Amino Acid Motifs: 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.Amino Acid 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.Molecular Sequence Data: 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.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Amino Acids: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Conserved 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.Cloning, Molecular: 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.Sequence Alignment: 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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Amino Acid Substitution: 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.Protein Structure, Tertiary: 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.Protein Binding: 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 Fusion Proteins: 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.DNA, Complementary: 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.Mutation: 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.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Structure-Activity Relationship: 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.Escherichia coli: 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, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Protein Conformation: 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).DNA Primers: 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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Bacterial Proteins: Proteins found in any species of bacterium.Sequence Homology, Nucleic Acid: 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.Consensus Sequence: 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.Peptides: 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.DNA: 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).Multigene Family: 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)Polymerase Chain Reaction: 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.Plasmids: 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.Transfection: 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, Essential: Amino acids that are not synthesized by the human body in amounts sufficient to carry out physiological functions. They are obtained from dietary foodstuffs.Protein Structure, Secondary: 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.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Membrane Proteins: 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.Amino Acid Transport Systems: Cellular proteins and protein complexes that transport amino acids across biological membranes.DNA-Binding Proteins: 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.Open Reading Frames: 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).Sequence Analysis, Protein: 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, Messenger: 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.Complementarity Determining Regions: 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).COS Cells: 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).)Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Saccharomyces cerevisiae: 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.Species Specificity: 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, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Repetitive Sequences, Nucleic Acid: 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).Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Cercopithecus aethiops: 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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Viral Proteins: Proteins found in any species of virus.Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Protein Processing, Post-Translational: 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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Nucleotide Motifs: Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.Epitopes: Sites on an antigen that interact with specific antibodies.HeLa Cells: 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.Kinetics: The rate dynamics in chemical or physical systems.Leucine: An essential branched-chain amino acid important for hemoglobin formation.Amino Acids, Aromatic: Amino acids containing an aromatic side chain.Receptors, Antigen, T-Cell, alpha-beta: 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, Branched-Chain: Amino acids which have a branched carbon chain.Nuclear Proteins: 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, Cultured: 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.Amino Acids, SulfurAspartic Acid: 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.Arabidopsis: 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.Proteins: 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.Signal Transduction: 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.PhosphoproteinsMolecular Weight: The sum of the weight of all the atoms in a molecule.Protein Sorting Signals: Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Clone Cells: 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)Alanine: 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.Genes, Bacterial: The functional hereditary units of BACTERIA.Lysine: An essential amino acid. It is often added to animal feed.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Isoleucine: 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, Basic: Amino acids with side chains that are positively charged at physiological pH.Amino Acid Transport Systems, Basic: Amino acid transporter systems capable of transporting basic amino acids (AMINO ACIDS, BASIC).Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.Point Mutation: 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.Codon: 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).Glycine: 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.Cattle: 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.Cytoplasm: 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)Proline: 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.Biological Transport: 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.Gene Library: 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.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.Arginine: An essential amino acid that is physiologically active in the L-form.Trypsin: 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.Genes: 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.Glutamine: 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 Interaction Domains and Motifs: 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: 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.Amino Acids, DiaminoValine: 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.Methionine: A sulfur-containing essential L-amino acid that is important in many body functions.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Phenylalanine: An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Repetitive Sequences, Amino Acid: A sequential pattern of amino acids occurring more than once in the same protein sequence.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Excitatory Amino Acids: 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.Blotting, Northern: 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.Nitrogen: 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.Promoter Regions, Genetic: 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.Tryptophan: 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.Macromolecular Substances: 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.Sequence Analysis: 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.Fungal Proteins: Proteins found in any species of fungus.Amino Acid Transport System A: 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, Neutral: Amino acids with uncharged R groups or side chains.Threonine: 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.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.Serine: 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.Helix-Turn-Helix Motifs: 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)Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Oligodeoxyribonucleotides: 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.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Genetic Complementation Test: 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.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Rabbits: 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.Saccharomyces cerevisiae Proteins: 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.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Chickens: 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.Tyrosine: A non-essential amino acid. In animals it is synthesized from PHENYLALANINE. It is also the precursor of EPINEPHRINE; THYROID HORMONES; and melanin.Endopeptidases: A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.Protein PrecursorsRNA: 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)Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Circular Dichroism: 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)Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Oligopeptides: Peptides composed of between two and twelve amino acids.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Chromatography, Gel: Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.Swine: 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).Gene Expression Regulation: 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.Peptide Mapping: 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.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Receptors, Amino Acid: 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.Exons: 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.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Blotting, Southern: 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.Temperature: 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.Chymotrypsin: 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.Chromatography, Ion Exchange: 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.Dietary Proteins: Proteins obtained from foods. They are the main source of the ESSENTIAL AMINO ACIDS.Magnetic Resonance Spectroscopy: 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).Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Computational Biology: 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.Genes, Fungal: The functional hereditary units of FUNGI.Glutamic Acid: A non-essential amino acid naturally occurring in the L-form. Glutamic acid is the most common excitatory neurotransmitter in the CENTRAL NERVOUS SYSTEM.Amino Acids, Cyclic: A class of amino acids characterized by a closed ring structure.Genetic Variation: Genotypic differences observed among individuals in a population.Amino Acyl-tRNA Synthetases: A subclass of enzymes that aminoacylate AMINO ACID-SPECIFIC TRANSFER RNA with their corresponding AMINO ACIDS.Sequence Homology: 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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Oligonucleotide Probes: 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.CHO Cells: 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.Aminoisobutyric Acids: A group of compounds that are derivatives of the amino acid 2-amino-2-methylpropanoic acid.Two-Hybrid System Techniques: 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.Protein Transport: 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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Mutation, Missense: 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)Molecular Structure: 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.Hydrogen-Ion Concentration: 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)Serine Endopeptidases: Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Tissue Distribution: 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.Histidine: An essential amino acid that is required for the production of HISTAMINE.Asparagine: 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)Models, Biological: 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.Binding, Competitive: 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.Repressor Proteins: 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.Alternative Splicing: 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.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Cystine: 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.Ligands: 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)Glycoproteins: Conjugated protein-carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins.Glycosylation: 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.Carbon Isotopes: 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.Plants: 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, Acidic: Amino acids with side chains that are negatively charged at physiological pH.Isoenzymes: Structurally related forms of an enzyme. Each isoenzyme has the same mechanism and classification, but differs in its chemical, physical, or immunological characteristics.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Genes, Viral: The functional hereditary units of VIRUSES.Large Neutral Amino Acid-Transporter 1: 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.

