Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Amino Acids: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Cyanogen Bromide: Cyanogen bromide (CNBr). A compound used in molecular biology to digest some proteins and as a coupling reagent for phosphoroamidate or pyrophosphate internucleotide bonds in DNA duplexes.Amino Acid Substitution: The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Molecular Weight: The sum of the weight of all the atoms in a molecule.Genes, Bacterial: The functional hereditary units of BACTERIA.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Recombinant Proteins: Proteins prepared by recombinant DNA technology.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Trypsin: A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 3.4.21.4.Bacterial Proteins: Proteins found in any species of bacterium.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.Kinetics: The rate dynamics in chemical or physical systems.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.Amino Acids, Essential: Amino acids that are not synthesized by the human body in amounts sufficient to carry out physiological functions. They are obtained from dietary foodstuffs.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Chymotrypsin: A serine endopeptidase secreted by the pancreas as its zymogen, CHYMOTRYPSINOGEN and carried in the pancreatic juice to the duodenum where it is activated by TRYPSIN. It selectively cleaves aromatic amino acids on the carboxyl side.Amino Acid Transport Systems: Cellular proteins and protein complexes that transport amino acids across biological membranes.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Chromatography, Ion Exchange: Separation technique in which the stationary phase consists of ion exchange resins. The resins contain loosely held small ions that easily exchange places with other small ions of like charge present in solutions washed over the resins.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Chromatography, Gel: Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Endopeptidases: A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Rabbits: The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Thermolysin: A thermostable extracellular metalloendopeptidase containing four calcium ions. (Enzyme Nomenclature, 1992) 3.4.24.27.Peptide Mapping: Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.Leucine: An essential branched-chain amino acid important for hemoglobin formation.Serine Endopeptidases: Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Amino Acids, Branched-Chain: Amino acids which have a branched carbon chain.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Viral Proteins: Proteins found in any species of virus.Amino Acids, Aromatic: Amino acids containing an aromatic side chain.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.Epitopes: Sites on an antigen that interact with specific antibodies.Genetic Complementation Test: A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.Amino Acids, SulfurProtein PrecursorsProtein Sorting Signals: Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Swine: Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).Genes, Fungal: The functional hereditary units of FUNGI.Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Enzyme Stability: The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Genes, Viral: The functional hereditary units of VIRUSES.Carboxypeptidases: Enzymes that act at a free C-terminus of a polypeptide to liberate a single amino acid residue.Chromatography, Affinity: A chromatographic technique that utilizes the ability of biological molecules to bind to certain ligands specifically and reversibly. It is used in protein biochemistry. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Isoenzymes: Structurally related forms of an enzyme. Each isoenzyme has the same mechanism and classification, but differs in its chemical, physical, or immunological characteristics.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Glycoproteins: Conjugated protein-carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins.Lysine: An essential amino acid. It is often added to animal feed.Alanine: A non-essential amino acid that occurs in high levels in its free state in plasma. It is produced from pyruvate by transamination. It is involved in sugar and acid metabolism, increases IMMUNITY, and provides energy for muscle tissue, BRAIN, and the CENTRAL NERVOUS SYSTEM.Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Peptide Hydrolases: Hydrolases that specifically cleave the peptide bonds found in PROTEINS and PEPTIDES. Examples of sub-subclasses for this group include EXOPEPTIDASES and ENDOPEPTIDASES.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Fungal Proteins: Proteins found in any species of fungus.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.Tissue Distribution: Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Biological Transport: The movement of materials (including biochemical substances and drugs) through a biological system at the cellular level. The transport can be across cell membranes and epithelial layers. It also can occur within intracellular compartments and extracellular compartments.Isoelectric Point: The pH in solutions of proteins and related compounds at which the dipolar ions are at a maximum.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.RNA: 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)DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Chemistry: A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.Genetic Variation: Genotypic differences observed among individuals in a population.Glycine: A non-essential amino acid. It is found primarily in gelatin and silk fibroin and used therapeutically as a nutrient. It is also a fast inhibitory neurotransmitter.Isoleucine: An essential branched-chain aliphatic amino acid found in many proteins. It is an isomer of LEUCINE. It is important in hemoglobin synthesis and regulation of blood sugar and energy levels.Glycosylation: The chemical or biochemical addition of carbohydrate or glycosyl groups to other chemicals, especially peptides or proteins. Glycosyl transferases are used in this biochemical reaction.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Chemical Phenomena: The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.Proline: A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Oligopeptides: Peptides composed of between two and twelve amino acids.Bacillus: A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.Pepsin A: Formed from pig pepsinogen by cleavage of one peptide bond. The enzyme is a single polypeptide chain and is inhibited by methyl 2-diaazoacetamidohexanoate. It cleaves peptides preferentially at the carbonyl linkages of phenylalanine or leucine and acts as the principal digestive enzyme of gastric juice.Disulfides: Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.Arginine: An essential amino acid that is physiologically active in the L-form.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Chromatography: Techniques used to separate mixtures of substances based on differences in the relative affinities of the substances for mobile and stationary phases. A mobile phase (fluid or gas) passes through a column containing a stationary phase of porous solid or liquid coated on a solid support. Usage is both analytical for small amounts and preparative for bulk amounts.COS Cells: CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Trypsin Inhibitors: Serine proteinase inhibitors which inhibit trypsin. They may be endogenous or exogenous compounds.Electrophoresis, Paper: Electrophoresis in which paper is used as the diffusion medium. This technique is confined almost entirely to separations of small molecules such as amino acids, peptides, and nucleotides, and relatively high voltages are nearly always used.Methionine: A sulfur-containing essential L-amino acid that is important in many body functions.Solubility: The ability of a substance to be dissolved, i.e. to form a solution with another substance. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Carbohydrates: The largest class of organic compounds, including STARCH; GLYCOGEN; CELLULOSE; POLYSACCHARIDES; and simple MONOSACCHARIDES. Carbohydrates are composed of carbon, hydrogen, and oxygen in a ratio of Cn(H2O)n.Oxidoreductases: The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)Antibodies, Monoclonal: Antibodies produced by a single clone of cells.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.Glutamine: A non-essential amino acid present abundantly throughout the body and is involved in many metabolic processes. It is synthesized from GLUTAMIC ACID and AMMONIA. It is the principal carrier of NITROGEN in the body and is an important energy source for many cells.Circular Dichroism: A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Aspartic Acid: One of the non-essential amino acids commonly occurring in the L-form. It is found in animals and plants, especially in sugar cane and sugar beets. It may be a neurotransmitter.Amino Acid Transport Systems, Basic: Amino acid transporter systems capable of transporting basic amino acids (AMINO ACIDS, BASIC).DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.Genetic Code: The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON).Glycoside HydrolasesImmunoblotting: Immunologic method used for detecting or quantifying immunoreactive substances. The substance is identified by first immobilizing it by blotting onto a membrane and then tagging it with labeled antibodies.Cross Reactions: Serological reactions in which an antiserum against one antigen reacts with a non-identical but closely related antigen.Amino Acids, Basic: Amino acids with side chains that are positively charged at physiological pH.Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.Ferredoxins: Iron-containing proteins that transfer electrons, usually at a low potential, to flavoproteins; the iron is not present as in heme. (McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Tryptophan: An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.Valine: 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.Plants, Medicinal: Plants whose roots, leaves, seeds, bark, or other constituent parts possess therapeutic, tonic, purgative, curative or other pharmacologic attributes, when administered to man or animals.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Amino Acids, DiaminoPseudomonas: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Fabaceae: The large family of plants characterized by pods. Some are edible and some cause LATHYRISM or FAVISM and other forms of poisoning. Other species yield useful materials like gums from ACACIA and various LECTINS like PHYTOHEMAGGLUTININS from PHASEOLUS. Many of them harbor NITROGEN FIXATION bacteria on their roots. Many but not all species of "beans" belong to this family.Streptomyces: A genus of bacteria that form a nonfragmented aerial mycelium. Many species have been identified with some being pathogenic. This genus is responsible for producing a majority of the ANTI-BACTERIAL AGENTS of practical value.Bacterial Outer Membrane Proteins: Proteins isolated from the outer membrane of Gram-negative bacteria.Serine: A non-essential amino acid occurring in natural form as the L-isomer. It is synthesized from GLYCINE or THREONINE. It is involved in the biosynthesis of PURINES; PYRIMIDINES; and other amino acids.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Geobacillus stearothermophilus: A species of GRAM-POSITIVE ENDOSPORE-FORMING BACTERIA in the family BACILLACEAE, found in soil, hot springs, Arctic waters, ocean sediments, and spoiled food products.Threonine: An essential amino acid occurring naturally in the L-form, which is the active form. It is found in eggs, milk, gelatin, and other proteins.Phenylalanine: An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.ChitinaseDNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Capsid Proteins: Proteins that form the CAPSID of VIRUSES.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Muscles: Contractile tissue that produces movement in animals.Lectins: Proteins that share the common characteristic of binding to carbohydrates. Some ANTIBODIES and carbohydrate-metabolizing proteins (ENZYMES) also bind to carbohydrates, however they are not considered lectins. PLANT LECTINS are carbohydrate-binding proteins that have been primarily identified by their hemagglutinating activity (HEMAGGLUTININS). However, a variety of lectins occur in animal species where they serve diverse array of functions through specific carbohydrate recognition.Isoelectric Focusing: Electrophoresis in which a pH gradient is established in a gel medium and proteins migrate until they reach the site (or focus) at which the pH is equal to their isoelectric point.Viral Structural Proteins: Viral proteins that are components of the mature assembled VIRUS PARTICLES. They may include nucleocapsid core proteins (gag proteins), enzymes packaged within the virus particle (pol proteins), and membrane components (env proteins). These do not include the proteins encoded in the VIRAL GENOME that are produced in infected cells but which are not packaged in the mature virus particle,i.e. the so called non-structural proteins (VIRAL NONSTRUCTURAL PROTEINS).Nitrogen: An element with the atomic symbol N, atomic number 7, and atomic weight [14.00643; 14.00728]. Nitrogen exists as a diatomic gas and makes up about 78% of the earth's atmosphere by volume. It is a constituent of proteins and nucleic acids and found in all living cells.Repetitive Sequences, Amino Acid: A sequential pattern of amino acids occurring more than once in the same protein sequence.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.Metalloendopeptidases: ENDOPEPTIDASES which use a metal such as ZINC in the catalytic mechanism.

