Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Proteins prepared by recombinant DNA technology.
The relationships of groups of organisms as reflected by their genetic makeup.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
Established cell cultures that have the potential to propagate indefinitely.
Proteins found in any species of bacterium.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
Amino acids that are not synthesized by the human body in amounts sufficient to carry out physiological functions. They are obtained from dietary foodstuffs.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
Transport proteins that carry specific substances in the blood or across cell membranes.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
Cellular proteins and protein complexes that transport amino acids across biological membranes.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Three regions (CDR1; CDR2 and CDR3) of amino acid sequence in the IMMUNOGLOBULIN VARIABLE REGION that are highly divergent. Together the CDRs from the light and heavy immunoglobulin chains form a surface that is complementary to the antigen. These regions are also present in other members of the immunoglobulin superfamily, for example, T-cell receptors (RECEPTORS, ANTIGEN, T-CELL).
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Proteins found in any species of virus.
The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.
Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.
Sites on an antigen that interact with specific antibodies.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
The rate dynamics in chemical or physical systems.
An essential branched-chain amino acid important for hemoglobin formation.
Amino acids containing an aromatic side chain.
T-cell receptors composed of CD3-associated alpha and beta polypeptide chains and expressed primarily in CD4+ or CD8+ T-cells. Unlike immunoglobulins, the alpha-beta T-cell receptors recognize antigens only when presented in association with major histocompatibility (MHC) molecules.
Amino acids which have a branched carbon chain.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
One of the non-essential amino acids commonly occurring in the L-form. It is found in animals and plants, especially in sugar cane and sugar beets. It may be a neurotransmitter.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
The sum of the weight of all the atoms in a molecule.
Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.
Deoxyribonucleic acid that makes up the genetic material of viruses.
A group of genetically identical cells all descended from a single common ancestral cell by mitosis in eukaryotes or by binary fission in prokaryotes. Clone cells also include populations of recombinant DNA molecules all carrying the same inserted sequence. (From King & Stansfield, Dictionary of Genetics, 4th ed)
A non-essential amino acid that occurs in high levels in its free state in plasma. It is produced from pyruvate by transamination. It is involved in sugar and acid metabolism, increases IMMUNITY, and provides energy for muscle tissue, BRAIN, and the CENTRAL NERVOUS SYSTEM.
The functional hereditary units of BACTERIA.
An essential amino acid. It is often added to animal feed.
A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.
An essential branched-chain aliphatic amino acid found in many proteins. It is an isomer of LEUCINE. It is important in hemoglobin synthesis and regulation of blood sugar and energy levels.
Amino acids with side chains that are positively charged at physiological pH.
Amino acid transporter systems capable of transporting basic amino acids (AMINO ACIDS, BASIC).
Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
A non-essential amino acid. It is found primarily in gelatin and silk fibroin and used therapeutically as a nutrient. It is also a fast inhibitory neurotransmitter.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)
A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.
The movement of materials (including biochemical substances and drugs) through a biological system at the cellular level. The transport can be across cell membranes and epithelial layers. It also can occur within intracellular compartments and extracellular compartments.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.
An essential amino acid that is physiologically active in the L-form.
A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 3.4.21.4.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
A non-essential amino acid present abundantly throughout the body and is involved in many metabolic processes. It is synthesized from GLUTAMIC ACID and AMMONIA. It is the principal carrier of NITROGEN in the body and is an important energy source for many cells.
Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.
Cyanogen bromide (CNBr). A compound used in molecular biology to digest some proteins and as a coupling reagent for phosphoroamidate or pyrophosphate internucleotide bonds in DNA duplexes.
A branched-chain essential amino acid that has stimulant activity. It promotes muscle growth and tissue repair. It is a precursor in the penicillin biosynthetic pathway.
A sulfur-containing essential L-amino acid that is important in many body functions.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
A sequential pattern of amino acids occurring more than once in the same protein sequence.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Endogenous amino acids released by neurons as excitatory neurotransmitters. Glutamic acid is the most common excitatory neurotransmitter in the brain. Aspartic acid has been regarded as an excitatory transmitter for many years, but the extent of its role as a transmitter is unclear.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
An element with the atomic symbol N, atomic number 7, and atomic weight [14.00643; 14.00728]. Nitrogen exists as a diatomic gas and makes up about 78% of the earth's atmosphere by volume. It is a constituent of proteins and nucleic acids and found in all living cells.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
Proteins found in any species of fungus.
A sodium-dependent neutral amino acid transporter that accounts for most of the sodium-dependent neutral amino acid uptake by mammalian cells. The preferred substrates for this transporter system include ALANINE; SERINE; and GLUTAMINE.
Amino acids with uncharged R groups or side chains.
An essential amino acid occurring naturally in the L-form, which is the active form. It is found in eggs, milk, gelatin, and other proteins.
Biochemical identification of mutational changes in a nucleotide sequence.
The process of cleaving a chemical compound by the addition of a molecule of water.
A non-essential amino acid occurring in natural form as the L-isomer. It is synthesized from GLYCINE or THREONINE. It is involved in the biosynthesis of PURINES; PYRIMIDINES; and other amino acids.
The first DNA-binding protein motif to be recognized. Helix-turn-helix motifs were originally identified in bacterial proteins but have since been found in hundreds of DNA-BINDING PROTEINS from both eukaryotes and prokaryotes. They are constructed from two alpha helices connected by a short extended chain of amino acids, which constitute the "turn." The two helices are held at a fixed angle, primarily through interactions between the two helices. (From Alberts et al., Molecular Biology of the Cell, 3d ed, p408-9)
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
Proteins obtained from ESCHERICHIA COLI.
Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.
A non-essential amino acid. In animals it is synthesized from PHENYLALANINE. It is also the precursor of EPINEPHRINE; THYROID HORMONES; and melanin.
A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
The process by which two molecules of the same chemical composition form a condensation product or polymer.
A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Any method used for determining the location of and relative distances between genes on a chromosome.
Peptides composed of between two and twelve amino acids.
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.
Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.
Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
Cell surface proteins that bind amino acids and trigger changes which influence the behavior of cells. Glutamate receptors are the most common receptors for fast excitatory synaptic transmission in the vertebrate central nervous system, and GAMMA-AMINOBUTYRIC ACID and glycine receptors are the most common receptors for fast inhibition.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
A serine endopeptidase secreted by the pancreas as its zymogen, CHYMOTRYPSINOGEN and carried in the pancreatic juice to the duodenum where it is activated by TRYPSIN. It selectively cleaves aromatic amino acids on the carboxyl side.
Separation technique in which the stationary phase consists of ion exchange resins. The resins contain loosely held small ions that easily exchange places with other small ions of like charge present in solutions washed over the resins.
Proteins obtained from foods. They are the main source of the ESSENTIAL AMINO ACIDS.
Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).
An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The functional hereditary units of FUNGI.
A non-essential amino acid naturally occurring in the L-form. Glutamic acid is the most common excitatory neurotransmitter in the CENTRAL NERVOUS SYSTEM.
A class of amino acids characterized by a closed ring structure.
Genotypic differences observed among individuals in a population.
A subclass of enzymes that aminoacylate AMINO ACID-SPECIFIC TRANSFER RNA with their corresponding AMINO ACIDS.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
CELL LINE derived from the ovary of the Chinese hamster, Cricetulus griseus (CRICETULUS). The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems for the study of genetic alterations in cultured mammalian cells.
A group of compounds that are derivatives of the amino acid 2-amino-2-methylpropanoic acid.
Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)
The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.
The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
An essential amino acid that is required for the production of HISTAMINE.
A non-essential amino acid that is involved in the metabolic control of cell functions in nerve and brain tissue. It is biosynthesized from ASPARTIC ACID and AMMONIA by asparagine synthetase. (From Concise Encyclopedia Biochemistry and Molecular Biology, 3rd ed)
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.
Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
A covalently linked dimeric nonessential amino acid formed by the oxidation of CYSTEINE. Two molecules of cysteine are joined together by a disulfide bridge to form cystine.
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Conjugated protein-carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins.
The chemical or biochemical addition of carbohydrate or glycosyl groups to other chemicals, especially peptides or proteins. Glycosyl transferases are used in this biochemical reaction.
Stable carbon atoms that have the same atomic number as the element carbon, but differ in atomic weight. C-13 is a stable carbon isotope.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
Amino acids with side chains that are negatively charged at physiological pH.
Structurally related forms of an enzyme. Each isoenzyme has the same mechanism and classification, but differs in its chemical, physical, or immunological characteristics.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The functional hereditary units of VIRUSES.
A CD98 antigen light chain that when heterodimerized with CD98 antigen heavy chain (ANTIGENS, CD98 HEAVY CHAIN) forms a protein that mediates sodium-independent L-type amino acid transport.
The commonest and widest ranging species of the clawed "frog" (Xenopus) in Africa. This species is used extensively in research. There is now a significant population in California derived from escaped laboratory animals.

Huckebein repressor activity in Drosophila terminal patterning is mediated by Groucho. (1/11917)

The Groucho corepressor mediates negative transcriptional regulation in association with various DNA-binding proteins in diverse developmental contexts. We have previously implicated Groucho in Drosophila embryonic terminal patterning, showing that it is required to confine tailless and huckebein terminal gap gene expression to the pole regions of the embryo. Here we reveal an additional requirement for Groucho in this developmental process by establishing that Groucho mediates repressor activity of the Huckebein protein. Putative Huckebein target genes are derepressed in embryos lacking maternal groucho activity and biochemical experiments demonstrate that Huckebein physically interacts with Groucho. Using an in vivo repression assay, we identify a functional repressor domain in Huckebein that contains an FRPW tetrapeptide, similar to the WRPW Groucho-recruitment domain found in Hairy-related repressor proteins. Mutations in Huckebein's FRPW motif abolish Groucho binding and in vivo repression activity, indicating that binding of Groucho through the FRPW motif is required for the repressor function of Huckebein. Taken together with our earlier results, these findings show that Groucho-repression regulates sequential aspects of terminal patterning in Drosophila.  (+info)

Two di-leucine-based motifs account for the different subcellular localizations of the human endothelin-converting enzyme (ECE-1) isoforms. (2/11917)

Endothelin-converting enzyme (ECE-1) is a type II integral membrane protein which plays a key role in the biosynthetic pathway of the vasoconstricting endothelins. Three ECE-1 isoforms, differing by their N-terminal cytoplasmic tails, are generated from a single gene. When expressed in CHO cells, they display comparable enzymatic activity but whereas ECE-1a is strongly expressed at the cell surface, ECE-1b is exclusively intracellular and ECE-1c presents an intermediate distribution. In the present study these different localizations were further described at the ultrastructural level, by electron microscope immunocytochemistry. To characterize the motifs responsible for the intracellular localization of ECE-1b we constructed chimeric proteins and point mutants. Two di-leucine-based motifs, contained in the N-terminal part of ECE-1b, were thus identified. One of these motifs (LV), displayed by both ECE-1b and ECE-1c, accounts for the reduced surface expression of ECE-1c as compared to ECE-1a. Mutation of both motifs (LL and LV) induces a very strong appearance of ECE-1b at the cell surface indicating that their presence in the N-terminal extremity of ECE-1b is critical for its exclusively intracellular localization.  (+info)

An Arabidopsis cDNA encoding a DNA-binding protein that is highly similar to the DEAH family of RNA/DNA helicase genes. (3/11917)

A cDNA encoding a putative RNA and/or DNA helicase has been isolated from Arabidopsis thaliana cDNA libraries. The cloned cDNA is 5166 bases long, and its largest open reading frame encodes 1538 amino acids. The central region of the predicted protein is homologous to a group of nucleic acid helicases from the DEAD/H family. However, the N- and C-terminal regions of the Arabidopsis cDNA product are distinct from these animal DEIH proteins. We have found that the C-terminal region contains three characteristic sequences: (i) two DNA-binding segments that form a probe helix (PH) involved in DNA recognition; (ii) an SV40-type nuclear localization signal; and (iii) 11 novel tandem-repeat sequences each consisting of about 28 amino acids. We have designated this cDNA as NIH (nuclear DEIH-boxhelicase). Functional character-ization of a recombinant fusion product containing the repeated region indicates that NIH may form homodimers, and that this is the active form in solution. Based on this information and the observation that the sequence homology is limited to the DEAH regions, we conclude that the biological roles of the plant helicase NIH differ from those of the animal DEIH family.  (+info)

A conserved motif N-terminal to the DNA-binding domains of myogenic bHLH transcription factors mediates cooperative DNA binding with pbx-Meis1/Prep1. (4/11917)

The t(1;19) chromosomal translocation of pediatric pre-B cell leukemia produces chimeric oncoprotein E2a-Pbx1, which contains the N-terminal transactivation domain of the basic helix-loop-helix (bHLH) transcription factor, E2a, joined to the majority of the homeodomain protein, Pbx1. There are three Pbx family members, which bind DNA as heterodimers with both broadly expressed Meis/Prep1 homeo-domain proteins and specifically expressed Hox homeodomain proteins. These Pbx heterodimers can augment the function of transcriptional activators bound to adjacent elements. In heterodimers, a conserved tryptophan motif in Hox proteins binds a pocket on the surface of the Pbx homeodomain, while Meis/Prep1 proteins bind an N-terminal Pbx domain, raising the possibility that the tryptophan-interaction pocket of the Pbx component of a Pbx-Meis/Prep1 complex is still available to bind trypto-phan motifs of other transcription factors bound to flanking elements. Here, we report that Pbx-Meis1/Prep1 binds DNA cooperatively with heterodimers of E2a and MyoD, myogenin, Mrf-4 or Myf-5. As with Hox proteins, a highly conserved tryptophan motif N-terminal to the DNA-binding domains of each myogenic bHLH family protein is required for cooperative DNA binding with Pbx-Meis1/Prep1. In vivo, MyoD requires this tryptophan motif to evoke chromatin remodeling in the Myogenin promoter and to activate Myogenin transcription. Pbx-Meis/Prep1 complexes, therefore, have the potential to cooperate with the myogenic bHLH proteins in regulating gene transcription.  (+info)