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)

*Protein primary structure

Amino acids are polymerised via peptide bonds to form a long backbone, with the different amino acid side chains protruding ... "Normalization of nomenclature for peptide motifs as ligands of modular protein domains". FEBS Letters. 513 (1): 141-144. doi: ... Protein sequencing Nucleic acid primary structure Translation Pseudo amino acid composition SANGER F (1952). "The arrangement ... listing the amino acids starting at the amino-terminal end through to the carboxyl-terminal end. Either a three letter code or ...

*Armadillo repeat

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 ...

*Beta-catenin

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) ...

*Cyclic di-GMP

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/ ...

*RGS18

This protein contains a conserved 120 amino acid motif called the RGS domain. The protein attenuates the signaling activity of ...

*Gluten immunochemistry

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 ...

*List of open-source health software

Wregex is an amino acid motif searching software for weighted regular expressions. It is available under the GNU GPL. Glucosio ...

*Ptc1

This recruitment takes place via a 4 amino acid motif in the Ste5 phosphosites. Ptc1 is also involved in regulating the osmotic ...

*TGF alpha

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 together ... TGF-α has been shown to inhibit gastric acid secretion. TGF-α can be produced in macrophages, brain cells, and keratinocytes. ...

*Protein inhibitor of activated STAT

Each SAP domain contains an LXXLL amino acid motif. L = leucine, and X = any amino acid. This motif is used to bind to nuclear ... motif, the RING-finger-like zinc-binding domain (RLD), the highly acidic domain (AD), the SUMO-interacting motif (SIM), and the ... contains a SUMO-interacting motif (SIM). The SIM motif may be needed for PIAS proteins to accurately recognize and interact ... The Pro-Ile-Asn-Ile-Thr (PINIT) motif was discovered in PIAS3L, an isoform of PIAS3. PIAS proteins tend to go back and forth ...

*Φ29 DNA polymerase

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. PMC 450017 ... 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 ...

*SALL4

Lauberth SM, Rauchman M (Aug 2006). "A conserved 12-amino acid motif in Sall1 recruits the nucleosome remodeling and ... Through a 12-amino acid sequence in its N-terminus (N-12a.a.), SALL4 binds to retinoblastoma binding protein 4 (RBBP4), a ... SALL4 has at least one canonical nuclear localization signal (NLS) with the K-K/R-X-K/R motif in the N-terminal portion of the ... SALL4 contains one zinc finger in its amino (N-) terminus and three clusters of zinc fingers that each coordinates zinc with ...

*GPX4

... shares the amino acid motif of selenocysteine, glutamine, and tryptophane (catalytic triad) with other glutathione ... In selenoproteins, the 21st amino acid selenocysteine is inserted in the nascent polypeptide chain during the process of ... During the catalytic cycle of GPx4, the active selenol (-SeH) is oxidized by peroxides to selenenic acid (-SeOH), which is then ... Grim JM, Hyndman KA, Kriska T, Girotti AW, Crockett EL (2011). "Relationship between oxidizable fatty acid content and level of ...

*PTK2

Tahiliani PD, Singh L, Auer KL, LaFlamme SE (March 1997). "The role of conserved amino acid motifs within the integrin beta3 ... A carboxy-terminal region of one hundred and fifty-nine amino acids, the focal adhesion targeting domain (FAT), has been shown ... The amino-terminal domains of FAK share a significant sequence similarity with the band 4.1 domain first identified in ... Between the amino and the carboxy regions lies the catalytic domain. Phosphorylation of the activation loop within this kinase ...

*SETDB1

The SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure. ...

*Karyopherin alpha 1

"RAG-1 interacts with the repeated amino acid motif of the human homologue of the yeast protein SRP1". Proc Natl Acad Sci U S A ... 1994). "The Vpr protein of human immunodeficiency virus type 1 influences nuclear localization of viral nucleic acids in ...

*RGS17

This protein contains a conserved, 120 amino acid motif called the RGS domain and a cysteine-rich region. The protein ...

*Molecular mimicry

For example, the QKRAA sequence is an amino acid motif in the third hypervariable region of HLA-DRB1*0401. This motif is also ... Assuming five to six amino acid residues are used to induce a monoclonal antibody response, the probability of 20 amino acids ... This motif occurs 37 times in the database. This would suggest that the linear amino acid sequence may not be an underlying ... The probability of finding a perfect match with a motif of 5 amino acids in length is 1 in 3.7 X 10−7 (0.055). Therefore, ...

*Cytochrome c

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 ... The dipole moment of cytochrome c is a result from a cluster of negatively charged amino acid side chains at the "back" of the ...

*Rev (HIV)

The arginine-rich motif (ARM) is located between amino acids 38-49 of the rev gene and forms an alpha-helical secondary ... Gorlich, D; Henklein, P; Laskey, RA; Hartmann, E (April 1996). "A 41 amino acid motif in importin-a confers binding to importin ... M10 is a mutated form of Rev and has a single amino acid substitution (Aspartic acid to Leucine). If delivered to cells, Rev ... Rev is a 13-kDa protein that is composed of 116 amino acids. Rev's sequence contains two specific domains which contribute to ...

*KPNB1

Görlich D, Henklein P, Laskey RA, Hartmann E (1996). "A 41 amino acid motif in importin-alpha confers binding to importin-beta ... Weis K, Ryder U, Lamond AI (1996). "The conserved amino-terminal domain of hSRP1 alpha is essential for nuclear protein import ...

*Importin α

Görlich, D; Henklein, P; Laskey, R A; Hartmann, E (1996-04-15). "A 41 amino acid motif in importin-alpha confers binding to ... NLS sequences can be monopartite (single cluster of basic amino acids) or bipartite (two clusters of basic amino acids with a ... This sequence occurs within the first 20 amino acid positions of the viral nucleoprotein and contains clusters of basic amino ... The IBB domain of importin α molecules contain many basic amino acid residues, similar to those found in NLS sequences. This ...

*RNA polymerase II holoenzyme

The CTD consists of repetitions of an amino acid motif, YSPTSPS, of which Serines and Threonines can be phosphorylated. The ... It has a kinase activity that phosphorylates the C-terminal domain (CTD) of Pol II at the amino acid serine. This switches the ... Major studies in which knockout of particular amino acids was achieved in the CTD have been carried out. The results indicate ... TFIIE may be involved in DNA melting at the promoter: it contains a zinc ribbon motif that can bind single-stranded DNA. TFIIE ...