The amino acid sequence of Neurospora NADP-specific glutamate dehydrogenase. The tryptic peptides. (1/190738)

The NADP-specific glutamate dehydrogenase of Neurospora crassa was digested with trypsin, and peptides accounting for 441 out of the 452 residues of the polypeptide chain were isolated and substantially sequenced. Additional experimental detail has been deposited as Supplementary Publication SUP 50052 (11 pages) with the British Library (Lending Division), Boston Spa, Wetherby, W. Yorkshire LS23 7BQ, U.K., from whom copies may be obtained under the terms given in Biochem J. (1975) 145, 5.  (+info)

The amino acid sequence of Neurospora NADP-specific glutamate dehydrogenase. Peptides from digestion with a staphylococcal proteinase. (2/190738)

The extracellular proteinase of Staphylococcus aureus strain V8 was used to digest the NADP-specific glutamate dehydrogenase of Neurospora crassa. Of 35 non-overlapping peptides expected from the glutamate content of the polypeptide chain, 29 were isolated and substantially sequenced. The sequences obtained were valuable in providing overlaps for the alignment of about two-thirds of the sequences found in tryptic peptides [Wootton, J. C., Taylor, J, G., Jackson, A. A., Chambers, G. K. & Fincham, J. R. S. (1975) Biochem. J. 149, 739-748]. The blocked N-terminal peptide of the protein was isolated. This peptide was sequenced by mass spectrometry, and found to have N-terminal N-acetylserine by Howard R. Morris and Anne Dell, whose results are presented as an Appendix to the main paper. The staphylococcal proteinase showed very high specificity for glutamyl bonds in the NH4HCO3 buffer used. Partial splits of two aspartyl bonds, both Asp-Ile, were probably attributable to the proteinase. No cleavage of glutaminyl or S-carboxymethylcysteinyl bonds was found. Additional experimental detail has been deposited as Supplementary Publication SUP 50053 (5 pages) with the British Library (Lending Division), Boston Spa, Wetherby, W. Yorkshire LS23 7BQ, U.K, from whom copies may be obtained under the terms given in Biochem. J. (1975) 1458 5.  (+info)

Novel regulation of the homeotic gene Scr associated with a crustacean leg-to-maxilliped appendage transformation. (3/190738)

Homeotic genes are known to be involved in patterning morphological structures along the antero-posterior axis of insects and vertebrates. Because of their important roles in development, changes in the function and expression patterns of homeotic genes may have played a major role in the evolution of different body plans. For example, it has been proposed that during the evolution of several crustacean lineages, changes in the expression patterns of the homeotic genes Ultrabithorax and abdominal-A have played a role in transformation of the anterior thoracic appendages into mouthparts termed maxillipeds. This homeotic-like transformation is recapitulated at the late stages of the direct embryonic development of the crustacean Porcellio scaber (Oniscidea, Isopoda). Interestingly, this morphological change is associated with apparent novelties both in the transcriptional and post-transcriptional regulation of the Porcellio scaber ortholog of the Drosophila homeotic gene, Sex combs reduced (Scr). Specifically, we find that Scr mRNA is present in the second maxillary segment and the first pair of thoracic legs (T1) in early embryos, whereas protein accumulates only in the second maxillae. In later stages, however, high levels of SCR appear in the T1 legs, which correlates temporally with the transformation of these appendages into maxillipeds. Our observations provide further insight into the process of the homeotic leg-to-maxilliped transformation in the evolution of crustaceans and suggest a novel regulatory mechanism for this process in this group of arthropods.  (+info)

The Drosophila kismet gene is related to chromatin-remodeling factors and is required for both segmentation and segment identity. (4/190738)

The Drosophila kismet gene was identified in a screen for dominant suppressors of Polycomb, a repressor of homeotic genes. Here we show that kismet mutations suppress the Polycomb mutant phenotype by blocking the ectopic transcription of homeotic genes. Loss of zygotic kismet function causes homeotic transformations similar to those associated with loss-of-function mutations in the homeotic genes Sex combs reduced and Abdominal-B. kismet is also required for proper larval body segmentation. Loss of maternal kismet function causes segmentation defects similar to those caused by mutations in the pair-rule gene even-skipped. The kismet gene encodes several large nuclear proteins that are ubiquitously expressed along the anterior-posterior axis. The Kismet proteins contain a domain conserved in the trithorax group protein Brahma and related chromatin-remodeling factors, providing further evidence that alterations in chromatin structure are required to maintain the spatially restricted patterns of homeotic gene transcription.  (+info)

The homeobox gene Pitx2: mediator of asymmetric left-right signaling in vertebrate heart and gut looping. (5/190738)

Left-right asymmetry in vertebrates is controlled by activities emanating from the left lateral plate. How these signals get transmitted to the forming organs is not known. A candidate mediator in mouse, frog and zebrafish embryos is the homeobox gene Pitx2. It is asymmetrically expressed in the left lateral plate mesoderm, tubular heart and early gut tube. Localized Pitx2 expression continues when these organs undergo asymmetric looping morphogenesis. Ectopic expression of Xnr1 in the right lateral plate induces Pitx2 transcription in Xenopus. Misexpression of Pitx2 affects situs and morphology of organs. These experiments suggest a role for Pitx2 in promoting looping of the linear heart and gut.  (+info)

Mrj encodes a DnaJ-related co-chaperone that is essential for murine placental development. (6/190738)

We have identified a novel gene in a gene trap screen that encodes a protein related to the DnaJ co-chaperone in E. coli. The gene, named Mrj (mammalian relative of DnaJ) was expressed throughout development in both the embryo and placenta. Within the placenta, expression was particularly high in trophoblast giant cells but moderate levels were also observed in trophoblast cells of the chorion at embryonic day 8.5, and later in the labyrinth which arises from the attachment of the chorion to the allantois (a process called chorioallantoic fusion). Insertion of the ROSAbetageo gene trap vector into the Mrj gene created a null allele. Homozygous Mrj mutants died at mid-gestation due to a failure of chorioallantoic fusion at embryonic day 8.5, which precluded formation of the mature placenta. At embryonic day 8.5, the chorion in mutants was morphologically normal and expressed the cell adhesion molecule beta4 integrin that is known to be required for chorioallantoic fusion. However, expression of the chorionic trophoblast-specific transcription factor genes Err2 and Gcm1 was significantly reduced. The mutants showed no abnormal phenotypes in other trophoblast cell types or in the embryo proper. This study indicates a previously unsuspected role for chaperone proteins in placental development and represents the first genetic analysis of DnaJ-related protein function in higher eukaryotes. Based on a survey of EST databases representing different mouse tissues and embryonic stages, there are 40 or more DnaJ-related genes in mammals. In addition to Mrj, at least two of these genes are also expressed in the developing mouse placenta. The specificity of the developmental defect in Mrj mutants suggests that each of these genes may have unique tissue and cellular activities.  (+info)

A Drosophila doublesex-related gene, terra, is involved in somitogenesis in vertebrates. (7/190738)

The Drosophila doublesex (dsx) gene encodes a transcription factor that mediates sex determination. We describe the characterization of a novel zebrafish zinc-finger gene, terra, which contains a DNA binding domain similar to that of the Drosophila dsx gene. However, unlike dsx, terra is transiently expressed in the presomitic mesoderm and newly formed somites. Expression of terra in presomitic mesoderm is restricted to cells that lack expression of MyoD. In vivo, terra expression is reduced by hedgehog but enhanced by BMP signals. Overexpression of terra induces rapid apoptosis both in vitro and in vivo, suggesting that a tight regulation of terra expression is required during embryogenesis. Terra has both human and mouse homologs and is specifically expressed in mouse somites. Taken together, our findings suggest that terra is a highly conserved protein that plays specific roles in early somitogenesis of vertebrates.  (+info)

Requirement of a novel gene, Xin, in cardiac morphogenesis. (8/190738)

A novel gene, Xin, from chick (cXin) and mouse (mXin) embryonic hearts, may be required for cardiac morphogenesis and looping. Both cloned cDNAs have a single open reading frame, encoding proteins with 2,562 and 1,677 amino acids for cXin and mXin, respectively. The derived amino acid sequences share 46% similarity. The overall domain structures of the predicted cXin and mXin proteins, including proline-rich regions, 16 amino acid repeats, DNA-binding domains, SH3-binding motifs and nuclear localization signals, are highly conserved. Northern blot analyses detect a single message of 8.9 and 5.8 kilo base (kb) from both cardiac and skeletal muscle of chick and mouse, respectively. In situ hybridization reveals that the cXin gene is specifically expressed in cardiac progenitor cells of chick embryos as early as stage 8, prior to heart tube formation. cXin continues to be expressed in the myocardium of developing hearts. By stage 15, cXin expression is also detected in the myotomes of developing somites. Immunofluorescence microscopy reveals that the mXin protein is colocalized with N-cadherin and connexin-43 in the intercalated discs of adult mouse hearts. Incubation of stage 6 chick embryos with cXin antisense oligonucleotides results in abnormal cardiac morphogenesis and an alteration of cardiac looping. The myocardium of the affected hearts becomes thickened and tends to form multiple invaginations into the heart cavity. This abnormal cellular process may account in part for the abnormal looping. cXin expression can be induced by bone morphogenetic protein (BMP) in explants of anterior medial mesoendoderm from stage 6 chick embryos, a tissue that is normally non-cardiogenic. This induction occurs following the BMP-mediated induction of two cardiac-restricted transcription factors, Nkx2.5 and MEF2C. Furthermore, either MEF2C or Nkx2.5 can transactivate a luciferase reporter driven by the mXin promoter in mouse fibroblasts. These results suggest that Xin may participate in a BMP-Nkx2.5-MEF2C pathway to control cardiac morphogenesis and looping.  (+info)