Drosophila and human RecQ5 exist in different isoforms generated by alternative splicing. (5/11917)

Members of the RecQ helicase superfamily have been implicated in DNA repair, recombination and replication. Although the genome of the budding yeast Saccharomyces cerevisiae encodes only a single member of this family, there are at least five human RecQ-related genes: RecQL, BLM, WRN, RecQ4 and RecQ5. Mutations in at least three of these are associated with diseases involving a predisposition to malignancies and a cellular phenotype that includes increased chromosome instability. Metazoan RecQ helicases are defined by a core region with characteristic helicase motifs and sequence similarity to Escherichia coli RecQ protein. This core region is typically flanked by extensive, highly charged regions, of largely unknown function. The recently reported human RecQ5, however, has only the core RecQ-homologous region. We describe here the identification of the Drosophila RecQ5 gene. We recovered cDNAs corresponding to three alternative splice forms of the RecQ5 transcript. Two of these generate nearly identical 54 kDa proteins that, like human RecQ5, consist of the helicase core only. The third splice variant encodes a 121 kDa isoform that, like other family members, has a C-terminal extension rich in charged residues. A combination of RACE and cDNA analysis of human RECQ5 demonstrates extensive alternative splicing for this gene also, including some forms lacking helicase motifs and other conserved regions.  (+info)

The acidic domain and first immunoglobulin-like loop of fibroblast growth factor receptor 2 modulate downstream signaling through glycosaminoglycan modification. (6/11917)

Fibroblast growth factor receptors (FGFRs) are membrane-spanning tyrosine kinases that have been implicated in a variety of biological processes including mitogenesis, cell migration, development, and differentiation. We identified a unique isoform of FGFR2 expressed as a diffuse band with an unusually large molecular mass. This receptor is modified by glycosaminoglycan at a Ser residue located immediately N terminal to the acidic box, a stretch of acidic amino acids. The acidic box and the glycosaminoglycan modification site are encoded by an alternative exon of the FGFR2 gene. The acidic box appears to play an important role in glycosaminoglycan modification, and the presence of this domain is required for modification by heparan sulfate glycosaminoglycan. Moreover, the presence of the first immunoglobulin-like domain encoded by another alternative exon abrogated the modification. The high-affinity receptor with heparan sulfate modification enhanced receptor autophosphorylation, substrate phosphorylation, and ternary complex factor-independent gene expression. It also sustained mitogen-activated protein kinase activity and increased eventual DNA synthesis, a long-term response to fibroblast growth factor stimulation, at physiological ligand concentrations. We propose a novel regulation mechanism of FGFR2 signal transduction through glycosaminoglycan modification.  (+info)

The net repressor is regulated by nuclear export in response to anisomycin, UV, and heat shock. (7/11917)

The ternary complex factors (TCFs) are targets for Ras/mitogen-activated protein kinase signalling pathways. They integrate the transcriptional response at the level of serum response elements in early-response genes, such as the c-fos proto-oncogene. An important aim is to understand the individual roles played by the three TCFs, Net, Elk1, and Sap1a. Net, in contrast to Elk1 and Sap1a, is a strong repressor of transcription. We now show that Net is regulated by nuclear-cytoplasmic shuttling in response to specific signalling pathways. Net is mainly nuclear under both normal and basal serum conditions. Net contains two nuclear localization signals (NLSs); one is located in the Ets domain, and the other corresponds to the D box. Net also has a nuclear export signal (NES) in the conserved Ets DNA binding domain. Net is apparently unique among Ets proteins in that a particular leucine in helix 1, a structural element, generates a NES. Anisomycin, UV, and heat shock induce active nuclear exclusion of Net through a pathway that involves c-Jun N-terminal kinase kinase and is inhibited by leptomycin B. Nuclear exclusion relieves transcriptional repression by Net. The specific induction of nuclear exclusion of Net by particular signalling pathways shows that nuclear-cytoplasmic transport of transcription factors can add to the specificity of the response to signalling cascades.  (+info)

Regulation of RelA subcellular localization by a putative nuclear export signal and p50. (8/11917)

Nuclear factor kappaB (NF-kappaB) represents a family of dimeric DNA binding proteins, the pleotropic form of which is a heterodimer composed of RelA and p50 subunits. The biological activity of NF-kappaB is controlled through its subcellular localization. Inactive NF-kappaB is sequestered in the cytoplasm by physical interaction with an inhibitor, IkappaBalpha. Signal-mediated IkappaBalpha degradation triggers the release and subsequent nuclear translocation of NF-kappaB. It remains unknown whether the NF-kappaB shuttling between the cytoplasm and nucleus is subjected to additional steps of regulation. In this study, we demonstrated that the RelA subunit of NF-kappaB exhibits strong cytoplasmic localization activity even in the absence of IkappaBalpha inhibition. The cytoplasmic distribution of RelA is largely mediated by a leucine-rich sequence homologous to the recently characterized nuclear export signal (NES). This putative NES is both required and sufficient to mediate cytoplasmic localization of RelA as well as that of heterologous proteins. Furthermore, the cytoplasmic distribution of RelA is sensitive to a nuclear export inhibitor, leptomycin B, suggesting that RelA undergoes continuous nuclear export. Interestingly, expression of p50 prevents the cytoplasmic expression of RelA, leading to the nuclear accumulation of both RelA and p50. Together, these results suggest that the nuclear and cytoplasmic shuttling of RelA is regulated by both an intrinsic NES-like sequence and the p50 subunit of NF-kappaB.  (+info)

