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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Kunes S, Chu T, Chiu M, Zhang E. A C-terminal motif targets hedgehog to axons, coordinating assembly of the Drosophila eye and brain. Developmental Cell [Internet]. 2006;10 (5) :635-46.
Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes ,1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a Bar Code format, ...
The purpose of this study was to investigate the blood stage of the malaria causing parasite, Plasmodium falciparum, to predict potential protein interactions between the parasite merozoite and the host erythrocyte and design peptides that could interrupt these predicted interactions. We screened the P. falciparum and human proteomes for computationally predicted short linear motifs (SLiMs) in cytoplasmic portions of transmembrane proteins that could play roles in the invasion of the erythrocyte by the merozoite, an essential step in malarial pathogenesis. We tested thirteen peptides predicted to contain SLiMs, twelve of them palmitoylated to enhance membrane targeting, and found three that blocked parasite growth in culture by inhibiting the initiation of new infections in erythrocytes. Scrambled peptides for two of the most promising peptides suggested that their activity may be reflective of amino acid properties, in particular, positive charge. However, one peptide showed effects which were ...
Many important interactions of proteins are facilitated by short, linear motifs (SLiMs) within a proteins primary sequence. Our aim was to establish robust methods for discovering putative functional motifs. The strongest evidence for such motifs is obtained when the same motifs occur in unrelated proteins, evolving by convergence. In practise, searches for such motifs are often swamped by motifs shared in related proteins that are identical by descent. Prediction of motifs among sets of biologically related proteins, including those both with and without detectable similarity, were made using the TEIRESIAS algorithm. The number of motif occurrences arising through common evolutionary descent were normalized based on treatment of BLAST local alignments. Motifs were ranked according to a score derived from the product of the normalized number of occurrences and the information content. The method was shown to significantly outperform methods that do not discount evolutionary relatedness, when ...
1] Tompa P (2011) Unstructural biology coming of age. Curr Opin Struct Biol 21: 419; [2] Babu MM et al. (2011) Intrinsically disordered proteins: regulation and disease. Curr Opin Struct Biol 21:432; [3] Diella F et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13:6580; [4] Davey NE et al. (2012) Attributes of short linear motifs. Mol Biosyst 8:268; [5] Davey NE, Trave G & Gibson TJ (2011) How viruses hijack cell regulation. Trends Biochem Sci 36:159; [6] Davey NE, Edwards RJ & Shields DC (2010) Computational identification and analysis of protein short linear motifs. Front Biosci 15:801; [7] Davey NE, Shields DC & Edwards RJ (2006): SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res. 34:3546; [8] Edwards RJ, Davey NE & Shields DC (2007): SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2:e967; ...
Shop Leucine-rich PPR motif-containing protein ELISA Kit, Recombinant Protein and Leucine-rich PPR motif-containing protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of pathway knowledge.
Many important regulatory interactions are mediated by short linear motif sequences, which are often embedded in disordered protein regions. These interactions tend to be transient, and therefore pose special experimental challenges. In order to develop precise tools for the manipulation and study of such interactions, accurate structural models are needed. However, due to weak binding affinity and the considerable flexibility of the peptide, structural modeling of peptide-mediated interactions presents a considerable challenge. In my talk I will present an overview of our research on peptide-mediated interactions. I will describe Rosetta FlexPepDock, the suite of protocols that we have developed, and applied, for the structure-based characterization and manipulation of peptide-mediated interactions. FlexPepDock is guided by observations of peptide binding strategies revealed from solved complex crystal structures. Efficient but focused sampling strategies have opened the way to model these ...
so sum1tar is basically summary 1 of the target motifs, those are the motifs i got from the motifenrichment analysis on my sequences using the motifenrich function inside the PWMenrich package. So i use scanWithPWM to get the highest score and i am not sure if the highest one represents the optimal position?. So after i have got the position , i hope to plot the sequence with the motif on top of the sequence somehow, i have tried using substring from the biostring package but only able to plot the sequences. So second question is about plotting the motif or highlighting the motif detected with the sequence. after we have detected the motifs, would there be any ways that i could highlight the motifs ? because so far i am only able to make a ranking table in the in the window and highlight the rough position just like the one in the manual. However i would like to see every single base pair with highlighted motifs in the sequence. The third quesiton is about pairwise alignment and motif anlysis, ...
We have extracted an extensive collection of recurrent structural motifs (RSMs), which consist of sequentially non-contiguous structural motifs (4-6 residues), each of which appears with very similar conformation in three or more mutually unrelated protein structures. We find that the proteins in our set are covered to a substantial extent by the recurrent non-contiguous structural motifs, especially the helix and strand regions. Computational alanine scanning calculations indicate that the average folding free energy changes upon alanine mutation for most types of non-alanine residues are higher for amino acids that are present in recurrent structural motifs than for amino acids that are not. The non-alanine amino acids that are most common in the recurrent structural motifs, i.e., phenylalanine, isoleucine, leucine, valine and tyrosine and the less abundant methionine and tryptophan, have the largest folding free energy changes. This indicates that the recurrent structural motifs, as we define them,
The eukaryotic linear motif (ELM resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). For |10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear mot …
BACKGROUND: Large datasets of protein interactions provide a rich resource for the discovery of Short Linear Motifs (SLiMs) that recur in unrelated proteins. However, existing methods for estimating the probability of motif recurrence may be biased by the size and composition of the search dataset, such that p-value estimates from different datasets, or from motifs containing different numbers of non-wildcard positions, are not strictly comparable. Here, we develop more exact methods and explore the potential biases of computationally efficient approximations.. RESULTS: A widely used heuristic for the calculation of motif over-representation approximates motif probability by assuming that all proteins have the same length and composition. We introduce pv, which calculates the probability exactly. Secondly, the recently introduced SLiMFinder statistic Sig, accounts for multiple testing (across all possible motifs) in motif discovery. However, it approximates the probability of all other possible ...
The motivating idea behind most discussions on motifs is the possibility of capturing the essential logic of genetic regulation by a small set of interaction circuits performing some specific functional tasks. While this hypothesis is, in principle, experimentally testable, experimental and theoretical work has hitherto considered essentially motifs in isolation, that is, excised from the biological environment in which the motifs instances are embedded.. We studied in detail the role of motifs in the case of the best-documented genetic sub-networks and biological functions where such motifs are found. In most cases, motifs do not seem to have a central regulatory role in the biological processes associated with each occurrence. The list of examples where enough biological information is available is, of course, limited, and further examples may subvert this picture. At the moment, it is a fact that all the examples studied highlight the high level of integration of different regulatory ...
This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, namely a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. [provided by RefSeq, Jul 2008 ...
Inspired by the main element role of super-helical motifs in molecular self-organization, several tandem heptad repeat peptides were used as building blocks to form well-ordered supramolecular nano-assemblies. structures at the nanoscale5,6,7. However, the formation of assemblies by such short peptides is limited mainly to -sheet business of the peptide motifs in the formed nanostructures8,9,10,11. While these assemblies offers remarkable mechanical, optical, piezolelctric and semiconductive proprieties, they lack the precise orientation of amino-acid residues needed for directed intermolecular business and specific interactions with target molecules such as DNA or other biopolymers12,13. Indeed, in many biological systems, the recognition of DNA is usually facilitated by ordered super-helical structural motifs14,15,16. This super-helical business commonly comprised of two or more Tegobuvir individual -helices that interact with each other via hydrophobic facets present in protein surfaces and ...
mouse Slo2 protein: a type of sodium-activated K+ channel, possess a typical PDZ binding motif at the carboxy-terminal end; NP_780671
This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly. In full display mode, each motif occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the + strand is shown.. The track may be configured to search for any short sequence of 2 - 30 bases in length. Sequences may include IUPAC ambiguity codes. To change the motif, open the tracks description page (by clicking the track control label or the mini-button to the left of the track), then type a new sequence into the text box.. To see how to create a bed file of the short match data see this mailing list question here.. ...
This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly. In full display mode, each motif occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the + strand is shown.. The track may be configured to search for any short sequence of 2 - 30 bases in length. Sequences may include IUPAC ambiguity codes. To change the motif, open the tracks description page (by clicking the track control label or the mini-button to the left of the track), then type a new sequence into the text box.. To see how to create a bed file of the short match data see this mailing list question here.. ...
This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly. In full display mode, each motif occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the + strand is shown.. The track may be configured to search for any short sequence of 2 - 30 bases in length. Sequences may include IUPAC ambiguity codes. To change the motif, open the tracks description page (by clicking the track control label or the mini-button to the left of the track), then type a new sequence into the text box.. ...
6 K in this function is the background entropy corrected for sample size, approximately 2 for E. coli (4), as was calculated in the example above. The frequencies, fi, are determined as in the example above from the aligned sequences of the prototype group for the given motif; the relative frequencies for the occurrence of each of the four bases are determined separately for each position of the motif. Fopt is the frequency found for the consensus base at a given position, and fobs is the frequency at which the base in the sequence of interest is found to occur in the same position of the prototype group.. A computer program was written that takes sequence as input, evaluates this function at each position within a window corresponding to the size of the motif of interest by using the prototype groups frequencies, divides the range of resultant index values into six qualitative levels from very good to very bad (attempts with 10 levels yielded no better performance), and codes the result in ...
Residues within a conserved amino acid motif of domains 1 and 4 of VCAM-1 are required for binding to VLA-4.. Journal of Cell Biology. 125:215-222. 1994 ...