Abstract. The use of recombinant peptides based upon the repeated amino acid sequences of Plasmodium has been proposed for malaria vaccines. By reducing homologies of such peptide vaccines to host proteins, the possibility of autoimmune complications may be reduced, and the effective immune response may be enhanced. The Wilbur and Lipman Wordsearch algorithm was used to identify homologous amino acid sequences between tandemly repeated Plasmodium amino acid sequences and the human and human viral sequences compiled in the National Biomedical Research Foundation database. Six published repetitive immunogenic amino acid sequences from the circumsporozoite (CS) antigen, ring-infected erythrocyte surface antigen (RESA), soluble (S) antigen, and falciparum interspersed repetitive antigen (FIRA) of P. falciparum, and the CS protein of P. vivax, were analyzed by computer. Matches of at least 4 amino acids were found for all sequences. In the database, 29 matches were found for human proteins and 26 matches
Chang, E., et al. N-Terminal Amino Acid Sequence Determination of Proteins by N-Terminal Dimethyl Labeling: Pitfalls and Advantages When Compared with Edman Degradation Sequence Analysis. Journal of Biomolecular Technology. 27(2). 07/03/2016.. ...
The complete amino acid sequence of bovine S antigen (48-kDa protein) has been determined by cDNA and partial amino acid sequencing. A 1623-base-pair (bp) cDNA contains an open reading frame coding for a protein of 404 amino acids (45,275 Da). Tryptic peptides and cyanogen bromide peptides of native bovine S antigen were purified and partially sequenced. All of these peptides were accounted for in the long open reading frame. Searching of the National Biomedical Research Foundation data bank revealed no extensive sequence homology between S antigen and other proteins. However, there are local regions of sequence similarity with alpha transducin, including the sites subject to ADP-ribosylation by Bordetella pertussis and cholera toxins and the phosphoryl binding-sites. Secondary structure prediction and circular dichroic spectroscopy show that S antigen is composed predominantly of beta-sheet conformation. Acid-catalyzed methanolysis suggests the presence of low levels of carbohydrate in the ...
Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory[citation needed]. Protein primary structures can be directly sequenced, or inferred from DNA sequences. Amino acids are polymerised via peptide bonds to form a long backbone, with the different amino acid side chains protruding along it. In biological systems, proteins are produced during translation by a cells ribosomes. Some organisms can also make short peptides by non-ribosomal peptide synthesis, which often use amino acids other than the standard 20, and may be cyclised, modified and cross-linked. Peptides can be synthesised chemically via a range of laboratory methods. Chemical methods typically synthesise peptides in the opposite order to ...
Genetic susceptibility to autoimmunity is frequently associated with specific MHC alleles. Diabetogenic MHC class II molecules, such as human HLA-DQ8 and mouse I-Ag7, typically have a small, uncharged amino acid residue at position 57 of their β chain (β57); this results in the absence of a salt bridge between β57 and Argα76, which is adjacent to the P9 pocket of the peptide-binding groove. However, the influence of Argα76 on the selection of the TCR repertoire remains unknown, particularly when the MHC molecule binds a peptide with a neutral amino acid residue at position P9. Here, we have shown that diabetogenic MHC class II molecules bound to a peptide with a neutral P9 residue primarily selected and expanded cells expressing TCRs bearing a negatively charged residue in the first segment of their complementarity determining region 3β. The crystal structure of one such TCR in complex with I-Ag7 bound to a peptide containing a neutral P9 residue revealed that a network of favorable ...
The invention provides a method for determining an amino acid sequence motif for a phosphorylation site of a protein kinase. In the method of the invention, a protein kinase is contacted with an oriented degenerate peptide library, peptides within the library which are substrates for the kinase are converted to phosphopeptides and the phosphopeptides are separated from non-phosphorylated peptides. The isolated phosphopeptides are sequenced and an amino acid sequence motif for the phosphorylation site is determined based upon the relative abundance of different amino acids residues at each degenerate position. The invention also provides peptide substrates for protein kinase A, cell cycle control kinases, src family kinases, the EGF receptor and p92.sup.c-fps/fes based upon amino acid sequence motifs for the phosphorylation sites of these kinases.
Proteins (/ˈproʊˌtiːnz/ or /ˈproʊti.ɪnz/) are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity.. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino ...
TY - JOUR. T1 - The hormonal control of glycogen metabolism. T2 - The amino acid sequence at the phosphorylation site of protein phosphatase inhibitor-1. AU - Cohen, Philip. AU - Rylatt, Dennis B.. AU - Nimmo, Gillian A.. PY - 1977/4/15. Y1 - 1977/4/15. UR - http://www.scopus.com/inward/record.url?scp=0017407844&partnerID=8YFLogxK. U2 - 10.1016/0014-5793(77)80147-6. DO - 10.1016/0014-5793(77)80147-6. M3 - Article. C2 - 193727. AN - SCOPUS:0017407844. VL - 76. SP - 182. EP - 186. JO - FEBS Letters. JF - FEBS Letters. SN - 0014-5793. IS - 2. ER - ...
TY - JOUR. T1 - Deduced primary structure of rat tryptophan-2,3-dioxygenase. AU - Maezono, Katsumi. AU - Tashiro, Kosuke. AU - Nakamura, Toshikazu. PY - 1990/7/16. Y1 - 1990/7/16. N2 - The complete amino acid sequence of the tryptophan 2, 3-dioxygenase (TO) of rat liver was determined from the nucleotide sequence of a full length TO cDNA isolated from a rat liver cDNA library and determined its primary structure. TO was encoded in a mRNA of about 1.7 kb containing an open reading frame of 1218 bp. According to the deduced amino acid sequence, the monomeric polypeptide of TO consisted of 406 amino acid residues with a calculated molecular weight of 47,796 daltons. It has twelve histidine residues around its hydrophobic region, which has homology with some heme proteins and oxygenase, suggesting that this hydrophobic region might to be the core of TO for the activity.. AB - The complete amino acid sequence of the tryptophan 2, 3-dioxygenase (TO) of rat liver was determined from the nucleotide ...
The amino acid sequences of the CT and TMD of NA are highly and moderately conserved, respectively, among the influenza A viruses. Yet the specific function and role of these amino acid sequences in virus biology remain unknown. Results presented in this report show that the specific amino acid residues are not absolutely required for the influenza virus life cycle, since either the complete or part of the NA TMD or CT can be replaced and modified, yet infectious viruses can be rescued and propagated. On the other hand, our data show that specific amino acids in some regions of the TMD and CT as well as a foreign TMD have a profound influence on virus biology, causing reduction in growth during multiple cycles of infection. Reduced yield of NA mutants can be attributed to decreased enzyme activity in the virion and a defect in budding at the cell surface.. Mutations in the TMD and CT of NA can affect protein expression, maturation, transport, incorporation into virions, and enzyme activity and ...
...COLLEGE STATION - Functional amino acids play a critical role in the d...In a journal article appearing in the American Society for Nutrition (... We need to move forward and capitalize on the potential of functional...A functional amino acid is an amino acid that can regulate key metabol...,AgriLife,scientist:,Functional,amino,acids,regulate,key,metabolic,pathways,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
The GLI oncogene, discovered by virtue of its amplification in human tumors, encodes a sequence-specific DNA-binding protein containing five zinc fingers. We have now characterized one member of a family of GLI-related zinc finger genes. A previously identified fragment of GLI3 genomic DNA was used to localize GLI3 to chromosome 7p13 and to isolate cDNA clones. Sequence analysis of these clones and identification of the GLI3 protein by using polyclonal antisera demonstrated that GLI3 encodes a protein of 1,596 amino acids and an apparent molecular mass of 190 kilodaltons. Amino acid sequence comparison with GLI demonstrated seven regions of similarity (53 to 88% identity), with the zinc fingers representing the most similar region. Furthermore, when produced in vitro, the GLI3 protein bound specifically to genomic DNA fragments containing GLI-binding sites. Amino acid sequence comparison with the product of another member of the GLI family, the Drosophila segment polarity gene cubitus ...
Ubiquitin is a 76-residue protein highly conserved among eukaryotes. Conjugation of ubiquitin to intracellular proteins mediates their selective degradation in vivo. We describe a family of four ubiquitin-coding loci in the yeast Saccharomyces cerevisiae. UB11, UB12 and UB13 encode hybrid proteins in which ubiquitin is fused to unrelated (tail) amino acid sequences. The ubiquitin coding elements of UB11 and UB12 are interrupted at identical positions by non-homologous introns. UB11 and UB12 encode identical 52-residue tails, whereas UB13 encodes a different 76-residue tail. The tail amino acid sequences are highly conserved between yeast and mammals. Each tail contains a putative metal-binding, nucleic acid-binding domain of the form Cys-X2-4-Cys-X2-15-Cys-X2-4-Cys, suggesting that these proteins may function by binding to DNA. The fourth gene, UB14, encodes a polyubiquitin precursor protein containing five ubiquitin repeats in a head-to-tail, spacerless arrangement. All four ubiquitin genes ...
The primary structure of porcine brain beta-tubulin was determined by automated and manual Edman degradation of six sets of overlapping peptides. The protein consists of 445 amino acid residues and has a minimum of six positions that are heterogeneous, indicating at least two beta-tubulins in porcine brain. Comparison of the optimally aligned sequences of alpha-tubulin and beta-tubulin indicates that 41% of their primary structures are identical. A region rich in glycyl residues is similar both in sequence and predicted secondary structure to the phosphate binding loop of several nucleotide binding enzymes. beta-Tubulin contains a highly acidic COOH-terminal region that resembles the NH2-terminus of troponin T.. ...