*BDP1

... contains a novel 55-amino-acid motif repeated nine times and maps closely to SMN1". Genomics. 70 (3): 315-26. doi:10.1006/geno. ...

*Mating of yeast

Presence of α-factor induces recruitment of Ptc1 to Ste5 via a 4 amino acid motif located within the Ste5 phosphosites. Ptc1 ...

*Phage display

PelB (an amino acid signal sequence that targets the protein to the periplasm where a signal peptidase then cleaves off PelB) ... "Comparison of bacterial and phage display peptide libraries in search of target-binding motif". Appl. Biochem. Biotechnol. 127 ... Usually peptides that can be fused to pVIII are 6-8 amino acids long. The size restriction seems to have less to do with ... Moreover, pIII allows for the insertion of larger protein sequences (>100 amino acids) and is more tolerant to it than pVIII. ...

*Plakoglobin

... is a member of the catenin family, since it contains a distinct repeating amino acid motif called the armadillo ... Troyanovsky SM, Troyanovsky RB, Eshkind LG, Leube RE, Franke WW (Nov 1994). "Identification of amino acid sequence motifs in ... Human plakoglobin is 81.7 kDa in molecular weight and 745 amino acids long. The JUP gene contains 13 exons spanning 17 kb on ... Franke WW, Goldschmidt MD, Zimbelmann R, Mueller HM, Schiller DL, Cowin P (Jun 1989). "Molecular cloning and amino acid ...
Although taking direct control of a cells motif system is a common and easy method for viruses to be able to thrive inside its host cell, it can take control by other means as well. One method is by indirectly influencing the motif control utilizing globular proteins and domains. Some examples of domains that do this are EBV BHRF-1, which binds specifically to BH3 motifs. Another example of this particular method would be STD viruses such as HIV or the bovine papillomavirus E6 oncoprotein. These particular viral proteins are able to bind onto paxillin, a cellular cytoskeletal protein.. Another mechanism of indirect motif control would be a viral infection leading to loss of the motif upon viral transferring into the host cell. The virus is able to do this by continually replicating itself and changing its genetic code via mutations until the sequence of the clone viral protein is virtually useless for the host cell. By becoming useless, the viral proteins are thus able to decouple from normal ...
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, ...
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,
Traditionally, protein-protein interactions were thought to be mediated by large, structured domains. However, it has become clear that the interactome comprises a wide range of binding interfaces with varying degrees of flexibility, ranging from rigid globular domains to disordered regions that natively lac Intrinsically Disordered Proteins
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 ...
mouse Slo2 protein: a type of sodium-activated K+ channel, possess a typical PDZ binding motif at the carboxy-terminal end; NP_780671
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 ...
The images below show the motif residues and the match residues superimposed. The carbon atoms are white in the motif and green in the match. Other atoms in the motif and match are colored by element. The C-alphas are shown as spheres, while the remaining motif and match atoms are shown in stick representation. The rest of the matching protein is shown in ribbon representation ...
Active Motif offers high-quality nuclear, cytoplasmic and whole-cell extracts from a variety of cell types and tissue sources that are ready to use as controls in a variety of applications, including TransAM™, gelshift and supershift assays, Western blo
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View mouse Trim33 Chr3:103279293-103358775 with: phenotypes, sequences, polymorphisms, proteins, references, function, expression
View mouse Trim21 Chr7:102557921-102565486 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
SU(HW) distribution relative to LADs is sequence driven and linked to CP190 binding.(A) Profiles of sequence motifs across aligned LAD borders. X-axis depicts t
We have recently shown that the ciliary trafficking of PC1 is regulated by specific BBS proteins and requires the presence of an intact PC1-CTT (Su et al., 2014). Here, we identified that multiple sequences and motifs in PC1-CTT contribute to the ciliary trafficking of PC1. PC1 and PC2 mutually promote the trafficking of each other to the primary cilium, and our results show that PC1 ciliary targeting is highly dependent on the dose of PC2 but not the VxP motifs in PC1 or PC2. GPS cleavage is not required for PC1 ciliary trafficking.. The most important sequences and motifs contributing to PC1 ciliary trafficking in the C-terminal tail we have identified are the coiled-coil motif that is the key for protein-protein interaction, the leucine residue adjacent to the G-protein-binding domain, and the highly conserved sequences containing multiple phosphorylation sites located N-terminal to the coiled-coil motif. The coiled-coil motif in PC1 has been shown to interact with many proteins including PC2 ...
Proteins belonging to the thioredoxin (Trx) superfamily are abundant in all organisms. They share the same structural features, arranged in a seemingly simple fold, but they perform a multitude of functions in oxidative protein folding and electron transfer pathways. We use the C-terminal domain of the unique transmembrane reductant conductor DsbD as a model for an in-depth analysis of the factors controlling the reactivity of the Trx fold. We employ NMR spectroscopy, x-ray crystallography, mutagenesis, in vivo functional experiments applied to DsbD, and a comparative sequence analysis of Trx-fold proteins to determine the effect of residues in the vicinity of the active site on the ionization of the key nucleophilic cysteine of the -CXXC- motif. We show that the function and reactivity of Trx-fold proteins depend critically on the electrostatic features imposed by an extended active-site motif.
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 ...
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 ...
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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 ...
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
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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 ...
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
... , Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
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.
... , Authors: Vanessa Cristina Arfelli, Leticia Fröhlich Archangelo. Published in: Atlas Genet Cytogenet Oncol Haematol.
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
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Nicely done, is it only one motif per hand? If so you could try doing another one like that just to make them visible from all angles... ReplyDelete ...
Looking for online definition of RNA binding motif protein 28 in the Medical Dictionary? RNA binding motif protein 28 explanation free. What is RNA binding motif protein 28? Meaning of RNA binding motif protein 28 medical term. What does RNA binding motif protein 28 mean?
Looking for online definition of RNA-binding motif protein 27 in the Medical Dictionary? RNA-binding motif protein 27 explanation free. What is RNA-binding motif protein 27? Meaning of RNA-binding motif protein 27 medical term. What does RNA-binding motif protein 27 mean?
