initially shown to recognize CpG motifs in bacterial DNA 6 . Later, surface plasmon resonance (SPR) was used to demonstrate a direct interaction between TLR9 and CpG DNA 44 , and, more recently, a bioinformatics approach was employed to model the 3D structure of the TLR9-CpG complex 45 . It should be noted that current technology now allows bridging SPR with protein identification by MS 46 .…”