A Dual Leucine-rich Repeat in Proteins from the Eukaryotic SAR Group.

Background: Leucine-rich repeats (LRRs) occurring in tandem are 20-29 amino acids long. Eleven LRR types have been recognized; they include plant-specific (PS) type with the consensus of LxxLxLxxNxL SGxIPxxIxxLxx of 24 residues and SDS22-like type with the consensus of LxxLxLxxNxL xxIxxIxxLxx of 22 residues.

Objective: A viral LRR protein in metagenome data indicated that most of the LRRs (5/6 = 0.

A crucial residue in the hydrophobic core of the solenoid structure of leucine rich repeats.

Leucine rich repeats (LRRs) with 20-30 residues form a super helix arrangement. Individual LRRs are separated into a highly conserved segment with a highly conserved (HCS) and a variable segment (VS). In LRRs short β-strands in HCS stack in parallel, while VS adopts various secondary structures.

A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats.

Leucine rich repeats (LRRs) are present in over 430 000 proteins from viruses to eukaryotes. The LRRs are 20 to 30 residues long and occur in tandem. Individual LRRs are separated into a highly conserved segment with the consensus of LxxLxLxxNxL or LxxLxLxxNxxL (HCS) and a variable segment (VS).

Super Secondary Structure Consisting of a Polyproline II Helix and a β-Turn in Leucine Rich Repeats in Bacterial Type III Secretion System Effectors.

Leucine rich repeats (LRRs) are present in over 100,000 proteins from viruses to eukaryotes. The LRRs are 20-30 residues long and occur in tandem. LRRs form parallel stacks of short β-strands and then assume a super helical arrangement called a solenoid structure.

Comparative Geometrical Analysis of Leucine-Rich Repeat Structures in the Nod-Like and Toll-Like Receptors in Vertebrate Innate Immunity.

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).

omega-Helices in proteins.

A modification of the alpha-helix, termed the omega-helix, has four residues in one turn of a helix. We searched the omega-helix in proteins by the HELFIT program which determines the helical parameters-pitch, residues per turn, radius, and handedness-and p = rmsd/(N - 1)(1/2) estimating helical regularity, where "rmsd" is the root mean square deviation from the best fit helix and "N" is helix length. A total of 1,496 regular alpha-helices 6-9 residues long with p < or = 0.

HELFIT: Helix fitting by a total least squares method.

The problem of fitting a helix to data arises in analysis of protein structure, in nuclear physics, and in engineering. A continuous helix is described by five parameters: helix axis, helix radius, and helix pitch. One of these helix parameters is frequently predefined in the helix fitting.

Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran.

TLR4 and MD-2 form a heterodimer that recognizes LPS (lipopolysaccharide) from Gram-negative bacteria. Eritoran is an analog of LPS that antagonizes its activity by binding to the TLR4-MD-2 complex. We determined the structure of the full-length ectodomain of the mouse TLR4 and MD-2 complex.

Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors.

Background: Toll-like receptors (TLRs) play a central role in innate immunity. TLRs are membrane glycoproteins and contain leucine rich repeat (LRR) motif in the ectodomain. TLRs recognize and respond to molecules such as lipopolysaccharide, peptidoglycan, flagellin, and RNA from bacteria or viruses.

3(10)-helices in proteins are parahelices.

The 3(10)-helix is characterized by having at least two consecutive hydrogen bonds between the main-chain carbonyl oxygen of residue i and the main-chain amide hydrogen of residue i + 3. The helical parameters--pitch, residues per turn, radius, and root mean square deviation (rmsd) from the best-fit helix--were determined by using the HELFIT program. All 3(10)-helices were classified as regular or irregular based on rmsd/(N - 1)1/2 where N is the helix length.

Structural principles of leucine-rich repeat (LRR) proteins.

LRR-containing proteins are present in over 2000 proteins from viruses to eukaryotes. Most LRRs are 20-30 amino acids long, and the repeat number ranges from 2 to 42. The known structures of 14 LRR proteins, each containing 4-17 repeats, have revealed that the LRR domains fold into a horseshoe (or arc) shape with a parallel beta-sheet on the concave face and with various secondary structures, including alpha-helix, 3(10)-helix, and pII helix on the convex face.