The computational analysis of eukaryotic promoters are among the most important and complex research domains that may contribute to complete gene identification. The current methods for promoter recognition are not sufficiently developed. Eukaryotic promoters contain a number of short motifs that may be used in promoter recognition. Having good computational models for these motifs can be crucial for increased efficiency of promoter recognition programs. This study proposes a combined statistical and LVQ neural network system as a computational model of the TAT A box motif of eukaryotic promoters. The methodology used is universal and applicable to any short functional motif in DNA. The statistical analysis of the core TAT A motif hexamer and its neighboring haxamers show strong regularities that can be used in motif recognition. Moreover, the positional distribution of the TAT A motif in terms of its distance from the transcription start site is very regular and is used in the statistical ...
In in vitro binding assays, D6PK could bind to polyacidic PIs and PtdOH in a K-rich motif-dependent manner. In vivo manipulation of PI or PtdOH metabolism led to the intracellular accumulation of YFP:D6PK and impaired its polar plasma membrane distribution but only manipulation of PtdIns4P synthesis affected YFP:D6PK solubility. At the same time, K-rich motif mutations in D6PK led to increased solubilization of the protein. This suggests that the intact K-rich domain is required for interactions with polyacidic phospholipids in different membranes and that the specific phospholipid composition in a given membrane might determine D6PK recruitment to different membranes. The D6PK interaction with multiple polyacidic phospholipids through ionic interactions resembles previously reported mechanisms for protein-phospholipid ionic interactions and is distinct from interactions mediated between phospholipids and globular protein domains (Hammond and Balla, 2015; Li et al., 2014).. PtdOH biosensors have ...
Viruses mimic host motifs to hijack the host cellular machinery. Their interaction with host protein domains is through Short Linear Motifs (SLiMs). SLiMs are short stretches of amino acids (~3-10) which are involved in post translational modifications (PTMs), protein-protein Interactions (PPIs), cell regulation and cell compartment targeting. To date, several studies have been conducted to identify PPIs, but no specific study to see how well different PPI capturing methods capture SLiMs-mediated interactions. The main objectives of this study are 1) to predict Domain Motif Interactions (DMIs) among viral and host proteins 2) to find whether virhostome (virus-human interaction) data is enriched for DMIs and, 3) to see which PPI method is better for studying DMIs. Results have shown that virhostome data is enriched for DMIs and can be a good source to study motif mimicry in viruses. The permutation test showed more enrichment for TAP data as compared to the Y2H data. Moreover, novel candidate ...
Like tyrosine phosphorylation, serine phosphorylation plays a critical role in regulating signaling for cell survival, apoptosis, or cell migration (21, 22). SXXE/D motifs, found in the cytoplasmic domains of many TNFR family members as well as their adaptor proteins, are involved in serine signal transduction. However, unlike PXSP or PS/SP motifs that are phosphorylated by MAPK/cdc2PK type kinases for β-stranded WW domain (ββ) interaction (23), SXXE/D motifs are phosphorylated by CK-II/IKK type kinases and have been shown to associate with TNFR1 (24). We demonstrated here that IKKβ and, to a lesser extent, IKKα can phosphorylate the "SXXE" motif of TNFR1 death domain.. In the helical death domain (αααααα) of Fas, the α-helix3 is involved in direct contact with FADD death domain within the α-helix2-α-helix3 region, which bears the SXXE/D motif (25). Besides, S215 of TRADD death domain and positive charge residues of both TRADD and TNFR1 death domains have been previously noted to ...
Methods and Results: In cultured endothelial cells, FcγRI-blocking antibodies prevented CRP antagonism of eNOS, and CRP activated Src via FcγRI. CRP-induced increases in FcγRIIB immunoreceptor tyrosine-based inhibitory motif phosphorylation and SH2 domain-containing inositol 5′-phosphatase 1 activation were Src-dependent, and Src inhibition prevented eNOS antagonism by CRP. Similar processes mediated eNOS antagonism by aggregated IgG used to mimic immune complex. Carotid artery re-endothelialization was evaluated in offspring from crosses of CRP transgenic mice (TG-CRP) with either mice lacking the γ subunit of FcγRI (FcRγ−/−) or FcγRIIB−/− mice. Whereas re-endothelialization was impaired in TG-CRP vs wild-type, it was normal in both FcRγ−/− TG-CRP and FcγRIIB−/− TG-CRP mice.. ...
High-throughput protein-RNA interaction data generated by CLIP-seq has provided an unprecedented depth of access to the activities of RNA-binding proteins (RBPs), the key players in co- and post-transcriptional regulation of gene expression. Motif discovery forms part of the necessary follow-up data analysis for CLIP-seq, both to refine the exact locations of RBP binding sites, and to characterize them. The specific properties of RBP binding sites, and the CLIP-seq methods, provide additional information not usually present in the classic motif discovery problem: the binding site structure, and cross-linking induced events in reads.
Implementation of Recursive Brute Force for Solving Motif Finding Problem on Multi-Core: 10.4018/ijsbbt.2013070101: Motif is an over-represented pattern in biological sequence. Motif discovery is a major challenge in bioinformatics. Pattern mismatches phenomena makes motif
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sample_1: Specifier Domain and GA motif region of B. subtilis tyrS T box leader RNA, [U-100% 13C; U-100% 15N], 1 mM; D2O 100%. sample_2: Specifier Domain and GA motif region of B. subtilis tyrS T box leader RNA, [U-100% 13C; U-100% 15N], 1 mM; D2O 10%; H2O 90%. sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 273 K ...
The address tags of the proteins utilize the cellular transportation system to go to different compartments of the cell. It is like mails, although there are addresses on them, they themselves will not go to the address; it depends on the post system to pick them up and deliver them to the right place. So whats the transportation system of the cell like? They are made of transmembrane proteins. The rumen sides of the transporter proteins can recognize and bind to the address tags on cargo proteins. The cytoplasmic side of the transporter proteins contains specific motifs. When the golgi bubbles out, different bubbles contains different sets of transporter proteins whose cytoplasmic motifs will decide where the bubble should go (The mechanism will not be discussed here). Now lets take a look at how granule resident proteins are sorted to the granule. By transporter, the sorting pathways can be divided into Mannose Phosphate Receptor (MPR)-dependent pathway and MPR-independent pathways. ...
We consider the planted (I, d) motif search problem, which consists of finding a substring of length I that occurs in a set of input sequences {si,. ..,s|s
The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.. ...
Tiwari, Santosh K. et al. Phylogenetic analysis, based on EPIYA repeats in the cagA gene of Indian Helicobacter pylori, and the implications of sequence variation in tyrosine phosphorylation motifs on determining the clinical outcome. Genet. Mol. Biol., 2011, vol.34, no.2, p.280-285. ISSN 1415- ...
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human EAST protein: an EGF receptor- & Eps15-associated protein; has src homology 3 & tyrosine-based activation motif domains; MW 52 kDa; amino acid sequence in first source
The Magdalene Motif is a circular motif with an openwork center. It creates a simple but striking wheel shape through chains and triple crochet stitches.
