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

Wei Zhou,Yuan Gao,Beiping Li,Zhengliang Qiu,Junjie Yue,Yan Li,Xichun Pan,Long Liang,Hong Zhou

doi:10.1186/1742-4682-10-18

Wei Zhou, Yuan Gao + Show 7 more

Open Access

https://doi.org/10.1186/1742-4682-10-18

Copy DOI

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.

Highlights

Toll-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
We can identify and characterise the Leucine rich repeat (LRR) region within hTLR9 that binds to CpG ODN with the higher affinity and further determine which specific residues are critical for ligand binding
Residues within LRR11 in hTLR9 provide the greatest number of interactions with CpG ODN The TLR9-ODN complex was modelled in three steps

Summary

Introduction

Toll-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. The specific sequence and structural requirements of the CpG DNA for the recognition of and binding to TLR9 are unknown. The surface-expressed TLRs primarily recognise structural components of pathogens, while the endosomal TLRs are dedicated to recognising nucleic acids [1]. Pathogen-binding ectodomains of mammalian TLRs comprise 19–25 extracellular leucine-rich repeats (LRRs) and a cytoplasmic toll/interleukin (IL)-1R (TIR) domain [3]. LRRs containing 24–29 amino acids are responsible for ligand recognition and binding, and the TIR domain is responsible for downstream signalling

Objectives

Results

Discussion

Conclusion