Kunes S, Chu T, Chiu M, Zhang E. A C-terminal motif targets hedgehog to axons, coordinating assembly of the Drosophila eye and brain. Developmental Cell [Internet]. 2006;10 (5) :635-46.
Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at http://elm.eu.org/ provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes ,1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a Bar Code format, ...
The purpose of this study was to investigate the blood stage of the malaria causing parasite, Plasmodium falciparum, to predict potential protein interactions between the parasite merozoite and the host erythrocyte and design peptides that could interrupt these predicted interactions. We screened the P. falciparum and human proteomes for computationally predicted short linear motifs (SLiMs) in cytoplasmic portions of transmembrane proteins that could play roles in the invasion of the erythrocyte by the merozoite, an essential step in malarial pathogenesis. We tested thirteen peptides predicted to contain SLiMs, twelve of them palmitoylated to enhance membrane targeting, and found three that blocked parasite growth in culture by inhibiting the initiation of new infections in erythrocytes. Scrambled peptides for two of the most promising peptides suggested that their activity may be reflective of amino acid properties, in particular, positive charge. However, one peptide showed effects which were ...
Many important interactions of proteins are facilitated by short, linear motifs (SLiMs) within a proteins primary sequence. Our aim was to establish robust methods for discovering putative functional motifs. The strongest evidence for such motifs is obtained when the same motifs occur in unrelated proteins, evolving by convergence. In practise, searches for such motifs are often swamped by motifs shared in related proteins that are identical by descent. Prediction of motifs among sets of biologically related proteins, including those both with and without detectable similarity, were made using the TEIRESIAS algorithm. The number of motif occurrences arising through common evolutionary descent were normalized based on treatment of BLAST local alignments. Motifs were ranked according to a score derived from the product of the normalized number of occurrences and the information content. The method was shown to significantly outperform methods that do not discount evolutionary relatedness, when ...
1] Tompa P (2011) Unstructural biology coming of age. Curr Opin Struct Biol 21: 419; [2] Babu MM et al. (2011) Intrinsically disordered proteins: regulation and disease. Curr Opin Struct Biol 21:432; [3] Diella F et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13:6580; [4] Davey NE et al. (2012) Attributes of short linear motifs. Mol Biosyst 8:268; [5] Davey NE, Trave G & Gibson TJ (2011) How viruses hijack cell regulation. Trends Biochem Sci 36:159; [6] Davey NE, Edwards RJ & Shields DC (2010) Computational identification and analysis of protein short linear motifs. Front Biosci 15:801; [7] Davey NE, Shields DC & Edwards RJ (2006): SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res. 34:3546; [8] Edwards RJ, Davey NE & Shields DC (2007): SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2:e967; ...
Shop Leucine-rich PPR motif-containing protein ELISA Kit, Recombinant Protein and Leucine-rich PPR motif-containing protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of pathway knowledge.
Many important regulatory interactions are mediated by short linear motif sequences, which are often embedded in disordered protein regions. These interactions tend to be transient, and therefore pose special experimental challenges. In order to develop precise tools for the manipulation and study of such interactions, accurate structural models are needed. However, due to weak binding affinity and the considerable flexibility of the peptide, structural modeling of peptide-mediated interactions presents a considerable challenge. In my talk I will present an overview of our research on peptide-mediated interactions. I will describe Rosetta FlexPepDock, the suite of protocols that we have developed, and applied, for the structure-based characterization and manipulation of peptide-mediated interactions. FlexPepDock is guided by observations of peptide binding strategies revealed from solved complex crystal structures. Efficient but focused sampling strategies have opened the way to model these ...
so sum1tar is basically summary 1 of the target motifs, those are the motifs i got from the motifenrichment analysis on my sequences using the motifenrich function inside the PWMenrich package. So i use scanWithPWM to get the highest score and i am not sure if the highest one represents the optimal position?. So after i have got the position , i hope to plot the sequence with the motif on top of the sequence somehow, i have tried using substring from the biostring package but only able to plot the sequences. So second question is about plotting the motif or highlighting the motif detected with the sequence. after we have detected the motifs, would there be any ways that i could highlight the motifs ? because so far i am only able to make a ranking table in the in the window and highlight the rough position just like the one in the manual. However i would like to see every single base pair with highlighted motifs in the sequence. The third quesiton is about pairwise alignment and motif anlysis, ...
We have extracted an extensive collection of recurrent structural motifs (RSMs), which consist of sequentially non-contiguous structural motifs (4-6 residues), each of which appears with very similar conformation in three or more mutually unrelated protein structures. We find that the proteins in our set are covered to a substantial extent by the recurrent non-contiguous structural motifs, especially the helix and strand regions. Computational alanine scanning calculations indicate that the average folding free energy changes upon alanine mutation for most types of non-alanine residues are higher for amino acids that are present in recurrent structural motifs than for amino acids that are not. The non-alanine amino acids that are most common in the recurrent structural motifs, i.e., phenylalanine, isoleucine, leucine, valine and tyrosine and the less abundant methionine and tryptophan, have the largest folding free energy changes. This indicates that the recurrent structural motifs, as we define them,
The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). For |10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear mot …
BACKGROUND: Large datasets of protein interactions provide a rich resource for the discovery of Short Linear Motifs (SLiMs) that recur in unrelated proteins. However, existing methods for estimating the probability of motif recurrence may be biased by the size and composition of the search dataset, such that p-value estimates from different datasets, or from motifs containing different numbers of non-wildcard positions, are not strictly comparable. Here, we develop more exact methods and explore the potential biases of computationally efficient approximations.. RESULTS: A widely used heuristic for the calculation of motif over-representation approximates motif probability by assuming that all proteins have the same length and composition. We introduce pv, which calculates the probability exactly. Secondly, the recently introduced SLiMFinder statistic Sig, accounts for multiple testing (across all possible motifs) in motif discovery. However, it approximates the probability of all other possible ...
The motivating idea behind most discussions on motifs is the possibility of capturing the essential logic of genetic regulation by a small set of interaction circuits performing some specific functional tasks. While this hypothesis is, in principle, experimentally testable, experimental and theoretical work has hitherto considered essentially motifs in isolation, that is, excised from the biological environment in which the motifs instances are embedded.. We studied in detail the role of motifs in the case of the best-documented genetic sub-networks and biological functions where such motifs are found. In most cases, motifs do not seem to have a central regulatory role in the biological processes associated with each occurrence. The list of examples where enough biological information is available is, of course, limited, and further examples may subvert this picture. At the moment, it is a fact that all the examples studied highlight the high level of integration of different regulatory ...
SCAN HISTORY OWL25_2 2 300 NSINGLE SPTR37_9f 2 125 NSINGLE INITIAL MOTIF SETS ADENOVSFIBRE1 Length of motif = 11 Motif number = 1 ADV fibre protein motif I - 1 PCODE ST INT EDDFNPVYPYE FIBP_ADE40 7 7 SDSFNPVYPYE FIBP_ADE07 26 26 EDDFNPVYPYG FIBP_ADE08 8 8 EDDFNPVYPYG FIBP_ADE09 8 8 EDTFNPVYPYD FIBP_ADE05 8 8 STSFNPVYPYE FIBP_ADE03 8 8 PANFDPVYPYD FIBP_ADECG 9 9 PANYDPVYPYD CA2FIBER 9 9 ADENOVSFIBRE2 Length of motif = 13 Motif number = 2 ADV fibre protein motif II - 1 PCODE ST INT DIPFITPPFASSN FIBP_ADE40 23 5 QHPFINPGFISPN FIBP_ADE07 42 5 NIPFLTPPFVSSN FIBP_ADE08 24 5 NIPFLTPPFVSSD FIBP_ADE09 24 5 TVPFLTPPFVSPN FIBP_ADE05 25 6 QHPFINPGFISPD FIBP_ADE03 24 5 PKPSTQPPFFNDR FIBP_ADECG 21 1 PGSSTQPPFFNNK CA2FIBER 21 1 ADENOVSFIBRE3 Length of motif = 15 Motif number = 3 ADV fibre protein motif III - 1 PCODE ST INT NGALTLKLGTGLNID FIBP_ADE40 57 21 GGSLQLKVGGGLTID FIBP_ADE07 76 21 NQNVSLKVGGGLTLQ FIBP_ADE08 58 21 NGNVSLKVGGGLTLQ FIBP_ADE09 58 21 NGMLALKMGNGLSLD FIBP_ADE05 59 21 SGSLQLKVGSGLTVD ...
This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, namely a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. [provided by RefSeq, Jul 2008 ...
Inspired by the main element role of super-helical motifs in molecular self-organization, several tandem heptad repeat peptides were used as building blocks to form well-ordered supramolecular nano-assemblies. structures at the nanoscale5,6,7. However, the formation of assemblies by such short peptides is limited mainly to -sheet business of the peptide motifs in the formed nanostructures8,9,10,11. While these assemblies offers remarkable mechanical, optical, piezolelctric and semiconductive proprieties, they lack the precise orientation of amino-acid residues needed for directed intermolecular business and specific interactions with target molecules such as DNA or other biopolymers12,13. Indeed, in many biological systems, the recognition of DNA is usually facilitated by ordered super-helical structural motifs14,15,16. This super-helical business commonly comprised of two or more Tegobuvir individual -helices that interact with each other via hydrophobic facets present in protein surfaces and ...
mouse Slo2 protein: a type of sodium-activated K+ channel, possess a typical PDZ binding motif at the carboxy-terminal end; NP_780671
This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly. In full display mode, each motif occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the + strand is shown.. The track may be configured to search for any short sequence of 2 - 30 bases in length. Sequences may include IUPAC ambiguity codes. To change the motif, open the tracks description page (by clicking the track control label or the mini-button to the left of the track), then type a new sequence into the text box.. To see how to create a bed file of the short match data see this mailing list question here.. ...
This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly. In full display mode, each motif occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the + strand is shown.. The track may be configured to search for any short sequence of 2 - 30 bases in length. Sequences may include IUPAC ambiguity codes. To change the motif, open the tracks description page (by clicking the track control label or the mini-button to the left of the track), then type a new sequence into the text box.. To see how to create a bed file of the short match data see this mailing list question here.. ...
This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly. In full display mode, each motif occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the + strand is shown.. The track may be configured to search for any short sequence of 2 - 30 bases in length. Sequences may include IUPAC ambiguity codes. To change the motif, open the tracks description page (by clicking the track control label or the mini-button to the left of the track), then type a new sequence into the text box.. ...
6 K in this function is the background entropy corrected for sample size, approximately 2 for E. coli (4), as was calculated in the example above. The frequencies, fi, are determined as in the example above from the aligned sequences of the prototype group for the given motif; the relative frequencies for the occurrence of each of the four bases are determined separately for each position of the motif. Fopt is the frequency found for the consensus base at a given position, and fobs is the frequency at which the base in the sequence of interest is found to occur in the same position of the prototype group.. A computer program was written that takes sequence as input, evaluates this function at each position within a window corresponding to the size of the motif of interest by using the prototype groups frequencies, divides the range of resultant index values into six qualitative levels from very good to very bad (attempts with 10 levels yielded no better performance), and codes the result in ...
SCAN HISTORY SPTR37_10f 2 45 NSINGLE INITIAL MOTIF SETS TYPE3IMSPROT1 Length of motif = 23 Motif number = 1 Type III IMS protein family motif I - 1 PCODE ST INT TEKPTPKKLKDAAKKGQSFKFKD SPAS_SHIFL 5 5 TEKPTKKRLEDSAKKGQSFKSKD SPAS_SALTY 6 6 TEQPTPKKIRDARKKGQVAKSKE YSCU_YERPS 6 6 TEQPTEKKLRDGRKEGQVVKSIE SSAU_SALTY 5 5 TEQPTDKKLEDAHRDGETAKSAD HRPN_BURSO 6 6 TELPSAKKIQKAREEGNVPKSME FLHB_HELPY 7 7 TEEPSAKKLSDARAKGDVIKSAD Q45997 11 11 TEAPSEKKISDATEKGNVPFSRE O54243 11 11 TEAPTPHRLEKAREEGQIPRSRE FLHB_ECOLI 9 9 TELPTDQKKQKAREEGRVLKSTE FLHB_BORBU 26 26 TEKATPKQIRDAREKGQVGQSQD O85098 5 5 SHGATPKKLSDARKRGQIPRSSD Y4YO_RHISN 9 9 TYPE3IMSPROT2 Length of motif = 19 Motif number = 2 Type III IMS protein family motif II - 1 PCODE ST INT DFVIEFILYMKDMMMDKQE SPAS_SHIFL 196 168 DAIAEYFLTMKDMKMDKEE SPAS_SALTY 197 168 DYAFEYYQYIKELKMSKDE YSCU_YERPS 202 173 DYSFQYYKIRKDLKMSKDD SSAU_SALTY 201 173 DFGIQRWLFIRDHRMSKDE HRPN_BURSO 203 174 DLAIKRRQYTNSLKMTKQE FLHB_HELPY 204 174 DYFWQRMRFMNRMRMTLQE Q45997 209 175 ...
Residues within a conserved amino acid motif of domains 1 and 4 of VCAM-1 are required for binding to VLA-4.. Journal of Cell Biology. 125:215-222. 1994 ...
View mouse Trim21 Chr7:102557921-102565486 with: phenotypes, sequences, polymorphisms, proteins, references, function, expression
View mouse Trim33 Chr3:103279293-103358775 with: phenotypes, sequences, polymorphisms, proteins, references, function, expression
Feature map marking the locations of 4G-, 3G- and 2G-containing motif occurrences in the G-rich motif group identified in the upstream regions of the organellar
For three decades, sequence logos are the de facto standard for the visualization of sequence motifs in biology and bioinformatics. Reasons for this success story are their simplicity and clarity. The number of inferred and published motifs grows with the number of data sets and motif extraction algorithms. Hence, it becomes more and more important to perceive differences between motifs. However, motif differences are hard to detect from individual sequence logos in case of multiple motifs for one transcription factor, highly similar binding motifs of different transcription factors, or multiple motifs for one protein domain. Here, we present DiffLogo, a freely available, extensible, and user-friendly R package for visualizing motif differences. DiffLogo is capable of showing differences between DNA motifs as well as protein motifs in a pair-wise manner resulting in publication-ready figures. In case of more than two motifs, DiffLogo is capable of visualizing pair-wise differences in a tabular form.