Jilbab instan tali cantik dengan motif kupu masih menjadi koleksi terlaris minggu ini, berbahan misby dengan motif kupu dan polka yang modern dilengkapi pet anti tembem yang modis sekali dipakai sebagai jilbab instan cantik sehari-hari.. ...
FBXL10b, 0.4 ml. This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box.
Parf my a parf movan kosmetika m e obsahovat a 25 l tek, kter EU uv d jako alergeny. V p rodn ch parf mech v ak nen ani jedna.
Amino Acid Motifs;Computational Biology;Conserved Sequence;Databases, Protein;Genes;Logistic Models;Predictive Value of Tests;Proteins;Sensitivity and Specificity;Genetics;Physiology;Classification;Gene ...
Testing nucleotide-protein interaction - posted in Biochemistry: Hi everybody I work with an intrinsically disordered protein with unknown function and no close homologs. Psi Blasts show some low degree of homology to ATPsaes, but with e-values above cutoff. Motif searches predict an incomplete Walker A motif. If so, only the GKS motif is conserved, but not the P-loop. The protein forms a stable complex with Ca-calmodulin. I tried atpase assays, but there was no activity. Upon addition...
2KUO: Structure and identification of ADP-ribose recognition motifs of aprataxin PNK-like factor (APLF) required for the interaction with sites of DNA damage response
The Samosa Motif is named for the Indian pastries that share its shape. It is a unique alternative for those who want to move beyond the granny square.
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Protein small structure motif search and statistics wrapped into integrated protein sequence and protein structure search agains PDB archive with fast phi/psi search and rich visualization capabilities
Protein small structure motif search and statistics wrapped into integrated protein sequence and protein structure search agains PDB archive with fast phi/psi search and rich visualization capabilities
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Mitogen-activated protein kinases (MAPKs) have a docking groove that interacts with linear "docking" motifs in binding partners. To determine the structural basis of binding specificity between MAPKs and docking motifs, we quantitatively analyzed the ability of 15 docking motifs from diverse MAPK partners to bind to c-Jun amino-terminal kinase 1 (JNK1), p38α, and extracellular signal-regulated kinase 2 (ERK2). Classical docking motifs mediated highly specific binding only to JNK1, and only those motifs with a sequence pattern distinct from the classical MAPK binding docking motif consensus differentiated between the topographically similar docking grooves of ERK and p38α. Crystal structures of four complexes of MAPKs with docking peptides, representing JNK-specific, ERK-specific, or ERK- and p38-selective binding modes, revealed that the regions located between consensus positions in the docking motifs showed conformational diversity. Although the consensus positions in the docking motifs ...
GIW93P01] Yoichi Iida, Takeshi Masuda: "Quantification Analysis of Translation Initiation Signal Sequences in Vertebrate mRNAs" [GIW93P02] Koji Tajima: "Multiple Sequence Alignment using Parallel Genetic Algorithms" [GIW93P03] Tsuyoshi Yoshizawa, Masaki Fumoto, Tamio Yasukawa: "Prediction of Protein Conformations by a Spin Glass Model (I)" [GIW93P04] Fumiyoshi Sasagawa, Koji Tajima: "Toward Prediction of Multi-states Secondary Structures of Protein by Neural Network" [GIW93P05] Kotoko Nakata: "Sequence Analysis of Zinc Finger DNA-Binding Protein" [GIW93P06] Kazuhiro Iida, Hiroshi Mamitsuka: "Protein Sequence Motif Extraction with a Probabilistic Logic Neural Network: Motif Evaluation on a 3-D Structure" [GIW93P07] Koichi Niijima, Shinichi Shimozono: "Learning Algorithms of Three Layered Neural Networks for Sequence Classification" [GIW93P08] Hidetoshi Tanaka, Kentaro Onizuka, Kiyoshi Asai: "Classification of Proteins via Successive State Splitting Algorithm of Hidden Markov Network" [GIW93P09] ...
Research interests in the Edwards lab stem from a fascination with the molecular basis of evolutionary change and how we can harness the genetic sequence patterns left behind to make useful predictions about contemporary biological systems. The core research in the lab is the study of Short Linear Motifs (SLiMs), which are short regions of proteins that mediate interactions with other proteins. This research originated with Richs postdoctoral research, during which he developed a bioinformatics (sequence analysis) method for rational design of biologically active short peptides. He subsequently developed SLiMDisc, one of the first algorithms for successfully predicting novel SLiMs from sequence data - and coined the term "SLiM" into the bargain - before developing the first SLiM prediction algorithm able to estimate the statistical significance of motif predictions (SLiMFinder), which greatly increased the reliability of predictions. SLiMFinder has since spawned a number of motif discovery ...
Both IFN-α and IFN-γ increased SAMHD1 mRNA and protein expression, and reduced miR-181a levels, particularly in microglia. Phosphorylated SAMHD1was not induced by interferons. Overexpression of miR-181a counteracted induction of SAMHD1 expression by interferons, and inhibition of miR-181a mimicked interferons treatment. Inhibition of JAK-STAT signaling pathways resulted in increased miR-181a levels and decreased SAMHD1 mRNA expression. Knock-down of SAMHD1 or overexpression of miR-181a enhanced HIV-1 infection, whereas inhibition of miR-181a reduced HIV-1 infection. However, inhibition of HIV-1 infection induced by IFN-α was not significantly affected by miR-181a and SAMHD1.. CONCLUSION ...
OMP85 is an evolutionarily conserved protein necessary for the assembly of integral beta-barrel proteins in bacteria. The authors show that OMP85 forms a channel and recognizes its unfolded subtrates through a C-terminal signature sequence.
thanks for your answer, but I do not want to look for motifs in proteins. I ask for initiation sites encoded by a specific DNA sequence motif for protzeins involved in DNA replication. For E.coli for example the Rep1-3 protein have some initiation sites. But to my knowledge there are no equivalent proteins in human. Searching the literature one can find lots of proteins involved in DNA replication like PCNA and others, but I did not find DNA sequnce motifs ...
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There is a lack of functional group diversity in the reverse turn motifs nucleating a β-sheet conformation in designed peptides, proteins and foldamers. The majority of these sequences consist of d-Pro-l-Pro, d-Pro-Gly or Asn-Gly as the turn inducing motif restricting their biological application and physico
UK-based antibiotics developer Motif Bio has made its debut on the London Stock Exchanges AIM board, raising £2.8 million.. The cash injection is a little below expectations of around £4 million but will help the company advance the development of lead compound iclaprim, that it maintains could be on the market within the next three years.. Shares started the day at just around 20 pence and, after rising to almost 48 pence in an initial flurry, had tracked back to around 31 pence at the time of writing, up 55 per cent.. Motifs listing comes at an opportune time given the rising interest in developing drugs to combat antibiotic-resistant superbugs, which led to the creation of a government-led taskforce in the UK last year and similar public and private initiatives around the world.. These are multi-pronged schemes designed to encourage the most appropriate use of currently-available drugs and prevent further resistance occurring, but all have the same ultimate objective of accelerating the ...