View mouse Trim21 Chr7:102557921-102565486 with: phenotypes, sequences, polymorphisms, proteins, references, function, expression
View mouse Trim33 Chr3:103279293-103358775 with: phenotypes, sequences, polymorphisms, proteins, references, function, expression
Feature map marking the locations of 4G-, 3G- and 2G-containing motif occurrences in the G-rich motif group identified in the upstream regions of the organellar
For three decades, sequence logos are the de facto standard for the visualization of sequence motifs in biology and bioinformatics. Reasons for this success story are their simplicity and clarity. The number of inferred and published motifs grows with the number of data sets and motif extraction algorithms. Hence, it becomes more and more important to perceive differences between motifs. However, motif differences are hard to detect from individual sequence logos in case of multiple motifs for one transcription factor, highly similar binding motifs of different transcription factors, or multiple motifs for one protein domain. Here, we present DiffLogo, a freely available, extensible, and user-friendly R package for visualizing motif differences. DiffLogo is capable of showing differences between DNA motifs as well as protein motifs in a pair-wise manner resulting in publication-ready figures. In case of more than two motifs, DiffLogo is capable of visualizing pair-wise differences in a tabular form.
Batten disease is a neurodegenerative disorder resulting from mutations in CLN3, a polytopic membrane protein, whose predominant intracellular destination in nonneuronal cells is the lysosome. The topology of CLN3 protein, its lysosomal targeting mechanism, and the development of Batten disease are poorly understood. We provide experimental evidence that both the N and C termini and one large loop domain of CLN3 face the cytoplasm. We have identified two lysosomal targeting motifs that mediate the sorting of CLN3 in transfected nonneuronal and neuronal cells: an unconventional motif in the long C-terminal cytosolic tail consisting of a methionine and a glycine separated by nine amino acids [M(X)9G], and a more conventional dileucine motif, located in the large cytosolic loop domain and preceded by an acidic patch. Each motif on its own was sufficient to mediate lysosomal targeting, but optimal efficiency required both. Interestingly, in primary neurons, CLN3 was prominently seen both in ...
In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which also appears in a variety of other molecules. Motifs do not allow us to predict the biological functions: they are found in proteins and enzymes with dissimilar functions. Because the relationship between primary structure and tertiary structure is not straightforward, two biopolymers may share the same motif yet lack appreciable primary structure similarity. In other words, a structural motif does not have to be associated with a sequence motif. Also, the existence of a sequence motif does not necessarily imply a distinctive structure. In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal double helical structure. ...
The chromo domain was originally identified as a protein sequence motif common to the Drosophila chromatin proteins, Polycomb (Pc) and heterochromatin protein 1 [HP1; Paro and Hogness (1991) Proc. Natl. Acad. Sci. USA, 88, 263-267; Paro (1990) Trends Genet., 6, 416-421]. Here we describe a second chromo domain-like motif in HP1. Subsequent refined searches identified further examples of this chromo domain variant which all occur in proteins that also have an N-terminally located chromo domain. Due to its relatedness to the chromo domain, and its occurrence in proteins that also have a classical chromo domain, we call the variant the chromo shadow domain. Chromo domain-containing proteins can therefore be divided into two classes depending on the presence, for example in HP1, or absence, for example in Pc, of the chromo shadow domain. We have also found examples of proteins which have two classical chromo domains. The Schizosaccharomyces pombe SWI6 protein, involved in repression of the silent ...
Red Hat Motif 2.1 for Linux Intel-compatible computers is the full OSF/Motif development system. As with previous versions of Red Hat Motif, Red Hat Motif 2.1 will enable you to use your Intel-compatible PC computer running Linux as a UNIX(r) Motif based workstation.For developers, Motif 2.1 makes creation of software applications and custom widgets simple. The many toolkit enhancements, new widgets, and UIL improvements allow you to port Motif-based applications easily across a variety of platforms.For end users, Red Hat Motif 2.1 improves the interface performance of their Motif-based applications. The virtual screen support unclutters their workspace by providing alternate locations for chosen windows, while providing greater consistency with PC environments.Red Hat Motif 2.1 New Features: Thread safe libraries Widget printing support Internationalization enhancements for vertical text, on-the-spot input and user defined characters for Asian languages See Red Hat Motif 2.1 Intel on the Store Page
Coronaviruses, including SARS-CoV-2, are proposed to use either the endocytic or non-endosomal pathway for cell entry (46). Our study provides biophysical evidence for the functionality of SLiMs in the cytoplasmic tails of ACE2 and integrin β3, which provide possible molecular links between the established (ACE2) and putative (integrin beta3) SARS-CoV-2 receptors and mediators of endocytosis and autophagy. Our finding that an endocytic AP2 μ2 binding motif exists in the ACE2 C-terminus and that such binding is negatively regulated by Tyr781 phosphorylation supports the possibility of clathrin-dependent endocytosis of SARS-CoV-2 upon receptor binding. It will, of course, be necessary to assess the biological relevance of the ACE2-AP2 μ2 interaction, particularly in light of its low affinity. Concerning the latter, we note that while affinities of AP2 core complexes for endocytic sorting signals are reported in the nanomolar range, measured KD values of the AP2 μ2 subunit alone vary between 10 ...
Sorry about my previous reply. The question was for DNA sequence motifs and my answer was for protein sequence motifs. The TFD database has several DNA sequence motifs found in yeast, however it is a Transcription Factor Database and would lack some of the types of sequence motifs that the original message was requesting. TFD is available as flat files, in a variety of formats, via anonymous ftp from look in the repository/TFD directory. TFD is the creation of D. Ghosh, NCBI. Mike ...
Previous studies have identified a number of mutants and/or motifs that affect ASIC channel trafficking and/or function [28-34]. Most of these studies focused on ASIC1a. Our results demonstrated that the LL motifs in ASIC2a are important for its trafficking and function. All the mutants that we studied here had increased surface level (Fig. 1). However, only the DAA mutant exhibited a significant increase in surface:total ratio while the AADAA mutant had a marginal effect (p = 0.049). These data, together with our current recordings, indicate that most of the effect on ASIC2a surface trafficking and channel function was mainly mediated by the second LL motif. We speculate that the exact location of the LL motif may contribute to the differences observed between mutating the two LL motifs. It remains unclear as to the exact mechanism of how the LL motifs regulate ASIC2a. Our data here showed that the AADAA and DAA mutants increased the maturation of N-linked glycans. N-glycosylation is an ...
TY - JOUR. T1 - Extracting Best Consensus Motifs from Positive and Negative Examples. AU - Tateishi, Erika. AU - Maruyama, Osamu. AU - Miyano, Satoru. PY - 1995/10/27. Y1 - 1995/10/27. N2 - We define the best consensus motif (BCM) problem motivated by the problem of extracting motifs from nucleic acid and amino acid sequences. A type over an alphabetΣ is a familyΩ of subsets of Σ. A motif π of type Ω is a stringπ=π_1…π_n of motif components, each of which stands for an element in Ω. The BCM problem for Ω is, given a yes-no sample S={(α^,(1),, β^,(1),),...,(α^,(m),, β^,(m),)} of pairs of strings inΣ with α^,(i),≠β^,(i), for 1≤i≤m, to find a motif π of type Ω that maximizes the number of good pairs in S, where (α^,(i),,β^,(i),) is good forπ if π accepts α^,(i), and rejects β^,(i),. We prove that the BCM problem is NP-complete even for a very simple type Ω_1={z,φ≠z⊆Σ}, which is used, in practice, for describing protein motifs in the PROSITE database. We also ...
Shop RNA-binding motif protein ELISA Kit, Recombinant Protein and RNA-binding motif protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
The cell-extrinsic apoptotic pathway triggers programmed cell death in response to certain ligands that bind to cell-surface death receptors. Apoptosis is essential for normal development and homeostasis in metazoans, and furthermore, selective activation of the cell-extrinsic pathway in tumor cells holds considerable promise for cancer therapy. We used phage display to identify peptides and synthetic antibodies that specifically bind to the human proapoptotic death receptor DR5. Despite great differences in overall size and structure, the DR5-binding peptides and antibodies shared a tripeptide motif, which was conserved within a disulfide-constrained loop of the peptides and the third complementarity determining region of the antibody heavy chains. The X-ray crystal structure of an antibody in complex with DR5 revealed that the tripeptide motif is buried at the core of the interface, confirming its central role in antigen recognition. We found that certain peptides and antibodies exhibited ...
One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of related data elements. With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation. Herein, we present a structured syntax of minimotifs and their functional annotation. A syntax-based model of minimotif function with established
C. elegans NAB-1 protein; contains similarity to Pfam domains PF07647 (SAM domain (Sterile alpha motif)), PF00595 (PDZ domain (Also known as DHR or GLGF)), PF00536 (SAM domain (Sterile alpha motif))contains similarity to Interpro domains IPR001660 (Sterile alpha motif SAM), IPR001478 (PDZ/DHR/GLGF ...
Activity of SRs is not only regulated by ligand binding but also by interacting cofactors. The best-described binding site for SR coregulators is the hydrophobic cleft in the LBD to which LxxLL motifs can bind. The AR LBD is unique in its preference for the interaction with cofactors carrying FxxLF motifs rather than LxxLL motifs (Dubbink et al., 2004; Hur et al., 2004). The AR itself also contains an FQNLF motif in the N-terminal domain, enabling interaction with the LBD (N/C interaction; Doesburg et al., 1997; He et al., 2000). The potential competition between the AR N-terminal FQNLF motif and similar motifs in cofactors for interaction with the LBD raises questions regarding the role of the N/C interaction in orchestrating cofactor interactions. To study AR N/C interactions in living cells, we tagged the AR at the N and C termini with YFP and CFP, respectively, or with CFP alone, and applied FRET and simultaneous FRET and FRAP experiments. In addition, to investigate cofactor interactions, ...