Batten disease is a neurodegenerative disorder resulting from mutations in CLN3, a polytopic membrane protein, whose predominant intracellular destination in nonneuronal cells is the lysosome. The topology of CLN3 protein, its lysosomal targeting mechanism, and the development of Batten disease are poorly understood. We provide experimental evidence that both the N and C termini and one large loop domain of CLN3 face the cytoplasm. We have identified two lysosomal targeting motifs that mediate the sorting of CLN3 in transfected nonneuronal and neuronal cells: an unconventional motif in the long C-terminal cytosolic tail consisting of a methionine and a glycine separated by nine amino acids [M(X)9G], and a more conventional dileucine motif, located in the large cytosolic loop domain and preceded by an acidic patch. Each motif on its own was sufficient to mediate lysosomal targeting, but optimal efficiency required both. Interestingly, in primary neurons, CLN3 was prominently seen both in ...
In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which also appears in a variety of other molecules. Motifs do not allow us to predict the biological functions: they are found in proteins and enzymes with dissimilar functions. Because the relationship between primary structure and tertiary structure is not straightforward, two biopolymers may share the same motif yet lack appreciable primary structure similarity. In other words, a structural motif does not have to be associated with a sequence motif. Also, the existence of a sequence motif does not necessarily imply a distinctive structure. In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal double helical structure. ...
The chromo domain was originally identified as a protein sequence motif common to the Drosophila chromatin proteins, Polycomb (Pc) and heterochromatin protein 1 [HP1; Paro and Hogness (1991) Proc. Natl. Acad. Sci. USA, 88, 263-267; Paro (1990) Trends Genet., 6, 416-421]. Here we describe a second chromo domain-like motif in HP1. Subsequent refined searches identified further examples of this chromo domain variant which all occur in proteins that also have an N-terminally located chromo domain. Due to its relatedness to the chromo domain, and its occurrence in proteins that also have a classical chromo domain, we call the variant the chromo shadow domain. Chromo domain-containing proteins can therefore be divided into two classes depending on the presence, for example in HP1, or absence, for example in Pc, of the chromo shadow domain. We have also found examples of proteins which have two classical chromo domains. The Schizosaccharomyces pombe SWI6 protein, involved in repression of the silent ...
Red Hat Motif 2.1 for Linux Intel-compatible computers is the full OSF/Motif development system. As with previous versions of Red Hat Motif, Red Hat Motif 2.1 will enable you to use your Intel-compatible PC computer running Linux as a UNIX(r) Motif based workstation.For developers, Motif 2.1 makes creation of software applications and custom widgets simple. The many toolkit enhancements, new widgets, and UIL improvements allow you to port Motif-based applications easily across a variety of platforms.For end users, Red Hat Motif 2.1 improves the interface performance of their Motif-based applications. The virtual screen support unclutters their workspace by providing alternate locations for chosen windows, while providing greater consistency with PC environments.Red Hat Motif 2.1 New Features: Thread safe libraries Widget printing support Internationalization enhancements for vertical text, on-the-spot input and user defined characters for Asian languages See Red Hat Motif 2.1 Intel on the Store Page
Coronaviruses, including SARS-CoV-2, are proposed to use either the endocytic or non-endosomal pathway for cell entry (46). Our study provides biophysical evidence for the functionality of SLiMs in the cytoplasmic tails of ACE2 and integrin β3, which provide possible molecular links between the established (ACE2) and putative (integrin beta3) SARS-CoV-2 receptors and mediators of endocytosis and autophagy. Our finding that an endocytic AP2 μ2 binding motif exists in the ACE2 C-terminus and that such binding is negatively regulated by Tyr781 phosphorylation supports the possibility of clathrin-dependent endocytosis of SARS-CoV-2 upon receptor binding. It will, of course, be necessary to assess the biological relevance of the ACE2-AP2 μ2 interaction, particularly in light of its low affinity. Concerning the latter, we note that while affinities of AP2 core complexes for endocytic sorting signals are reported in the nanomolar range, measured KD values of the AP2 μ2 subunit alone vary between 10 ...
Sorry about my previous reply. The question was for DNA sequence motifs and my answer was for protein sequence motifs. The TFD database has several DNA sequence motifs found in yeast, however it is a Transcription Factor Database and would lack some of the types of sequence motifs that the original message was requesting. TFD is available as flat files, in a variety of formats, via anonymous ftp from ncbi.nlm.nih.gov look in the repository/TFD directory. TFD is the creation of D. Ghosh, NCBI. Mike ...
Previous studies have identified a number of mutants and/or motifs that affect ASIC channel trafficking and/or function [28-34]. Most of these studies focused on ASIC1a. Our results demonstrated that the LL motifs in ASIC2a are important for its trafficking and function. All the mutants that we studied here had increased surface level (Fig. 1). However, only the DAA mutant exhibited a significant increase in surface:total ratio while the AADAA mutant had a marginal effect (p = 0.049). These data, together with our current recordings, indicate that most of the effect on ASIC2a surface trafficking and channel function was mainly mediated by the second LL motif. We speculate that the exact location of the LL motif may contribute to the differences observed between mutating the two LL motifs. It remains unclear as to the exact mechanism of how the LL motifs regulate ASIC2a. Our data here showed that the AADAA and DAA mutants increased the maturation of N-linked glycans. N-glycosylation is an ...
TY - JOUR. T1 - Extracting Best Consensus Motifs from Positive and Negative Examples. AU - Tateishi, Erika. AU - Maruyama, Osamu. AU - Miyano, Satoru. PY - 1995/10/27. Y1 - 1995/10/27. N2 - We define the best consensus motif (BCM) problem motivated by the problem of extracting motifs from nucleic acid and amino acid sequences. A type over an alphabetΣ is a familyΩ of subsets of Σ. A motif π of type Ω is a stringπ=π_1…π_n of motif components, each of which stands for an element in Ω. The BCM problem for Ω is, given a yes-no sample S={(α^,(1),, β^,(1),),...,(α^,(m),, β^,(m),)} of pairs of strings inΣ with α^,(i),≠β^,(i), for 1≤i≤m, to find a motif π of type Ω that maximizes the number of good pairs in S, where (α^,(i),,β^,(i),) is good forπ if π accepts α^,(i), and rejects β^,(i),. We prove that the BCM problem is NP-complete even for a very simple type Ω_1={z,φ≠z⊆Σ}, which is used, in practice, for describing protein motifs in the PROSITE database. We also ...
Shop RNA-binding motif protein ELISA Kit, Recombinant Protein and RNA-binding motif protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
The cell-extrinsic apoptotic pathway triggers programmed cell death in response to certain ligands that bind to cell-surface death receptors. Apoptosis is essential for normal development and homeostasis in metazoans, and furthermore, selective activation of the cell-extrinsic pathway in tumor cells holds considerable promise for cancer therapy. We used phage display to identify peptides and synthetic antibodies that specifically bind to the human proapoptotic death receptor DR5. Despite great differences in overall size and structure, the DR5-binding peptides and antibodies shared a tripeptide motif, which was conserved within a disulfide-constrained loop of the peptides and the third complementarity determining region of the antibody heavy chains. The X-ray crystal structure of an antibody in complex with DR5 revealed that the tripeptide motif is buried at the core of the interface, confirming its central role in antigen recognition. We found that certain peptides and antibodies exhibited ...
One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of related data elements. With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation. Herein, we present a structured syntax of minimotifs and their functional annotation. A syntax-based model of minimotif function with established
C. elegans NAB-1 protein; contains similarity to Pfam domains PF07647 (SAM domain (Sterile alpha motif)), PF00595 (PDZ domain (Also known as DHR or GLGF)), PF00536 (SAM domain (Sterile alpha motif))contains similarity to Interpro domains IPR001660 (Sterile alpha motif SAM), IPR001478 (PDZ/DHR/GLGF ...
Activity of SRs is not only regulated by ligand binding but also by interacting cofactors. The best-described binding site for SR coregulators is the hydrophobic cleft in the LBD to which LxxLL motifs can bind. The AR LBD is unique in its preference for the interaction with cofactors carrying FxxLF motifs rather than LxxLL motifs (Dubbink et al., 2004; Hur et al., 2004). The AR itself also contains an FQNLF motif in the N-terminal domain, enabling interaction with the LBD (N/C interaction; Doesburg et al., 1997; He et al., 2000). The potential competition between the AR N-terminal FQNLF motif and similar motifs in cofactors for interaction with the LBD raises questions regarding the role of the N/C interaction in orchestrating cofactor interactions. To study AR N/C interactions in living cells, we tagged the AR at the N and C termini with YFP and CFP, respectively, or with CFP alone, and applied FRET and simultaneous FRET and FRAP experiments. In addition, to investigate cofactor interactions, ...
Background Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions. Methodology/Principal Findings Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have a related cellular or molecular function, the prediction is more likely to be accurate. This filter was implemented in Minimotif Miner using function annotations from the Gene Ontology. We have also combined two filters that are based on entirely different principles and this combined filter has a better
Offers an approach for motif discovery based on a Bayesian approach. BAMM!motif is an application that exploits Bayesian Markov Models (BaMMs) to perform its predictions. It consists of four distinct modules allowing users to: (i) investigate nucleotide sequence to determine high-order motifs; (ii) explore model repositories with a feature for searching given motifs against a pre-computed database; and (iii) detect motifs occurrences from sequences.
PTMs (posttranslational modifications) such as ubiquitylation, sumoylation, acetylation and protein methylation are pivotal modifiers that determine the activation, deactivation or subcellular localization of signaling proteins, facilitating the initiation, amplification and transduction of signaling. Accumulating evidence suggest that several key signaling molecules in Hippo signaling pathway are tightly regulated by various types of PTMs. Malfunction of these critical signaling modules such as YAP/TAZ, MAT1/2 and LATS1/2 due to deregulated PTMs has been linked to a variety of human diseases such as cancer. In this review article, we summarized the current understanding of the impact of PTMs in regulating Hippo signaling pathway and further discussed the potential therapeutic intervention from the view of PTMs and Hippo pathway.
May play a role in the process of differentiation and maturation of neuronal cells (By similarity). May regulate the activity of TRIM17 (By similarity). Is a negative regulator of PAX6 expression (By similarity).
Bacterial surfaces are complex, built of from membranes, peptide-glycans and, importantly, proteins. The proteins play crucial roles as the key regulator of how the bacterium interacts with its environment. A full catalog of the motifs in coiled-coil proteins and their relative conservation grade is a pre-requisite to target the protein-protein interaction that bacterial surface protein makes to host proteins. Here, we present a greedy approach to iteratively identify conserved motifs in large sequence collections, identify all occurrences of these motifs and mask them. Remaining unmasked sequences are subjected to the second round of motif detection until no more significant motifs can be found or all protein segments have been assigned to a motif. We present the results for the S. pyogenes M protein. Given the speed and flexibility of our approach, we believe it will be useful in breaking analyzing surface protein of pathogens as these proteins are under high selective pressure and therefore cannot be
This gene was identified by involvement in some t(X;14) translocations associated with mature T-cell proliferations. This region has a complex gene structure, with a common promoter and 5 exon spliced to two different sets of 3 exons that encode two different proteins. This gene represents the downstream 8 kDa protein that localizes to mitochondria.[provided by RefSeq, Mar 2009 ...
Ret finger proteinRING finger protein 76, RFPtripartite motif protein TRIM27, RNF76RFP transforming protein, Tripartite motif-containing protein 27, tripartite motif-containing 27, tripartite motif containing 27, zinc finger protein ...
Accuracy. If you search with a simple motif, you can adjust the accuracy of the motif to the match on the sequence. If you type in a simple motif and let the accuracy be 80%, the motif search algorithm runs through the input sequence and finds all subsequences of the same length as the simple motif such that the fraction of identity between the subsequence and the simple motif is at least 80%. A motif match is added to the sequence as an annotation with the exact fraction of identity between the subsequence and the simple motif. If you use a list of motifs, the accuracy applies only to the simple motifs in the list ...
One focus of our research is to further our understanding of the physico-chemical properties of non-canonical nucleic acid structures. In this work, DNA hairpins are used to mimic a common motif present in RNA, i.e., a stem-loop motif with a bulge or inte
Ji, H. H., & Ostap, E. M. (2020). The regulatory protein 14-3-3β binds to the IQ motifs of myosin-IC independent of phosphorylation. Journal of Biological Chemistry, 295(12), 3749-3756. https://doi.org/10.1074/jbc. ...
C. elegans ETR-1 protein; contains similarity to Pfam domain PF00076 (RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain))contains similarity to Interpro domains IPR012677 (Nucleotide-binding, alpha-beta plait), IPR000504 (RNA-binding region RNP-1 (RNA recognition motif ...
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Active Motif, Inc. is a privately held biotechnology company focused on supplying innovative kits and reagents for epigenetics and nuclear function research. We are always looking for highly motivated individuals to join our team.
TRIM37 (tripartite motif-containing 37), Authors: Elif Ayse Erson,.M Elizabeth Petty. Published in: Atlas Genet Cytogenet Oncol Haematol.
Evidence 3: Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr: putative ...
Evidence 3: Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt: putative ...
UHMK1 (U2AF homology motif kinase 1), Authors: Vanessa Cristina Arfelli, Leticia Fröhlich Archangelo. Published in: Atlas Genet Cytogenet Oncol Haematol.
Active Motif offers a variety of ChIP Accessory Products that make it even easier to perform successful ChIP when working with our ChIP-IT Express Kitsand our Specialized ChIP-IT Kits.
Active Motif offers research kits, assays and biocomputing systems that help researchers study the function, regulation and interactions between genes, proteins and metabolic pathways.
Active Motif offers research kits, assays and biocomputing systems that help researchers study the function, regulation and interactions between genes, proteins and metabolic pathways.
Motif Bio Plc (LON:MTFB) CEO Dr Graham Lumsden talks to DirectorsTalk about the dosing of the first patient in the iclaprim Phase 3 trials to treat skin in
Fine materials and design for this Skirt With Jacquard Plaid Motif by Emporio Armani Women. Take a look at the official online boutique now.