A method is provided for isolating and identifying a recombinant clone having a DNA segment therein coding for at least one desired heterologous polypeptide, at least a short amino acid sequence of which is known, by effecting cDNA synthesis on a mixture of mRNAs containing the mRNA coding for the desired polypeptide, isolating the resultant cDNA mixture, inserting the resultant cDNA into recombinant cloning vehicles, transforming hosts with the vehicles, separating the transformants and isolating and identifying a recombinant clone containing a DNA segment which is homologous over at least a portion thereof to at least one oligonucleotide probe specific for the DNA segment; wherein the probe is an extension of the nucleotide sequence of an oligonucleotide primer having a nucleotide sequence complementary to a region of the target mRNA coding for a portion of the known amino acid sequence, and is complementary to a longer region of the target mRNA coding for a longer portion of the known amino acid
A method is provided for isolating and identifying a recombinant clone having a DNA segment therein coding for at least one desired heterologous polypeptide, at least a short amino acid sequence of which is known, by effecting cDNA synthesis on a mixture of mRNAs containing the mRNA coding for the desired polypeptide, isolating the resultant cDNA mixture, inserting the resultant cDNA into recombinant cloning vehicles, transforming hosts with the vehicles, separating the transformants and isolating and identifying a recombinant clone containing a DNA segment which is homologous over at least a portion thereof to at least one oligonucleotide probe specific for the DNA segment; wherein the probe is an extension of the nucleotide sequence of an oligonucleotide primer having a nucleotide sequence complementary to a region of the target mRNA coding for a portion of the known amino acid sequence, and is complementary to a longer region of the target mRNA coding for a longer portion of the known amino acid
The amino acid sequences of 301 glycosyl hydrolases and related enzymes have been compared. A total of 291 sequences corresponding to 39 EC entries could be classified into 35 families. Only ten sequences (less than 5% of the sample) could not be assigned to any family. With the sequences available for this analysis, 18 families were found to be monospecific (containing only one EC number) and 17 were found to be polyspecific (containing at least two EC numbers). Implications on the folding characteristics and mechanism of action of these enzymes and on the evolution of carbohydrate metabolism are discussed. With the steady increase in sequence and structural data, it is suggested that the enzyme classification system should perhaps be revised. ...
The supernumerary subunit g is found in all mitochondrial ATP synthases. Most of the conserved amino acid residues are present in the membrane C-terminal part of the protein that contains a dimerization motif GXXXG. In yeast, alteration of this motif leads to the loss of subunit g and of supramolecular structures of the ATP synthase with concomitant appearance of anomalous mitochondrial morphologies. Disulfide bond formation involving an engineered cysteine in position 109 of subunit g and the endogenous cysteine 28 of subunit e promoted g + g, e + g, and e + e adducts, thus revealing the proximity in the mitochondrial membrane of several subunits e and g. Disulfide bond formation between two subunits g in mitochondria increased the stability of an oligomeric structure of the ATP synthase in digitonin extracts. These data suggest the participation of the dimerization motif of subunit g in the formation of supramolecular structures and is in favor of the existence of ATP synthase associations, in ...
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1993) The download the paraphrase of shem nh vii1 nag hammadi and manichaean lifetime equations through a internal detail into a right story-layered Africville at the electrical arrangement then in guy. 1978) In: Atlas of Protein Sequence and Structure, Suppl. 2 National Biomedical Research Foundation, Washington, DC.
The detection of HIV-1 p24 antigen in diagnostic tests relies on antibodies binding to conserved areas of the protein to cover the full range of HIV-1 subtypes. Using a panel of 43 different virus-like particles (VLPs) expressing Gag from clinical HIV-1 isolates, we previously found that some highly sensitive tests completely failed to detect p24 of certain VLPs, seemingly unrelated to their subtype. Here we aimed to investigate the reason for this failure, hypothesising that it might be due to single amino acid variations in conserved epitopes. Using amino acid alignment, we identified single amino acid variations at position 16 or 170 of p24, unique to those VLPs that failed to be detected in certain diagnostic tests. Through DNA-mutagenesis, these amino acids were changed to ones more commonly found at these positions. The impact of these changes on p24 detection was tested in commercial diagnostic tests as well as by Western Blot and ELISA, using epitope-specific antibodies. Changing positions 16 or
The observed gene overlays in the viruses ФX174 and SV40 show a surprising economy of information storage; two different amino acid sequences are read in different frames from the same stretch of DNA.
Amino acid sequence in DENV2 NS2B/NS3 protease. The residues marked in bold are part of NS2B amino acid sequence. The residues marked in underline are His-tag.
A standard technique to confirm the amino acid sequence of a molecule, Peptide Mapping Analysis uses multiple enzyme digest strategy to break apart a protein into smaller peptide fragments which are subsequently analysed on the mass spectrometer.. Peptide fragments digested with different enzymes will highly likely provide overlapping amino acid sequence data, allowing for the accurate determination and confirmation of the amino acid sequence of the full length of a target protein molecule.. An added value of Peptide Mapping Analysis is that modifications such as C-terminal truncations and/or N-terminal modifications may also be detected.. For more information please email [email protected] ...
DNA damage can result in a variety of mutations, including point mutations, frameshift mutations, and chromosomal mutations. Point mutations include changes in DNA sequence due to substitution of one base for another during DNA replication. For example, the DNA sequence AATTCGCATTG could be replicated as AACTCGCCTTG. Changes in DNA sequence may or may not result in changes in amino acid sequence when the mutated DNA is used to code for protein. When DNA is translated into proteins, every three nucleotide bases (a codon) code for one amino acid. However, many amino acids are coded for by more than one codon. Thus, if a mutation occurs such that the mutated sequence codes for the same amino acid sequence as the old sequence, this is called a silent mutation. In evolutionary terms, this is also referred to as a neutral mutation. Silent (or neutral) mutations may also occur if there is a change in the amino acid sequence, but this does not alter the structure of the protein. However, if a point ...
An increasing number of proteins with weak sequence similarity have been found to assume similar three-dimensional fold and often have similar or related biochemical or biophysical functions. We propose a method for detecting the fold similarity between two proteins with low sequence similarity based on their amino acid properties alone. The method, the proximity correlation matrix (PCM) method, is built on the observation that the physical properties of neighboring amino acid residues in sequence at structurally equivalent positions of two proteins of similar fold are often correlated even when amino acid sequences are different. The hydrophobicity is shown to be the most strongly correlated property for all protein fold classes. The PCM method was tested on 420 proteins belonging to 64 different known folds, each having at least three proteins with little sequence similarity. The method was able to detect fold similarities for 40% of the 420 sequences. Compared with sequence comparison and ...
The results above define the location of the cleavage site in QSOX1A as occurring between the peptide sequence used to raise the anti-QSOX1A antibody and the TM domain (Figure 5A). To identify potential proteases responsible for the cleavage of QSOX1A, we first searched the UniProt database [26] for all proteases that are known to be present within the human ER and Golgi apparatus (Supplementary Table S1 at http://www.biochemj.org/bj/454/bj4540181add.htm). The resulting list of proteases was analysed manually with regard to their substrate specificities and consensus cleavage patterns. Three of the PPCs (proprotein convertases), PCSK3, PCSK6 and PCSK7, particularly stood out as they cleave at dibasic motifs, two of which are present in the QSOX1A amino acid sequence. The QSOX1A amino acid sequence also was analysed for potential cleavage sites using the ProP 1.0 Server [27]. Two of the predicted PPC cleavage sites are present in the region of interest with cleavage occurring C-terminally of ...
SEC72 encodes the 23-kD subunit of the Sec63p complex, an integral ER membrane protein complex that is required for translocation of presecretory proteins into the ER of Saccharomyces cerevisiae. DNA sequence analysis of SEC72 predicts a 21.6-kD protein with neither a signal peptide nor any transmembrane domains. Antibodies directed against a carboxyl-terminal peptide of Sec72p were used to confirm the membrane location of the protein. SEC72 is not essential for yeast cell growth, although an sec72 null mutant accumulates a subset of secretory precursors in vivo. Experiments using signal peptide chimeric proteins demonstrate that the sec72 translocation defect is associated with the signal peptide rather than with the mature region of the secretory precursor. ...
SEC72 encodes the 23-kD subunit of the Sec63p complex, an integral ER membrane protein complex that is required for translocation of presecretory proteins into the ER of Saccharomyces cerevisiae. DNA sequence analysis of SEC72 predicts a 21.6-kD protein with neither a signal peptide nor any transmembrane domains. Antibodies directed against a carboxyl-terminal peptide of Sec72p were used to confirm the membrane location of the protein. SEC72 is not essential for yeast cell growth, although an sec72 null mutant accumulates a subset of secretory precursors in vivo. Experiments using signal peptide chimeric proteins demonstrate that the sec72 translocation defect is associated with the signal peptide rather than with the mature region of the secretory precursor. ...
