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)

*Ancestral reconstruction

These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the ... amino acid) sequence of proteins by Frederick Sanger in 1955, Zuckerkandl and Pauling postulated that such sequences could be ... Pupko, T.; Pe, I.; Shamir, R.; Graur, D. (2000). "A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences ... Yang, Ziheng; Kumar, Sudhir; Nei, Masatoshi (1995). "A new method of inference of ancestral nucleotide and amino acid sequences ...

*Molecular phylogenetics

... including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test (testing best-fitting ... Modern sequence comparison techniques overcome this objection by the use of multiple sequences. Once the divergences between ... At any location within such a sequence, the bases found in a given position may vary between organisms. The particular sequence ... These have been replaced in recent times largely by DNA sequencing, which produces the exact sequences of nucleotides or bases ...

*Protein primary structure

Protein sequencing Nucleic acid primary structure Translation Pseudo amino acid composition SANGER F (1952). "The arrangement ... Amino acids are polymerised via peptide bonds to form a long backbone, with the different amino acid side chains protruding ... Protein sequence is typically notated as a string of letters, listing the amino acids starting at the amino-terminal end ... as well as mixtures or ambiguous amino acids (similar to nucleic acid notation). Peptides can be directly sequenced, or ...

*KDEL (amino acid sequence)

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 ...

*KKXX (amino acid sequence)

... 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 ...

*N-acyl phosphatidylethanolamine-specific phospholipase D

The NAPEPLD cDNA sequence predicts 396 amino acid sequences in both mice and rats, which are 89% and 90% identical to that of ... "Amino Acid Sequencing". W.M. Keck Facility at Yale. 2006-10-23. Retrieved 2009-01-12. The Procise 494 cLC is described from the ... Regulation of Fatty Acid Ethanolamide Biosynthesis by Bile Acids". Structure. 23 (3): 598-604. doi:10.1016/j.str.2014.12.018. ... Bile acids bind with high affinity to selective pockets in this cavity, enhancing dimer assembly and enabling catalysis. NAPE- ...

*Complement component 1s

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. ... Partial sequence determination of the heavy chain and identification of the peptide bond cleaved during activation". European ... Tosi M, Duponchel C, Meo T, Julier C (December 1987). "Complete cDNA sequence of human complement Cls and close physical ...

*Endothiapepsin

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, ...

*SPINK1

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 ...

*Glutamate-cysteine ligase

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 ...

*HIST1H3B

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". ...

*H3F3A

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 ...

*HIST1H2BE

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 ...

*HIST1H2BG

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 ...

*Histone H2B type 1-C

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 ...

*HIST1H2BF

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 ...

*Myelin basic protein

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. ...

*HIST2H3PS2

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. ( ...

*HIST2H3C

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 ...

*Glycyl endopeptidase

Ritonja, A.; Buttle, D.J.; Rawlings, N.D.; Turk, V.; Barrett, A.J. (1989). "Papaya proteinase IV amino acid sequence". FEBS ...

*ITIH3

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 ...

*Richard Perham

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; ...

*Dihydrofolate reductase

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, ... Folic acid is necessary for growth, and the pathway of the metabolism of folic acid is a target in developing treatments for ... Masters JN, Attardi G (1983). "The nucleotide sequence of the cDNA coding for the human dihydrofolic acid reductase". Gene. 21 ...

*ITIH1

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 ...

*STIM2

... 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 ...

*Phage display

... were expressed both with and without the signal sequence. PelB (an amino acid signal sequence that targets the protein to the ... Moreover, pIII allows for the insertion of larger protein sequences (>100 amino acids) and is more tolerant to it than pVIII. ... Usually peptides that can be fused to pVIII are 6-8 amino acids long. The size restriction seems to have less to do with ... Direct Interaction Rescue or by adding an 8-10 amino acid linker between the cDNA and pIII at the C-terminus. pVIII is the main ...