Az első luxus parfüméria - művészi parfümök, tiszta bőrápolás, smink, úri borotválkozás, királyi hajkefe és fogkefe, enteriőrillatosítás
Members of this enzyme family typically share two conserved amino acid motifs. The first motif, or string of consecutive amino ... The second conserved motif is DFGWG (Aspartic acid, Phenylalanine, Glycine, Tryptophan, Glycine) and it is typically found near ... Phylogenetic analysis using full-length amino acid sequences of functionally characterized BAHD enzymes by D'Auria (2006) and ... Aspartic acid) and it is typically found in the central region of the protein. The Histidine in this motif has also been shown ...
Calmodulin contains 148 amino acids and has 4 calcium-binding EF hand motifs. Its functions include roles in growth and the ... Li Z, Sacks DB (Feb 2003). "Elucidation of the interaction of calmodulin with the IQ motifs of IQGAP1". J. Biol. Chem. 278 (6 ...
The pentatricopeptide repeat (PPR) is a 35-amino acid sequence motif. Pentatricopeptide-repeat-containing proteins are a family ... They are distinguished by the presence of tandem degenerate PPR motifs and by the relative lack of introns in the genes coding ...
... identification of amino acid sequence motifs governing subunit stoichiometry". Neuron. 11 (6): 1049-56. doi:10.1016/0896-6273( ... The receptor can be activated by a range of simple amino acids including glycine, β-alanine and taurine, and can be selectively ... The glycine receptor (abbreviated as GlyR or GLR) is the receptor of the amino acid neurotransmitter glycine. GlyR is an ...
McLachlan A, Cullis PG, Cornell HJ (October 2002). "The use of extended amino acid motifs for focussing on toxic peptides in ... The IRP lies within a 25 amino-acid long region that is resistant to pancreatic proteases. The 25mer is also resistant to Brush ... HLA-DQ proteins present polypeptide regions of proteins of about 9 amino acids and larger in size (10 to 14 residues in ... Α2-gliadin differs from the other α-gliadins, specifically because it contains an insert of 14 amino acids. This particular ...
The Sac1 phosphatase domain encompasses approximately 400 amino acids and consists of seven conserved motifs. It harbors the ... In humans, the FIG4 gene localizes on chromosome 6 and encodes a Sac3 protein of 907 amino acids. Sac3 is characterized as a ...
The WH2 domain is an ~18-21 amino acids actin-binding motif. This domain was first recognized as an essential element for the ... The human COBL gene encodes a 1261-amino acid protein with a mass of about 136 kDa. The mouse protein is 1337 amino acids long ... Cobl Homology domains contain three motifs following the consensus KrRAPpPP (first described as "KRAP" motif of unknown ... The WH2 motif in WASp recruits ATP-G-actin that binds to either Arp2 or Arp3 to complete the formation of a trimeric actin ...
It has a motif domain between the amino acids 35 and 43. Due to the alternative splicing, two isoforms of this same protein ... Isoform 2 consists just of 151 amino acids, having a mass of 16,667 Da. Small GTPases of the RAB superfamily are recognized as ... Even though these RAB family proteins are highly homologous to each other (RAB2A and RAB2B have 85.8% amino acid identity), the ...
Peifer M, Berg S, Reynolds AB (1994). "A repeating amino acid motif shared by proteins with diverse cellular roles". Cell. 76 ( ... Eukaryotic Linear Motif resource motif class TRG_NLS_Bipartite_1 Eukaryotic Linear Motif resource motif class TRG_NLS_MonoCore_ ... 2 Eukaryotic Linear Motif resource motif class TRG_NLS_MonoExtC_3 Eukaryotic Linear Motif resource motif class TRG_NLS_MonoExtN ... An armadillo repeat is the name of a characteristic, repetitive amino acid sequence of about 40 residues in length that is ...
Peifer M, Berg S, Reynolds AB (March 1994). "A repeating amino acid motif shared by proteins with diverse cellular roles". Cell ... Liu J, Xing Y, Hinds TR, Zheng J, Xu W (June 2006). "The third 20 amino acid repeat is the tightest binding site of APC for ... First, they might reach or even surpass the length of 30 amino acids in length, and contact the ARM domain on an excessively ... There is one requirement, though: substrates of GSK3 need to be pre-phosphorylated four amino acids downstream (C-terminally) ...
SMG stands for the conserved amino acid motif of Ser-Met-Gly. Upon closure, these residues interact with L-ornithine. The ... Orotic acid is a product of this pathway. Increased levels of orotic acid in urine can be an indicator that a patient is ... Postranscriptional modification leaves the mature peptide with 322 amino acids and a weight of 36.1 kD. The protein is located ... Anabolic OTC facilitates the sixth step in the biosynthesis of the amino acid arginine in prokaryotes. In contrast, mammalian ...
... whose members have certain conserved motifs in their extracellular amino-acid domain. The IL-2 receptor belongs to this chain, ...
The EGF receptor is characterized by having an extracellular domain that has numerous amino acid motifs. EGFR is essential for ... TGF-α is synthesized internally as part of a 160 (human) or 159 (rat) amino acid transmembrane precursor. The precursor is ... 50 amino acids of TGF-α, and a 35-residue-long cytoplasmic domain. In its smallest form, TGF-α has six cysteines linked ... TGF-α has been shown to inhibit gastric acid secretion. TGF-α can be produced in macrophages, brain cells, and keratinocytes. ...
The C terminus contain a LPXTG sequence motif and hydrophobic amino acid segments attached to peptidoglycan. The C-terminal ... the wall-anchoring LPTXG motif, a hydrophobic transmembrane region and a cytoplasmic tail of positively charged amino acid ... SdrG stands for serine-aspartate dipeptide repeats, which as its name suggests, contains repeats of two amino acids, serine and ...
The KIAA1211L protein has one domain called the DUF4592 motif and spans amino acids 131-239. This domain is highly conserved ... Additionally, this location (amino acids 24-43) is positively charged, probably due to the high amount of lysine at this ... The amino acids conserved among all the KIAA1211L orthologs are depicted in the conceptual translation. The KIAA1211L gene is ... KIAA1211 is located on chromosome 4 and has 1233 amino acids. Its percent identity to KIAA1211L is 21%. The KIAA1211 has an ...
The catalytic center is formed by several motifs containing a number of conserved amino acid residues. Eukaryotic RNA ... Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the aspartic acid residues of these motifs are implied in the ... Birnaviral RNA replicase is unique in that it lacks motif C (GDD) in the palm. Mononegaviral RdRP (PDB 5A22) has been ... This RNA-directed RNA polymerase possesses a number of short regions and motifs homologous to other RNA-directed RNA ...
For example, RNP in snRNPs have an RNA-binding motif in its RNA-binding protein. Aromatic amino acid residues in this motif ... they provide a rough model of the structure which allows for predictions of the identity of significant amino acids and ... This nucleic acid binding is strengthened by electrostatic attraction between the positive lysine side chains and the negative ... Nucleoproteins are any proteins that are structurally associated with nucleic acids, either DNA or RNA. Typical nucleoproteins ...
UBA domains have a common sequence motif of approximately 45 amino acid residues. They fold into three-helix bundle structures ... Hofmann K, Bucher P (May 1996). "The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination ...
There is also a predicted sumoylation motif from amino acid 212 to 221. C19orf44 is predicted to be localized in the nucleus or ... The amino acid sequence for C19orf44 was found to be serine rich using tools on EMBL-EBI. Additionally, there is a domain of ... It contains 10 exons that code for a 657 amino acid protein. There are 7 splice variants that exist for C19orf44. C19orf44 is ... located from amino acid 474 to 641. C19orf44 has experimentally determined phosphorylation sites at the S114 and S213 positions ...
These proteins have either an EAL or an HD-GYP amino acid motif. Processes that are known to be regulated by cyclic di-GMP, at ... These proteins typically have a characteristic GGDEF motif, which refers to a conserved sequence of five amino acids. ... Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid P. Ross Nature, 1987 Benach, J; Swaminathan ... "Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid". Nature. 325 (6101): 279-81. doi:10.1038/ ...
This protein contains a conserved 120 amino acid motif called the RGS domain. The protein attenuates the signaling activity of ...
... sequence motifs and amino acid composition". Bioinformatics. 22 (10): 1158-65. doi:10.1093/bioinformatics/btl002. PMID 16428265 ... predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices". Amino ... Du P, Cao S, Li Y (November 2009). "SubChlo: predicting protein subchloroplast locations with pseudo-amino acid composition and ... Tusnády, Gábor E.; Simon, István (Oct 1998). "Principles governing amino acid composition of integral membrane proteins: ...
They are common in protein-protein interaction motifs and are typically 20-29 amino acids in length. All major classes of LRRs ... The LRRN3 protein is 708 amino acids in length. The molecular weight of this protein is 79,424 Daltons, with an isoelectric ... Leucine-rich repeats are unusually rich in the hydrophobic amino acid leucine. ...
This recruitment takes place via a 4 amino acid motif in the Ste5 phosphosites. Ptc1 is also involved in regulating the osmotic ...
A coronavirus cleavage site is predicted at the 235 amino acid position. There are also tyrosine motif locations between amino ... The full C16orf46 protein is 417 amino acids long. It has no isoforms, and its most distant ortholog, Rhincodon typus (whale ... acids 42-45 and 251-252. mRNA folding on the 5' UTR predicts a stem loop twice in the area between base pairs 47-90. C16orf46 ...
These amino acids form the DDE motif that coordinate divalent metal ions (Mg2+ or Mn2+). These metal ions are essential for the ... A loop containing amino acid residues 140-149 is located in the catalytic-core domain and is important for IN function as ... 2. The catalytic core domain (CCD), which encompasses amino acids 51- 212, contains the active site of IN but it can't catalyze ... 3. The C-terminal domain (CTD), which encompasses amino acids 213-288, binds DNA nonspecifically and its interaction with NTD ...
As predicted amino acids in the conserved WRKYGQK signature motif contact the W-box DNA. WRKY Transcription Factor Family at ... The W box is a deoxyribonucleic acid (DNA) cis-regulatory element sequence, (T)TGAC(C/T), which is recognized by the family of ... Nucleic Acids Research. 41 (21): 9764-9778. doi:10.1093/nar/gkt732. PMC 3834811. PMID 23975197. Yamasaki, K.; Kigawa T; ...
This motif is composed of four amino acids at the end of the protein sequence. The most common retention sequences are KDEL for ... The N-terminus (one end) of a polypeptide chain (i.e., a protein) contains a few amino acids that work as an address tag, which ... The first 5-30 amino acids polymerized encode a signal peptide, a molecular message that is recognized and bound by a signal ... either secreted constitutively with no tag or secreted in a regulatory manner involving clathrin and paired basic amino acids ...
Bernad A, Blanco L, Salas M (September 1990). "Site-directed mutagenesis of the YCDTDS amino acid motif of the phi 29 DNA ... Involvement of two amino acid residues highly conserved in proofreading DNA polymerases". EMBO J. 15 (5): 1182-92. doi:10.1002/ ... His61 and Phe69 of the highly conserved ExoII motif are essential for interaction with the terminal protein". Nucleic Acids Res ... Truniger V, Blanco L, Salas M (1999). "Role of the "YxGG/A" motif of Phi29 DNA polymerase in protein-primed replication". J Mol ...
The putative 622-amino acid protein has a leucine-zipper motif at its N-terminus. Fanconi anemia is an autosomal recessive ... Blom E, van de Vrugt HJ, de Vries Y, de Winter JP, Arwert F, Joenje H (January 2004). "Multiple TPR motifs characterize the ...
... rich in hydroxylated amino acids such as serine, threonine, and proline, and poor in acidic amino acids like aspartic acid and ... "Functional characterization of sequence motifs in the transit peptide of Arabidopsis small subunit of rubisco". Plant ... Chloroplast transit peptides exhibit huge variation in length and amino acid sequence.[42] They can be from 20-150 amino acids ... Tic100 is a nuclear encoded protein that's 871 amino acids long. The 871 amino acids collectively weigh slightly less than 100 ...
Needleman, S. y Wunsch, C. (1970). "A general method applicable to the search for similarities in the amino acid sequence of ... "PRINTS-a protein motif fingerprint database". Protein Engineering 7 (7). ISSN 1741-0134, Páxs. 841-848. ... "Similar amino acid sequences: chance or common ancestry?". Science 214 (4517).. ... "Nucleic Acids Research 22 (17).. *↑ Un bo recurso de introdución a EMBnet é a páxina What is EMBnet? Arquivado 07 de setembro ...
In humans, RAD51 is a 339-amino acid protein that plays a major role in homologous recombination of DNA during double strand ... Wong AK, Pero R, Ormonde PA, Tavtigian SV, Bartel PL (Dec 1997). "RAD51 interacts with the evolutionarily conserved BRC motifs ... They each share about 25% amino acid sequence identity with RAD51 and with each other.[28] ... "Nucleic Acids Research. 25 (19): 3868-74. doi:10.1093/nar/25.19.3868. PMC 146972 . PMID 9380510.. ...
Four hydrogen bonds form between polar side chains on TBP amino acid (Asn27, Asn117, Thr82, Thr173)( and bases in the minor ... One study found less than 30% of 1031 potential promoter regions contain a putative TATA box motif in humans.[9] In Drosophila, ... "Nucleic Acids Research. 9 (19): 5145-58. doi:10.1093/nar/9.19.5145. PMC 327505. PMID 6171774.. ... The TATA box was the first eukaryotic core promoter motif to be identified in 1978 by American biochemist David Hogness[1] ...
The single-letter amino acid abbreviation (e.g., K for Lysine) and the amino acid position in the protein ... motif (DNA-binding protein motif that recognize specific DNA sequence). They also share the feature of long 'tails' on one end ... compared amino acid compositions in the same histone from different organisms, and compared amino acid sequences of the same ... 3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone". The Journal of ...
"for his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active ... "for his profoundly characteristic narrative art with motifs from the life of the Jewish people"[۵] ... "for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA"[۲۹] ... "for their contributions concerning the determination of base sequences in nucleic acids"[۲۹] ...
The microbes are also responsible for metabolising the carbohydrates and amino acids present in the tea leaves.[15][16][17] ... The press forces the tea into a metal form that is occasionally decorated with a motif in sunken-relief. Due to its efficiency ... Wet pile fermented pu'er has higher levels of caffeine and much higher levels of gallic acid compared with traditionally aged ...
... as all ingested SOD is broken down into amino acids before being absorbed. However, ingestion of SOD bound to wheat proteins ... The Ni-hook contains the motif His-Cys-X-X-Pro-Cys-Gly-X-Tyr; it provides most of the interactions critical for metal binding ... and their active sites contain the same type and arrangement of amino acid side-chains. They are usually dimers, but ... superoxide inactivates the citric acid cycle enzyme aconitase, can poison energy metabolism, and releases potentially toxic ...
The ubiquitin protein itself is 76 amino acids long and was named due to its ubiquitous nature, as it has a highly conserved ... which contains a specific motif (i.e., HbYX motif). The ATPases C-termini bind into pockets in the top of the 20S, and tether ... The mechanism for unfolding of globular proteins is necessarily general, but somewhat dependent on the amino acid sequence. ... The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into ...