Background Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions. Methodology/Principal Findings Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have a related cellular or molecular function, the prediction is more likely to be accurate. This filter was implemented in Minimotif Miner using function annotations from the Gene Ontology. We have also combined two filters that are based on entirely different principles and this combined filter has a better
Offers an approach for motif discovery based on a Bayesian approach. BAMM!motif is an application that exploits Bayesian Markov Models (BaMMs) to perform its predictions. It consists of four distinct modules allowing users to: (i) investigate nucleotide sequence to determine high-order motifs; (ii) explore model repositories with a feature for searching given motifs against a pre-computed database; and (iii) detect motifs occurrences from sequences.
PTMs (posttranslational modifications) such as ubiquitylation, sumoylation, acetylation and protein methylation are pivotal modifiers that determine the activation, deactivation or subcellular localization of signaling proteins, facilitating the initiation, amplification and transduction of signaling. Accumulating evidence suggest that several key signaling molecules in Hippo signaling pathway are tightly regulated by various types of PTMs. Malfunction of these critical signaling modules such as YAP/TAZ, MAT1/2 and LATS1/2 due to deregulated PTMs has been linked to a variety of human diseases such as cancer. In this review article, we summarized the current understanding of the impact of PTMs in regulating Hippo signaling pathway and further discussed the potential therapeutic intervention from the view of PTMs and Hippo pathway.
May play a role in the process of differentiation and maturation of neuronal cells (By similarity). May regulate the activity of TRIM17 (By similarity). Is a negative regulator of PAX6 expression (By similarity).
Bacterial surfaces are complex, built of from membranes, peptide-glycans and, importantly, proteins. The proteins play crucial roles as the key regulator of how the bacterium interacts with its environment. A full catalog of the motifs in coiled-coil proteins and their relative conservation grade is a pre-requisite to target the protein-protein interaction that bacterial surface protein makes to host proteins. Here, we present a greedy approach to iteratively identify conserved motifs in large sequence collections, identify all occurrences of these motifs and mask them. Remaining unmasked sequences are subjected to the second round of motif detection until no more significant motifs can be found or all protein segments have been assigned to a motif. We present the results for the S. pyogenes M protein. Given the speed and flexibility of our approach, we believe it will be useful in breaking analyzing surface protein of pathogens as these proteins are under high selective pressure and therefore cannot be
This gene was identified by involvement in some t(X;14) translocations associated with mature T-cell proliferations. This region has a complex gene structure, with a common promoter and 5 exon spliced to two different sets of 3 exons that encode two different proteins. This gene represents the downstream 8 kDa protein that localizes to mitochondria.[provided by RefSeq, Mar 2009 ...
Ret finger proteinRING finger protein 76, RFPtripartite motif protein TRIM27, RNF76RFP transforming protein, Tripartite motif-containing protein 27, tripartite motif-containing 27, tripartite motif containing 27, zinc finger protein ...
Accuracy. If you search with a simple motif, you can adjust the accuracy of the motif to the match on the sequence. If you type in a simple motif and let the accuracy be 80%, the motif search algorithm runs through the input sequence and finds all subsequences of the same length as the simple motif such that the fraction of identity between the subsequence and the simple motif is at least 80%. A motif match is added to the sequence as an annotation with the exact fraction of identity between the subsequence and the simple motif. If you use a list of motifs, the accuracy applies only to the simple motifs in the list ...
One focus of our research is to further our understanding of the physico-chemical properties of non-canonical nucleic acid structures. In this work, DNA hairpins are used to mimic a common motif present in RNA, i.e., a stem-loop motif with a bulge or inte
Ji, H. H., & Ostap, E. M. (2020). The regulatory protein 14-3-3β binds to the IQ motifs of myosin-IC independent of phosphorylation. Journal of Biological Chemistry, 295(12), 3749-3756. ...
C. elegans ETR-1 protein; contains similarity to Pfam domain PF00076 (RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain))contains similarity to Interpro domains IPR012677 (Nucleotide-binding, alpha-beta plait), IPR000504 (RNA-binding region RNP-1 (RNA recognition motif ...
We use cookies to ensure that we give you the best experience on our website. If you click Continue well assume that you are happy to receive all cookies and you wont see this message again. Click Find out more for information on how to change your cookie settings ...
Active Motif, Inc. is a privately held biotechnology company focused on supplying innovative kits and reagents for epigenetics and nuclear function research. We are always looking for highly motivated individuals to join our team.
TRIM37 (tripartite motif-containing 37), Authors: Elif Ayse Erson,.M Elizabeth Petty. Published in: Atlas Genet Cytogenet Oncol Haematol.
Evidence 3: Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr: putative ...
Evidence 3: Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt: putative ...
UHMK1 (U2AF homology motif kinase 1), Authors: Vanessa Cristina Arfelli, Leticia Fröhlich Archangelo. Published in: Atlas Genet Cytogenet Oncol Haematol.
Active Motif offers a variety of ChIP Accessory Products that make it even easier to perform successful ChIP when working with our ChIP-IT Express Kitsand our Specialized ChIP-IT Kits.
Active Motif offers research kits, assays and biocomputing systems that help researchers study the function, regulation and interactions between genes, proteins and metabolic pathways.
Active Motif offers research kits, assays and biocomputing systems that help researchers study the function, regulation and interactions between genes, proteins and metabolic pathways.
Motif Bio Plc (LON:MTFB) CEO Dr Graham Lumsden talks to DirectorsTalk about the dosing of the first patient in the iclaprim Phase 3 trials to treat skin in
Fine materials and design for this Skirt With Jacquard Plaid Motif by Emporio Armani Women. Take a look at the official online boutique now.
Az első luxus parfüméria - művészi parfümök, tiszta bőrápolás, smink, úri borotválkozás, királyi hajkefe és fogkefe, enteriőrillatosítás
v t e (Amino acids, Amino acid motifs, All stub articles, Molecular biology stubs). ... any amino acid X- any amino acid ER retention KDEL (amino acid sequence) COPI Signal peptide Protein targeting Martin J. ... KKXX and for some proteins XKXX is a target peptide motif located in the C terminus in the amino acid structure of a protein ... The abbreviation KKXX is formed by the corresponding standard abbreviations for lysine (K) and any amino acid (X). This letter ...
Articles with short description, Short description matches Wikidata, Amino acids, Amino acid motifs, Peptide sequences). ... H-Histidine D-Aspartic acid E-Glutamic acid L-Leucine Three letter code is: His-Asp-Glu-Leu. ER retention KKXX (amino acid ... KDEL is a target peptide sequence in mammals and plants located on the C-terminal end of the amino acid structure of a protein ... The abbreviation KDEL is formed by the corresponding letters to each amino acid. This letter system was defined by the IUPAC ...
v t e (Protein pages needing a picture, Amino acid motifs, All stub articles, Molecular biology stubs). ... The pentatricopeptide repeat (PPR) is a 35-amino acid sequence motif. Pentatricopeptide-repeat-containing proteins are a family ... They are distinguished by the presence of tandem degenerate PPR motifs and by the relative lack of introns in the genes coding ...
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) ...
The last three amino acids of the CaaX motif are removed later. There are four binding pockets in FTase, which accommodate the ... is an aliphatic amino acid, and 'X' is variable). The carboxyl-terminal amino acid (X) discriminates FTase's targets from those ... last four amino acids on the carboxyl-terminus of a protein. Only those with a suitable CaaX motif can bind ('C' is Cysteine, ' ... Farnesyltransferase (FTase) adds a 15-carbon isoprenoid called a farnesyl group to proteins bearing a CaaX motif: a four-amino ...
The WH2 domain is an ~18-21 amino acids actin-binding motif. This domain was first recognized as an essential element for the ... The human COBL gene encodes a 1261-amino acid protein with a mass of about 136 kDa. The mouse protein is 1337 amino acids long ... Cobl Homology domains contain three motifs following the consensus KrRAPpPP (first described as "KRAP" motif of unknown ... The WH2 motif in WASp recruits ATP-G-actin that binds to either Arp2 or Arp3 to complete the formation of a trimeric actin ...
It has a motif domain between the amino acids 35 and 43. Due to the alternative splicing, two isoforms of this same protein ... Isoform 2 consists just of 151 amino acids, having a mass of 16,667 Da. Small GTPases of the RAB superfamily are recognized as ... Even though these RAB family proteins are highly homologous to each other (RAB2A and RAB2B have 85.8% amino acid identity), the ...
Peifer M, Berg S, Reynolds AB (1994). "A repeating amino acid motif shared by proteins with diverse cellular roles". Cell. 76 ( ... Eukaryotic Linear Motif resource motif class TRG_NLS_Bipartite_1 Eukaryotic Linear Motif resource motif class TRG_NLS_MonoCore_ ... 2 Eukaryotic Linear Motif resource motif class TRG_NLS_MonoExtC_3 Eukaryotic Linear Motif resource motif class TRG_NLS_MonoExtN ... An armadillo repeat is the name of a characteristic, repetitive amino acid sequence of about 40 residues in length that is ...
Members of this enzyme family typically share two conserved amino acid motifs. The first motif, or string of consecutive amino ... The second conserved motif is DFGWG (Aspartic acid, Phenylalanine, Glycine, Tryptophan, Glycine) and it is typically found near ... Phylogenetic analysis using full-length amino acid sequences of functionally characterized BAHD enzymes by D'Auria (2006) and ... Aspartic acid) and it is typically found in the central region of the protein. The Histidine in this motif has also been shown ...