*Aspergillopepsin I

Amino acid sequence of the enzyme". Bioorg. Khim. 12: 1030-1047. Yagi, F.; Fan, J.; Tadera, K.; Kobayashi, A. (1986). " ... Effects of acid protease-specific inhibitors on the acid proteases from Aspergillus niger var. macrosporus". J. Biochem. 80: ... Aspergillopepsin I (EC 3.4.23.18, Aspergillus acid protease, Aspergillus acid proteinase, Aspergillus aspartic proteinase, ... Aspergillus saitoi acid proteinase, pepsin-type aspartic proteinase, Aspergillus niger acid proteinase, sumizyme AP, proctase P ...
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.. ...
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 ...
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 ...
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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 ...
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.
Proteins belonging to the thioredoxin (Trx) superfamily are abundant in all organisms. They share the same structural features, arranged in a seemingly simple fold, but they perform a multitude of functions in oxidative protein folding and electron transfer pathways. We use the C-terminal domain of the unique transmembrane reductant conductor DsbD as a model for an in-depth analysis of the factors controlling the reactivity of the Trx fold. We employ NMR spectroscopy, x-ray crystallography, mutagenesis, in vivo functional experiments applied to DsbD, and a comparative sequence analysis of Trx-fold proteins to determine the effect of residues in the vicinity of the active site on the ionization of the key nucleophilic cysteine of the -CXXC- motif. We show that the function and reactivity of Trx-fold proteins depend critically on the electrostatic features imposed by an extended active-site motif.
The 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.
Alignment of the amino acid sequences of the nine elephant γ genes.The deduced amino acid sequences of three γ chain-coding exons and two membrane exons of ni
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. ...
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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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 amino acid sequences of ten proteins with intracellular half-lives less than 2 hours contain one or more regions rich in proline (P), glutamic acid (E), serine (S), and threonine (T). These PEST regions are generally, but not always, flanked by clusters containing several positively charged amino acids. Similar inspection of 35 proteins with intracellular half-lives between 20 and 220 hours revealed that only three contain a PEST region. On the basis of this information, it was anticipated that caseins, which contain several PEST sequences, would be rapidly degraded within eukaryotic cells. This expectation was confirmed by red blood cell-mediated microinjection of 125I-labeled caseins into HeLa cells where they exhibited half-lives of less than 2 hours. The rapid degradation of injected alpha- and beta-casein as well as the inverse correlation of PEST regions with intracellular stability indicate that the presence of these regions can result in the rapid intracellular degradation of the ...
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 ...
This program is about how to generate protein sequences (random sequences of 100amino acid) and these sequences should be stored in a database type file. The sequence analysis gave the bioscience researches a new direction. This project works for generating new sequences of proteins. These sequences might already exist in nature and having similarity with any organism. Through this software new random sequences may be generated and saved to a file on users machine. Saving to file helps to compare different sequences as well as the complete information may be placed at the same place ...
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 ...
The inverse protein folding problem, the problem of finding which amino acid sequences fold into a known three-dimensional (3D) structure, can be effectively attacked by finding sequences that are most compatible with the environments of the residues in the 3D structure. The environments are described by: (i) the area of the residue buried in the protein and inaccessible to solvent; (ii) the fraction of side-chain area that is covered by polar atoms (O and N); and (iii) the local secondary structure. Examples of this 3D profile method are presented for four families of proteins: the globins, cyclic AMP (adenosine 3,5-monophosphate) receptor-like proteins, the periplasmic binding proteins, and the actins. This method is able to detect the structural similarity of the actins and 70- kilodalton heat shock proteins, even though these protein families share no detectable sequence similarity. ...
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 ...
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 ...
To study the regulation of CYP4F gene expression by LPS and clofibrate as well as the involvement of PPARα in wild-type and PPARα knockout mice, mouse CYP4F isoforms must be first identified. Five new mouse CYP4F cDNAs have been identified from mouse brain and kidney; two of them are used in our gene regulation study, namely, CYP4F15 and CYP4F16. Both clones contain full-length open reading frames with the conserved family 4 consensus sequence and heme-binding region. Two in-frame initiation methionines are present in CYP4F15 cDNA, separated by four amino acid residues. However, the second initiation methionine of CYP4F15 showed higher homology with other CYP4Fs with similar length and hydrophobicity of the N-terminal inner membrane domain. Therefore, we think that the second ATG is the real initiation codon used for protein expression. CYP4F15 encodes a protein with 529 amino acid residues with a predicted molecular weight of 60,628, whereas CYP4F16 encodes 524 amino acid residues with an ...
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), ...
Patenting around nuisance prior art. Patenting gene sequences. Patenting nucleotide and amino acid sequences in view of electronic sequence database searches
EST). A short partial sequence, typically 200-400 bp long, of a complementary DNA (cDNA) clone. Because cDNAs are prepared by reverse transcription of messenger RNA molecules, ESTs act as markers for genes that are expressed in particular tissues or organs. EST sequence data are held on databases, and researchers use computer programs to search for sequences that correspond to, say, a partial amino-acid sequence for a protein under investigation. The EST sequence can then be used to construct a DNA probe to locate the respective clone from a DNA library. ...
Amino acid sequence from degu islet amyloid-derived insulin shows unique sequence characteristics.: The main protein of enriched and purified amyloid from Octod
In the present study, we reported that Ufm1 acts as a new post‐translational UBL modifier, based on the following criteria: (1) It is a small protein of 9.1 kDa with a ubiquitin‐fold structure. (2) Ufm1 is synthesized in a precursor form, and the extra amino‐acid residues at the C‐terminal side need to be processed to expose the Gly residue. (3) The C‐terminal processing and exposure of glycine residue are essential to the formation of Ufm conjugates in the cells. (4) Ufm1 has specific E1‐like (Uba5) and E2‐like (Ufc1) enzymes for activation and conjugation, respectively. Intriguingly, many UBL modifiers are evolutionarily conserved from yeast to human, except interferon‐inducible UBL modifiers, such as UCRP/ISG15, Fat10, and Fau1/MNSFβ (Nakamura et al, 1995; DCunha et al, 1996; Liu et al, 1999). Ufm1, Uba5, and Ufc1 found in the present study are conserved in various multicellular organisms (Figures 1B, 2A and 4A), but not in both budding and fission yeasts, suggesting that ...