"Nucleic Acids Res. 28 (18): 3558-63. PMC 110727. PMID 10982876. doi:10.1093/nar/28.18.3558.. ... A iniciación da tradución alternativa e os mecanismos de empalme ou splicing alteran as secuencias amino- e carboxilo-terminais ... "DNA ligase III is recruited to DNA strand breaks by a zinc finger motif homologous to that of poly(ADP-ribose) polymerase. ... "Nucleic Acids Res. 23 (23): 4836-43. PMC 307472. PMID 8532526. doi:10.1093/nar/23.23.4836.. ...
Mineral Nutrients and Amino Acids May or Must be Added.[87] Voluntary and mandatory fortification was described for various ... bind to a conserved Leu-Xaa-Xaa-Leu-Ala-Pro motif present in all substrates identified so far.. ... Ascorbic acid is a weak sugar acid structurally related to glucose. In biological systems, ascorbic acid can be found only at ... The biosynthesis of ascorbic acid in vertebrates starts with the formation of UDP-glucuronic acid. UDP-glucuronic acid is ...
In mammals, amino acid sensing and additional signals such as growth factors and reactive oxygen species regulate the activity ... The generated PtdIns(3)P is used as a docking point for proteins harboring a PtdIns(3)P binding motif. WIPI2, a PtdIns(3)P ... Z. Yang, J. Huang, J. Geng, U. Nair, and D. J. Klionsky, 'Atg22 Recycles Amino Acids to Link the Degradative and Recycling ... This allows unneeded proteins to be degraded and the amino acids recycled for the synthesis of proteins that are essential for ...
In an effort to localize the amino acid motif responsible for granule targeting, we constructed additional fusion proteins and ... TNF is primarily produced as a 233-amino acid-long type II transmembrane protein arranged in stable homotrimers.[24][25] From ... cellular response to amino acid stimulus. • negative regulation of extrinsic apoptotic signaling pathway in absence of ligand. ... The common house mouse TNFα and human TNF are structurally different.[28] The 17-kilodalton (kDa) TNF protomers (185-amino acid ...
The Wiskott-Aldrich Syndrome protein (WASp) is a 502-amino acid protein expressed in cells of the hematopoietic system. In the ... It is located towards the C-terminal end of the protein and contains four motifs: two verprolin homology motifs (VV) binds ... The presence of a number of different motifs suggests they are regulated by a number of different stimuli, and interact with ... and the acidic motif (A) binds Arp2/3.[8] In isolation, the VCA region is constitutively active. However, in full-length N-WASp ...
Miyakawa T, Obaru K, Maeda K, Harada S, Mitsuya H (2002). „Identification of amino acid residues critical for LD78beta, a ... The BBXB motif of RANTES is the principal site for heparin binding and controls receptor selectivity". J. Biol. Chem. 276 (14 ... "Nucleic Acids Res. 18 (6): 1513-6. PMC 330519 . PMID 2183196. doi:10.1093/nar/18.6.1513.. CS1 одржавање: Експлицитна употреба ... Addition of ethanolamine-phosphoglycerol to specific glutamic acid residues on EF-1 alpha". J. Biol. Chem. 264 (24): 14334-41. ...
39-80 amino acid residues) are also present. These larger cathelicidins display repetitive proline motifs forming extended ... Cathelicidins range in size from 12 to 80 amino acid residues and have a wide range of structures.[8] Most cathelicidins are ... although amino acid residues thought to be important in such protease inhibition are usually lacking. ... linear peptides with 23-37 amino acid residues, and fold into amphipathic α-helices. Additionally cathelicidins may also be ...
Isoform "a" of human CASS4 is considered the predominant species, and at 786 amino acids is the longest one.[10] Amino acid ... CAS proteins have an amino terminal SH3 domain enabling interaction with poly-proline motif-containing proteins such as FAK. ... 786 amino acids, considered the major isoform), the third one contains 6 exons and encodes a shorter isoform b (732 amino acids ... The CASS4 C-terminus has a short region of CAS family homology, but lacks obvious similarity at the level of primary amino acid ...
With the combination of two potent dopamine transporter (DAT) binding motifs attached to the tropane ring, the p-iodophenyl ... tropane-2 beta-carboxylic acid ester and amide analogues. New high-affinity and selective compounds for the dopamine ... 2-Amino-1,2-dihydronaphthalene. *2-Aminoindane. *5-(2-Aminopropyl)indole. *2-Aminotetralin ...
... beyond the twenty canonical amino acids found in nature, to include an unnatural amino acid as well. The unnatural amino acid ... Class I has two highly conserved sequence motifs. It aminoacylates at the 2'-OH of a terminal adenosine nucleotide on tRNA, and ... the tRNA with the amino acid. Once the tRNA is charged, a ribosome can transfer the amino acid from the tRNA onto a growing ... and redox-active amino acids.[14] Another use is introducing amino acids bearing reactive functional groups for chemically ...
Sequence motif. Short amino acid sequences within proteins often act as recognition sites for other proteins.[26] For instance ... The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino ... amino acids. All proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a ... If amino acids are present in the environment, microorganisms can conserve energy by taking up the amino acids from their ...
Purification and partial amino acid sequence analysis of human erythrocyte acetylcholinesterase.. FEBS Lett. 1989, 247 (2): 279 ... 1vzj: STRUCTURE OF THE TETRAMERIZATION DOMAIN OF ACETYLCHOLINESTERASE: FOUR-FOLD INTERACTION OF A WWW MOTIF WITH A LEFT-HANDED ...
... are folded chains of a large number of different amino acids called polypeptides. The amino acid sequence of any polypeptide ... Such a name is given because this arrangement is the same folding motif used in other heme/globin proteins such as myoglobin.[ ... Variations in hemoglobin amino acid sequences, as with other proteins, may be adaptive. For example, hemoglobin has been found ... Hemoglobin has a quaternary structure characteristic of many multi-subunit globular proteins.[34] Most of the amino acids in ...
All cytochrome c proteins contain a characteristic CXXCH (cysteine-any-any-cysteine-histidine) amino acid motif that binds heme ... Its primary structure consists of a chain of about 100 amino acids. Many higher-order organisms possess a chain of 104 amino ... Its amino acid sequence is highly conserved in eukaryotes, differing by only a few residues. In more than thirty species, 34 of ... Amino acid sequences in cytochrome c proteins from different species, adapted from Strahler, Arthur; Science and Earth History ...
The combination of corn and beans provided the Mesa Verdeans with the amino acids of a complete protein. When conditions were ... Common motifs in the rock art of the region include, anthropomorphic figures in procession and during copulation or childbirth ... patterns that resemble symbols used in pottery and zigzag that represent stitches used in basket making are common motifs. The ...
"SAP97 is associated with the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor GluR1 subunit". The Journal of ... 97 to GluR-A alpha-amino-5-hydroxy-3-methyl-4-isoxazole propionate receptor subunit is determined by a novel sequence motif". ... "SAP97 is associated with the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor GluR1 subunit". The Journal of ... Bassand P, Bernard A, Rafiki A, Gayet D, Khrestchatisky M (Jun 1999). "Differential interaction of the tSXV motifs of the NR1 ...
Human ALOX5 is a soluble, monomeric protein consisting of 673 amino acids with a molecular weight of ~78 kDa. Structurally, ... Variant alleles involved deletions (one or two) or additions (one, two, or three) of Sp1 motifs to the five tandem motifs ... Arachidonic acidEdit. ALOX5 metabolizes the omega-6 fatty acid, Arachidonic acid (AA, i.e. 5Z,8Z,11Z,15Z-eicosatrienoic acid), ... Eicosapentaenoic acidEdit. ALOX5 metabolizes the omega-3 fatty acid, Eicosapentaenoic acid (EPA, i.e. 4Z,8Z,11Z,14Z,17Z- ...
Serotonin is synthesized from an amino acid called L-tryptophan. Active transport system regulates the uptake of tryptophan ... The same motif can be found in reboxetine where it is constrained in a morpholine ring system. Some studies have been made ... This structural motif has potential for high affinity binding to biogenic amine transports.[28] Drugs containing an ...
cellular response to amino acid starvation. • positive regulation of programmed cell death. • negative regulation of apoptotic ... Specifically it contains a Cy1 motif in the N-terminal half, and weaker Cy2 motif in the C-terminal domain that allow it to ... "Cyclin-binding motifs are essential for the function of p21CIP1". Molecular and Cellular Biology. 16 (9): 4673-4682. doi ...
... those with a specific amino acid sequence (or motif) of glutamic acid-leucine-arginine (or ELR for short) immediately before ... they share gene sequence and amino acid sequence homology. They all also possess conserved amino acids that are important for ... The CC chemokine (or β-chemokine) proteins have two adjacent cysteines (amino acids), near their amino terminus. There have ... A loop of approximately ten amino acids follows the first two cysteines and is known as the N-loop. This is followed by a ...
... that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes ... 1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). ... N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence ...
Amino Acid Motifs (en); motifs dacides aminés (fr) Three-dimensional protein structural elements that are composed of a ... Amino Acid Motifs Three-dimensional protein structural elements that are composed of a combination of secondary structures. ... Media in category "Amino acid motifs". The following 52 files are in this category, out of 52 total. ... Retrieved from "https://commons.wikimedia.org/w/index.php?title=Category:Amino_acid_motifs&oldid=333987164" ...
... severe motifs; M, mild motifs; C, cerebral malaria motifs; N, severe malaria NUD motifs; NS, nonsevere malaria NUD motifs; R, ... Specific PfEMP1-DBL1α amino acid motifs correlated with rosetting and severe malaria, with motif location corresponding to ... Amino acids involved in receptor binding are indicated by blue dots, and amino acids essential for binding are represented by ... PfEMP1-DBL1α amino acid motifs in severe disease states of Plasmodium falciparum malaria. Johan Normark, Daniel Nilsson, Ulf ...
We present a new framework for global and localalignment of amino acid sequences based on hierarchicalmotif vectors that ... for global and local alignment of amino acid sequences based on hierarchical motif vectors that characterize local amino acid ... We then formulate different schemes for aligning amino acid sequences based on their respective motif vectors globally as well ... sequence alignment; amino acid sequence analysis;physico-chemical profiles; motif vectors; waveletdecomposition. ...
A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinsons disease. Jill A. ... A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinsons disease ... A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinsons disease ... A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinsons disease ...
"Amino Acid Motifs" by people in this website by year, and whether "Amino Acid Motifs" was a major or minor topic of these ... "Amino Acid Motifs" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical Subject ... Amino Acid Motifs*Amino Acid Motifs. *Amino Acid Motif. *Motif, Amino Acid ... Below are the most recent publications written about "Amino Acid Motifs" by people in Profiles. ...
Two of seven amino acid substitutions in the proline-rich motif of ExoP affected EPS I production, indicating that most of the ... Substitution of specific amino acid residues in the proline-rich motif of the ExoP protein.To analyze the relevance of the ... Specific Amino Acid Substitutions in the Proline-Rich Motif of the Rhizobium meliloti ExoP Protein Result in Enhanced ... Specific Amino Acid Substitutions in the Proline-Rich Motif of the Rhizobium meliloti ExoP Protein Result in Enhanced ...
Amino acid preferences at each position in the motif are presented, as are dot matrix sequence comparisons between several of ... Amino acid preferences at each position in the motif are presented, as are dot matrix sequence comparisons between several of ... Occurrence of a Repeating 11-Mer Amino Acid Sequence Motif in Diverse Organisms. Author(s): Leon Dure III. Department of ... Abstract: A repeating 11-mer amino acid sequence motif, first recognized in plant seed proteins, has been observed in such ...
... ... We previously identified 3S, a critical conserved motif of gp41 that induces the NKp44L ligand of an activating NK receptor. In ... Generation of antibodies in mice against the W614 specific position in the 3S motif elicited a capacity to neutralize cross- ... Results: Here, we show that specific substitutions in the 3S motif reduce viral infection without affecting gp41 production, ...
Thomsen, M. C. F., & Nielsen, M. (2012). Seq2Logo: a method for construction and visualization of amino acid binding motifs and ... Thomsen, MCF & Nielsen, M 2012, Seq2Logo: a method for construction and visualization of amino acid binding motifs and ... Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence ... Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence ...
E. FRIEDERICH et al., "An actin-binding site containing a conserved motif of charged amino acid residues is essential for the ... An actin-binding site containing a conserved motif of charged amino acid residues is essential for the morphogenic effect of ... "An Actin-binding Site Containing a Conserved Motif of Charged Amino Acid Residues Is Essential for the Morphogenic Effect of ... "An Actin-binding Site Containing a Conserved Motif of Charged Amino Acid Residues Is Essential for the Morphogenic Effect of ...
Single amino acid substitutions defined the critical amino acid peptide motif as RRKQXK-PXXF. This motif probably exhibits a ... We have identified a highly conserved 12-amino acid motif in the transcription factor Sall1 that is sufficient for the ... Single amino acid substitutions defined the critical amino acid peptide motif as RRKQXK-PXXF. This motif probably exhibits a ... We have identified a highly conserved 12-amino acid motif in the transcription factor Sall1 that is sufficient for the ...
We found that susceptibility to PD can be explained by a specific combination of amino acids at positions 70-74 on the HLA-DRB1 ... The association of specific combinations of amino acids that participate in critical peptide-binding pockets of the HLA class ... We found that susceptibility to PD can be explained by a specific combination of amino acids at positions 70-74 on the HLA-DRB1 ... The association of specific combinations of amino acids that participate in critical peptide-binding pockets of the HLA class ...
Vibrational spectroscopy of a non-aromatic amino acid-based model peptide: Identification of the gamma-turn motif of the ...
Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power.. ... Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power.. ... Amino Acid Sequence, Computer Graphics, Computer Simulation, Information Systems, Models, Molecular, Protein Conformation, ... Amino acid sequence patterns suggested to characterize specific recurrent turn conformation in protein are tested as to their ...
... motif vectors to represent local amino acid sequence configurations for predicting the functional attributes of amino acid ... Hierarchical motif vectors for prediction of functional sites in amino acid sequences using quasi-supervised learning. ... The motif vectors are constructed via wavelet decomposition on the variations of physico-chemical amino acid properties along ... We then formulate a prediction scheme for the functional attributes of amino acid sites in terms of the respective motif ...
... classifying and curating information about short linear motifs (SLiMs). For ,10 years, this resource has provided the ... The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, ... Amino Acid Motifs* * Databases, Protein* * Internet * Multiprotein Complexes / chemistry * Protein Interaction Domains and ... The eukaryotic linear motif resource ELM: 10 years and counting Nucleic Acids Res. 2014 Jan;42(Database issue):D259-66. doi: ...