SMG stands for the conserved amino acid motif of Ser-Met-Gly. Upon closure, these residues interact with L-ornithine. The ... Orotic acid is a product of this pathway. Increased levels of orotic acid in urine can be an indicator that a patient is ... Postranscriptional modification leaves the mature peptide with 322 amino acids and a weight of 36.1 kD. The protein is located ... Anabolic OTC facilitates the sixth step in the biosynthesis of the amino acid arginine in prokaryotes. In contrast, mammalian ...
For example, RNP in snRNPs have an RNA-binding motif in its RNA-binding protein. Aromatic amino acid residues in this motif ... they provide a rough model of the structure which allows for predictions of the identity of significant amino acids and ... This nucleic acid binding is strengthened by electrostatic attraction between the positive lysine side chains and the negative ... Lysine residues in the helical portion of RNA-binding proteins help to stabilize interactions with nucleic acids. ...
UBA domains have a common sequence motif of approximately 45 amino acid residues. They fold into three-helix bundle structures ... Hofmann K, Bucher P (May 1996). "The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination ...
There is also a predicted sumoylation motif from amino acid 212 to 221. C19orf44 is predicted to be localized in the nucleus or ... The amino acid sequence for C19orf44 was found to be serine rich using tools on EMBL-EBI. Additionally, there is a domain of ... It contains 10 exons that code for a 657 amino acid protein. There are 7 splice variants that exist for C19orf44. C19orf44 is ... located from amino acid 474 to 641. C19orf44 has experimentally determined phosphorylation sites at the S114 and S213 positions ...
These proteins have either an EAL or an HD-GYP amino acid motif. Processes that are known to be regulated by cyclic di-GMP, at ... These proteins typically have a characteristic GGDEF motif, which refers to a conserved sequence of five amino acids. ... 1987). "Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid". Nature. 325 (6101): 279-281. doi: ...
This protein contains a conserved 120 amino acid motif called the RGS domain. The protein attenuates the signaling activity of ...
Calmodulin contains 148 amino acids and has 4 calcium-binding EF hand motifs. Its functions include roles in growth and the ... Li Z, Sacks DB (Feb 2003). "Elucidation of the interaction of calmodulin with the IQ motifs of IQGAP1". J. Biol. Chem. 278 (6 ...
It contains a divalent cation tolerance protein CutA motif from amino acids 57-88. No transmembrane domains or N-terminal ... Chemically significant amino acid changes in conserved regions of the c4orf36 protein were found with NCBI SNPGeneView. GRCh38 ... C4orf36 encodes a 117 amino acid protein with a molecular weight of 13.28 kDa and an isoelectric point of 9.54. ... "GenomeNet MOTIF Search". GenomeNet. Archived from the original on 2011-08-17. "PSORTII Prediction". PSORTII. Archived from the ...
This recruitment takes place via a 4 amino acid motif in the Ste5 phosphosites. Ptc1 is also involved in regulating the osmotic ...
A coronavirus cleavage site is predicted at the 235 amino acid position. There are also tyrosine motif locations between amino ... The full C16orf46 protein is 417 amino acids long. It has no isoforms, and its most distant ortholog, Rhincodon typus (whale ... acids 42-45 and 251-252. mRNA folding on the 5' UTR predicts a stem loop twice in the area between base pairs 47-90. C16orf46 ...
The amino acid sequence of Cl6a contains the NaSpTx family 1 motif KHKWCK. Cl6a highly resembles a similar sequence with other ... Toxins of NaSpTx family 1 are characterized by containing the following motif present in the amino acid sequence of the toxins ... For instance, the amino acid sequence of Cl6a shows 67% sequence similarity with Hainantoxin (HNTX) III and 97% with huwentoxin ... Cl6a is a 33 amino acid residue peptide toxin with a molecular weight of 3775.6 Dalton. Its molecular structure encompasses six ...
... identification of amino acid sequence motifs governing subunit stoichiometry". Neuron. 11 (6): 1049-56. doi:10.1016/0896-6273( ... The receptor can be activated by a range of simple amino acids including glycine, β-alanine and taurine, and can be selectively ... The glycine receptor (abbreviated as GlyR or GLR) is the receptor of the amino acid neurotransmitter glycine. GlyR is an ...
DUF 4587 is usually between 64 and 79 amino acids long and contains the two sequence motifs QNAQ and HHH. PRR29 is predicted to ... It contains one proline-rich region motif that extends from amino acid 39 to 107. The secondary structure is characterized by ... Its name is derived from the chain of 5 proline amino acids located toward the end of the protein. The primary domain within ... PRR29 contains a proline rich region within its sequence from amino acids 73 to 166. A domain of unknown function, DUF 4587, is ...
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 ...
These amino acids form the DDE motif that coordinate divalent metal ions (Mg2+ or Mn2+). These metal ions are essential for the ... A loop containing amino acid residues 140-149 is located in the catalytic-core domain and is important for IN function as ... 2. The catalytic core domain (CCD), which encompasses amino acids 51- 212, contains the active site of IN but it can't catalyze ... 3. The C-terminal domain (CTD), which encompasses amino acids 213-288, binds DNA nonspecifically and its interaction with NTD ...
The Sac1 phosphatase domain encompasses approximately 400 amino acids and consists of seven conserved motifs. It harbors the ... In humans, the FIG4 gene localizes on chromosome 6 and encodes a Sac3 protein of 907 amino acids. Sac3 is characterized as a ...
As predicted amino acids in the conserved WRKYGQK signature motif contact the W-box DNA. WRKY Transcription Factor Family at ... The W box is a deoxyribonucleic acid (DNA) cis-regulatory element sequence, (T)TGAC(C/T), which is recognized by the family of ... Nucleic Acids Research. 41 (21): 9764-9778. doi:10.1093/nar/gkt732. PMC 3834811. PMID 23975197. Yamasaki, K.; Kigawa T; ...
This motif is composed of four amino acids at the end of the protein sequence. The most common retention sequences are KDEL for ... The N-terminus (one end) of a polypeptide chain (i.e., a protein) contains a few amino acids that work as an address tag, which ... The first 5-30 amino acids polymerized encode a signal peptide, a molecular message that is recognized and bound by a signal ... either secreted constitutively with no tag or secreted in a regulatory manner involving clathrin and paired basic amino acids ...
Bernad A, Blanco L, Salas M (September 1990). "Site-directed mutagenesis of the YCDTDS amino acid motif of the phi 29 DNA ... Involvement of two amino acid residues highly conserved in proofreading DNA polymerases". EMBO J. 15 (5): 1182-92. doi:10.1002/ ... His61 and Phe69 of the highly conserved ExoII motif are essential for interaction with the terminal protein". Nucleic Acids Res ... Truniger V, Blanco L, Salas M (1999). "Role of the "YxGG/A" motif of Phi29 DNA polymerase in protein-primed replication". J Mol ...
The putative 622-amino acid protein has a leucine-zipper motif at its N-terminus. Fanconi anemia is an autosomal recessive ... Blom E, van de Vrugt HJ, de Vries Y, de Winter JP, Arwert F, Joenje H (January 2004). "Multiple TPR motifs characterize the ...
... whose members have certain conserved motifs in their extracellular amino-acid domain. The IL-2 receptor belongs to this chain, ...
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. ...
In SARS-CoV, the causative agent of SARS, the N protein is 422 amino acid residues long and in SARS-CoV-2, the causative agent ... Parts of the IDR, particularly a conserved sequence motif rich in serine and arginine residues (the SR-rich region), may also ...
... denotes any amino acid except for those in the string. For example, {ST} denotes any amino acid other than S or T. If a pattern ... signifies a single amino acid or a gap, and each * indicates one member of a closely related family of amino acids. The authors ... each denoting a specific amino acid or a set of amino acids; a string of characters drawn from the alphabet denotes a sequence ... In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be ...
2800 amino acids. Teneurins are highly conserved within and between species. The primary structure, or amino acid sequence ... two EF-hand-like motifs near the centre, and a number of conserved tyrosine phosphorylation sites. The proline-rich stretches ... There are 41 amino acids in TCAPs, except for TCAP-3 from Ten-m3, which has 40. TCAPs show structural homology to the CRF ... The linker region is made up of ~200 amino acid residues and is found immediately distal to the transmembrane domain. This is ...
GFP's fluorophore is made up of three cyclized amino acids within the beta-barrel structure: Serine65-Tyrosine66-Glycine67. ... Spinach is an 84-nucleotide-long structure with two helical strands and an internal bulge with a G-quadruplex motif. It is at ...
... identification of a repeated basic amino acid motif within the C-terminal binding region". Journal of Virology. 66 (9): 5347-56 ... amino acid analysis and amino terminal amino acid sequence". Science. 207 (4430): 525-6. Bibcode:1980Sci...207..525K. doi: ... Bruce Merrifield, using solid phase peptide synthesis, one amino acid at a time. He later won the Nobel Prize in chemistry. ... Tan YH, Barakat F, Berthold W, Smith-Johannsen H, Tan C (August 1979). "The isolation and amino acid/sugar composition of human ...
Some examples also contain stretches of basic amino acids, or stretches of aromatic amino acids thought to reside in the ... Class II viroporins possess a helix-turn-helix motif with both helices crossing the membrane; in class IIA both termini are ... Viroporins are usually small - under 100 or 120 amino acid residues - and contain at least one region capable of folding into ...