A method was developed to purify human smooth muscle filamin in high yield and structural domains were defined by using mild proteolysis to dissect the molecule into intermediate-sized peptides. Unique domains were defined and aligned by using high-resolution peptide mapping of iodinated peptides on cellulose plates. The amino- and carboxyl-terminal orientation of these domains within the molecule was determined by amino acid sequence analysis of several aligned peptides. In addition to the three unique domains which were identified, a number of smaller and larger fragments were also characterized and aligned within the intact molecule. These structural domains and related peptides provide a useful set of defined fragments for further elucidation of structure-function relationships. The two known functionally important binding sites of filamin, the self-association site and the actin-binding site, have been localized. Self-association of two monomers in a tail-to-tail orientation involves a ...
Because of the relatively weak hydrophobicity of HR8, the topology and geometry of PS1 "TMD7," wherein the catalytic aspartate D385 resides, remain controversial. To obtain information about the hydrophilicity of HR8 when incorporated in an active γ-secretase complex, we generated single-Cys mt PS1 at 29 consecutive amino acid residues in and around HR8 (R377-T406). Again, some mutants (i.e., G382C, G384C, D385C, G394C, G402C, D403C, and W404C) lost protein expression or activity and thus were excluded from additional analysis (supplemental Fig. 1B, available at www.jneurosci.org as supplemental material). Labeling experiments using intact cells revealed that consecutive amino acid residues from K395 to S401, and T406, were reactive with MTSEA-biotin (Fig. 4 A). The labeling of all these residues was inhibited by preincubation with MTSES or MTSET, suggesting that this entire region resides in a hydrophilic environment accessible from the extracellular side (HL7) (Fig. 4 B). Given that H351 ...
I know that there are polar uncharged amino acids (serine, threonine, asparagine, glutamine, cysteine) and polar charged amino acids (the basic and acidic amino acids). Does the charge on the acidic and basic amino acids make them more polar and hydrophilic than the uncharged polar amino acids? Moreover, cysteine is classified as an uncharged amino acid, but because it has an ionizable side chain, would it be more polar than serine, asparagine, etc.? ...
Information about approximately 38,000 full-length cDNA clones that were completely sequenced in the Rice full-length cDNA project is shown in the database. The full-length cDNA clones were collected from various tissues treated under various stress conditions. The database contains not only information about complete nucleotide sequences and encoded amino acid sequences, but also results of homology searches against public databases, mapping information, information about patterns of alternative splicing, protein domains and transmembrane structures, and information about cellular localizations and gene functions annotated with Gene Ontology.. ...
Proteins are macromolecules that play important roles in life processes such as catalyzing biological reactions, forming DNA strands, sending signals within systems, and transportation of substances in the body. They are composed of amino acid subunits, which in specific combinations form peptides linked by a C-N peptide bond. Chains of peptides are called polypeptides, or proteins.. Proteins are folded into specific spatial conformations by non-covalent bonds such as hydrogen bonding, ionic bonding, disulfide bonds, Van der Waals forces and hydrophobic interactions. There are four types of structures: primary, secondary, tertiary and quaternary. Primary structure is the linear amino acid sequence, whilst the secondary structure is coiling or folding of the amino acid sequence. The tertiary structure is the three-dimensional globular structure of the protein, and the quaternary structure is the interaction of multiple polypeptides. All these structures denote the final shape of a specific ...
A region of HIF-1α encompassing amino acid residues 400-600 is necessary and sufficient for O2-regulated ubiquitination and degradation (23, 32, 74). VHL interacts, via its β-domain, with amino acid residues 532-585 of HIF-1α (55, 75). Because the ubiquitination and degradation of other key regulatory proteins such as IκB are regulated by phosphorylation, great effort was made to identify phosphorylatable (serine, threonine, tyrosine) residues of HIF-1α that were important for regulation of protein half-life, but to no avail. Instead, Pro-564 is hydroxylated in an O2-dependent manner, and this modification is required for VHL binding (25, 27, 87). Pro-402 represents a second site of hydroxylation and VHL binding (48). Pro-402 and Pro-564 are each contained within a similar amino acid sequence (LXXLAP, where A is alanine, L is leucine, P is proline, and X is any amino acid). HIF-2α and HIF-3α expression are also regulated by prolyl hydroxylation and VHL binding (20, 49, 50).. Three prolyl ...
I was wondering if I did something wrong with the deletion, it seems pretty self explanatory but I just want to make sure I did this right. 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 dont get it ...
A comparison between the triplets tentatively deduced by these methods with the changes in amino acid sequence produced by mutation shows a fair measure of agreement. - Francis Crick quotes from BrainyQuote.com
package transeq import ( "bufio" "bytes" "context" "encoding/binary" "fmt" "io" "runtime" "sync" ) var ( letterCode = map[byte]uint8{ A: aCode, C: cCode, T: tCode, G: gCode, N: nCode, U: uCode, } standard = map[string]byte{ "TTT": F, "TCT": S, "TAT": Y, "TGT": C, "TTC": F, "TCC": S, "TAC": Y, "TGC": C, "TTA": L, "TCA": S, "TAA": *, "TGA": *, "TTG": L, "TCG": S, "TAG": *, "TGG": W, "CTT": L, "CCT": P, "CAT": H, "CGT": R, "CTC": L, "CCC": P, "CAC": H, "CGC": R, "CTA": L, "CCA": P, "CAA": Q, "CGA": R, "CTG": L, "CCG": P, "CAG": Q, "CGG": R, "ATT": I, "ACT": T, "AAT": N, "AGT": S, "ATC": I, "ACC": T, "AAC": N, "AGC": S, "ATA": I, "ACA": T, "AAA": K, "AGA": R, "ATG": M, "ACG": T, "AAG": K, "AGG": R, "GTT": V, "GCT": A, "GAT": D, "GGT": G, "GTC": V, "GCC": A, "GAC": D, "GGC": G, "GTA": V, "GCA": A, "GAA": E, "GGA": G, "GTG": V, "GCG": A, "GAG": E, "GGG": G, } ) ...
A protease is any enzyme that performs proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link amino acids together in the polypeptide chain forming the protein. Proteases are used throughout an organism for various metabolic processes. Proteases control a great variety of physiological processes that are critical for life, including the immune response, cell cycle, cell death, wound healing, food digestion, and protein and organelle recycling. On the basis of the type of the key amino acid in the active site of the protease and the mechanism of peptide bond cleavage, proteases can be classified into six groups: cysteine, serine, threonine, glutamic acid, aspartate proteases, as well as matrix metalloproteases. Proteases can not only activate proteins such as cytokines, or inactivate them such as numerous repair proteins during apoptosis, but also expose cryptic sites, such as occurs with β-secretase during amyloid precursor protein processing, shed various