TY - JOUR. T1 - Insulin regulation of a novel WD-40 repeat protein in adipocytes. AU - Rodgers, B. D.. AU - Levine, M. A.. AU - Bernier, M.. AU - Montrose-Rafizadeh, C.. PY - 2001. Y1 - 2001. N2 - A 400 bp PCR product generated with degenerate primers derived from the glucagon-like peptide-1 receptor was used to screen a rat skeletal muscle cDNA library. The predicted amino acid sequence of the 978 bp open reading frame has a predicted Mr of 35 804, an estimated isoelectric point (pI) of 5.31 and contains seven WD-40 repeats, which are common to G-protein beta subunits (Gβ). Although chemically and structurally similar to Gβ subunits, the predicted amino acid sequence, when compared with the previously cloned Gβ isoforms, was found to be only 31-41% similar and thus was named Gβ-like (GβL, Gable). Western blotting of whole-cell lysates and immunoprecipitates of membrane and cytosolic fractions of HEK 293 cells stably overexpressing a carboxy-terminal His-tagged GβL indicates that the ...
A polynucleotide sequence for the mouse ortholog of human zalphal 1 has been identified and is shown in SEQ ID NO:84 and the corresponding amino acid sequence shown in jEQ ID NO: 85. AnalYsis of the mouse zalphal 1 polypeptide encoded by the DNA\ sequence of SEQ ID N0(84)revealed an open reading frame encodmg 529 amino acids (SEQ ID NO:85) comprising a predicted secretory signal peptide of 19 amino acid residues (residue 1 (Met) to residue 19 (Ser) of SEQ ID NO:85), and a mature polypeptide of 510 amino acids (residue 20 (Cys) to residue 529 (Ser) of SEQ ID N0:2). In addition to the WSXWS motif (SEQ ID N0:3) corresponding to residues 214 to 218 of SEQ ID N0:85, the receptor comprises a cytokine-binding domain of approximately 200 amino acid residues (residues 20 (Cys) to 237 (His) of SEQ ID N0:85); a domam linker (residues 120 (Pro) to 123 (Pro) of SEQ ID NO:85); a penultimate strand region (residues 192 (Lys) to 202 (Ala) of SEQ ID NO:85); a transmembrane domain (residues 238 (Met) to 254 (Leu) ...
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Adducin is a membrane-skeletal protein which is a candidate to promote assembly of a spectrin-actin network in erythrocytes and at sites of cell-cell contact in epithelial tissues. The complete sequence of both subunits of human adducin, alpha (737 amino acids), and beta (726 amino acids) has been deduced by analysis of the cDNAs. The two subunits have strikingly conserved amino acid sequences with 49% identity and 66% similarity, suggesting evolution by gene duplication. Each adducin subunit has three distinct domains: a 39-kD NH2-terminal globular protease-resistant domain, connected by a 9-kD domain to a 33-kD COOH-terminal protease-sensitive tail comprised almost entirely of hydrophilic amino acids. The tail is responsible for the high frictional ratio of adducin noted previously, and was visualized by EM. The head domains of both adducin subunits exhibit a limited sequence similarity with the NH2-terminal actin-binding motif present in members of the spectrin superfamily and actin gelation ...
Maloy W.L.; Nathenson S.G.; Coligan J.E., 1981: Primary structure of murine major histo compatibility complex allo antigens amino acid sequence of the amino terminal 98 residues of the h 2d b glyco protein
The glycoprotein encoded by this gene is a cell surface antigen that is expressed in greater than 95% of human colon cancers. The open reading frame encodes a 319-amino acid polypeptide having a putative secretory signal sequence and 3 potential glycosylation sites. The predicted mature protein has a 213-amino acid extracellular region, a single transmembrane domain, and a 62-amino acid intracellular tail. The sequence of the extracellular region contains 2 domains characteristic of the CD2 subgroup of the immunoglobulin (Ig) superfamily. [provided by RefSeq, Jul 2008 ...
The Cycle 1 results indicate that the N-terminal amino acid residue is D (aspartic acid). The Cycle 2 results indicate that the second amino acid group from the N-terminal is V (valine). Analysis to the 21st residue reveals the sequence from the N-terminal to be: Asp-Val-Val-Met-Thr-Gln-Thr-Pro-Leu-Thr-Leu-Ser-Val-Thr-Ile-Gly-Gln-Pro-Ala-Ser-Ile.. ...
TY - JOUR. T1 - The amino acid sequences of the phosphorylated sites in troponin-I from rabbit skeletal muscle. AU - Huang, T. S.. AU - Bylund, D. B.. AU - Stull, J. T.. AU - Krebs, E. G.. PY - 1974/6/15. Y1 - 1974/6/15. UR - http://www.scopus.com/inward/record.url?scp=0016165471&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0016165471&partnerID=8YFLogxK. U2 - 10.1016/0014-5793(74)80738-6. DO - 10.1016/0014-5793(74)80738-6. M3 - Article. C2 - 4369265. AN - SCOPUS:0016165471. VL - 42. SP - 249. EP - 252. JO - FEBS Letters. JF - FEBS Letters. SN - 0014-5793. IS - 3. ER - ...
Fig. 4 shows the amino acid sequences of the predicted proteins of AtFpg-1, -1a, -2, -3, and -4. Exons 1, 2, 3, 5, 6, and 7 were entirely conserved in all the Arabidopsis cDNA clones. The polypeptide chains encoded by exons 1, 5, 6,and 7 represent the major conserved regions between Arabidopsis and bacterial FPGs , showing between 29 and 54% identity between Arabidopsis and E. coli amino acid sequences. The N-terminal sequence of exon 1 and the lysine of exon 5 (K155) of E. coli FPG have been associated with the active site. The predicted amino acid sequence coded by exon 1 shows a surprising relationship to a sequence from DNA photolyase, another DNA repair enzyme but one quite unrelated to FPG (Fig. 5). If this relates to DNA binding, it might explain how AtFPG-2, which lacks the C-terminal DNA-binding region present in AtFPG-1 (or the zinc-finger of E. coli FPG) might have the DNA cleavage activities measured by Gao and Murphy (Photochem. Photobiol., in press). The optional exons are exon 4 ...
We have cloned the cDNA encoding a murine GDNF inducible transcription factor designated mGIF. It is homolgous to two human genes, TIEG (Subramaniam et al., 1995) and EGR-α (Blok et al., 1995). TIEG was cloned from fetal osteoblastic cells and found to be induced by TGF-β and by epidermal growth factor (EGF), whereas EGR-α was cloned from prostate carcinoma cells and found to be induced by EGF and repressed by androgens. TIEG and EGRα have identical amino acid sequences except for 12 residues absent in the N terminus of EGRα. Thus, TIEG and EGRα appear to be encoded by the same gene. Sequence comparison between murine mGIF and these two human proteins indicates 85% amino acid identity. Comparison of their nucleotide sequences revealed that although these cDNAs are homologous within their open reading frame, more diversity exists in their 3′ untranslated regions. Both the human and murine proteins are rich in proline. mGIF has two proline-rich regions; one contains 17 prolines of 90 ...
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The following experiments were conducted to discern which domains or regions of XB130 are crucial for its Rac-dependent peripheral translocation. XB130 contains a variety of domains that in principle might contribute to its peripheral (membrane and/or lamellipodial) redistribution (Fig. 6A). Key candidate regions included the two pleckstrin homology domains, PH1 (aa 175-271) and PH2 (aa 353-446), which might be involved in the interaction between proteins and membrane phospholipids; the so called unique region (aa 491-648), which holds the lowest amino acid sequence homology to AFAP-110; the coiled-coiled motif (aa 652-750), which shows similarity to a region in AFAP-110 that harbors a leucine zipper motif for protein-protein interaction and a 17-residue stretch that is essential for F-actin binding or cross-linking; the N-terminus (aa 2-169), which contains SH3- and SH2-domain binding motifs, several tyrosine kinase target residues (e.g. Y54), as well as a putative actin-binding motif (see the ...
Structure- Type I MHC- It has a 45 KD alpha chain associated noncovalently with a 12 KD beta 2 microglobulin molecule. Alpha chain is a trans membraneglycoprotein encoded by A, B, C region in human HLA complexes and by K, D/L region in mice. Association of alpha chain and beta 2 microglobulin require for expression of class I molecule on cell membrane. Alpha chain bind to plasma membrane by its hydrophobic transmembrane segment and hydrophilic cytoplasmic tail. Alpha chain is made up of three external domain(α1,α2,α3). Each domain have 90 amino acid, a trans membrane domain have 25 hydrophobic amino acid, a short segment of hydrophilic amino acid and a cytoplasmic segment of 30 amino acid. Peptide which bind to class I MHC is made up of 8-9 amino acid ...
Whilst the fact that the single-letter codes do not all match the first letter of the amino acid that they correspond to is somewhat confusing to begin with is is worth remembering that most proteins of interest contain hundreds of amino acid residues. To illustrate how useful the amino acid codes can be lets have a look at a rather small imaginary protein with only seven residues: Alanine-Phenylalanine-Proline-Leucine-Serine-Valine-Valine-Arginine This is already irritatingly long if you have to write it out more than once. So, using the three-letter codes we have instead: ALA-PHE-PRO-LEU-SER-VAL-VAL-ARG This is already a great improvement in terms of reducing the length of the sequence that we have to write (and it remains fairly human-readable since the codes are just the first part of the amino acid names). However, if our protein had a more realistic number of residues e.g. 700 instead of 7 then this is clearly still going to be a fairly long piece of text when fully written out. Finally ...
This program uses protein sequences to compute a distance matrix, under four different models of amino acid replacement. It can also compute a table of similarity between the amino acid sequences. The distance for each pair of species estimates the total branch length between the two species, and can be used in the distance matrix programs FITCH, KITSCH or NEIGHBOR. This is an alternative to use of the sequence data itself in the parsimony program PROTPARS. The program reads in protein sequences and writes an output file containing the distance matrix or similarity table. The five models of amino acid substitution are one which is based on the Jones, Taylor and Thornton (1992) model of amino acid change, the PMB model (Veerassamy, Smith and Tillier, 2004) which is derived from the Blocks database of conserved protein motifs, one based on the PAM matrixes of Margaret Dayhoff, one due to Kimura (1983) which approximates it based simply on the fraction of similar amino acids, and one based on a ...
