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.

Numerous variants of leucine rich repeats in proteins from nucleo-cytoplasmic large DNA viruses.

Leucine rich repeats (LRRs) occurring in tandem are 20-29 amino acids long. Eleven LRR types have been recognized. Sequence features of LRRs from viruses were investigated using over 600 LRR proteins from 89 species.

Withdrawal Notice: Novel Sequence Features of Leucine-rich Repeats in Proteins from Nucleocytoplasmic Large DNA Viruses.

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Sequence features, structure, ligand interaction, and diseases in small leucine rich repeat proteoglycans.

Small leucine rich repeat proteoglycans (SLRPs) are a group of active components of the extracellular matrix in all tissues. SLRPs bind to collagens and regulate collagen fibril growth and fibril organization. SLRPs also interact with various cytokines and extracellular compounds, which lead to various biological functions such cell adhesion and signaling, proliferation, and differentiation.

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.

Shrinking of repeating unit length in leucine-rich repeats from double-stranded DNA viruses.

Leucine-rich repeats (LRRs) are present in over 563,000 proteins from viruses to eukaryotes. LRRs repeat in tandem and have been classified into fifteen classes in which the repeat unit lengths range from 20 to 29 residues. Most LRR proteins are involved in protein-protein or ligand interactions.

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).

Molecular Dynamics Study of the Changes in Conformation of Calmodulin with Calcium Binding and/or Target Recognition.

Calmodulin is a calcium binding protein with two lobes, N-lobe and C-lobe, which evolved from duplication and fusion of a single precursor lobe of a pair of EF-hand. These two lobes of calmodulin show subtle differences in calcium binding and target recognition; these are important for the functions of calmodulin. Since the structures, especially main chain conformations, of two EF-lobes in holo-form are quite similar; this is a good example to evaluate the effect of side chains for structural dynamics.

Interaction sites of PEF proteins for recognition of their targets.

The EF-hand is a helix-loop-helix motif observed mainly in intracellular calcium binding proteins. The EF-hand usually occurs as a pair, EF-lobe, which is a unit of evolution and structure. Penta EF-hand (PEF) proteins form a unique group including calpain, sorcin, grancalcin, ALG-2, and peflin.

Polyproline II Helix as a Recognition Motif of Plant Peptide Hormones and Flagellin Peptide flg22.

Background: Plant peptide hormones play a crucial role in plant growth and development. A group of these peptide hormones are signaling peptides with 5 - 23 amino acids. Flagellin peptide (flg22) also elicits an immune response in plants.

Leucine Rich Repeat Proteins: Sequences, Mutations, Structures and Diseases.

Mutations in the genes encoding Leucine Rich Repeat (LRR) containing proteins are associated with over sixty human diseases; these include high myopia, mitochondrial encephalomyopathy, and Crohn's disease. These mutations occur frequently within the LRR domains and within the regions that shield the hydrophobic core of the LRR domain. The amino acid sequences of fifty-five LRR proteins have been published.

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.

Conformational landscape mapping the difference between N-lobes and C-lobes of calmodulin.

Calmodulin is a calcium binding protein that consists of four EF-hand domains. The two EF-lobes of calmodulin, called the N-lobe and the C-lobe, arose from duplication and fusion of a precursor EF-hand. The amino acid sequences and the structures of the N-lobe and of the C-lobe are quite similar to each other.

Structural and functional diversity of EF-hand proteins: Evolutionary perspectives.

We have classified 865 sequences of EF-hand proteins from five proteomes into 156 subfamilies. These subfamilies were put into six groups. Evolutionary relationships among subfamilies and groups were analyzed from the inferred ancestral sequence for each subfamily.

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).

HVM: a web-based tool for alignment of EF-hand lobes relative to their local pseudo two-fold axes.

We have developed a method to align a pair of EF-hand domains, an EF-lobe, using the symmetry axis that is intrinsic to the EF-lobe itself. The coordinate system for the alignment is dependent only on the symmetry of the EF-lobe. The absolute positions of each component in the structure can be described in this coordinate system.

Structural differences among subfamilies of EF-hand proteins--a view from the pseudo two-fold symmetry axis.

We have analyzed the conformations of EF-lobes, adjacent pairs of EF-hand domains, in a coordinate system based on the approximate two-fold (z) axis that relates the two EF-hands. Two parameters - dE(ø), the azimuthal angle between the y-axis and the projection of the offset vector to helix E onto the yz-plane, and δdF(ø), the difference angle between the two helices (F1 and F2) of odd and even domains--characterize the openness of a single EF-hand domain and of an EF-lobe, respectively. We describe and compare values of dE(ø) and of δdF(ø) for EF-hand proteins of five subfamilies--CTER, CPV, S100, PARV, CALP--in calci- and apo- forms, with and without bound target proteins.

Analysis of the movements of helices in EF-hands.

We have developed a method to place an EF-lobe in a coordinate system that recognizes the similarity of its two EF-hand domains as well as their relationship by a pseudo-two fold axis, z. The x-axis connects the center of mass, calculated from α-carbons of helices E1 and F1, with the center of mass of E2 and F2. The resulting coordinate system is intrinsic to each EF-lobe and requires no comparison with other EF-lobes.

Structure and characterization of the 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Aeropyrum pernix.

The first enzyme in the shikimic acid biosynthetic pathway, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS), varies significantly in size and complexity in the bacteria and plants that express it. The DAH7PS from the archaebacterium Aeropyrum pernix (DAH7PS(Ap)) is among the smallest and least complex of the DAH7PS enzymes, leading to the hypothesis that DAH7PS(Ap) would not be subject to feedback regulation by shikimic acid pathway products. We overexpressed DAH7PS(Ap) in Escherichia coli, purified it, and characterized its enzymatic activity.

Non-globular structures of tandem repeats in proteins.

There are two classes of tandem repeats in proteins - globular and non-globular. There are two subclasses of non-globular repeats. The first, such as collagen, form stable helices.

Flexible structures and ligand interactions of tandem repeats consisting of proline, glycine, asparagine, serine, and/or threonine rich oligopeptides in proteins.

Tandem repeats occur in 14% of all proteins. The repeat unit lengths range from a single amino acid to more than 100 residues and the repeat number is sometimes over 100. Understanding the structures, functions, and evolution of these repeats is a significant goal in both proteomics and genomics.

Cell signaling, beyond cytosolic calcium in eukaryotes.

Calcium functions as a secondary messenger within the cytosols of eukaryotes. This serves as a reference point to evaluate three related questions:Exploration of these three interrelated questions indicates the importance of more sensitive techniques and of a refined concept of information transfer and transduction. 1.

Initial three-dimensional reconstructions of protein kinase C delta from two-dimensional crystals on lipid monolayers.

Two-dimensional crystals of protein kinase C delta (PKCdelta) and of its regulatory domain (RDdelta) were grown on lipid monolayers and analyzed by electron microscopy at tilt angles varying from -50 degrees to +55 degrees. Although the crystals exhibit pseudo-3-fold symmetry, analysis of difference phase residuals indicates that there is only one way to align the crystals for merging so the data were processed in plane group P1. Three-dimensional reconstructions generated for several two-dimensional crystals each of PKCdelta and RDdelta show good agreement and are consistent with membrane attachment via a single C1 subdomain, a small surface contact by one or two loops from the C2 domain, and, in intact PKCdelta, a small appendage from the catalytic domain, probably V5.

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.