Homology modeling of human Toll‐like receptors TLR7, 8, and 9 ligand‐binding domains

Toll‐like receptors (TLRs) play a key role in the innate immune system. The TLR7, 8, and 9 compose a family of intracellularly localized TLRs that signal in response to pathogen‐derived nucleic acids. So far, there are no crystallographic structures for TLR7, 8, and 9. For this reason, their ligand‐binding mechanisms are poorly understood. To enable first predictions of the receptor–ligand interaction sites, we developed three‐dimensional structures for the leucine‐rich repeat ectodomains of human TLR7, 8, and 9 based on homology modeling. To achieve a high sequence similarity between targets and templates, structural segments from all known TLR ectodomain structures (human TLR1/2/3/4 and mouse TLR3/4) were used as candidate templates for the modeling. The resulting models support previously reported essential ligand‐binding residues. They also provide a basis to identify three potential receptor dimerization mechanisms. Additionally, potential ligand‐binding residues are identified using combined procedures. We suggest further investigations of these residues through mutation experiments. Our modeling approach can be extended to other members of the TLR family or other repetitive proteins.

[1]  N. Gay,et al.  Structure and function of Toll receptors and their ligands. , 2007, Annual review of biochemistry.

[2]  S. Paik,et al.  Crystal Structure of the TLR1-TLR2 Heterodimer Induced by Binding of a Tri-Acylated Lipopeptide , 2007, Cell.

[3]  Y. Kuroki,et al.  Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors , 2007, BMC Genomics.

[4]  Sarah E. Ewald,et al.  The ectodomain of Toll-like receptor 9 is cleaved to generate a functional receptor , 2008, Nature.

[5]  Janusz M Bujnicki,et al.  Protein‐Structure Prediction by Recombination of Fragments , 2006, Chembiochem : a European journal of chemical biology.

[6]  N. Gay,et al.  Conserved Features in the Extracellular Domain of Human Toll-like Receptor 8 Are Essential for pH-dependent Signaling* , 2006, Journal of Biological Chemistry.

[7]  Kengo Kinoshita,et al.  PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces , 2005, Bioinform..

[8]  D. Davies,et al.  Leucine-rich repeats and pathogen recognition in Toll-like receptors. , 2003, Trends in immunology.

[9]  I. Wilson,et al.  Crystal Structure of Human Toll-Like Receptor 3 (TLR3) Ectodomain , 2005, Science.

[10]  J. Gibrat,et al.  GOR method for predicting protein secondary structure from amino acid sequence. , 1996, Methods in enzymology.

[11]  Hayyoung Lee,et al.  Crystal Structure of the TLR4-MD-2 Complex with Bound Endotoxin Antagonist Eritoran , 2007, Cell.

[12]  M. Frank,et al.  Structure-function relationships of Toll-like receptor domains through homology modelling and molecular dynamics. , 2007, Biochemical Society transactions.

[13]  D. Davies,et al.  Structural Basis of Toll-Like Receptor 3 Signaling with Double-Stranded RNA , 2008, Science.

[14]  Peng Jiang,et al.  RISP: A web-based server for prediction of RNA-binding sites in proteins , 2008, Comput. Methods Programs Biomed..

[15]  Janusz M. Bujnicki,et al.  MetaMQAP: A meta-server for the quality assessment of protein models , 2008, BMC Bioinformatics.

[16]  A. Kaur,et al.  The evolution of vertebrate Toll-like receptors. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[17]  J. Metzger,et al.  Toll‐like receptor 9 binds single‐stranded CpG‐DNA in a sequence‐ and pH‐dependent manner , 2004, European journal of immunology.

[18]  Liam J. McGuffin,et al.  The ModFOLD server for the quality assessment of protein structural models , 2008, Bioinform..

[19]  A. Sali,et al.  Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.

[20]  D. Davies,et al.  The dsRNA binding site of human Toll‐like receptor 3 , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Shandar Ahmad,et al.  PSSM-based prediction of DNA binding sites in proteins , 2005, BMC Bioinformatics.

[22]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[23]  Arne Elofsson,et al.  Identification of correct regions in protein models using structural, alignment, and consensus information , 2006, Protein science : a publication of the Protein Society.

[24]  K. Ginalski.  Comparative modeling for protein structure prediction. , 2006, Current opinion in structural biology.

[25]  R Langridge,et al.  Improvements in protein secondary structure prediction by an enhanced neural network. , 1990, Journal of molecular biology.

[26]  S. Akira,et al.  Toll-like receptors in innate immunity. , 2004, International immunology.

[27]  Pierre Baldi,et al.  Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data , 2005, Data Mining and Knowledge Discovery.

[28]  D. Davies,et al.  The molecular structure of the Toll-like receptor 3 ligand-binding domain. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[29]  A. Bowie,et al.  The family of five: TIR-domain-containing adaptors in Toll-like receptor signalling , 2007, Nature Reviews Immunology.

[30]  Burkhard Rost,et al.  The PredictProtein server , 2003, Nucleic Acids Res..

[31]  Igor B. Kuznetsov,et al.  DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins , 2007, Bioinform..

[32]  Jae-Hyung Lee,et al.  Genetics, Development and Cell Biology Publications Genetics, Development and Cell Biology Rnabindr: a Server for Analyzing and Predicting Rna-binding Sites in Proteins Rnabindr: a Server for Analyzing and Predicting Rna-binding Sites in Proteins , 2022 .

[33]  Shandar Ahmad,et al.  Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information , 2004, Bioinform..

[34]  B. Monks,et al.  Ligand-induced conformational changes allosterically activate Toll-like receptor 9 , 2007, Nature Immunology.

[35]  R. Medzhitov,et al.  Two Modes of Ligand Recognition by TLRs , 2007, Cell.

[36]  Liangjiang Wang,et al.  BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences , 2006, Nucleic Acids Res..

[37]  Shaila C. Rössle,et al.  LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs) , 2008, BMC Structural Biology.

[38]  Gajendra P.S. Raghava,et al.  Prediction of RNA binding sites in a protein using SVM and PSSM profile , 2008, Proteins.

[39]  András Fiser,et al.  ModLoop: automated modeling of loops in protein structures , 2003, Bioinform..

[40]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[41]  Torsten Schwede,et al.  Automated protein structure homology modeling: a progress report. , 2004, Pharmacogenomics.

[42]  K. Heeg,et al.  Immunostimulatory CpG Oligonucleotides Form Defined Three‐Dimensional Structures: Results from an NMR Study , 2007, ChemMedChem.