For release 67 we changed how we store the protein function predictions from SIFT and PolyPhen so that they also can be used for more than just Ensembl transcripts, including RefSeq transcripts. We use these tools to compute the predicted effect of every possible amino acid substitution in the human proteome (over 2 billion predictions!). Now, the complete set of predictions for a particular protein are retrieved using the protein sequence itself as an identifier rather than an Ensembl stable identifier (we actually use the MD5 hash of the sequence). This means that you can retrieve predictions for any protein that has the same amino acid sequence as an Ensembl translation. So if you work with RefSeq transcripts, you can now get SIFT and PolyPhen predictions for any missense variants that fall in the 95% of RefSeq transcripts that match an Ensembl transcript exactly, using both the Variant Effect Predictor (VEP) and the Variation API.. New in release 67 are also predictions from both classifier ...
Collins, J.H.; Elzinga, M., 1975: The primary structure of actin from rabbit skeletal muscle. Completion and analysis of the amino acid sequence
Both thrombin and trypsin are serine-proteases known to possess PAR-dependent vascular effects (see the Introduction). The vascular effects of thrombin and trypsin were similar in that both proteases were more potent relaxant than contractile agonists (Fig. 1), consistent with the observations of other investigators (Muramatsu et al., 1992; Hwa et al., 1996; Komuro et al., 1997). Furthermore, the protease activity responsible for activation of contractile receptors showed similar kinetics between thrombin and trypsin and contraction was a slower response than relaxation (Fig. 2). It is possible that the release of endothelial factors may play a role in generating a faster relaxant than contractile response or that the relaxant second messenger system is more rapidly activated. The differences in the time to achieve maximal relaxant and maximal contractile responses could also be due to the cleavage site amino acid sequence differences between the relaxant and contractile PARs such that enzymatic ...
Hello all- I am looking for insight into how to determine the amino acid sequence of a peptide bound by MHC I. Is it possible to purify the MHC away from the cells, and then the peptide from the MHC? Or is this technically not feasible at this time. Thanks Kajetan -------------- next part -------------- A non-text attachment was scrubbed... Name: Kajetan-Groicher.vcf Type: text/x-vcard Size: 427 bytes Desc: Card for Kajetan H. Groicher Url : http://iubio.bio.indiana.edu/bionet/mm/immuno/attachments/19991113/ebfcbaa7/Kajetan-Groicher.bin ...
develop a new model summarizing the entire process of transcription and translation with your lab group you will be asked to communicate share amino acid sequence chart dna.. ...
Synopsis Proteins evolved from a common ancestor are said to be homologues and to constitute a "family" with potentially similar structures, functions, and interactions. The problem of identifying "real" protein families based on amino acid sequence conservation is still doubtful because algorithms that search for pairwise homologies can miss important relations and produce false hits. Problem of reconstructing the evolutionary relationships amongst proteins and of classifying them into families from a topological point of view was addressed by defining the Protein Homology Network (PHN). In the PHN, proteins are seen as nodes connected by links that represent the homology relations inferred by sequence similarity. In such a representation, protein families should appear as dense clusters disconnected from the rest of the network. The availability of a large number of sequenced genomes now allows us to map the full set of protein similarity relationships into a Protein Homology Network (PHN), ...
The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino ... Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence ... amino acids. All proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a ... Sequence motif. Short amino acid sequences within proteins often act as recognition sites for other proteins.[22] For instance ...
The complete amino acid sequence". European Journal of Biochemistry. 169 (3): 547-53. doi:10.1111/j.1432-1033.1987.tb13644.x. ... The complete amino acid sequence". European Journal of Biochemistry. 169 (3): 547-53. doi:10.1111/j.1432-1033.1987.tb13644.x. ... Cyanogen bromide cleavage and N-terminal sequences of the fragments". The Biochemical Journal. 215 (3): 565-71. doi:10.1042/ ... Partial sequence determination of the heavy chain and identification of the peptide bond cleaved during activation". European ...
Amino acid or cDNA sequencing Determination of amino acid sequence. See also[edit]. *Ero1 ... Glycoproteins are proteins which contain oligosaccharide chains (glycans) covalently attached to amino acid side-chains. The ... but also on tyrosine or non-canonical amino acids such as hydroxylysine & hydroxyproline. ... Compositional analysis following acid hydrolysis Identifies sugars that the glycoprotein contains and their stoichiometry. ...
The complete amino acid sequence". J. Biol. Chem. 246 (18): 5770-84. PMID 5096093. Saxe DF, Takahashi N, Hood L, Simon MI (1985 ... Carnegie PR (1972). "Amino acid sequence of the encephalitogenic basic protein from human myelin". Biochem. J. 123 (1): 57-67. ... Gibson BW, Gilliom RD, Whitaker JN, Biemann K (1984). "Amino acid sequence of human myelin basic protein peptide 45-89 as ... "Complete amino acid sequence of PO protein in bovine peripheral nerve myelin". J. Biol. Chem. 262 (9): 4208-14. PMID 2435734. ...
Purification, properties, and amino acid sequence". The Journal of Biological Chemistry. 254 (22): 11475-84. PMID 500653.. ... thymidylic acid, and certain amino acids. While the functional dihydrofolate reductase gene has been mapped to chromosome 5, ... Masters JN, Attardi G (1983). "The nucleotide sequence of the cDNA coding for the human dihydrofolic acid reductase". Gene. 21 ... translation repressor activity, nucleic acid binding. • sequence-specific mRNA binding. • NADP binding. ...
Purification and amino acid sequence.». Eur. J. Biochem. 188 (3): 501-6. PMID 2110056. doi:10.1111/j.1432-1033.1990.tb15428.x. ... Amino acid sequence of the reduced S-aminoethylated protein.». Arch. Biochem. Biophys. 179 (1): 189-99. PMID 843082. doi: ...
... is a 9-amino acid peptide chain. The amino acid sequence of bradykinin is: Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg ( ... Bradykinin is a physiologically and pharmacologically active peptide of the kinin group of proteins, consisting of nine amino ...
Barkholt, V. (1987). "Amino acid sequence of endothiapepsin. Complete primary structure of the aspartic protease from Endothia ... Endothiapepsin (EC 3.4.23.22, Endothia aspartic proteinase, Endothia acid proteinase, Endothia parasitica acid proteinase, ...
Amino acid sequence of the reduced S-aminoethylated protein". Archives of Biochemistry and Biophysics. 179 (1): 189-99. doi: ... Purification and amino acid sequence". European Journal of Biochemistry / FEBS. 188 (3): 501-6. doi:10.1111/j.1432-1033.1990. ... Yamamoto T, Nakamura Y, Nishide J, Emi M, Ogawa M, Mori T, Matsubara K (Oct 1985). "Molecular cloning and nucleotide sequence ...
The complete amino acid sequence". European Journal of Biochemistry. 169 (3): 547-553. doi:10.1111/j.1432-1033.1987.tb13644.x. ... This peptide coupling is unique in that it occurs between the amino moiety of the cysteine and the terminal carboxylic acid of ... to metabolize γ-GC and GSH into its constituent amino acids. GCL enzymatic activity generally dictates cellular GSH levels and ...
Isolation and amino acid sequence". J. Biochem. 90 (4): 1205-11. PMID 7309716. Kardalinou E, Eick S, Albig W, Doenecke D (1993 ... 2003). "The DNA sequence and analysis of human chromosome 6". Nature. 425 (6960): 805-11. doi:10.1038/nature02055. PMID ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 1986). "Enhancer-facilitated expression of prokaryotic and eukaryotic genes using human histone gene 5' regulatory sequences". ...
Isolation and amino acid sequence". J. Biochem. 90 (4): 1205-11. PMID 7309716. Kato S, Sekine S, Oh SW, et al. (1995). " ... Nucleic Acids Res. 15 (7): 2871-89. doi:10.1093/nar/15.7.2871. PMC 340704 . PMID 3031613. "Entrez Gene: H3F3A H3 histone, ... evidence that basally expressed histone genes have intervening sequences and encode polyadenylylated mRNAs". Proc. Natl. Acad. ... "The Groucho/transducin-like enhancer of split transcriptional repressors interact with the genetically defined amino-terminal ...
Isolation and amino acid sequence". J. Biochem. 85 (2): 615-24. PMID 422550. Dobner T, Wolf I, Mai B, Lipp M (1992). "A novel ... 2003). "The DNA sequence and analysis of human chromosome 6". Nature. 425 (6960): 805-11. doi:10.1038/nature02055. PMID ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
Isolation and amino acid sequence". J. Biochem. 85 (2): 615-24. PMID 422550. Frohm M, Gunne H, Bergman AC, et al. (1996). " ... 2003). "The DNA sequence and analysis of human chromosome 6". Nature. 425 (6960): 805-11. doi:10.1038/nature02055. PMID ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
Isolation and amino acid sequence". J. Biochem. 85 (2): 615-24. PMID 422550. Albig W, Doenecke D (1998). "The human histone ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
Isolation and amino acid sequence". J. Biochem. 85 (2): 615-24. PMID 422550. Albig W, Doenecke D (1998). "The human histone ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
Isolation and amino acid sequence". J. Biochem. 90 (4): 1205-11. PMID 7309716. Goto H, Tomono Y, Ajiro K, et al. (1999). " ... 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Nucleic Acids Res. 31 (3): 878-85. doi:10.1093/nar/gkg176. PMC 149197 . PMID 12560483. Wang Y, Wysocka J, Sayegh J, et al. ( ...
Isolation and amino acid sequence". J. Biochem. 90 (4): 1205-11. PMID 7309716. Díaz-Jullien C, Pérez-Estévez A, Covelo G, ... Nucleic Acids Res. 31 (3): 878-885. doi:10.1093/nar/gkg176. PMC 149197 . PMID 12560483. Yoon HG, Chan DW, Huang ZQ, Li J, ... regulatory sequences". Biochem Cell Biol. 64 (4): 277-289. doi:10.1139/o86-039. PMID 3013246. "Entrez Gene: HIST2H3C histone ...
In general, prediction tools take as input information about a protein, such as a protein sequence of amino acids, and produce ... Emanuelsson O (Dec 2002). "Predicting protein subcellular localisation from amino acid sequence information". Briefings in ...
Findlay JB, Brew K (1972). «The complete amino-acid sequence of human -lactalbumin.». Eur. J. Biochem. 27 (1): 65-86. DOI: ... Prager EM, Wilson AC (1988). «Ancient origin of lactalbumin from lysozyme: analysis of DNA and amino acid sequences». J. Mol. ... Giuffrida MG, Cavaletto M, Giunta C, et al. (1998). «The unusual amino acid triplet Asn-Ile-Cys is a glycosylation consensus ... identification and characterisation of plasmids containing human alpha-lactalbumin cDNA sequences». Nucleic Acids Res. 9 (1): ...