The distinct subcellular redistribution of p53 and p73 in MDM2-expressing cells suggests the existence of structural differences between the proteins. Whereas the oligermerization domain of p53 and p73 share 33% identity, the extreme CT (outside of the oligermerization domain) of the two proteins is much less conserved. Inspection of the primary amino acid sequence reveals that the p53 CT contains five lysine residues that are not conserved in p73. In addition, we showed recently that under conditions where p53 is highly ubiquitinated, p73 exhibits a much lower tendency for ubiquitination (10) . According to the current model of p53 nuclear export, the p53 NES is inactive when p53 is in tetramer. Ubiquitination of the p53 CT lysine residues by MDM2 results in the revealing of the NES that then permits p53 to be nuclear-exported (5, 6, 7) . It is therefore possible that the NES of p73 is unable to be activated because of its lack of the corresponding lysine residues available for ubiquitination. ...
Abstract: Proteomic studies of some human tissues and organs (skeletal muscles, myometrium, motor zone of the brain, prostate), and also cultivated myoblasts revealed 41 of 300 identified proteins, in which the present of certain variants of amino acids (conflicts) was recognized at several positions. Among the 93 registered amino acids conflicts, seven cases represented the results of the protein polymorphisms caused by corresponding substitution of individual amino acid. Moreover, among prostate proteins the proteomic analysis revealed two isoforms of prostate-specific antigen, formed due to alternative splicing. Thus, our results have shown, that proteomic technologies allow to specify effectively the features of primary structures and to characterize various kinds of polymorphism in many human proteins ...
AA Edit 1.2 displays the primary structure of the protein as a sequence of single-character amino acid codes. The sequence can be copied and pasted using the normal keyboard shortcuts. (For example, on Windows, ctrl-c for copy, and ctrl-v for paste.). For proteins which contain "mutable" segments, a new sequence can be pasted into the "AASeq" box. When you click the "change" button, the recipe attempts to mutate each segment to the new value entered.. The recipe does not attempt to change non-mutable segments. It does not change any segments where the current amino acid is the same as the new amino acid. It does not change any segments where the new amino acid code is not one of the 20 amino acids recognized by Foldit.. In puzzles with ligands, the ligand may be represented by one or more segments which return amino acid type "unk" instead of one of the normal codes. The recipe changes "unk" to "x" for display purposes. Since "x" is also not one of the recognized Foldit codes, its ignored when ...
Third Class Lever Definition 140404 What Makes Things Move Levers In The Human Body Physics Simple Machine Third Class Levers And Examples Youtube Third Class Lever Definition, Lever Kullabs Third Class Lever Definition, Lever Students Britannica Kids Homework Help Third Class Lever Definition, Third Class Lever Definition 140404 What Makes Things Move Levers In The Human Body, ...
A simple convention is used to write the structure and name of the peptide. The amino acid unit having free -NH2 group is called N-terminal end whereas the amino acid unit with free -COOH group is called C-terminal end. The structure is written with N-terminal end to the left and C-terminal end to the right. The base name of the peptide is taken from the C-terminal amino acid unit. Other amino acid units are taken to be substituents of this acid and the suffix ine of their name is replaced with yl. In case of polypeptides and proteins, the abbreviated names of amino acid units are used. Let us write the structure of a tripeptide formed from glycine, alanine and serine .. ...
select ?title ?sequence where{ ?s,http://www.w3.org/1999/02/22-rdf-syntax-ns#type,,http://bio2rdf.org/drugbank_vocabulary:Enzyme, . ?s ,http://purl.org/dc/terms/title, ?title . ?s,http://bio2rdf.org/drugbank_vocabulary:amino-acid-sequence,?sequence FILTER regex(?title, ??term, i) } limit ?? ...
NPC1s amino acid sequence homology to PATCHED, human HMG-CoA reductase and SCAP. Credit: Reprinted with permission from AAAS / Carstea et al., Science 277:228, 1997." />NPC1s amino acid sequence homology to PATCHED, human HMG-CoA reductase and SCAP. Credit: Reprinted with permission from AAAS / Carstea et al., Science 277:228, 1997. In the 1990s, the Ara Parseghian Foundation donated money to the National I. 0 Comments. ...
Mutations can occur randomly during DNA replication. The chance of a mutation occurring is increased by exposure to certain chemicals and radiations- these are known as mutagens. If a mutation results in cancer, the mutagens responsible are known as carcinogens.. Examples of mutations include addition, deletion and substitution of nucleotide bases. The majority of mutations are not harmful or fatal. Most mutations are neutral, a small number are harmful and a small number give a new characteristic that gives the organism a selective advantage.. If the mutation occurs in a gene, it can alter the amino acid sequence coded. Modifying the amino acid sequence of a polypeptide chain can have various consequences including modifying protein structure. Hydrogen, ionic and disulphide bonds hold the tertiary and quaternary structures of proteins together. Amino acid changes can disrupt these bonds- or even create new bonds. This can transform the structure of a protein. Structural modifications of a ...
A significant number of proteins, especially large proteins, have a structure divided into several independent domains. These domains can often perform specific functions in a protein. For example, a cell membrane receptor might have an extracellular domain to bind a target molecule and an intracellular domain that binds other proteins inside the cell, thereby transducing a signal across the cell membrane.. The domain of a protein is determined by the secondary structure of a protein there are four main types of domain structures: alpha-helix, beta-sheet, beta-turns, and random coil.. The alpha-helix is when the poly-peptide chain forms a helix shape with the amino acids side chains sticking out, usually about 10 amino acids long. The alpha-helix gets its strength by forming internal hydrogen bonds, that occur between amino acid 1 and 4 along the length of the helix. A high concentration of Glycines in a row tend towards the alpha-helix conformation.. The beta-sheet structure is composed of ...
Did you know that in 2007 alone, 33.2 million people lived with AIDS? Of this number, 2.1 million died, including 330,000 children. AIDS is now a pandemic, ravaging sub-Saharan Africa and retarding economic growth. Research has been done in a multitude of labs across the country concerning HIV, its deadly retrovirus. Recent researchers have identified antibodies in the first loop (ECL1) of CCR5 of HIV exposed but uninfected individuals. This means that these antibodies could resist the HIV infection. It would be interesting to analyze and target the specific amino acid residues in this loop to determine which amino acids are involved in antibody binding to CCR5. Studies have been done that showed that amino acid substitutions in positions Alanine-95 and Alanine-96 increased antibody-peptide binding compared to that of the wild-type peptide Aspartate-95 and Phenylalanine-96. ...
Serine proteases represent over a third of all known proteolytic enzymes and are implicit in a wide range of physiological processes including digestion, immunity, blood clotting, fibrinolysis, reproduction and protein folding [1]. The proteolytic mechanism of these proteases involves nucleophilic attack of the carbonyl atom of the substrate peptide bond by a catalytic serine (Ser) residue in the active site of the enzyme. In addition to the nucleophilic Ser residue, this reaction is dependent on two other amino acids in the catalytic site, Histidine (His) and an Aspartate (Asp) that together form what is referred to as the catalytic triad (or a dyad in some cases) [2]. The presence of this catalytic triad in at least four distinct protein folds indicates evolutionary success in four different contexts [3].. The MEROPS classification system (http://merops.sanger.ac.uk/) has grouped proteases into clans that typically have structural homology and/or the same linear order of catalytic triad ...
