Structure modeling of Toll-like receptors

Toll-like receptors (TLRs) recognize invasion of microbial pathogens and initiate innate immune responses that are essential for inhibiting pathogen dissemination and for the development of acquired immunity. To understand how these receptors work, it is crucial to investigate them from a structural perspective. High-throughput genome sequencing projects have led to the identification of more than 3,000 TLR sequences. However, only several structures of TLRs have been determined because structure determination by X-ray diffraction or nuclear magnetic resonance spectroscopy experiments remains difficult and time-consuming. Protein structure modeling methods are powerful tools for bridging the gap between sequence determination and structure determination. Due to different repeat numbers and distinct arrangements of leucine-rich repeats (LRRs) contained in TLR ectodomains, an automated homology modeling method often failed to predict a proper model. Here, we describe an LRR template assembly method for homology modeling of TLRs. This method was successfully validated through the comparison of a predicted model with the crystal structures, and showed better performance than other Protein structure modeling tools. The resulting models can be used to perform protein-ligand interaction studies or to design mutagenesis experiments, and hence to investigate TLR ligand-binding mechanisms.