... spans 110,720 base pairs, and contains 827 amino acids. There are two isoforms of the gene transcript that exist by ... LRSAM1 is also known as leucine rich repeat and sterile alpha motif protein 1. The value for the protein is .29 and the ...
34 amino acids long) and TPR2 which spans from amino acids 626 to 659 (also 34 amino acids long). TTC39B contains three ... TPR motifs that are arranged one in front of another create a right-handed helical structure with an amphipathic channel which ... It is located from amino acid 142 until 568 (a length of 427 amino acids). Proteins of this family also contain a TPR_2 domain ... It is located from amino acid 600 until 658 (a length of 59 amino acids). The TPR domains are found in many proteins that ...
... motif with a conserved Histidine-Aspartic acid-XXY motif in the catalytic center. The following 28 species are assigned to the ... that have amino acid sequences that are at least 85% identical to those encoded by all other members of the species. Marmots ...
On the other hand, the substitution rate of mt-proteins is very low, thus amino acid changes accumulate slowly (with ... new insights into the role of non-canonical DNA structures and sequence motifs". PLOS ONE. 8 (3): e59907. Bibcode:2013PLoSO... ... Schatz G, Haslbrunner E, Tuppy H (March 1964). "Deoxyribonucleic acid associated with yeast mitochondria". Biochemical and ... Nucleic Acids Research. 47 (D1): D29-D32. doi:10.1093/nar/gky843. PMC 6324066. PMID 30247677. Gu Z, Li J, Gao S, Gong M, Wang J ...
Along with Isabella Karle, a frequent collaborator, he has also pioneered the use of alpha-amino isobutyric acid to induce and ... and has investigated structural elements playing a key role in the formation of secondary structural motifs such as helices, ...
Other mutations observed include a nonsense mutation, an in-frame deletion of amino acids and an entire gene deletion. De novo ... SON contains various domains such as the RS-rich domain, a G-patch domain and a double-stranded RNA-binding motif. The presence ... SON is a large protein consisting of 2426 amino acids and repeat sequences. SON is located within the human chromosomal region ...
Trp is an amino acid named tryptophan. The Trp ring obtains its name from the high levels of tryptophan found in the C-terminal ... The GIN domain is a head domain named after its sequence motif GIN (Glycine-Isoleucine-Asparagine) motif. It has an all-beta ... It contains sequence motifs, of which there is a strong similarity with other TAA heads. This indicates that there is a lot of ... The YadA head domain has eight repeat motifs, each fourteen residues in length. The Trp ring is the second-most-common TAA head ...
... is a 101-amino acid integral membrane protein likely with a topology such that both the N-terminus and the C-terminus ... Biochemical studies have shown that a conserved sequence motif D-Y-L-S-F at the C-terminus, as well as the overall length of ...
SNO donors target specific amino acids motifs; post-translational modification leads to changes in protein activity, protein ... The addition of a nitroso group to a sulfur atom of an amino acid residue of a protein is known as S-nitrosylation or S- ... S-Nitrosothiols may arise from condensation from nitrous acid and a thiol: RSH + HONO ⟶ RSNO + H 2 O {\displaystyle {\ce {RSH ... upon treatment with acids: RSNO + H + ⟶ RSH + NO + {\displaystyle {\ce {RSNO + H+ -> RSH + NO+}}} and they can transfer nitroso ...
Uncharacterized protein C17orf78 isoform 2 (C17orf78-203) has a span of 159 amino acids, constituted from 5 exon regions, which ... "Motif Scan". Retrieved 2020-05-21. "Human BLAT Search". Retrieved 2020-12-18. (CS1 errors: ... Uncharacterized protein C17orf78 isoform 1 (C17orf78-204) has a span of 275 amino acids, including all 7 exons. C17orf78 ... Myristolyation has been predicted to occur on C17orf78 by the ExPASy tool Motif Scan. C17orf78 orthologs have been identified ...
This approach uses protein sequence data and the chemical and physical interactions of the encoded amino acids to predict the 3 ... It has been predicted that at least 16,000 protein structures will need to be determined in order for all structural motifs to ... Highly accurate modeling is considered to require at least 50% amino acid sequence identity between the unknown protein and the ...
... which has 76 amino acid residues arranged into a "beta-grasp" protein fold consisting of a five-strand antiparallel beta sheet ... UBLs that are capable of conjugation (sometimes known as Type I) have a characteristic sequence motif consisting of one to two ... Nucleic Acids Research. 46 (D1): D447-D453. doi:10.1093/nar/gkx1041. PMC 5753239. PMID 29106644. Hochstrasser M (March 2009). " ... Nucleic Acids Research. 39 (8): 3204-23. doi:10.1093/nar/gkq1228. PMC 3082918. PMID 21169198. Hennell James R, Caceres EF, ...
MHC-β is a 223 kDa protein composed of 1935 amino acids. MHC-β is a hexameric, asymmetric motor forming the bulk of the thick ... that dimerize and multimerize into a coiled-coil motif to form the light meromyosin (LMM), thick filament rod. The 9 nm alpha- ...
Of the twenty common naturally occurring amino acids, only proline is likely to adopt the cis isomer of the peptide bond, ... Articles with short description, Short description matches Wikidata, Protein structural motifs, Helices). ... However, peptide bonds that replace proline with another N-substituted amino acid (such as sarcosine) are also likely to adopt ... This PPII conformation is also common in proteins and polypeptides with other amino acids apart from proline. Similarly, a more ...
... binds to three conserved amino acids through hydrogen bonds. These amino acids include three Aspartate residues. NAD+ and NADP+ ... due to its characteristics this ncRNA resembles previous regulatory motifs called riboswitches, icd-II ncRNA motif has been ... Isocitrate binds within the active site to a conserved sequence of about eight amino acids through hydrogen bonds. These acids ... Two aspartate amino acid residues (below left) are interacting with two adjacent water molecules (w6 and w8) in the Mn2+ ...
... glycine refers to the amino acid glycine; however, the watch company is named for the Wisteria genus of plant (fleur de Glycine ... when plant-inspired motifs and floral designs were in fashion. Fleur de Glycine was chosen due to its vining growth structure ...
... both are phosphorylation sites with locations at amino acid 210 and 224. A natural variant is found at amino acid 110 (Glutamic ... C3orf62 has a KKXX-like motif and is predicted to be localized in the nucleus. Expression of C3orf62 remains highest in whole ... C3orf62 human protein (Q6ZUJ4) is 267 amino acids long, and has a molecular mass of 30,194 Daltons. The isoelectric point of ... C3orf62 has a KKXX-like motif in the C-terminus meaning C3orf62 may be responsible for retrieval of endoplasmic reticulum (ER) ...
... including many proteins of over 2500 amino acids. A number of the members of this family have been designated adhesins, ... A bacterial adhesin formed as a 50-nm monomeric rigid rod based on a 19-residue repeat motif rich in beta strands and turns". J ... Its sequence contains two regions of tandem 19-residue repeats, where the repeat motif consists of short beta-strands separated ...
Fourthly, a six amino acid insert in the twenty-first spectrin motif with unknown function has been reported. Alpha II-spectrin ... Thirdly, an insert of five amino acids in the fifteenth spectrin motif bears a highly antigenic epitope resembling an ankyrin- ... First, a cardiac-specific, 21 amino acid sequence insert in the 21st spectrin repeat, termed alpha II-cardi+, was identified as ... Secondly, another insert of 20 amino acids in the 10th spectrin repeat, termed SH3i+, contains protein kinase A and protein ...
The DNA-Pkcs protein is a serine/threonine protein kinase comprising a single polypeptide chain of 4,128 amino acids. DNA-PKcs ... Ko L, Cardona GR, Chin WW (May 2000). "Thyroid hormone receptor-binding protein, an LXXLL motif-containing protein, functions ... Nucleic Acids Res. 27 (17): 3494-502. doi:10.1093/nar/27.17.3494. PMC 148593. PMID 10446239. ...
Szczepanek T, Lazowska J (July 1996). "Replacement of two non-adjacent amino acids in the S.cerevisiae bi2 intron-encoded RNA ... based in their shared structural motifs: H1: LAGLIDADG family - H2: GIY-YIG family - H3: H-N-H family - H4: His-Cys box family ... "Two homologous mitochondrial introns from closely related Saccharomyces species differ by only a few amino acid replacements in ... Perler FB (January 2002). "InBase: the Intein Database". Nucleic Acids Res. 30 (1): 383-4. doi:10.1093/nar/30.1.383. PMC 99080 ...
It is a protein with 148 amino acids and a molecular weight of 16 kDa that comprises four ankyrin repeats. The name of p16 is ... Serrano M, Hannon GJ, Beach D (December 1993). "A new regulatory motif in cell-cycle control causing specific inhibition of ...
The fifth ORF codes for nucleic-acid binding protein. This is the protein that helps the DNA or RNA connect with amino acids. ... The first ORF codes for a 194 kDa polypeptide with conserved motifs of replication related proteins of positive strand RNA ... Nucleic acid hybridizationis also used to detect GVA. In this method, a small sample of the infected plant is taken and then ... "Nucleic Acid Hybridization - MeSH - NCBI". Retrieved 16 November 2020. Wang, Qiaochun; Mawassi, Munir; Li ...
Amino Acid Motifs * Amino Acid Sequence * Animals * Cell Line * Female * Hepatocytes / parasitology* ... Two proteins with 6-cys motifs are required for malarial parasites to commit to infection of the hepatocyte Mol Microbiol. 2005 ...
Amino acid/motif. Phenotypic consequences. Hemagglutinin. Cleavage site motif: -RRKR¯G-. Polybasic cleavage motif sequence ...