Base substitution: In this of mutation the single nucleotide base is substituted with another in DNA (/or) RNA molecule Frame shift (deletion or addition): In this method the amino acid sequence at protein translation is attained through deletion (and addition) of nucleotides. This is done because this initiate a change in the interpretation frame of the codons in the mRNA. Another variation is where when the number of nucleotides implanted or removed is not a multiple of three. Missense mutation In this type […]. ...
In this work, we have performed an exhaustive bioinformatic analysis of the human genome to try to identify new serine proteases that could contain different catalytic domains within the same polypeptide chain. These bioinformatic searches led us to find a region in chromosome 16p11.2 putatively encoding a new polyprotease. After completing the cloning process using liver cDNA as template, we confirmed that the identified sequence was a new polyserine proteinase that we called polyserase-3 to underline its structural relationship with the previously described polyserases-1 and -2 [3,9]. However, the polyserase-3 architecture is less complex than the exhibited by the two other human polyproteases. Thus, this new polyserase is composed of two serine protease domains preceded by a signal peptide, whereas both polyserase-1 and polyserase-2 contain three catalytic domains in a single polypeptide chain.. A comparative structural analysis also revealed that polyserase-3 is more closely related to ...
Globular proteins = enzymes and catalysts Fibrous proteins = structural or connective role. Structure - function relationships Some residues and chains are just disordered
L 117 peptide: has same amino acid sequence as somatotropin 110-127 except that amino acid at position 117 is replaced by leucine; stimulates Nb2 mitogenesis
BioCentrum is a privately-owned biotechnology service and product provider. The company conducts its own research, development and implementation projects in the area of microbiology and protein chemistry. The special interest is focused on bacterial virulence factors as potential therapeutic targets for drug development and on antibacterial peptides exerting an antibiotic activity.
DNA sequence of human 5-HT2 receptor cDNA and deduced amino acid sequence of the human (H), rat (R), and mouse (M) 5-HT2 receptors. The seven proposed transmembrane domains are bracketed. Intron exon junctions are indicated by arrows, and exons are labeled E1, E2, and E3. Amino acids in rat or mouse receptors that are different than those in the human are shown as opposed to identical residue, which are designated with dots. ...
The protein encoded by this gene is a member of a family of actin-related proteins (ARPs) which share significant amino acid sequence identity to…
In this work the affinity maturation of the murine anti c-myc-peptide antibody 9E10 was analysed. Therefore Fab fragments with reversed mutations directed towards germline genes were genetically produced and characterised for their binding to the human c-myc peptide. The epitope recognized by 9E10 consists of the amino acid sequence EQKLISEEDLLRKR of which the key positions LISEXXL are very selectively recognized. The maturation of 9E10 leads to a 3300-fold higher affinity, which is achieved by a faster association as well as by a slower dissociation of the complex. For the gain in affinity formation of additional contacts to the peptide is less important than conformational and/or flexibility changes of the CDRs which are involved in binding. The exceptionally long CDR-H3 contributes essentially to the affinity maturation. The variable light domain serves thereby with its long CDR-L1 and -L3 as a binding platform for the flexible CDR-H3. Changes in specificity of 9E10 are primarily due to ...
The TMDOCK web server predicts formation of dimeric complexes by single-spanning transmembrane (TM) proteins. It calculates thermodynamic stabilities, 3D structures, and spatial positions in membranes of parallel homodimers of TM alpha-helices. Please see instruction . Note that input amino acid sequence must be longer than TM helix, unless user wants to look at homodimerization of shorter peptides. The location of TM helix in amino acid sequence will be refined by server automatically ...
In article ,DEernisse-2506951545380001 at deernisse.fullerton.edu,, Doug Eernisse ,DEernisse at fullerton.edu, wrote: ,In article ,ts15-2306951442190001 at 128.253.38.30,, ts15 at cornell.edu (Ted ,Schultz) wrote: ... ,, I understand that protein ,, parsimony can also be applied in PHYLIP, though I have never tried this. , ,I believe the standard (universal) codon translation protein ,parsimony (ProtPars) is used as default, with no option to do parsimony with ,equal weighting or protein parsimony based on other codes. One should ,still be able to use equal weighting if the data are not treated as ,protein data. Is this still correct, Joe? PROTPARS is not able in version 3.5 to handle codes other than the Universal code. Our discrete-characters parsimony program does not allow more than two states, and in that is much less general than PAUP. So no, you cant do equal weighting which I take to mean any amino acid can change to any other. You could fake it if there were 5 or fewer amino acids ...
You can figure out how much protein you need if you know how much you weigh. Each day, kids need to eat about 0.5 grams of protein for every pound (0.5 kilograms) they weigh. Thats a gram for every 2 pounds (1 kilogram) you weigh. Your protein needs will grow as you get bigger, but then they will level off when you reach adult size. Adults, for instance, need about 60 grams per day. More about amino acids Proteins are sometimes described as long necklaces with differently shaped beads. Each bead is a small amino acid. These amino acids can join together to make thousands of different proteins. Scientists have found many different amino acids in protein, but 22 of them are very important to human health. Why are proteins important? Proteins are very important for your body so you can grow and be strong. Proteins are large molecules made up of long chains of amino acid subunits. Some of these amino acids are nutritionally essential as they cannot be made or stored within the body and so must come ...
PMAP-36: 36-residue C-terminal region of pig myeloid antibacterial peptide; a highly cationic sequence; strong tendency to form an amphipathic alpha-helix; has potent antibacterial activity against Gram-(-) and Gram-(+) bacteria; amino acid sequence given in first source (residue 131-166 of pre-proPMAP-36)
for a maximum yield of a1-fragment cations from oligopeptide cations grazing along a hydrocarbon surface. Some amino acids can produce a1-fragment cations at two different grazing velocity intervals ...
Previous studies suggest that PKGI compartmentation has an important role in regulating its phosphorylation of select targets. However, it is unknown whether such mechanisms might also regulate PKGI posttranslational modifications that are important for some of its activities. Previously, we observed that cGMP stimulates PKGI proteolysis and the generation of a COOH-terminal kinase fragment, PKGI-γ, that localizes to the nucleus of SMC and transactivates gene expression (83). Moreover, we recently showed that PKGI-γ nuclear localization plays an important role in regulating SMC differentiation because mutant PKGI-γ that does not enter the nucleus does not increase the expression of SMC contractile proteins (14). On the basis of insights from the NH2-terminal amino acid sequence of immunopurified nuclear PKGI-γ and the putative structure of protease recognition domains, we examined whether PCs might contribute to PKGI cleavage and nuclear PKGI-γ localization (41). During these studies, we ...