Ritonja, A.; Buttle, D.J.; Rawlings, N.D.; Turk, V.; Barrett, A.J. (1989). "Papaya proteinase IV amino acid sequence". FEBS ...
cDNA and deduced amino-acid sequence". Eur. J. Biochem. 212 (3): 771-6. doi:10.1111/j.1432-1033.1993.tb17717.x. PMID 7681778. ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
Perham, Richard N; Baumeister, Wolfgang; Johnson, Louise; Steven, Alasdair (1975). Instrumentation in amino acid sequence ... Instrumentation in amino acid sequence analysis. London New York: Academic Press. ISBN 9780125512503. Perham, Richard N; ...
cDNA and deduced amino-acid sequence". Eur. J. Biochem. 212 (3): 771-6. doi:10.1111/j.1432-1033.1993.tb17717.x. PMID 7681778. ... 1992). "Human inter-alpha-trypsin inhibitor: full-length cDNA sequence of the heavy chain H1". Biochim. Biophys. Acta. 1132 (1 ... their identification by electrophoresis and partial sequencing. Differential reactivity with concanavalin A". Biol. Chem. Hoppe ...
... of amino acid sequence conserved) and STIM2 (31% identical; 46% of amino acid sequence conserved). Unicellular eukaryotes such ... of the amino acid sequence of STIM1). Only the extreme of the C-terminal region shows a significant sequence divergence. The ... Human STIM2 consists of 833 amino acid residues (aas) (105-115 kDa) (Fig. 1), 148 additional aas compared to human STIM1. Their ... 1). Mouse STIM2 shares a 92% identity with human STIM2 in the aminoacid sequence according to the pairwise alignment generated ...
Liu J, Sessa WC (1994). "Identification of covalently bound amino-terminal myristic acid in endothelial nitric oxide synthase ... 1997). "Large-scale concatenation cDNA sequencing". Genome Res. 7 (4): 353-8. doi:10.1101/gr.7.4.353. PMC 139146 . PMID 9110174 ... Zhou W, Parent LJ, Wills JW, Resh MD (1994). "Identification of a membrane-binding domain within the amino-terminal region of ... 1985). "Amino terminal myristylation of the protein kinase p60src, a retroviral transforming protein". Science. 227 (4685): 427 ...
Filters include the use of a scoring scheme, comparison of scan numbers versus sequence of common ions to be MS/MS, and ... A method for locating pattern matches in amino acids by use of various and sequential filters capable of determining inner ... 7. A method for pattern matching unique sequences in multiple samples of amino acids comprising the steps of: a. analyzing a ... 9. A method for pattern matching unique sequences in multiple samples of amino acids comprising the steps of: a. analyzing a ...
Amino acid sequence definition at Dictionary.com, a free online dictionary with pronunciation, synonyms and translation. Look ... amino acid sequence. noun 1. the unique sequence of amino acids that characterizes a given protein ...
The structure of a protein may be directly sequenced or inferred from the sequence of DNA. ... The protein primary structure conventionally begins at the amino-terminal (N) end and continues until the carboxyl-terminal (C ... Each protein or peptide consists of a linear sequence of amino acids. ... Amino Acids and Protein Sequences. News-Medical. https://www.news-medical.net/life-sciences/Amino-Acids-and-Protein-Sequences. ...
The amino acid sequence of dog (Canis familiaris) hemoglobin.. Brimhall B, Duerst M, Jones RT. ... The manual sequencing of the tryptic peptic from the alpha and beta chains of dog hemoglobin is described, including evidence ... Although the actual sequence was published in 1970, the evidence on which it was based has not previously appeared. ...
... Dan Jacobson DANJ at JHUHYG.BITNET Sat Nov 2 15:30:24 EST 1991 *Previous message ... take the amino aci d composition of a peptide fragment and find the location of the peptide in a larger amino acid sequence. I ... accross an article describing software designed to do just that as well as some other functions in volved in protein sequencing ...
Any amino acid sequence that contains post-translationally modified amino acids may be described as the amino acid sequence ... 2) Amino acids: Amino acids are those L-amino acids commonly found in naturally occurring proteins and are listed in WIPO ... V. SEQUENCE IDENTIFIER. 37 CFR 1.821(c) requires that each disclosed nucleic acid or amino acid sequence in the application ... 37 CFR 1.821 Nucleotide and/or amino acid sequence disclosures in patent applications.. *(a) Nucleotide and/or amino acid ...
Prediction of protein antigenic determinants from amino acid sequences Message Subject (Your Name) has sent you a message from ... A method is presented for locating protein antigenic determinants by analyzing amino acid sequences in order to find the point ... Prediction of protein antigenic determinants from amino acid sequences. T P Hopp and K R Woods ... This is accomplished by assigning each amino acid a numerical value (hydrophilicity value) and then repetitively averaging ...
This specificity may not be conferred at the amino acid level, as sequences encoding the amino-terminal 15 amino acid residues ... Secretion signals have been mapped in several Yop proteins to sequences encoding the amino-terminal 15 amino acid residues (11 ... A conserved amino acid sequence directing intracellular type III secretion by Salmonella typhimurium. Edward A. Miao and Samuel ... The amino acid sequence of SspH1 and SlrP also sets them apart from other family members. Although they do contain the ...
The assumed specifically active fragment of bovine fibrinopeptide B with the amino acid sequence 15-21 and the fragment 12-21 ... 1. The assumed specifically active fragment of bovine fibrinopeptide B with the amino acid sequence 15-21 and the fragment 12- ... Synthesis of a fragment of bovine fibrinopeptide B with the amino acid sequence 12-21. ...
The calculated molar ratios of the amino acids and the percentages of the N- or C-terminal amino acid residues of the supposed ... The amino acid sequence of the peptide moiety of the pseudomurein from Methanobacterium thermoautotrophicum.. König H, Kandler ... The amino acid sequence of the peptide subunits of the peptide moiety of the sacculus polymer (pseudomurein) of ... Methanobacterium thermoautotrophicum was elucidated by analysing overlapping peptides obtained from partial acid hydrolsates of ...
KDEL is a target peptide sequence in the amino acid structure of a protein which prevents the protein from being secreted from ... ER retention KKXX (amino acid sequence) Endoplasmic reticulum protein retention receptors KDELR1 KDELR2 KDELR3 Mariano ... K-Lysine D-Aspartic acid E-Glutamic acid L-Leucine Therefore, the sequence in three letter code is: Lys-Asp-Glu-Leu. The ... The abbreviation KDEL is formed by the corresponding letters to each amino acid. This letter system was defined by the IUPAC ...
... any amino acid X- any amino acid ER retention KDEL (amino acid sequence) Martin J. Vincent; Annelet S. Martin; Richard W. ... 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 ...
If youre curious to see how PROBCONS performs on nucleotide sequence, try out PROBCONSRNA, an experimental version of PROBCONS ... Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences. RUN. ABOUT. DOWNLOAD. HELP. ...
... amino acid sequence explanation free. What is amino acid sequence? Meaning of amino acid sequence medical term. What does amino ... Looking for online definition of amino acid sequence in the Medical Dictionary? ... amino acid sequence. Also found in: Dictionary. amino acid sequence. the order in which AMINO ACIDS are placed along a protein ... uncharacterized amino acid sequences predicted from genome DNA sequences, and amino acid sequences of known function.. A "game ...
Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-amino-acid amidohydrolase from Agrobacterium ... Chain A: N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE. Chain Downloadable Files. Download FASTA File. View Sequence & DSSP Image. ... Sequence Display for the Entities in PDB 1FO6 The graphical representation below shows this entrys sequences as reported in ... Sequence & Structure Relationships. Enable Jmol to view annotations in 3D.. Display Jmol. Redundancy Reduction and Sequence ...
A new method of inference of ancestral nucleotide and amino acid sequences.. Z Yang, S Kumar and M Nei ... A new method of inference of ancestral nucleotide and amino acid sequences.. Z Yang, S Kumar and M Nei ... A new method of inference of ancestral nucleotide and amino acid sequences.. Z Yang, S Kumar and M Nei ... A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum ...
Mutated Sequence: TAC TGG CG TTA GRR GAT ATA ACT. mRNA Sequence: AUG ACC GC AAU CAA CUA UAU UGA. Amino Acid Sequence: met thr ... Similar Discussions: Determining mutated, mRNA, Amino Acid sequence * Acidity/basicity of amino acids (Replies: 1) ... The filled in answers are in bold And Im completely lost with the Amino Acid sequence, my TA did this in class and I still ... What mechanism is responsible for the sequencing of amino acids? (Replies: 1) ...
... Lai C.-Y., Nakai N., Chang D. ... Elucidation of the amino acid sequence of fructose-1,6-bis-phosphate aldolase from rabbit muscle has made it possible to assign ... p>This will take you to the BLAST page where you can edit options ,/p>,p>,a href="/help/sequence-searches">More..,/a>,/p>. Wed ...
Acids as Inhibitors of Protein Tyrosine Phosphatase 1B ... Oxalyl-Aryl-Amino Benzoic Acid inhibitors of PTP1B, compound 17 ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1ONY Legend Entity #1 , Chains: A Protein-tyrosine phosphatase, non- ... Blast this sequence against all of PDB Archive.. Rank. In each cluster, the chains are sorted (i.e. ranked) according to the ...
... consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found ... High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed ... These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes ... Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, ...
Amino acid sequence. About microscopic forms of life, including Bacteria, Archea, protozoans, algae and fungi. Topics relating ... How do I find amino acid sequence for different sub-units for cholera toxin ? ?. Please help me. Share link or etc. ...
The same way that pretty much any amino acid sequence (or better yet, nucleotide sequence) of sufficient length can be used to ... Viral Amino acid sequence. About microscopic forms of life, including Bacteria, Archea, protozoans, algae and fungi. Topics ... Viral Amino acid sequence. by Layd33foxx » Tue Mar 13, 2012 12:01 am ... How can a viral amino acid sequence be used to identify a virus? ... Nucleic acids are better for that.. Anyway, if you get some ...