The AIM Center is funded by NIH grant P20GM121176, and it endows the state of New Mexico and the surrounding region with a state-of-the-art biomedical center and an intellectual and technological hub for cutting-edge research. On a larger scale, the AIM Center promises to be a nationally important center for the advancement of research on autophagy. ...
Search for Functionally Significant Motifs and Amino Acid Residues of Actin. Molecular Biology. 52(1), 136-151. 31/1/2018. ... Search for Functionally Significant Motifs and Amino Acid Residues of Actin. 0 ...
A common conserved amino acid motif module shared by bacterial and intercellular adhesins: bacterial adherence mimicking cell- ... A common conserved amino acid motif module shared by bacterial and intercellular adhesins: bacterial adherence mimicking cell- ... Short motif sequences determine the targets of the prokaryotic CRISPR defence system F. J. M. Mojica, C. Díez-Villaseñor, J. ...
... enzyme prefers individual amino acids at each subsite in isolation or prefers to cleave combinations of amino acids as a motif ... enzyme prefers individual amino acids at each subsite in isolation or prefers to cleave combinations of amino acids as a motif ... enzyme prefers individual amino acids at each subsite in isolation or prefers to cleave combinations of amino acids as a motif ... enzyme prefers individual amino acids at each subsite in isolation or prefers to cleave combinations of amino acids as a motif ...
TriPepSVM - de novo prediction of RNA-binding proteins based on short amino acid motifs. by admin · November 9, 2018. ... TriPepSVM - de novo prediction of RNA-binding proteins based on short amino acid motifs. Source: Viral Bioinformatics ... or disordered low-complexity regions of RBPs have been identified to play an important role in interactions with nucleic acids ... the 18th annual Nucleic Acids Research web server issue 2020 , #Bioinformatics Vol 48, Issue W1 , https://bit.ly/2VmTV4a ...
Identification of the amino acid sequence motif of alpha-synuclein responsible for macrophage activation, doi: 10.1016/j.bbrc. ... YUHSpace: Identification of the amino acid sequence motif of alpha-synuclein responsible for macrophage activation. menu ... Amino Acid Motifs/genetics ; Animals ; Cell Line ; DNA Mutational Analysis ; Humans ; Macrophage Activation*/genetics ; ... Identification of the amino acid sequence motif of alpha-synuclein responsible for macrophage activation ...
Amino Acid Motifs. *ArnT. *Arrestin. *Arrestins. *ATP-Binding Cassette Transporters. *Bacterial Proteins ...
Thus, the peptide motif demonstrated potent inhibition of two functionally distinct subunits of Stx. Watanabe-Takahashi, Tamada ... A monomeric peptide with the same motif, however, did not bind to the B-subunit pentamer. Instead, the monomer inhibited ... On the other hand, a monomeric peptide containing the same motif occupies the Stx catalytic cavity, suggesting that this ... peptide motif can inhibit two subunits of Stx. ... which has a synthetic amino acid βAla in its motif, better ...
Amino acid motifs in P. indica In order to screen the genome of P. indica for known and unknown motifs in the amino acid ... A search for motifs (Table S12 and S13) in the amino acid sequences of these heterogeneous proteins identified a group of 25 ... amino acid permeases, transmembrane amino acid transporter proteins, nucleobase cation symporters, ABC-2 type transporters, and ... 1) Secreted proteins were predicted using TargetP and SignalP as described in material and methods, amino acid motifs in P. ...
3.3.3 Phloem Thioredoxin h 8211; charged amino acids as PD motifs --. 3.3.4 Proteolytic processing facilitates transport of ... charged amino acids as PD motifs -- 3.3.4 Proteolytic processing facilitates transport of CmPP36 -- 3.3.5 A short PD-targeting ... 3.3.5 A short PD-targeting motif in phloem HSC70 --. 3.3.6 The elusive nature of PD-targeting signals --. 3.4 Conclusions and ... motif in phloem HSC70 -- 3.3.6 The elusive nature of PD-targeting signals -- 3.4 Conclusions and future prospects -- ...
Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing ... Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing ... Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing ... title = "Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid ...
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid ... MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid ... sequence motifs, and amino acid composition ...
HCDR3 amino acid motifs that are associated with influenza responses.. In some respects, the Ab fold that forms the framework ... Indeed, several specific amino acid patterns have been identified in Ab CDRs as comprising canonical motifs for interaction ... Interestingly, each of these genetic features (common V or D gene usage and convergent amino acid motifs and indels) has been ... The Ab protein remarkably mimics the interaction of the carbohydrate sialic acid by placing its amino acid structure into the ...
  • To explore the relationships between sequence and disease states or parasite phenotype, we acquired a set of DBL1α sequences from children with severe and mild malaria and developed specific algorithms to identify sequence-motifs (MOTIFF) and examined them for correlations with observed phenotypes. (pnas.org)
  • We present a new framework for global and local alignment of amino acid sequences based on hierarchical motif vectors that characterize local amino acid configurations. (actapress.com)
  • The motif vectors are constructed by carrying out wavelet decomposition on numeric property sequences obtained by replacing each amino acid in a sequence with their respective properties, and concatenating such profiles obtained for a large number of physico-chemical properties into a single column vector. (actapress.com)
  • We then formulate different schemes for aligning amino acid sequences based on their respective motif vectors globally as well as locally subject to measures of statistical significance. (actapress.com)
  • Experiment results indicate that the motif vectors accurately capture the amino acid composition at and around individual sites along sequences and allow associating sequence segments sharing similar functional attributes. (actapress.com)
  • Although the amino acid sequences of the N-terminal ExoP domain and the similar proteins were only weakly conserved, these proteins displayed structural similarities, since they were characterized by two putative transmembrane helices and a conserved proline-rich amino acid motif located on the periplasmic side, very close to the second membrane helix ( 2 , 6 , 28 , 32 ). (asm.org)
  • Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. (dtu.dk)
  • The motif vectors are constructed via wavelet decomposition on the variations of physico-chemical amino acid properties along the sequences. (iyte.edu.tr)
  • E-values refer to the significance of each motif found within the CIR sequences. (nih.gov)
  • The frequency (percentage) of CIR sequences within the whole repertoire, clade A1 or whole sub-families A and B containing each motif is shown. (nih.gov)
  • A) Similarity plot of the aligned capsid amino acid sequences of 64 enterovirus prototype strains. (asm.org)
  • Primer sequences are shown directly below the amino acid motif sequences. (asm.org)
  • Three conserved protein motifs were identified by aligning the VP3 and VP1 sequences of prototype EV strains. (asm.org)
  • In this system, nucleotide sequences which are at least 75% identical (85% amino acid identity) are considered to represent strains of the same serotype ( 12 - 14 , 19 , 20 ). (asm.org)
  • Deduced amino acid sequences constantly showed the toxic motifs. (mdpi.com)
  • A comparison of the amino acid sequences and phylogenetic analysis of 31 full-length cDNAs of maize ( Zea mays ) AQPs shows that they comprise four different groups of highly divergent proteins. (plantphysiol.org)
  • Amino acid sequence identities vary from 16% to 100%, but all sequences share structural motifs and conserved amino acids necessary to stabilize the two loops that form the aqueous pore. (plantphysiol.org)
  • We report here a whole genome analysis of the olfactory receptor genes of Bos taurus using conserved OR gene-specific motifs and known OR protein sequences from diverse species. (biomedcentral.com)
  • Identifying motifs in biological sequences is an important challenge in biology. (merlot.org)
  • To our knowledge all currently available methods search motifs in protein sequences at the amino acid level, sometimes. (merlot.org)
  • To our knowledge all currently available methods search motifs in protein sequences at the amino acid level, sometimes allowing degenerate motifs to comply with point variations [1, 2]. (merlot.org)
  • Given a set of protein sequences known to be involved in a common biological system (positive set) and a set of protein sequences known not to be involved in that system (negative set) our method is able to identifiy motifs that are frequent in positive sequences while infrequent or absent in negative sequences. (merlot.org)
  • These motifs did have some predictive ability in searching for the known epitopes among a set of decoy sequences. (mcponline.org)
  • PEST motifs are sequences rich in Pro, Glu, Asp, Ser and Thr which have been proposed to constitute protein instability determinants. (cnrs.fr)
  • AC: A Compression Tool for Amino Acid Sequences. (bioportfolio.com)
  • art method for lossless compression of amino acid sequences. (bioportfolio.com)
  • The Variability of Amino Acid Sequences in Hepatitis B Virus. (bioportfolio.com)
  • OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs. (bioportfolio.com)
  • A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. (bioportfolio.com)
  • Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences. (bioportfolio.com)
  • The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. (bioportfolio.com)
  • Alignment of sequences around putative catalytic residues in known cutinases and this enzyme indicated that the three residues (S119, D199, H214) which form a catalytic triad in lipases, esterases, and serine proteases are conserved in this enzyme along with the consensus sequence lipase box GXSXG motif around a catalytic serine (Fig. 1 ). (asm.org)
  • Phylogenetic analysis using full-length amino acid sequences of functionally characterized BAHD enzymes by D'Auria (2006) and Stewart et al. (wikipedia.org)
  • A repeating 11-mer amino acid sequence motif, first recognized in plant seed proteins, has been observed in such diverse organisms as the nematode Caenorhabditis elegans and the eubacteria Haemophilus influenzae and Dienococcus radiodurans. (eurekaselect.com)
  • Amino acid preferences at each position in the motif are presented, as are dot matrix sequence comparisons between several of the proteins harboring the repeating motif. (eurekaselect.com)
  • Although implicated in plant abiotic stress tolerance, no molecular function for the proteins carrying the motif has yet been uncovered. (eurekaselect.com)
  • This motif probably exhibits a more general role in regulating gene expression, since other proteins containing this domain, including all Sall family members and an unrelated zinc finger protein Ebfaz, mediate transcriptional repression and associate with NuRD. (escholarship.org)
  • Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power. (ac.be)
  • Amino acid sequence patterns suggested to characterize specific recurrent turn conformation in protein are tested as to their predictive power in a database containing 75 proteins of known structure. (ac.be)
  • About 10% of the fungal genes induced during the biotrophic colonization encoded putative small secreted proteins (SSP), including several lectin-like proteins and members of a P. indica -specific gene family (DELD) with a conserved novel seven-amino acids motif at the C-terminus. (pubmedcentralcanada.ca)
  • VQ motif-containing (VQ) proteins are plant-specific proteins that interact with WRKY transcription factors and play important roles in plant growth, development and stress response. (biomedcentral.com)
  • The CsVQ proteins all contained the typical conserved motif FxxhVQxhTG, and most proteins were localized in the nucleus. (biomedcentral.com)
  • Most divergent are the small and basic integral proteins in which the first of the two highly conserved Asn-Pro-Ala motifs of the pore is not conserved, but is represented by alanine-proline-threonine or alanine-proline-serine. (plantphysiol.org)
  • Finding motifs specific to proteins involved in the same process can help deciphering the determinants of their fate and thus be used in identifying new candidate proteins involved in important biological systems. (merlot.org)
  • The identified motifs can then be used to mine the wealth of protein data now available, in order to identify new previously uncharacterized proteins involved in biological processes of importance. (merlot.org)
  • The APOBEC3 proteins are a mammalian-specific family of nucleic acid cytidine deaminases that block retroviral infection. (mdpi.com)
  • A BLAST search revealed that the deduced amino acid sequence of this protein did not exhibit homology with any of the known lipases, and the enzyme was found to be weakly (12 to 20%) homologous to proteins belonging to the cutinase family. (asm.org)
  • In this study, we have identified 11 Arabidopsis genes encoding novel proteins, termed RICs (for Rop-interactive CRIB motif-containing proteins), that contain a CRIB (for Cdc42/Rac-interactive binding) motif required for their specific interaction with GTP-bound Rop1. (elsevier.com)
  • Here, using a customized workflow, we report genes encoding GAST proteins, identify novel motifs and evolutionary patterns contributing to the subfunctionalization of GAST domains, and explore functional conservation across diverse plant groups. (plantphysiol.org)
  • Thus, our study identifies GAST s and their encoded proteins, uncovers their structure, novel motifs, and evolutionary pattern among plants, and suggests their functional conservation. (plantphysiol.org)
  • An actin-binding site containing a conserved motif of charged amino acid residues is essential for the morphogenic effect of villin. (ugent.be)
  • In this paper, the functional significance of this conserved motif is further studied by the analysis of mutants in conserved residues Asn387, Ser388, and Gly391. (neb.com)
  • Here, we further attenuated WNV by mutating the asparagine to serine or glutamine in addition to mutating other residues in the NS1 130-132 glycosylation motif. (utmb.edu)
  • Reference: Identification of amino acid residues in the human immunodeficiency virus type-1 reverse transcriptase tryptophan-repeat motif that are required for subunit interaction using infectious virions. (neb.com)
  • Here, we analyzed the contributions of amino acid residues comprising the Trp-motif to RT subunit interaction and function. (neb.com)
  • Our results reveal important inter- and intra-subunit interactions of residues in the Trp-motif. (neb.com)
  • We propose a method that allows to identify emerging motifs based both on conservation of amino acids and on the physico-chemical properties of these residues. (merlot.org)
  • Interestingly, acute depletion of phosphatidylinositol 4-phosphate (PtdIns4P) at the Golgi complex reduced GAP-43 membrane binding, highlighting a new, pivotal role for this anionic lipid and supporting the idea that basic amino acid residues are involved in the electrostatic interactions between GAP-43 and membranes of the Golgi complex where they are S-acylated. (portlandpress.com)
  • Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. (dtu.dk)
  • One of these peptides, MMA-tet (containing the following motif, Met-Met-Ala-Arg-Arg-Arg-Arg), inhibits the major Stx family members (e.g. (nature.com)
  • By contrast, HC-10 did not react with six additional peptides, each bearing motif amino acid substitutions present in HC-10-not-reactive HLA-I allospecificities. (jimmunol.org)
  • Though the epitopes were not directly evident, subtle motifs were found among the top binding peptides for each antibody. (mcponline.org)
  • We have identified a highly conserved 12-amino acid motif in the transcription factor Sall1 that is sufficient for the recruitment of NuRD. (escholarship.org)