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Immunoglobulin superfamily member 2; IgSF2; Cell surface glycoprotein V7; Glu-Trp-Ile EWI motif-containing protein 101; EWI-101; AltName: CD_antigen=CD101; Precursor ...
Principal Investigator:YUBISUI Toshitsugu, Project Period (FY):1994 - 1995, Research Category:Grant-in-Aid for international Scientific Research, Section:Joint Research
The di-Arg ER retention motif is defined by two consecutive arginine residues (RR) or with a single residue insertion (RXR). The motif is completed by an adjacent hydrophobic/arginine residue which may be on either side of the Arg pair ...
All these proteins share a number of conserved sequence motifs. Some of them are specific to this family while others are shared by other ATP-binding proteins or by proteins belonging to the helicases `superfamily [4]. One of these motifs, called the D-E-A-D-box, represents a special version of the B motif of ATP-binding proteins. Some other proteins belong to a subfamily which have His instead of the second Asp and are thus said to be D-E-A-H-box proteins [3,5,6]. Proteins currently known to belong to this subfamily are: ...
Diril, M. K., Schmidt, S., Krauß, M., Gawlik, V., Joost, H.-G., Schürmann, A., Haucke, V. and Augustin, R. (2009), Lysosomal localization of GLUT8 in the testis - the EXXXLL motif of GLUT8 is sufficient for its intracellular sorting via AP1- and AP2-mediated interaction. The FEBS Journal, 276: 3729-3743. doi: 10.1111/j.1742-4658.2009.07089.x ...
5000 Indian designs and motifs by Indian Institute of Art in Industry (Calcutta, India); 1 edition; First published in 1965; Subjects: Decoration and ornament, Decoration and ornament, Indic, Indic Decoration and ornament; Places: India
Jual jilbab bergo tali cantik terbaru cocok dipakai sebagai jilbab cantik bergo harian masakini, jilbab bergo tali motif cantik, hijab bergo tali
duplication: two beta(3)-alpha motifs are related by pseudo twofold symmetry; single antiparrallel beta-sheet, order:321456, shaped into a half-barrel; helical linker region ...
Proteins internalized at the cell surface by clathrin-mediated endocytosis contain specific sorting sequences that bind to the internalization machinery. The best characterized of these is the tyrosine-based YXXΦ motif (in which X is any residue and Φ is a bulky, hydrophobic residue). This binds to a specific region in the μ2 subunit of the AP2 clathrin adaptor protein, and structural studies have shown that the spacing between the Y and Φ residues is crucial. Ruth Murrell and co-workers now unveil a novel type of tyrosine-based endocytic motif (p. 3073). They have used site-directed mutagenesis and CD8-based chimeras to analyse endocytosis of P2X4 receptors, ATP-gated cation channels that rapidly cycle off the plasma membrane. These receptors possess consensus YXXΦ motifs, but surprisingly these are inaccessible to AP2 and not needed for endocytosis. Instead, the authors show, a downstream YXXGΦ motif is required. Determining the structure of a YXXGΦ-μ2 complex, they demonstrate that ...
The Gram-negative, intracellular bacterium Chlamydia trachomatis causes acute and chronic urogenital tract infection, potentially leading to infertility and ectopic pregnancy. The only partially characterized cytotoxin CT166 of serovar D exhibits a DXD motif, which is important for the enzymatic activity of many bacterial and mammalian type A glycosyltransferases, leading to the hypothesis that CT166 possess glycosyltransferase activity. CT166-expressing HeLa cells exhibit actin reorganization, including cell rounding, which has been attributed to the inhibition of the Rho-GTPases Rac/Cdc42. Exploiting the glycosylation-sensitive Ras(27H5) antibody, we here show that CT166 induces an epitope change in Ras, resulting in inhibited ERK and PI3K signaling and delayed cell cycle progression. Consistent with the hypothesis that these effects strictly depend on the DXD motif, CT166 with the mutated DXD motif causes neither Ras-ERK inhibition nor delayed cell cycle progression. In contrast, CT166 with the
The C-type lectin-like receptor 2 (CLEC-2)activates platelets through Src and Syk tyrosine kinases via a single cytoplasmic YxxL motif known as a hem immunoreceptor tyrosine-based activation motif (hemITAM).Here, we demonstrate using sucrose gradient ultracentrifugation and methyl--cyclodextrin treatment that CLEC-2 translocates to lipid rafts upon ligand engagement and that translocation is essential for hemITAM phosphorylation and signal initiation. HemITAM phosphorylation, but not translocation, is also critically dependent on actin polymerization,Rac1 activation, and release of ADP and thromboxane A2 (TxA2). The role of ADP and TxA2 in mediating hosphorylation is dependent on ligand engagement and rac activation but is independent of platelet aggregation. In contrast,tyrosine phosphorylation of the GPVIFcR -chain ITAM, which has 2 YxxL motifs,is independent of actin polymerization and secondary mediators. These results reveal a unique series of proximal events in CLEC-2 phosphorylation ...
The supernumerary subunit g is found in all mitochondrial ATP synthases. Most of the conserved amino acid residues are present in the membrane C-terminal part of the protein that contains a dimerization motif GXXXG. In yeast, alteration of this motif leads to the loss of subunit g and of supramolecular structures of the ATP synthase with concomitant appearance of anomalous mitochondrial morphologies. Disulfide bond formation involving an engineered cysteine in position 109 of subunit g and the endogenous cysteine 28 of subunit e promoted g + g, e + g, and e + e adducts, thus revealing the proximity in the mitochondrial membrane of several subunits e and g. Disulfide bond formation between two subunits g in mitochondria increased the stability of an oligomeric structure of the ATP synthase in digitonin extracts. These data suggest the participation of the dimerization motif of subunit g in the formation of supramolecular structures and is in favor of the existence of ATP synthase associations, in ...
Institut National de la Sante et de la Recherche Medicale U124-IRCL, Lille, France. The BTB/POZ domain defines a newly characterized protein-protein interaction interface. It is highly conserved throughout metazoan evolution and generally found at the NH2 terminus of either actin-binding or, more commonly, nuclear DNA-binding proteins. By mediating protein binding in large aggregates, the BTB/POZ domain serves to organize higher order macromolecular complexes involved in ring canal formation or chromatin folding ...
EcoKI cuts or modifies DNA according to the methylation states of specific adenine residues in its target recognition site. If these residues are unmethylated the DNA is cut, often thousands of base pairs away from the recognition site. Communication between EcoKI bound to the recognition site and the cleavage site occurs by DNA translocation, which is driven by ATP hydrolysis. The amino acid sequence of the subunit required for restriction contains seven motifs that are conserved in the DEAD box family of proteins. This family is a sub-group of the superfamily of DNA and RNA helicases. Previous studies on DEAD box proteins have found these motifs are involved in the ATPase and helicase activities of these proteins. To assess the importance of the DEAD box motifs in the restriction of DNA by EcoKI, amino acid residues in each of the seven motifs were changed and the effects of these substitutions on restriction were investigated. Eight proteins, each containing a different amino acid ...

