title: Comparative Geometrical Analysis of Leucine-Rich Repeat Structures in the Nod-Like and Toll-Like Receptors in Vertebrate Innate Immunity.
abstract: The NOD-like receptors (NLRs) and Toll-like receptors (TLRs) are pattern recognition receptors that are involved in the innate, pathogen pattern recognition system. The TLR and NLR receptors contain leucine-rich repeats (LRRs) that are responsible for ligand interactions. In LRRs short β-strands stack parallel and then the LRRs form a super helical arrangement of repeating structural units (called a coil of solenoids). The structures of the LRR domains of NLRC4, NLRP1, and NLRX1 in NLRs and of TLR1-5, TLR6, TLR8, TLR9 in TLRs have been determined. Here we report nine geometrical parameters that characterize the LRR domains; these include four helical parameters from HELFIT analysis. These nine parameters characterize well the LRR structures in NLRs and TLRs; the LRRs of NLR adopts a right-handed helix. In contrast, the TLR LRRs adopt either a left-handed helix or are nearly flat; RP105 and CD14 also adopt a left-handed helix. This geometrical analysis subdivides TLRs into four groups consisting of TLR3/TLR8/TLR9, TLR1/TLR2/TRR6, TLR4, and TLR5; these correspond to the phylogenetic tree based on amino acid sequences. In the TLRs an ascending lateral surface that consists of loops connecting the β-strand at the C-terminal side is involved in protein, protein/ligand interactions, but not the descending lateral surface on the opposite side.
authors: The Institute of Tandem Repeats, Sapporo 060-8556, Japan. norio_irreko@outlook.jp.
authors: Norio
authors: N
authors: Matsushima
authors: The Institute of Tandem Repeats, Sapporo 060-8556, Japan. miya_hokkaido@hotmail.com.
authors: Hiroki
authors: H
authors: Miyashita
authors: Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar 210646/377, Mongolia. enkhb2003@yahoo.com.
authors: Purevjav
authors: P
authors: Enkhbayar
authors: Department of Biology, University of Virginia, Charlottesville, VA 22904, USA. rhk5i@virginia.edu.
authors: Robert H
authors: RH
authors: Kretsinger
mesh_terms: D000818:Animals; D006801:Humans; D007113:Immunity, Innate; D007930:Leucine; D020449:Repetitive Sequences, Amino Acid; D051193:Toll-Like Receptors / Q000737:chemistry* / Q000378:metabolism; D014714:Vertebrates / Q000276:immunology*
chemical_list: D051193:Toll-Like Receptors; D007930:Leucine
keywords: CD14; NLRs; RP105; TLRs; dimer; helix; receptor