We suggest mixing the two enzyme buffers 1:1 GluC:AspN buffer. The Endo- proteinase GluC would prefer to have the E-E dipeptide present to stimulate activity and Endoproteinase AspN requires Zn, which is present in the AspN buffer. Still use a 1:20 (wt/wt) ratio of enzyme to substrate for each enzyme. There will be some reduction in the cleavage of your substrate protein since the two proteases will be chewing each other. It has been our experience that these conditions work well enough to get a high degree of digestion. You may need to adjust the individual amounts of each enzyme if you are missing a desired fragment, assuming that the reactions will be analyzed by some MS technique. If you prefer to do the reactions sequentially, do the Endoproteinase GluC reaction first as Endoproteinase AspN has difficulty digesting intact pro- teins. All digestions should be performed at 37°C ...
The traditional view has been that a proteins primary (amino acid) sequence determines its fold and therefore its function. It has been assumed, therefore, that any proteins with similar primary sequence will have similar functions and vice versa. The newer view is that this is a bunch of washed up crap. Obviously primary sequence will determine the fold and we still use primary sequence to determine the level of homology between two proteins of unknown structure. However, its not always safe to assume that the resulting percentage is of any true value without functional data ...
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With evidence accumulating that ligand-induced receptor conformation plays a pivotal role in signaling, receptors with structural modifications that activate only certain pathways provide a valuable tool for elucidating the mechanisms that account for pluridimensional efficacy. Shenoy and others used evolutionary trace analysis to rationally modify the β2AR amino acid residues at positions 68 (threonine), 132 (tyrosine), and 219 (tyrosine) to generate a mutant receptor known as β2AR TYY (Shenoy et al., 2006). Cellular studies using β2AR TYY demonstrate uncoupling of the receptor from its G protein and subsequently no cAMP production upon stimulation (Shenoy et al., 2006). Remarkably, this genetically engineered receptor maintains the ability to recruit β-arrestin and induce ERK signaling but with modified kinetics compared with the wild-type β2AR. The increase in phosphorylated ERK seems to peak later than that seen upon stimulation of wild-type β2ARs, is absolutely sensitive to siRNA ...
The invention pertains to a single polypeptide chain binding molecule which has binding specificity and affinity substantially similar to the binding specificity and affinity of the light and heavy ch
Consensus-Degenerate Hybrid Oligonucleotide Primer (CODEHOP) PCR primers derived from amino acid sequence motifs which are highly conserved between members of a protein family have proven to be highly effective in the ...
Every protein in a cell is created through the transcription of a specific sequence, that is part of the DNA. This transcription provides the sequence in which amino acids are to be linked, to form a protein.
An immunoassay is reported which uses, as a label, an expressible DNA fragment encoding the α-peptide of β-galactosidase. This inactive peptide consists of 97 amino acid residues containing an amino-terminal portion of the enzyme. Antigen (an anti-thyrotropin immunoglobulin) immobilized in microtiter wells is allow
A process for amplifying any target nucleic acid sequence contained in a nucleic acid or mixture thereof comprises treating separate complementary strands of the nucleic acid with a molar excess of tw
This chapter begins with a discussion on a cyclic-di-GMP (c-di-GMP), a self-associating messenger molecule. The proteins involved in c-di-GMP formation, recognition, and degradation are drawn primarily from large gene families which have multiple representatives encoded by most bacterial genomes. Degradation of c-di-GMP is mediated by two families of specific PDEs called EAL and HDGYP proteins based on a stereotyped amino acid sequence and these proteins once again have a broad and frequently redundant phylogenetic distribution. motif present in their active sites. The chapter focuses on the EAL proteins that are most abundant and structurally best characterized. The exact separation between the c-di-GMP switch and the N-terminal β-strand of the PilZ domain varies in different family members, as does the conformation of this β-strand in some family members, which enables the switch to effect distinct changes in interdomain interactions in different PilZ domain-containing receptors. Ironically, neither
4F2hc is a type-II glycoprotein that form covalently-bound heterodimers with several described light chains and whose main function is the transport of amino acids. Likewise, the heavy chain interacts with β-integrins mediating integrin-dependent events such as survival, proliferation, migration and even transformation. Its large C-terminal domain resembles α-amylases structure, but lacking catalytic residues and thus enzymatic activity. In fact, this ectodomain contains the N-terminal domain A, a TIM barrel, connected by 6 residues in α-helix to the C-terminal domain C, comprised of a β-sandwich. Spectroscopic/structural characterization of recombinant 4F2hc-ED shows that its structure in solution is quite similar to that of the crystal, being compact and thermally stable. Moreover, this ectodomain is unable to homodimerize by itself, remaining monomeric in solution. According to the data obtained, the folding/unfolding mechanism of 4F2hc-ED may occur following a 4-state model with 2 ...
By making a single substitution in the amino acid sequence of a modern enzyme, scientists at Brookhaven Lab have changed its function into that of a theoretical distant ancestor, providing the first experimental evidence for the common origin of the two distinct enzyme types.
LOC FOR DETECTION OF HYBRIDIZATION OF NUCLEIC ACID SEQUENCES WITH PCR AMPLIFICATION USING LINKER PRIMERS - diagram, schematic, and image 08 ...
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Cited for: VARIANTS EIEE6 PHE-17 DEL; THR-68; ASN-79; CYS-84; PRO-98; GLN-101; TRP-101; ARG-108; ASP-127; ARG-199; SER-227; THR-227; SER-232; ARG-233; VAL-342; ASP-343; TRP-351; SER-359; ARG-363; ARG-384; CYS-393; HIS-393; VAL-400; VAL-403; PHE-406; GLY-626; ASP-762; THR-785; ILE-812; ARG-842; 854-GLY-LEU-855 DEL; CYS-859; GLN-862; PRO-890; CYS-932; PRO-933; CYS-946; HIS-946; ARG-950; LYS-954; LYS-956; LEU-957; ILE-976; VAL-979; ARG-993; 999-ASN-LEU-1000 DELINS LEU-ILE-SER; LYS-1208; LYS-1221; PHE-1230; ASP-1238; ALA-1266; ASN-1288; VAL-1320; PRO-1326; GLY-1350; ARG-1358; PRO-1370; HIS-1378; THR-1378; ILE-1394; TYR-1396; SER-1417; PHE-1423; ALA-1429 DEL; VAL-1433; LYS-1450; SER-1451; LYS-1454; HIS-1462; LYS-1476; LYS-1503; GLY-1544; GLU-1586; ARG-1588; HIS-1592; PRO-1592; SER-1605; GLU-1637; THR-1638; CYS-1648; GLU-1653; PRO-1660; PRO-1667; LEU-1668; ILE-1672; THR-1673; THR-1683; ASP-1684; TRP-1688; ARG-1714; ASN-1763; ASN-1770; PHE-1770; THR-1770; THR-1780; VAL-1783; LYS-1787; PRO-1832; ...
PACMANS is software using a bioinformatically informed algorithm to predict, design, and disrupt protease-on-protease hydrolysis. This program uses a substrate proteases amino acid sequence and a protease-ases specificity matrix from MEROPS to produce a ranked list of the most likely hydrolyzed segments of the substrate proteases amino acid sequence. This program is currently implemented in a downloadable MATLAB Application (below) and will soon be available online through this website for users without access MATLAB.. This work has been published by Ferrall-Fairbanks et al in Protein Science.. ...