... cNLSs are short linear motifs, rich in basic amino acids. Monopartite cNLSs are comprised of one basic cluster, typified by the ... Sequence motif analysis Is the Subject Area "Sequence motif analysis" applicable to this article? Yes. No. ... and X represents any amino acid) [39].Thus, all TNRC6A P3 and/ or P5 cavity mutants adhere to this general monopartite ... motifs (termed GW repeats) that are located throughout the length of the protein (Fig 1A); while the N-terminal GW motifs ...
Amino Acid Motifs. 1. 2014. 980. 0.030. Why? HIV Infections. 1. 2017. 15382. 0.030. Why? ...
Betulinic, oleanolic, and ursolic acids are the most medicinally important TAs and are mainly found in plants of the mint ... Triterpenic acids (TAs), a large group of natural compounds with diverse biological activity, are produced by several plant ... Every colored box represents a specific motif. The amino acid sequences of motifs used to design primers are shown with an ... en-28-oic acid, BA), oleanolic acid (3β-hydroxyolean-12-en-28-oic acid, OA), and ursolic acid (3β-hydroxyurs-12-en-28-oic acid ...
O-fucosylation stabilizes the TSR3 motif in thrombospondin-1 by interacting with nearby amino acids and protecting a disulfide ... Galectins compose a protein family defined by a conserved sequence motif conferring affinity for β-galactose-containing glycans ... Thrombospondin type-1 repeats (TSRs) are small protein motifs containing six conserved cysteines forming three disulfide bonds ... motifs. Here we report that heparin and tetrasaccharide fragments of heparin are able to inhibit CCL5-CCR1 binding, with IC50 ...
Recent results show that GPCRs are characterized with structural motifs that preferentially associate with cholesterol. An ... Putative cholesterol recognition/interaction amino acid consensus (CRAC) motifs in human GPCRs. (a) CRAC motifs in ... cholesterol recognition/interaction amino acid consensus) motif [89, 90], CCM (cholesterol consensus motif) [29], SSD (sterol- ... represents between one and five residues of any amino acid [90]. We recently reported the presence of CRAC motifs in ...
HIERARCHICAL MOTIF VECTORS FOR AMINO ACID SEQUENCE ALIGNMENT. Bilge Karaçalı Izmir. doi: 10.2316/J.2012.216.764-0055 Abstract ... AN EVALUATION OF MOTIF DETECTION TOOLS. Alin G. Voina, Petre G. Pop, Mircea F. Vaida Technical University of Cluj Napoca,. doi ...
... along the length of the insulin receptor and at least six insulin-binding sequence motifs. The amino acid sequence motifs ... We also discuss the potential of sequence motifs, and the insulin-binding scoring matrix, to diagnose insulin binding to other ... identify putative insulin-binding sequence motifs *develop a preliminary insulin-binding scoring matrix that could be used in ... Identification of putative insulin binding motifs of the insulin receptor. Steve Bottomley1, Jessica Mitchell2, Brian Plewright ...
Distinct amino acid motifs carrying multiple positive charges regulate membrane targeting of dysferlin and MG53. PLoS One 2018; ... aa, amino acid; ANOVA, analysis of variance; CaV3.2, calcium channels 3.2; ICa3.1, CaV3.1 current; ICa3.2, CaV3.2 current; I ... aa, amino acid; AAV, adeno-associated virus; CaV3.2, calcium channels 3.2; DEPP, disorder-enhanced phosphorylation predictor; ... PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta 2010;1804:996-1010.. * Cited Here , ...
involved_in cellular response to amino acid starvation IMP Inferred from Mutant Phenotype. more info ... DSRM; Double-stranded RNA binding motif. cl21453. Location:262 → 495. PKc_like; Protein Kinases, catalytic domain. ... HIV-1 Tat, specifically amino acids 49-57, increases activation of PKR in Leishmania-infected macrophages. PubMed ... DSRM; Double-stranded RNA binding motif. cd14047. Location:260 → 536. STKc_EIF2AK2_PKR; Catalytic domain of the Serine/ ...
... and T-cell receptor amino acid sequences and motifs. Bioinformatics 2019, 35, 2974-2981. [Google Scholar] [CrossRef][Green ... such as hydrophobicity of amino acids at certain positions or common motifs [26,27,28]. ... the nucleotide-to-amino acid (nt:aa) ratio found in individual mice; (b) as in (a), but for degree of sharedness and with boxes ... the nucleotide-to-amino acid (nt:aa) ratio found in individual mice; (b) as in (a), but for degree of sharedness and with boxes ...
the 10-amino acid LC8 binding motif is capitalized. †non-native residues added to the N-terminus of each peptide to increase ... d-g) The I/I0 data are alternatively plotted as the average intensity ratio for each 10-amino acid motif versus the molar ratio ... Plots of the average peak intensity (I/I0) for each 10-amino acid motif in dLBD, and in each of QT2-4 and QT4-6 constructs ... "Plots of the average peak intensity (I/I0) for each 10-amino acid motif in dLBD, and in each of QT2-4 and QT4-6 constructs ...
... amino acids Q226 and G228 by H3 numbering). Avian consensus sequences at other motifs/amino acid positions in proteins of ... multiple arginine amino acids in this motif would be predicted to result in a highly pathogenic phenotype in chickens. ... Besides the multibasic cleavage site, the virus had typical avian consensus amino acid residues in the HA protein at positions ... Although there were several amino acid differences compared with older North American H7 HA1 protein sequences (27-32 changes ...
Each match receives a score, indicating how well it fits the motif. OPTIONS (DEFAULT SETTINGS) -h Show all options and their ... GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re- ... glam2scan - finds a GLAM2 motif in a database SYNOPSIS. glam2scan [options] alphabet my_motif.glam2 my_seqs.fa An alphabet ... Each match receives a score, indicating how well it fits the motif. OPTIONS (DEFAULT SETTINGS) -h Show all options and their ...
Biochemical properties of hepatitis C virus RNA-dependent RNA polymerase and identification of amino acid sequence motifs ...
Candidate PAs are reported in species with predicted (VXXXD) and unexpected (IXXXN) amino acid motifs in their homospermidine ... A parallel sequence proceeding via the stereoisomeric epoxide 44 led to the necic acid segment 75 of the alkaloid (+)-usaramine ... Results: Monoesters of retronecine with senecioic, hydroxysenecioic or syringic acids were identified in roots of Alafia cf. ... The first, starting from methyl (R)-(-)-3-hydroxy-2-methylpropionate, proceeded in 19 steps to integerrinecic acid lactone (5) ...
The H5N1 Inventory is an inclusive compilation of amino acid changes and/or motifs identified within each viral protein that ... H5N1 virus (A/Vietnam/1203/2004) amino acid numbering for the mature proteins has been used throughout. ... has developed an inventory of amino acid mutations in H5N1 viruses that is intended to be used by the influenza surveillance ... mutations or motifs that were introduced into HPAI H5N1 viruses by reverse genetics or arose through repeated passage in the ...
The amino acid motifs for binding to the erythrocyte DARC reside in region II. PkDBP is encoded by an α-gene and therefore ... These forms, known as Fya and Fyb, are the result of a single amino acid substitution [7] in the domain that binds with PkDBP ... can be explained by the fact that PkDBPαII and PvDBPII are orthologues which have similar critical domain and amino acid ...
Recognition of conserved amino acid motifs of common viruses and its role in autoimmunity. M Sospedra, Y Zhao, H Hausen, PA ...
The short N-terminal domains share ,20% identical amino acids, but contain conserved motifs. A fusion protein consisting of the ... containing several essential motifs, which is followed by the kinase catalytic domain comprising the C-terminus of the protein ...
Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic ... Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic ... Using solution-state NMR spectroscopy, we demonstrate that the 200 amino acid Argiope trifasciata AcSp1 repeat unit contrasts ...
For example, the helix-turn-helix motif comprises two coiled sequences of amino acids, ... with the protein sequence of amino acids to indicate how the amino acids at different points along a protein chain fold ... The researchers carried out a blind test on NMR data from a 70-amino acid protein called mth1743 from the microbe ... Wheres the motif? Although nature can create almost unlimited variations on protein sequences, a limited number of motifs ...
The MADS domain and core motifs of the sweet potato MADS-box genes were identified by motif analysis. We identified 19 MADS-box ... The MADS domain and K domain of the sweet potato MADS-box genes were identified by motif analysis. We identified 19 MADS-box ... conjugated phenolic acids and minerals, which has high edible, forage and medicinal value, and is also an important energy crop ... conjugated phenolic acids, and minerals, which have high edible, forage, and medicinal value, and is also an important energy ...
Although this simple amino acid motif is commonly found throughout nature, it does not generally result in fluorescence. What ... The packing of amino acid residues inside the beta barrel is extremely stable, which results in a very high fluorescence ... More than 30 amino acid alterations to the structure were required for the creation of the first-generation monomeric DsRed ... It is remarkable that the principle fluorophore is derived from a triplet of adjacent amino acids: the serine, tyrosine, and ...
... and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, ... Moreover, their annotation is based on the presence of conserved amino acid motifs and structural features or limited homology. ... and is decreased in glucose minimal media enriched with amino acids [44]. The repression of genes involved in amino acid ... based on the presence of conserved amino acid motifs, structural features or limited identity, have not yet been fully ...