Category:Amino acid motifs - Wikimedia CommonsCategory:Amino acid motifs - Wikimedia Commons

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" ...
more infohttps://commons.wikimedia.org/wiki/Category:Amino_acid_motifs

PfEMP1-DBL1α amino acid motifs in severe disease states of Plasmodium falciparum malaria | PNASPfEMP1-DBL1α amino acid motifs in severe disease states of Plasmodium falciparum malaria | PNAS

... 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 ...
more infohttp://www.pnas.org/content/104/40/15835

A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinsons disease | PNASA specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinson's disease | PNAS

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 ...
more infohttps://www.pnas.org/content/116/15/7419.short?rss=1&utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+pnas%2FSMZM+%28Current+Issue%29

A conserved 12-amino acid motif in Sall1 recruits the nucleosome remodeling and deacetylase corepressor complexA conserved 12-amino acid motif in Sall1 recruits the nucleosome remodeling and deacetylase corepressor complex

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 ...
more infohttps://escholarship.org/uc/item/15q6p0q9

Abstract] HIERARCHICAL MOTIF VECTORS FOR AMINO ACID SEQUENCE ALIGNMENTAbstract] HIERARCHICAL MOTIF VECTORS FOR AMINO ACID SEQUENCE ALIGNMENT

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. ...
more infohttp://actapress.com/Abstract.aspx?paperId=45053

YUHSpace: Identification of the amino acid sequence motif of alpha-synuclein responsible for macrophage activationYUHSpace: Identification of the amino acid sequence motif of alpha-synuclein responsible for macrophage activation

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 ...
more infohttps://ir.ymlib.yonsei.ac.kr/handle/22282913/103483

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...

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 ...
more infohttps://jb.asm.org/content/180/2/395?ijkey=09b3e80ca266bd3ad3966c69817ad1f123c278a4&keytype2=tf_ipsecsha

Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indicaEndophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica

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. ...
more infohttp://pubmedcentralcanada.ca/pmcc/articles/PMC3192844/

Imperfect interface of Beclin1 coiled-coil domain regulates homodimer and heterodimer formation with Atg14L and UVRAG.Imperfect interface of Beclin1 coiled-coil domain regulates homodimer and heterodimer formation with Atg14L and UVRAG.

Amino Acid Motifs. Amino Acid Sequence. Apoptosis Regulatory Proteins / metabolism*. Autophagy. Class III Phosphatidylinositol ... Another prominent feature of the Beclin 1 CC structure is the unusually high composition of charged amino acid residues, as ... Beclin 1 self-association is independent of autophagy induction by amino acid deprivation and rapamycin treatment. J. Cell ... are directly involved in Beclin 1-Atg14L interaction because mutating these amino acids to hydrophobic leucine residue nearly ...
more infohttp://www.biomedsearch.com/nih/Imperfect-interface-Beclin1-coiled-coil/22314358.html

Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS).  - PubMed -...Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS). - PubMed -...

Conserved amino acid motifs within CIR sequences. Amino acid motifs present within the CIR repertoire were identified by MEME ... Members of each sub-family displayed different amino acid motifs, and were thus predicted to have undergone functional ... Relationships between CIR amino acid sequences. Similarities between CIR sequences were visualized using a network created in ... clade A1 or whole sub-families A and B containing each motif is shown. Examples of motif arrangement in CIR proteins are shown ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/22458863?dopt=Abstract

Sensitive, Seminested PCR Amplification of VP1 Sequences for Direct Identification of All Enterovirus Serotypes from Original...Sensitive, Seminested PCR Amplification of VP1 Sequences for Direct Identification of All Enterovirus Serotypes from Original...

B) Amino acid motifs used in primer design and schematic representation of the steps in the CODEHOP VP1 RT-snPCR assay. ... Consensus amino acid motifs are shown. Asterisks indicate that the residue directly above the asterisk is present at that ... Primer sequences are shown directly below the amino acid motif sequences. Ambiguity codes are as follows: R, A or G; Y, C or T ... Consensus degenerate primers for the cDNA and PCR1 steps were designed from conserved amino acid motifs in the aligned capsid ...
more infohttps://jcm.asm.org/content/44/8/2698

Outline of Clock GenesOutline of Clock Genes

About 40 amino acid motif.. BTRC, SLMB. FBXL3. JETLAG. SM00256. IPR001810. WD40. WD-40 repeats is involved in protein-protein ... PAS (PERIOD ARNT SIM)domains were found in proteins involved in sensing for environmental signals.About 100 amino acid motif.. ... 40 amino acid.. BTRC, SLMB. SM00320. IPR001680 LRR. Leucine-rich repeats. Protein-binding. One unit consists of 22~28mino acid. ... About 60 amino acids. The N-terminal basic region (15 aa) is involved in DNA binding. C-terminal HLH involved in dimerization. ...
more infohttps://staff.aist.go.jp/s-hanai/clockbase/005_outline.html

A survey of machine learning methods for secondary and supersecondary protein structure prediction. - NextBio articleA survey of machine learning methods for secondary and supersecondary protein structure prediction. - NextBio article