  • The production of the acidic exopolysaccharide succinoglycan (EPS I) by Rhizobium meliloti exoP * mutants expressing an ExoP protein lacking its C-terminal cytoplasmic domain and by mutants characterized by specific amino acid substitutions in the proline-rich motif (RX 4 PX 2 PX 4 SPKX 9 IXGXMXGXG) located from positions 443 to 476 of the ExoP protein was analyzed. (asm.org)
  • Specific substitutions within the 3S peptide motif were prepared by directed mutagenesis. (nih.gov)
  • Here, we show that specific substitutions in the 3S motif reduce viral infection without affecting gp41 production, while decreasing both its capacity to induce NKp44L expression on CD4(+) T cells and its sensitivity to autologous NK cells. (nih.gov)
  • Single amino acid substitutions defined the critical amino acid peptide motif as RRKQXK-PXXF. (escholarship.org)
  • To test whether UIM-mediated binding results in substrate preference, these scientists generated a panel of USP25 mutants carrying substitutions of functional amino acids in UIMs and analyzed their interaction with and catalytic activity toward Lys48- or Lys63-linked ubiquitin chains. (eurekalert.org)
  • At a given position in the sequence, the nature and physico-chemical properties of amino acids in protein families is more conserved than the amino acid itself. (merlot.org)
  • Thus, the peptide motif demonstrated potent inhibition of two functionally distinct subunits of Stx. (nature.com)
  • Mutants in phi 29 DNA polymerase residue Tyr390 of this conserved motif had been previously described to be affected in DNA-dependent dNTP binding. (neb.com)
  • 1. A peptide consisting of the amino acid sequence of FIG. 1 (SEQ ID NO:68) from about the lysine residue at amino acid 676 to about the valine residue at amino acid 1255. (google.com)
  • The Histidine in this motif has also been shown to act as a catalytic residue in many BAHD enzymes. (wikipedia.org)
  • Amino Acid Motifs" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (umassmed.edu)
  • We propose hierarchical motif vectors to represent local amino acid sequence configurations for predicting the functional attributes of amino acid sites on a global scale in a quasi-supervised learning framework. (iyte.edu.tr)
  • The amino acid motifs and phylogenetic analyses indicated that MeGSTs were divided into 9 classes. (springer.com)
  • Phylogenetic analysis revealed that the GAST-Cysteine Rich1 motif evolved early in the S. moellendorffii GAST, which further acquired subfunctionalization through successive conjugation of other motifs and remained conserved across plants, as supported by their collinearity. (plantphysiol.org)
  • Interestingly, the PTL motif is conserved in other members of the fos multigene family. (cnrs.fr)
  • The association of specific combinations of amino acids that participate in critical peptide-binding pockets of the HLA class II molecule implicates antigen presentation in PD pathogenesis and provides further support for genetic control of neuroinflammation in disease. (escholarship.org)
  • While the subsite specificity of thrombin is understood, it is not clear whether the enzyme prefers individual amino acids at each subsite in isolation or prefers to cleave combinations of amino acids as a motif. (monash.edu)
  • The regulatory domain of MyoD is approximately 70 amino acids in length and includes both a basic DNA binding motif and a bHLH dimerization motif. (fishersci.com)
  • The C-terminal cytoplasmic domain contains a putative ATP binding motif ( 6 ). (asm.org)
  • We also found that PopP2 harbors a putative eukaryotic transcriptional repressor motif (ethylene-responsive element binding factor-associated amphiphilic repression or EAR), which is known to be involved in the recruitment of transcriptional co-repressors. (frontiersin.org)
  • We have previously shown that FYCO1 binds to LC3B via a 19-amino acid sequence containing a putative core LC3-interacting region (LIR) motif. (rcsb.org)
  • The putative 622-amino acid protein has a leucine-zipper motif at its N-terminus. (wikipedia.org)
  • We then formulate a prediction scheme for the functional attributes of amino acid sites in terms of the respective motif vectors using the quasi-supervised learning algorithm that carries out predictions for all sites in consideration using only the experimentally verified sites. (iyte.edu.tr)
  • The tetravalent peptide has a synthetic amino acid, β−Ala, in each functional motif. (nature.com)
  • Two major sub-families were identified, which have been named A and B. Members of each sub-family displayed different amino acid motifs, and were thus predicted to have undergone functional divergence. (nih.gov)
  • To address the functional significance of the LIR motif of FYCO1, we generated FYCO1 knock-out cells that subsequently were reconstituted with GFP-FYCO1 WT and LIR mutant constructs. (rcsb.org)
  • Our data show that FYCO1 requires a functional LIR motif to facilitate efficient maturation of autophagosomes under basal conditions, whereas starvation-induced autophagy was unaffected. (rcsb.org)
  • Gibberellic Acid Stimulated Transcript-Related 9 ) suggests hormonal regulation, novel roles in seed germination, and functional conservation among diverse plant groups. (plantphysiol.org)
  • We show that a DEEDh (the five catalytic amino acids) motif drives nucleotide excision. (rcsb.org)
  • Specific PfEMP1-DBL1α amino acid motifs correlated with rosetting and severe malaria, with motif location corresponding to distinct regions of receptor interaction. (pnas.org)
  • The propensity of both the side chain and the backbone carbonyls of the polyproline type II helix to participate in the interface interaction makes it an excellent recognition motif. (hindawi.com)
  • FBPs mediate protein-protein interaction with roughly 50 amino acids within their structural motifs. (news-medical.net)
  • We found that mutation of critical basic amino acids drastically reduced membrane interaction and hence S-acylation of GAP-43. (portlandpress.com)
  • Finally, phosphorylation motifs (standard, degenerate, and multiply phosphorylated) were extracted from the data set with the Motif-X algorithm. (nih.gov)
  • Consensus degenerate primers were designed from a conserved VP3 motif and a distal VP1 motif for the first PCR. (asm.org)
  • Consensus-degenerate hybrid oligonucleotide primers were designed from an internal VP1 motif and used with the same distal VP1 motif for the second, seminested PCR step. (asm.org)
  • Generation of antibodies in mice against the W614 specific position in the 3S motif elicited a capacity to neutralize cross-clade viruses, notable in its magnitude, breadth, and durability. (nih.gov)
  • 15. The diagnostic composition of claim 14, wherein said compounds are nucleic acid molecules or antibodies. (freepatentsonline.com)
  • Intermolecular interactions mediated by proline-rich motifs (PRMs) are observed in many facets of the immune response. (hindawi.com)
  • Genome-wide distribution of the repressed genes of Lactobacillus helveticus CM4 in response to amino acids on the genome map ( a ) and locations from the origin with the repressive effects ( b ). a Location of the repressed genes by amino acids on a previously reported physical map of Lactobacillus helveticus CM4 chromosomal DNA [ 20 ]. (biomedcentral.com)
  • b Locations of the repressed genes from the origin and the repressive effects by amino acids in CM4. (biomedcentral.com)
  • Gibberellic Acid Stimulated Transcript ( GAST )-like genes encode small polypeptides, some of which have been implicated in diverse biological processes regulating plant growth and development. (plantphysiol.org)
  • Computational modeling predicts that these GAST genes are regulated by several factors, including the phytohormones gibberellin and abscisic acid, through conserved cis-motifs present in their promoters, and that they might act as signaling molecules in a complex feedback loop. (plantphysiol.org)
  • The second conserved motif is DFGWG (Aspartic acid, Phenylalanine, Glycine, Tryptophan, Glycine) and it is typically found near the carboxyl terminus of the protein and is thought to participate in CoA binding (D'Auria, 2006). (wikipedia.org)
  • Together, these findings suggest that agrin-induced phosphorylation of the β subunit motif increases the stoichiometry of rapsyn binding to the AChR, thereby helping to stably cluster the receptor and anchor it at high density in the postsynaptic membrane. (jneurosci.org)
  • Because of the large size of the data set, both novel and known phosphorylation motifs were extracted using the Motif-X algorithm, including those representative of potential ordered phosphorylation events. (nih.gov)
  • Consensus amino acid motifs are shown. (asm.org)
  • A ribosome only binds to the RER once a specific protein-nucleic acid complex forms in the cytosol. (wikipedia.org)
  • [email protected]#To establish 293T cell lines stably expressing Calpain-cleavage related α3 cytoplasmic tail mutants, and to explore the effect of amino acid motifs in integrin β3 cytoplasmic tail on αⅡbβ3-mediated cell function. (bvsalud.org)
  • Cnx1E Asp274 mutants accumulate the Moco precursor adenylated molybdopterin, thus providing the molecular framework required for subsequent research work devoted to elucidate the mechanism behind molybdate insertion into the MPT dithiolene motif which is intrinsically tied to Moco formation. (portlandpress.com)
  • 10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear motifs. (nih.gov)
  • Remarkably, mutation of the EAR motif disabled PopP2 avirulence function as measured by the development of hypersensitive response, electrolyte leakage, defense marker gene expression and bacterial growth in Arabidopsis. (frontiersin.org)
  • Interestingly, a mutation at a SUMO- interacting motif (SIM), but not the catalytic sites within the mature Trx2 protein, completely blocks Trx2 processing with no effect on Trx2 mitochondrial targeting. (frontiersin.org)
  • Irp5 shows 41% similarity to EntE, the 2,3-dihydroxybenzoic acid-activating enzyme utilized in enterobactin synthesis of Escherichia coli . (asm.org)
  • This enzyme could effectively degrade the high-molecular-weight compound polylactic acid, as well as other biodegradable plastics, including polybutylene succinate, poly (ε-caprolactone), and poly(3-hydroxybutyrate). (asm.org)
  • Members of this enzyme family typically share two conserved amino acid motifs. (wikipedia.org)
  • Overall, we showed that changing the asparagine of the NS1 130 glycosylation motif to a serine or glutamine attenuated WNV further than the asparagine to alanine substitution. (utmb.edu)
  • Spot technique-based experiments showed that 667 recognizes a linear epitope of 12 amino acids located in the variable region A of the receptor binding domain. (cnrs.fr)
  • Alanine scanning experiments showed that six amino acids within the epitope are critical for MAb binding. (cnrs.fr)
  • In rheumatoid arthritis (RA), the shared epitope (SE), a five-amino acid sequence motif encoded by RA-associated HLA - DRB1 alleles, is the single most significant genetic risk factor. (wn.com)
  • A monomeric peptide with the same motif, however, did not bind to the B-subunit pentamer. (nature.com)
  • The incipient formation of cisplatin-derived complexes with the recognized biological amino acid targets L-histidine (His) and L-methionine (Met) has been investigated revealing the primary platination event to be mainly directed at the Nπ atom of the imidazole side chain of His and to the thiomethyl sulfur of Met. (unich.it)
  • Importantly, our data also indicate that the PopP2 conserved repressor motif could contribute to the effector accumulation in plant cells. (frontiersin.org)
  • This graph shows the total number of publications written about "Amino Acid Motifs" by people in this website by year, and whether "Amino Acid Motifs" was a major or minor topic of these publications. (umassmed.edu)
  • motifs d'acides aminés (fr) Three-dimensional protein structural elements that are composed of a combination of secondary structures. (wikimedia.org)
  • Many of these patterns are found to be associated with local structures that differ from the motifs originally used to derive them. (ac.be)
  • Tiemann, B., Gerardy-Schahn, R., and Bakker, H. (2013) LARGE2 generates the same xylose and glucuronic acid containing glycan structures as LARGE. (mh-hannover.de)
  • To investigate whether preferred peptide motifs for cleavage could be identified for thrombin, we exposed a phage-displayed peptide library to thrombin. (monash.edu)
  • The results revealed that thrombin selected for amino acid motifs in cleavage sites. (monash.edu)
  • The contribution of these hypothetical motifs to substrate cleavage efficiency was further investigated using the B1 IgG-binding domain of streptococcal protein G as a model substrate. (monash.edu)
  • Introduction of further P(3)-P(1) and P(1)-P(1) -P(3) amino acid motifs into the loop region yielded greater cleavage efficiencies, suggesting that the susceptibility of a protein substrate to cleavage by thrombin is influenced by these motifs, perhaps because of cooperative effects between subsites closest to the scissile peptide bond. (monash.edu)
  • The signals for GAP-43 S-acylation are confined to the first 13 amino acids, including the S-acylatable cysteines 3 and 4 embedded in a hydrophobic region, followed by a cluster of basic amino acids. (portlandpress.com)
  • phi 29 DNA polymerase shares with other alpha-like DNA polymerases several regions of amino acid similarity. (neb.com)
  • The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). (nih.gov)
  • Structural analysis of crystals of mammalian AQPs and amino acid sequence comparisons of all AQPs show that they have six membrane-spanning alpha helices with N and C termini that face the cytosol. (plantphysiol.org)
  • The structural modification includes addition or deletion of a leucine-based motif or parts thereof. (google.com)
  • We previously identified 3S, a critical conserved motif of gp41 that induces the NKp44L ligand of an activating NK receptor. (nih.gov)
  • Our study reveals that a unique SUMO-interacting motif of Trx2 is critical for its mitochondrial processing and subsequent anti-oxidant/antisenescence activities. (frontiersin.org)
  • Glycerol molecules move in a single file through an equally narrow amphipathic channel in which the NPA motifs also play a critical role. (plantphysiol.org)
  • and (b) a selective expansion of Vδ1 cells bearing recurrent junctional amino acid motifs. (jci.org)
  • Members of Gibberellic Acid Stimulated Transcript ( GAST ) gene family are regulated by GA and encode small polypeptides that have a C-terminal domain of ∼60 amino acids. (plantphysiol.org)
  • [10] The first 5-30 amino acids polymerized encode a signal peptide , a molecular message that is recognized and bound by a signal recognition particle (SRP). (wikipedia.org)
  • The irp1 gene consists of 9,486 bp capable of encoding a 3,161-amino-acid high-molecular-weight protein 1 (HMWP1) polypeptide with a predicted mass of 384.6 kDa. (asm.org)
  • Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange formats. (nih.gov)
  • Furthermore, unstructured or disordered low-complexity regions of RBPs have been identified to play an important role in interactions with nucleic acids. (4virology.net)
  • Leon Dure III, " Occurrence of a Repeating 11-Mer Amino Acid Sequence Motif in Diverse Organisms", Protein & Peptide Letters (2001) 8: 115. (eurekaselect.com)
  • Betha, AK, Williams, AM & Martinis, SA 2007, ' Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing activity ', Biochemistry , vol. 46, no. 21, pp. 6258-6267. (illinois.edu)
  • ExoP consists of 786 amino acids and can be divided into an N-terminal domain (positions 1 to 481), mainly located in the periplasm, and a C-terminal cytoplasmic domain (positions 482 to 786) ( 6 ). (asm.org)
  • [email protected]#293T cell lines stably co-expressing human wild type integrin αⅡb and full length β3 or mutant β3, including β3-ΔNITY (β3 cytoplasmic tail NITY motif deleted), β3-Δ754 (β3 cytoplasmic tail TNITYRGT motif deleted) and β3-Δ759 (β3 cytoplasmic tail RGT motif deleted) were established. (bvsalud.org)