Lauberth SM, Rauchman M. A conserved 12-amino acid motif in Sall1 recruits the nucleosome remodeling and deacetylase ... Our studies have demonstrated that TTP regulates glucose, fatty acid and branched-chain amino acid metabolism in the liver and ... mechanism of TTP regulation of branched-chain amino acid levels and 4) role of TTP in cardiac metabolism. ... Future goals are to refine the use of ALDH and fatty acid desaturases inhibitors to target cancer stem cells residual after ...
Analysis of repetitive amino acid motifs reveals the essential features of spider dragline silk proteins. AD Malay, K Arakawa, ...
  • The results indicate at least seven putative insulin-binding regions (R1 to R7) along the length of the insulin receptor and at least six insulin-binding sequence motifs. (
  • We also discuss the potential of sequence motifs, and the insulin-binding scoring matrix, to diagnose insulin binding to other peptides or proteins. (
  • If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press). (
  • Biochemical properties of hepatitis C virus RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity. (
  • Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. (
  • The chart shows the underlying distribution of phospho-peptide motifs in a PhosphoScan ® LC-MS/MS experiment using 581 nonredundant Lys-C/tryptic peptides generated from 293T cells treated with Calyculin A #9902 (10 nM, 30 min) and immunoprecipitated with PTMScan ® Phospho-Ser/Thr Motif [pS/T] Immunoaffinity Beads. (
  • Peptides are then subjected to immunoaffinity purification using a PTMScan ® Motif Antibody conjugated to protein A agarose beads. (
  • Unbound peptides are removed through washing, and the captured PTM-containing peptides are eluted with dilute acid. (
  • GYISTRVGM) of NS3 of dengue virus types 1 and 3 (named DENV-1/3), and their respective modified epitope peptides, DENV-2/4-9L (GYISTRVE L ) and DENV-1/3-9L (GYISTRVG L ), in which the C-terminal residue M of the original epitope peptide was replaced by L, in order to provide the complete H-2Kd- binding motif. (
  • [ 52 ] Based on these findings, short (28-33 amino acids) synthetic peptides were designed, which represent portions of these longer B-cell epitopes. (
  • while the N-terminal GW motifs confer binding to Ago proteins [ 5 , 8 , 9 ], the C-terminal GW repeats are important for the recruitment of the PAN2-PAN3 and CCR4-NOT deadenylase complexes [ 10 - 15 ] for poly(A) tail removal, a process termed deadenylation. (
  • Like most proteins, transcription factors are made up of chains of amino acids that fold into a specific three-dimensional (3D) structurewith a region that recognizes and binds to a specific DNA sequence. (
  • A few prominent kinases targeting a handful of substrate consensus motifs account for a majority of the tens of thousands of known and predicted sites on more than 13,000 human proteins (1-3). (
  • These motifs allow molecules of melanocyte inducing transcription factor to interact with each other or with other proteins that have a similar structure, creating a two-protein unit (dimer) that functions as a transcription factor. (
  • Proteins arising from the Avh superfamily have very different amino acid sequences but share two common motifs at one end of the protein (N-terminus). (
  • The readily identified RXLR and dEER motifs (single letter code for amino acids) are required for entry of the proteins into plant host cells. (
  • Similar motifs are also found in the effector proteins produced by the malarial parasite Plasmodium as it invades red blood cells. (
  • The team also detected some conserved amino acid motifs (W, Y and L) at the other end (C terminus) of some of the proteins that have been selected over years of evolution. (
  • Furthermore, while the first motif occurs in almost all EnvZ homologues, the second motif is only found in species that have MzrA, indicating co-evolution of the two proteins. (
  • Proteins of the TFF family are characterized by obtaining a minimum of 1 copy of the trefoil motif, a 40-amino acid domain that contains 3 conserved disulfides. (
  • Trefoil Factors are stable secretory proteins expressed in gastrointestinal mucosa which protect the mucosa from insults, stabilize the mucus layer and affect healing of the epithelium.TFF2 inhibits gastric acid motility & secretion. (
  • Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). (
  • We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery. (
  • However, the same motif may occur in proteins or enzymes with different functions. (
  • MYMV was found to be closely related to KA27 DNA B in amino acid sequence identity of BV1 (94.1%) and BC1 (97.6%) proteins and in the organization of nuclear localization signal (NLS), nuclear export signal (NES) and phosphorylation sites. (
  • 2013}. However, the proteins in our Serpentinomonas strains lack the specific motif in the c-rings that is proposed to be critica! (
  • Proteins are large biomolecules consisting of one or more long chains of amino acid residues. (
  • The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. (
  • There are three GW182 paralogs in vertebrates, namely, TNRC6A (also known as GW182), TNRC6B and TNRC6C, which share a characteristic architecture of a central ubiquitin associated domain (UBA) domain and a C-terminal RNA recognition motif (RRM) that are flanked by long stretches of sequences of intrinsic disorder ( Fig 1A ) [ 16 ]. (
  • GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. (
  • The scientists probed the recently published genome sequences of both organisms using bioinformatic tools that can look for specific amino acid sequences or motifs. (
  • Based on their partial amino acid sequences, full-length cDNAs were cloned. (
  • Sequences of ARF-GAP domains show no recognizable similarity to those of other GAPs, and contain a characteristic Cys-X(2)-Cys-X(16-17)-Cys-X(2)-Cys motif. (
  • We characterize variant diversity, amino acid mutation frequency, functionality and associations with COVID-19 infections in one of the largest datasets of SARS-CoV-2 genome sequences collected from wastewater in the New York metropolitan area. (
  • The peptide sequences were used to isolate BnSCE3 cDNA, which was shown to contain an open reading frame of 1170 bp encoding a protein of 389 amino acids, including a leader peptide of 25 amino acids. (
  • The main module page also shows the location of these motifs within the upstream sequences of the module member genes. (
  • cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. (
  • PKR activity modulation by phosphomimetic mutations of serine residues located three aminoacids upstream of double-stranded RNA binding motifs. (
  • T, changing serine to cysteine at amino acid position 1218. (
  • The enzymes belong to the SGNH protein family, which use a catalytic triad of Ser-Asp-His, with serine as the nucleophile of the GDSL motif. (
  • The transcription factor ASCIZ (ATMIN, ZNF822) has an unusually high number of recognition motifs for the product of its main target gene, the hub protein LC8 (DYNLL1). (
  • GYISTRVEM) spinning the amino acid residues 298-306 of NS3 of dengue virus types 2 and 4 was substituted for L to prepare the peptide Den2.4-9L with a complete H-2Kd-binding motif. (
  • Immunogenic amino acid motifs and linear epitopes of COVID-19 mRNA vaccines. (
  • Detailed knowledge of the Mamu-B*08 peptide-binding motif enabled us to identify six additional novel Mamu-B*08-restricted SIV-specific CD8(+) T cell immune responses directed against epitopes in Gag, Vpr, and Env. (
  • All seven regions encoding Mamu-B*08-restricted CD8+ T cell epitopes also exhibit amino acid replacements typically seen only in the presence of Mamu-B*08, suggesting that the variation we observe is indeed selected by CD8+ T cell responses. (
  • The deleted genes include amino acids and sugar transporters, RNA polymerase sigma-70 factor, and fatty acids metabolisms. (
  • Improvement of phi29 DNA polymerase amplification performance by fusion of DNA binding motifs. (
  • Peptide (C)DSRPGPEDGENTAQWR, corresponding to amino acid residues 33-48 of rat Presenilin-2 (Accession O88777 ). (
  • XV" YOL105C 1 15 18 YOL105C "Putative integral membrane protein containing novel cysteine motif. (
  • The libraries are comprised of stabilized, alpha-helical polypeptides having a similar tertiary structure but different amino acid residues at specific, "variable" positions in the sequence. (
  • Two of the regions, called the helix-loop-helix motif and the leucine-zipper motif, are critical for protein interactions. (
  • Some MITF gene variants change the amino acids used to make melanocyte inducing transcription factor, which alters the helix-loop-helix or leucine-zipper motif. (
  • This mutation is in the granin site at the amino acid positions 1214-1223 and the leucine zipper at amino acid positions 1209-1230. (
  • The structure of BRCA1 is not strikingly homologous to other known molecules apart from the presence of a ring zinc finger domain and a 10 amino acid granin motif which are thought to be significant due to fact that they both are conserved in humans and other species studied. (
  • Thrombospondin type-1 repeats (TSRs) are small protein motifs containing six conserved cysteines forming three disulfide bonds that can be modified with an O -linked fucose. (
  • Confirmation that HUS and TTP are clearly different diseases, despite their clinical similarities, followed the discovery of the von Willebrand factor (vWF)-cleaving metalloprotease ADAMTS13 (A disintegrin and metalloprotease with a thrombospondin type 1 motif, member 13). (
  • The second novel missense mutation was g.1380 G>A, changing glutamic acid to lysine at the amino acid position 421. (
  • The candidate cysteines are part of a motif that is conserved in the RNase E protein family, and mutation of these residues causes the partial loss of zinc, the complete disruption of the tetramer into dimers, and effective catalytic inactivation. (
  • The WHO Collaborating Center for Influenza Reference and Research at the Centers for Disease Control and Prevention in Atlanta, with input from many influenza subject matter experts from around the world, has developed an inventory of amino acid mutations in H5N1 viruses that is intended to be used by the influenza surveillance and research community as a tool to inform the influenza knowledge base for surveillance and public health preparedness. (
  • Motif mimicry tolerates mutations, evolves quickly to modify interactions with the host, and enables modular interactions with protein complexes. (
  • Similarly, the peptide Den1.3-9L with the binding motif was prepared from dengue virus types 1 and 3. (