Amino Acid Motifs Artificial Intelligence Computational Biology Models, Molecular Protein Structure, Secondary Proteins ...
more infohttp://www.nextbio.com/b/search/article.nb?id=22987348

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis | BMC Bioinformatics | Full TextMeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis | BMC Bioinformatics | Full Text

Fatty acid oxidation. Cellular amino acid metabolic process (+7). Thioredoxin-disulfide reductase activity ... Nucleic Acids Res. 2009; 37:166-9.View ArticleGoogle Scholar. *. Sartor MA, Ade A, Wright Z, States D, Omenn GS, Athey B, et al ... Nucleic Acids Res. 2008; 37:619-22.View ArticleGoogle Scholar. *. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, ... Nucleic Acids Res. 2012; 41:64-69.View ArticleGoogle Scholar. *. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, ...
more infohttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0453-z

Stavros Group: Mick StaniforthStavros Group: Mick Staniforth

Unravelling the Photoprotection Properties of Mycosporine Amino Acid Motifs. J. M. Woolley, M. Staniforth, M. D. Horbury, G. W ... amino acids and beyond. M. Staniforth and V.G. Stavros, Proc. R. Soc. A, 469 (2013) 20130458 ... First Step toward a Universal Fluorescent Probe: Unravelling the Photodynamics of an Amino-Maleimide Fluorophore. M. Staniforth ...
more infohttps://warwick.ac.uk/fac/sci/chemistry/research/stavros/stavrosgroup/groupmembers/mick

The Hp UreI urea channel hexamera, Ribbon diagram of he | Open-iThe Hp UreI urea channel hexamera, Ribbon diagram of he | Open-i

Amino Acid Motifs. *Crystallography, X-Ray. *Hydrogen-Ion Concentration. *Models, Molecular. *Protein Multimerization ... The bundle defines a previously unobserved fold comprising a two-helix hairpin motif repeated three times around the central ... The bundle defines a previously unobserved fold comprising a two-helix hairpin motif repeated three times around the central ...
more infohttps://openi.nlm.nih.gov/detailedresult.php?img=PMC3974264_nihms416126f1&req=4

Conceptual and ortholog-based maximum likelihood phylog | Open-iConceptual and ortholog-based maximum likelihood phylog | Open-i

Amino Acid Motifs. *Biosynthetic Pathways/genetics. *Fungal Proteins/genetics. *Molecular Sequence Annotation ...
more infohttps://openi.nlm.nih.gov/detailedresult.php?img=PMC4117958_12864_2013_6290_Fig2_HTML&req=4

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...

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 ...
more infohttp://abi.inf.uni-tuebingen.de/Publications/MultiLocGCB/

Amphioxus (Branchiostoma floridae) has orthologs of vertebrate odorant receptors | BMC Evolutionary Biology | Full TextAmphioxus (Branchiostoma floridae) has orthologs of vertebrate odorant receptors | BMC Evolutionary Biology | Full Text

We have also identified highly conserved amino acid motifs that may be important for maintaining receptor conformation or ... we identified three OR-specific amino acid motifs common in cephalochordate, fish and mammalian and ORs. Here, we show that ... By exposing conserved amino acid motifs and testing the ability of those motifs to discriminate between ORs and non-OR GPCRs, ... Key amino acid motifs. To identify amino acid motifs common in vertebrate and B. floridae ORs, we constructed an alignment of ...
more infohttps://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-9-242

Hla-drb1Hla-drb1

A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in .... *. ... In rheumatoid arthritis (RA), the shared epitope (SE), a five-amino acid sequence motif encoded by RA-associated HLA-DRB1 ...
more infohttps://wn.com/HLA-DRB1

A Screen for New Trithorax Group Genes Identified little imaginal discs, the Drosophila melanogaster Homologue of Human...A Screen for New Trithorax Group Genes Identified little imaginal discs, the Drosophila melanogaster Homologue of Human...

... a bipartite nuclear localization signal is found at amino acids 1599-1616. Each of these amino acid motifs is found in human ... This domain has a previously described amino acid motif called ARID (AT-rich interaction domain; Herrscheret al. 1995). Among ... Amino acid motifs were determined using the Profilescan program and PsortII programs. Protein alignments were performed on the ... The protein contains a number of amino acid motifs found in both trithorax and Polycomb group genes. It contains an N-terminal ...
more infohttp://www.genetics.org/content/156/2/645

Frontiers | A Haloarchaeal Small Regulatory RNA (sRNA) Is Essential for Rapid Adaptation to Phosphate Starvation Conditions |...Frontiers | A Haloarchaeal Small Regulatory RNA (sRNA) Is Essential for Rapid Adaptation to Phosphate Starvation Conditions |...

CPXCG denotes an amino acid motif of zinc finger protein. The S-layer is indicated by blue triangles. ... For example, more than 30 genes were transiently induced in H. volcanii after a shift from casamino acids to glucose, but had ... For H. salinarum it has been experimentally shown that pho-boxes, the binding motifs of PhoU regulators, are present in the ... compare the terminator motif in Figure 1A). Therefore, it was decided to unravel whether the sRNA132 has any effect on the ...
more infohttps://www.frontiersin.org/articles/10.3389/fmicb.2019.01219/full

Tau GSTs involved in regulation of leaf abscission by comparison the gene profiling of Me GSTs in various abscission-promoting...Tau GSTs involved in regulation of leaf abscission by comparison the gene profiling of Me GSTs in various abscission-promoting...

The motif lengths with 11 and 50 amino acids long were confirmed by MEME analysis (Fig. 2; Additional file 3: Figure S1). In ... The amino acid motifs and phylogenetic analyses indicated that MeGSTs were divided into 9 classes. The global expression ... Further, the phylogenetic tree and amino acid motifs prediction and analysis were carried out. A globe microarray analysis was ... the TCHQD GST genes have motifs 1, 4, and 6; the GHR GST genes have motifs 4 and 6; the EF1Bγ GST genes have motifs 1, 4, 9, 10 ...
more infohttps://link.springer.com/article/10.1186%2Fs12863-018-0627-6
  • 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)
  • motifs d'acides aminés (fr) Three-dimensional protein structural elements that are composed of a combination of secondary structures. (wikimedia.org)
  • Not only their ARM domains resemble each other in both architecture and ligand binding capacity, but the N-terminal β-TrCP-binding motif is also conserved in plakoglobin, implying common ancestry and shared regulation with β-catenin. (wikipedia.org)