Use the Protease Finder to identify individual proteases that can be used to cleave a distinct peptide bond within your specific protein or peptide sequence.
A current barrier for successful rational drug design is the lack of understanding of the structure space provided by the proteins in a cell that is determined by their sequence space. The protein sequences capable of folding to functional three-dimensional shapes of the proteins are clearly different for different organisms, since sequences obtained from human proteins often fail to form correct three-dimensional structures in bacterial organisms. In analogy to the question "What kind of things do people say?" we therefore need to ask the question "What kind of amino acid sequences occur in the proteins of an organism?" An understanding of the sequence space occupied by proteins in different organisms would have important applications for "translation" of proteins from the language of one organism into that of another and design of drugs that target sequences that might be unique or preferred by pathogenic organisms over those in human hosts. Here we describe the development of a biological ...
Intrinsically unstructured/disordered proteins have no single well-defined tertiary structure in their native, functional state. Our server recognizes such regions from the amino acid sequence based on the estimated pairwise energy content. The underlying assumption is that globular proteins are composed of amino acids which have the potential to form a large number of favorable interactions, whereas intrinsically unstructured proteins (IUPs) adopt no stable structure because their amino acid composition does not allow sufficient favorable interactions to form ...
Biology Assignment Help, Homologous proteins - amino acid sequence in fasta format, Please answer the following question on Sequence Y: Protein databases 1. What sequence from which organism is this sequence most similar to? 2. Can you find any homologues of this protein in other organisms? Can you find any clues to
Looking for online definition of nonpolar amino acid in the Medical Dictionary? nonpolar amino acid explanation free. What is nonpolar amino acid? Meaning of nonpolar amino acid medical term. What does nonpolar amino acid mean?
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Looking for Major histocompatibility complex protein? Find out information about Major histocompatibility complex protein. In vertebrates, a family of genes that encode cell surface glycoproteins that regulate interactions among cells of the immune system, some components of the... Explanation of Major histocompatibility complex protein
The lamin B receptor is a previously identified integral membrane protein in the nuclear envelope of turkey erythrocytes that associates with the nuclear intermediate filament protein lamin B (Worman, H. J., J. Yuan, G. Blobel, and S. D. Georgatos. 1988. Proc. Natl. Acad. Sci. USA. 85:8531-8534). In the present report, we use cell fractionation and antibodies against the lamin B receptor to localize it to an 8-M urea-extracted membrane fraction of chicken liver nuclei, supporting an inner nuclear membrane localization. We deduced the amino acid sequence of the chicken lamin B receptor from overlapping clones obtained by screening cDNA libraries with a probe generated by the polymerase chain reaction with primers based on the partial protein sequence of the isolated protein. The mature lamin B receptor has a calculated molecular mass of 73,375 D and eight segments of hydrophobic amino acids that could function as transmembrane domains as determined by hydropathy analysis. Preceding the first ...
The oxidation of the methionine residues of human growth hormone (hGH) and human chorionic somatomammotropin (hCS) to methionine sulfoxide by hydrogen peroxide has been studied. The kinetics of oxidation of individual methionine residues has been measured by reverse-phase high pressure liquid chromatography tryptic peptide mapping. Met-170 is completely resistant to oxidation in both hormones. The other 3 methionine residues in hCS (Met-64, Met-96, and Met-179) have markedly different reaction rates. Oxidation of the methionine residues does not appear to cause gross conformational changes in either hGH or hCS, as judged by CD and 1H NMR spectroscopy. Oxidation of Met-14 and Met-125 in hGH has little effect on affinity of the hormone for lactogenic receptors or on its potency in the Nb2 rat lymphoma in vitro bioassay for lactogenic hormones. The oxidation of Met-64 and/or Met-179 in hCS reduces profoundly both its affinity for lactogenic receptors and its in vitro biological potency. It is inferred by
Mitogen-activated protein kinases (MAPKs) constitute a major signaling pathway in cells, and are involved in processes controlling gene expression, cell division, cell survival, apoptosis, metabolism, differentiation and motility [1]. The conventional mammalian pathway consists of a cascade of three serine/threonine kinases referred to as MAPK kinase kinase, MAPK kinase and MAPK. The MAPKs are divided into four different subfamilies; the extracellular signal-regulated kinases 1/2 (ERK1/2), the c-JUN N-terminal kinases 1-3 (JNK1-3) or stress-activated protein kinases (SAPKα, β and γ), the p38 MAPKs (p38 α, β, γ and δ), and the big MAPKs (BMK1/ERK5). The atypical MAPK pathway is not organized in the normal three tier cascade, and includes ERK3/4, ERK7/8 and Nemo-like kinase (NLK) [1]. Both the conventional and the unconventional pathway can phosphorylate protein substrates and other protein kinases called mitogen-activated protein kinase-activated protein kinases (MAPKAPK). The MAPKAPK ...
Kit 30500-050 Kit 30500-096 DNA marker 81-0020 DNA marker 81-0100 DNA marker 82-0100 DNA marker 82-0200 DNA marker 82-0500 DNA marker 82-1000 DNA marker 83-2500 DNA marker 83-5000 DNA Aptamers AD-155-B DNA Aptamers AD-155-F DNA Aptamers AD-155-U Peptide Aptamers AP-302-B Peptide Aptamers AP-302-F Peptide Aptamers AP-302-U Peptide Aptamers AP-304-B Peptide Aptamers AP-304-F Peptide Aptamers AP-304-U Peptide Aptamers AP-306-B Peptide Aptamers AP-306-F Peptide Aptamers AP-306-U Peptide Aptamers AP-308-B Peptide Aptamers AP-308-F Peptide Aptamers AP-308-U Peptide Aptamers AP-309-B Peptide Aptamers AP-309-F Peptide Aptamers AP-309-U Peptide Aptamers AP-310-B Peptide Aptamers AP-310-F Peptide Aptamers AP-310-U Peptide Aptamers AP-312-B Peptide Aptamers AP-312-F Peptide Aptamers AP-312-U Peptide Aptamers AP-315-B Peptide Aptamers AP-315-F Peptide Aptamers AP-315-U Peptide Aptamers AP-318-B Peptide Aptamers AP-318-F Peptide Aptamers AP-318-U Peptide Aptamers AP-319-B Peptide Aptamers AP-319-F Peptide Aptamers
An accurate method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been developed for quantitative analysis of calcitonin and insulin in different commercially available pharmaceutical products. Tryptic peptides derived from these polypeptides were chemically modified at their C-terminal lysine-residues with 2-methoxy-4,5-dihydro-imidazole (light tagging) as standard and deuterated 2-methoxy-4,5-dihydro-imidazole (heavy tagging) as internal standard (IS). The heavy modified tryptic peptides (4D-Lys tag), differed by four atomic mass units from the corresponding light labelled counterparts (4H-Lys tag). The normalized peak areas (the ratio between the light and heavy tagged peptides) were used to construct a standard curve to determine the concentration of the analytes. The concentrations of calcitonin and insulin content of the analyzed pharmaceutical products were accurately determined, and less than 5% error was obtained between the ...