... in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, ... The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the ... RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences Nucleic Acids Res. 2003 Jul 1;31(13):3537-9. doi: ... It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the ...
Research Topics about Experts and Doctors on amino acid sequence in Cambridge, Massachusetts, United States ... The predicted amino acid sequence of the pgm gene is highly conserved in E. coli, Acetobacter xylinum, Saccharomyces cerevisiae ... Lane W, Galat A, Harding M, Schreiber S. Complete amino acid sequence of the FK506 and rapamycin binding protein, FKBP, ... You are here: Locale , United States , Massachusetts , Experts and Doctors on amino acid sequence in Cambridge, Massachusetts, ...
Publications about Experts and Doctors on amino acid sequence in Houston, Texas, United States ... Yang C, Huang W, Chirala S, Wakil S. Complete amino acid sequence of the thioesterase domain of chicken liver fatty acid ... Experts and Doctors on amino acid sequence in Houston, Texas, United States. Summary. Locale: Houston, Texas, United States ... You are here: Locale , United States , Texas , Experts and Doctors on amino acid sequence in Houston, Texas, United States ...
  • These results show that although the sequences of NA CT and TMD per se are not absolutely essential for the virus life cycle, specific amino acid sequences play a critical role in providing structural stability, enzyme activity, and lipid raft association of NA. (asm.org)
  • Together with American colleagues, the Mainz researchers have reported in the latest edition of the scientific journal Science Advances that the interactions of specific amino acid sequences of the protein molecules generate water domains with increased order and stronger hydrogen bonds. (mpg.de)
  • For many purposes the primary amino acid sequence of a protein can be directly used to predict important structural parameters. (caltech.edu)
  • In turn, each residue's contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold analysis from sequence data. (biomedcentral.com)
  • In particular we study the effect of minor mutations of insulin's primary amino acid sequence on its interaction with 1,2-Dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) model lipid layers. (frontiersin.org)
  • These signals are insensitive to frameshift mutations ( 12 ), suggesting that the recognized signal lies within the mRNA sequence. (pnas.org)
  • This mRNA code has a sequence of codons, which provides the order of assembling various amino acids together. (biologywise.com)
  • From the strand of mRNA, that is transported in the cytoplasm, tRNA (transfer RNA) carry the information about the sequence, to a ribosome site for protein assembly. (biologywise.com)
  • This study aimed to obtain the complete cDNA coding sequences of aqp1 and aqp3 from the gills of Protopterus annectens , and to determine their branchial mRNA and protein expression levels during the induction, maintenance and arousal phases of aestivation. (frontiersin.org)
  • In other aspects, replicable recombinant cloning vehicles are provided which code for plant 1-deoxyxylulose-5-phosphate synthases, or for a base sequence sufficiently complementary to at least a portion of 1-deoxyxylulose-5-phosphate synthase DNA or RNA to enable hybridization therewith. (osti.gov)
  • In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding a plant 1-deoxyxylulose-5-phosphate synthase. (osti.gov)
  • 2. A recombinant expression vector comprising the nucleic acid of claim 1 operably linked to a transcription regulatory element. (patents.com)
  • This letter system was defined by the IUPAC and IUBMB in 1983, and is as follows: K-Lysine D-Aspartic acid E-Glutamic acid L-Leucine Therefore, the sequence in three letter code is: Lys-Asp-Glu-Leu. (wikipedia.org)
  • The Cycle 1 results indicate that the N-terminal amino acid residue is D (aspartic acid). (shimadzu.com)
  • The existence of heavy chain variable region subgroups is also deduced, from a comparison of these two sequences with those of another γ 1 chain, Eu, a μ chain, Ou, and the partial sequence of a fourth γ 1 chain, Ste. Carbohydrate has been found to be linked to an aspartic acid residue in the variable region of one of the γ 1 chains, Cor. (biochemj.org)
  • Among the influenza A viruses, both the cytoplasmic tail (CT) and transmembrane domain (TMD) amino acid sequences of NA are highly conserved, yet their function(s) in virus biology remains unknown. (asm.org)
  • In addition, we also made two chimeric NA by replacing the CT proximal one-third amino acids of the NA TMD [NA(1T2N)NA] and the entire NA TMD (NATRNA) with that of human transferrin receptor (TR) (a type II transmembrane glycoprotein). (asm.org)
  • The HA protein, a type I transmembrane protein, is responsible for binding to the cell surface sialic acid (the receptor), eliciting neutralizing antibodies, and mediating virus entry into the cell by fusion of the viral membrane with the endosomal membrane ( 46 ). (asm.org)
  • Three CD36 domains were identified including cytoplasmic, transmembrane and exoplasmic sequences. (mdpi.com)
  • Specifically defined" means those amino acids other than "Xaa" and those nucleotide bases other than "n" defined in accordance with the World Intellectual Property Organization (WIPO) Handbook on Industrial Property Information and Documentation, Standard ST.25: Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in Patent Applications (1998), including Tables 1 through 6 in Appendix 2, herein incorporated by reference. (uspto.gov)
  • Modifications, e.g. , methylated bases, may be described as set forth in WIPO Standard ST.25 (1998), Appendix 2, Table 2, but shall not be shown explicitly in the nucleotide sequence. (uspto.gov)
  • three bases provide the code for each amino acid. (thefreedictionary.com)
  • Using the single-letter code, plug in the amino acids you wish to locate and Sequencher will find and highlight the bases within the sequence that code for those amino acids. (genecodes.com)
  • Sequencher can easily go to the next set of bases that comply with the search by selecting the Find Next button in the Find Amino Acids window. (genecodes.com)
  • In aqueous solutions they are dipolar ions (zwitterions, or hybrid ions) that react with strong acids or bases in a way that leads to the neutralization of the negatively or positively charged ends, respectively. (britannica.com)
  • Because of their reactions with strong acids and strong bases, the amino acids act as buffers-stabilizers of hydrogen ion (H + ) or hydroxide ion (OH − ) concentrations. (britannica.com)
  • Such a cleavage is essential for viral infectivity because in the acidic pH of the endosome it exposes a membrane fusion peptide at the amino terminus of the HA2 subunit required for membrane fusion ( 26 ). (asm.org)
  • A method for locating pattern matches in amino acids by use of various and sequential filters capable of determining inner sample pattern matches, inner group pattern matches, and word matching for purposes of further analysis or data mining. (google.com)
  • This analysis employs the Edman method (sequential cleaving of amino acids from the N-terminal of the protein to determine the amino acid sequence), which is the most reliable method for determining amino acid sequences. (shimadzu.com)
  • Besides, experimental procedures reveal that C. sticklandii degrades amino acids in a preferential and sequential way. (biomedcentral.com)
  • We report the amino acid sequence of a 299-residue segment from the α chain of the human platelet membrane glycoprotein Ib. (elsevier.com)
  • 37 CFR 1.821 Nucleotide and/or amino acid sequence disclosures in patent applications. (uspto.gov)
  • b) Patent applications which contain disclosures of nucleotide and/or amino acid sequences, in accordance with the definition in paragraph (a) of this section, shall, with regard to the manner in which the nucleotide and/or amino acid sequences are presented and described, conform exclusively to the requirements of §§ 1.821 through 1.825 . (uspto.gov)
  • 37 CFR 1.821(a) presents a definition for "nucleotide and/or amino acid sequences. (bitlaw.com)
  • The requirement for compliance in 37 CFR 1.821(c) is directed to "disclosures of nucleotide and/or amino acid sequences. (bitlaw.com)
  • All sequence information, whether claimed or not, that meets the length thresholds in 37 CFR 1.821(a) is subject to the rules. (bitlaw.com)
  • 1) If the "Sequence Listing" required by § 1.821(c) is submitted on paper: The "Sequence Listing," setting forth the nucleotide and/or amino acid sequence and associated information in accordance with paragraph (b) of this section, must begin on a new page and must be titled "Sequence Listing. (bitlaw.com)
  • 2) If the "Sequence Listing" required by § 1.821(c) is submitted on compact disc: The "Sequence Listing" must be submitted on a compact disc in compliance with § 1.52(e) . (bitlaw.com)
  • The presentation of the "Sequence Listing" and other materials on compact disc under § 1.821(c) does not substitute for the Computer Readable Form that must be submitted on disk, compact disc, or tape in accordance with § 1.824 . (bitlaw.com)
  • The preceding steps should be repeated with a different fragment pattern so that the overall protein sequence can be reconstructed with minimal errors. (news-medical.net)
  • 1. The assumed specifically active fragment of bovine fibrinopeptide B with the amino acid sequence 15-21 and the fragment 12-21 containing the tripeptide residue Asp 12 -Arg 13 -Pro 14 have been synthesized. (springer.com)
  • 9. The antigenic conjugate as claimed in claim 5, wherein the amino acid sequence of the coupled-fragment is SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7 or a combination thereof. (freepatentsonline.com)
  • It has been shown previously that NA is not required for virus replication or budding except in the final step of releasing the virus particles from the cell surface sialic acid receptor as well as preventing aggregation among the progeny virus particles ( 29 ). (asm.org)
  • Herein, the authors focus on the formation of self-assembled particles using an amphiphilic amino acid (AA) sequence derived by solid-phase peptide synthesis (SPPS) and describe its purifn. (unibas.ch)
  • Bacteria may use gluconeogenesis (Fig. 1 ) to synthesize glucose from nonsugar C 2 or C 3 compounds or the intermediates of the tricarboxylic acid (TCA) cycle when there is not sufficient hexose in their niches ( 17 , 24 , 26 , 27 ). (asm.org)
  • A variety of anaerobic bacteria have developed specific pathways to degrade amino acids by fermentation processes. (biomedcentral.com)
  • These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. (mdpi.com)