  • Subcutaneous immunization of BALB/c mice with Den1.3-9L emulsified with complete Freund adjuvant (CFA) induced the CTLs which lysed the target cells (P815) pulsed with peptide Den1.3-9L as well as those pulsed with peptide Den1.3 corresponding to the amino acid residues 299-307 (GYISTRVGM) of NS3 of dengue virus serotypes 1 and 3. (
  • CTL epitope peptide for providing the complete MHC class I binding motif augments the immunogenicity to induce specific CTLs. (
  • 1] They with a binding motif, which is determined by recognize specific structures on the surface of peptide length, and a.a. residues called anchor target cells as their antigens, which are composed residues. (
  • Mice were immunized by subcutaneous motif induced CTLs more efficiently than the injection with 1 n mole of the peptide original ones of dengue viruses, which did not emulsified with complete Freund adjuvant possess complete binding motif. (
  • We therefore defined a detailed peptide-binding motif for Mamu-B*08 and investigated binding similarities between the macaque and human MHC class I molecules. (
  • The remarkable similarity of the peptide-binding motifs and repertoires for Mamu-B*08 and HLA-B*2705 suggests that the nature of the peptide bound by the MHC class I molecule may play an important role in control of immunodeficiency virus replication. (
  • Peptide confirmation Confirmed by amino acid analysis and mass spectrometry. (
  • The gene from Y. pestis KIM possesses a unique second transversion (G·C→T·A) at amino acid 146 causing substitution of aspartic acid (encoded by GAU) with tyrosine (encoded by UAU). (
  • The ARF-GAP domain comprises a central three-stranded beta-sheet flanked by five alpha-helices, with a Zn(2+) ion coordinated by the four cysteines of the cysteine-rich motif. (
  • The other region, known as the basic motif, binds to specific areas of DNA, allowing the dimer to control gene activity. (
  • The MITF gene variants that cause Tietz syndrome either delete or change a single protein building block (amino acid) in the basic motif region of the melanocyte inducing transcription factor structure. (
  • Sequence homology analysis of these genes with other species threonyl-tRNA synthetase showed that the shorter gene did not possess motif-2 and motif-3 of catalytic core that were conserved in class II aminoacyl-tRNA synthetases. (
  • On the other hand, the longer gene had almost all amino acids that were expected to be involved in substrate binding and catalytic activity. (
  • Analysis of this HA gene shows that it is closely related to avian A(H5) viruses in HA clade and lacked amino acid changes that improve recognition of mammalian receptors or fusion of the viral membrane with the host endosomal membranes. (
  • SLC10A7, encoded by the so-called SLC10A7 gene, is the seventh member of a human sodium/bile acid cotransporter family, known as the SLC10 family. (
  • The only known distinction between most sequenced isolates of aspA from Y. pestis and the active gene in Yersinia pseudotuberculosis (the immediate progenitor of Y. pestis ) is a single base transversion (G·C→T·A) causing replacement of leucine (encoded by UUG) for valine (encoded by GUG) at amino acid position 363. (
  • Dengue viruses, of which there are four acids. (
  • TFF2 Human Recombinant includes a 40-amino acid trefoil motif containing three conserved intramolecular disulfide bonds and was purified by proprietary chromatographic techniques. (
  • Dr. Duckett earned his PhD degree in Biochemistry from the University of Dundee under the mentorship of Professor David M. J. Lilley, a Member of Royal Society and the Director of the Cancer Research UK Nucleic Acid Structure Research Group, where Derek had a remarkable string of studies that defined the structures for DNA and RNA four-way helical junctions, and how these interact with resolving enzymes (Duckett, et al. (
  • In strain O26 21765 , the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair , iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. (
  • 2. The library of claim 1, which contains at least 10.sup.3 members, and amino acid variations occur in at least three different residue positions in the exposed region of the at least one polypeptide. (
  • 3. The library of claim 1, wherein amino acid variations occur at contiguous residue positions in the exposed region of the at least one polypeptide. (
  • 4. The library of claim 1, wherein amino acid variations occur at residue positions in the exposed regions of two adjacent.alpha. (
  • 5. The library of claim 1, wherein amino acid variations occur in a total of at least two different residue positions in the exposed regions of each polypeptide. (
  • 6. The library of claim 1, wherein the first polypeptide contains a terminal bridge segment linking an end of the first polypeptide to an adjacent end of the second polypeptide, the first exposed region further includes this bridge segment and amino acid variations occur in this bridge segment. (
  • Ankyrin repeats are about 33 amino acids long and occur in at least four consecutive copies. (
  • Although distinct amino acid motifs containing consecutive prolines (polyP) cause ribosome stalling, which necessitates recruitment of the translation elongation factor P (EF-P), they occur strikingly often in bacterial proteomes. (
  • Opacity-associated protein A LysM-like domain, Opacity-associated protein A N-terminal motif [Interproscan]. (
  • Motifs are typically the most conserved regions of PROTEIN DOMAINS and are critical for domain function. (
  • Crafting these residues, which are located in loop regions between TPR motifs, onto the monomeric consensus TPR protein CTPR3 induced the formation of oligomers. (
  • These forms, known as Fy a and Fy b , are the result of a single amino acid substitution [ 7 ] in the domain that binds with PkDBPαII. (
  • The MADS domain and core motifs of the sweet potato MADS-box genes were identified by motif analysis. (
  • 30 amino acid motif that precedes the kinase domain in types I and II TGF beta receptors. (
  • Moreover, the prediction of GluP structure revealed interesting signatures: a rhomboid domain and two tetracopeptide repeat (TPR) motifs. (
  • We show that the I PPPL motif in the HAMP domain is required for dimerization of EnvZ. (
  • The second motif, VVPPA, which is located in the periplasmic domain, was found to be required for interaction with the modulator protein MzrA. (
  • The main innovation of GLAM2 is that it allows insertions and deletions in motifs. (
  • In previous A(H5N1) outbreaks and zoonosis the NA stalk region often had deletions (e.g., a 20 amino acid deletion at positions 49-68 relative to A/goose/Guangdong/1/1996) that enhances replication and/or pathogenesis in terrestrial poultry and mice ( 4-6 ). (
  • Homology Mouse, human - 13/14 amino acid residues identical. (
  • Computational modelling of diatom silicic acid transporters predicts a conserved fold with implications for their function and evolution. (
  • Ankyrin repeats are tandemly repeated modules of about 33 amino acids. (
  • 11. The library of claim 1, wherein each polypeptide contains a heptad of amino acid residues with positions denoted abcdefg, where a and d are said hydrophobic residues. (
  • TFF-2 Human Recombinant produced in E.Coli is a single, non-glycosylated, polypeptide chain containing 106 amino acids (24-129) and having a total molecular mass of 12 kDa. (
  • Here we have investigated the roles of two polyP motifs in the osmosensor and histidine kinase EnvZ. (
  • Return of valine for leucine at position 363 of the Y. pestis enzyme restored normal turnover ( k cat 86±2 s −1 ) provided that the amino acid substitution at position 146 was also reversed. (
  • Galectins compose a protein family defined by a conserved sequence motif conferring affinity for β-galactose-containing glycans. (
  • CXCL12/SDF-1 alpha is 89 amino acids (aa) in length with a predicted molecular weight of 10 kDa, CXCL12/SDF-1 beta is 93 aa in length with a predicted molecular weight of 10.6 kDa, and CXCL12/SDF-1 gamma is 119 aa in length with a predicted molecular weight of 13.7 kDa. (
  • Eight StCRK members were identified, with amino acid size from 459 to 686 aa, molecular weight of 50.75-77.50 kD, and isoelectric point of 5.84-8.75. (
  • The H5N1 Inventory is an inclusive compilation of amino acid changes and/or motifs identified within each viral protein that affect one or more biological properties, provided in broad categories. (
  • The 7.8 kb mRNA encodes a protein of 1863 amino acids. (
  • As a food source, casein supplies essential amino acids as well as some carbohydrates and the inorganic elements calcium and phosphorus. (
  • Recent results show that GPCRs are characterized with structural motifs that preferentially associate with cholesterol. (
  • Differences in the predicted protein functional domains encoded among SIT clades suggest that the divergence of clades resulted in functional diversification among S ITs, and suggests that diatoms' dominant ability to take up silicic acid from seawater in diverse environmental conditions may have been affected. (
  • 9. The library of claim 1, wherein the unique variation of amino acid residues in the exposed region is accomplished using representative amino acids that display the basic physico-chemical properties associated with naturally occurring amino acids, but exclude many of these naturally occurring amino acids. (
  • Twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic or natural amino acids. (
  • 20% identical amino acids, but contain conserved motifs. (
  • Shiga toxin type 1 (Stx1) is identical to the toxin produced by Shigella spp or differs by only one amino acid. (
  • After purification to near homogeneity, the products were subjected to biochemical analysis and found to exhibit similar secondary, tertiary and quaternary (tetrameric) structures as well as comparable Michaelis constants for l -aspartic acid. (
  • High resolution HLA analysis reveals independent class I haplotypes and amino-acid motifs protective for multiple sclerosis. (
  • Transcription factor binding motifs help to elucidate regulatory mechanism. (
  • MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. (
  • A consequence of having odd number of transmembrane passes is that the amino and carboxy terminals are localized on opposite sides of the cellular membrane. (
  • It is established that cells of Yersinia pestis , the causative agent of bubonic plague, excrete l -aspartic acid at the expense of exogenous l -glutamic acid during expression of the low-calcium response. (
  • This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence. (
  • Variable Consequences of Membrane Targeting Motifs for Genetically Encoded Voltage Indicators Biophysical Journal . (