Cleave amino acid sequence with enzyme - MATLAB cleaveCleave amino acid sequence with enzyme - MATLAB cleave

... an amino acid sequence, into parts at the cleavage sites specific for Enzyme, a character vector specifying a name or ... Short amino acid sequence to search for in SeqAA. , a larger sequence. PeptidePattern. can be any of the following: *. ... Sequence. field that contains an amino acid sequence, such as returned by fastaread. , getgenpept. , genpeptread. , getpdb. , ... an amino acid sequence, into parts at the cleavage sites specific for Enzyme. , a character vector specifying a name or ...
more infohttp://www.mathworks.com/help/bioinfo/ref/cleave.html?requestedDomain=www.mathworks.com&nocookie=true

Cleave amino acid sequence with enzyme - MATLAB cleaveCleave amino acid sequence with enzyme - MATLAB cleave

... an amino acid sequence, into parts at the cleavage sites specific for Enzyme, a character vector specifying a name or ... Short amino acid sequence to search for in SeqAA. , a larger sequence. PeptidePattern. can be any of the following: *. ... Sequence. field that contains an amino acid sequence, such as returned by fastaread. , getgenpept. , genpeptread. , getpdb. , ... an amino acid sequence, into parts at the cleavage sites specific for Enzyme. , a character vector specifying a name or ...
more infohttp://www.mathworks.com/help/bioinfo/ref/cleave.html?requestedDomain=true&nocookie=true

DNA vs amino acid sequencesDNA vs amino acid sequences

... Joe Felsenstein joe at evolution.genetics.washington.edu Mon Jun 26 16:12:22 EST 1995 *Previous ... which I take to mean any amino acid can change to any other. You could fake it if there were 5 or fewer amino acids by recoding ... Previous message: DNA vs amino acid sequences *Next message: DNA vs amino acid sequences ... DNA vs amino acid sequences *Next message: DNA vs amino acid sequences ...
more infohttp://www.bio.net/bionet/mm/mol-evol/1995-June/003006.html

DNA vs amino acid sequencesDNA vs amino acid sequences

... Christopher L. Schardl clscha00 at ukcc.uky.edu Thu Jun 15 10:01:52 EST 1995 *Previous message: ... 1993 Confidence in evolutionary trees from biological sequence data. Nature 364: 440-442. Lockhart, P. J., Steel, M. A., Hendy ... M. D., and Penny, D., 1994 Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology ...
more infohttp://www.bio.net/bionet/mm/mol-evol/1995-June/002952.html

Amino acid sequence | Define Amino acid sequence at Dictionary.comAmino acid sequence | Define Amino acid sequence at Dictionary.com

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 ...
more infohttp://www.dictionary.com/browse/amino-acid-sequence

Patent US6891154 - Amino acid sequence pattern matching - Google PatentsPatent US6891154 - Amino acid sequence pattern matching - Google Patents

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 ...
more infohttp://www.google.com/patents/US6891154?dq=6,757,682

Amino-acid sequence in a hypertensin.  - PubMed - NCBIAmino-acid sequence in a hypertensin. - PubMed - NCBI

PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
more infohttps://www.ncbi.nlm.nih.gov/pubmed/13321895?dopt=Abstract

Design of temperature-sensitive mutants solely from amino acid sequence | PNASDesign of temperature-sensitive mutants solely from amino acid sequence | PNAS

... hydrophobic amino acids typically have little effect, whereas replacement by bulky aromatic amino acids (especially Trp) and ... Design of temperature-sensitive mutants solely from amino acid sequence. Ghadiyaram Chakshusmathi, Kajari Mondal, G. Santosh ... Design of temperature-sensitive mutants solely from amino acid sequence. Ghadiyaram Chakshusmathi, Kajari Mondal, G. Santosh ... Design of temperature-sensitive mutants solely from amino acid sequence Message Subject (Your Name) has sent you a message from ...
more infohttps://www.pnas.org/content/101/21/7925?ijkey=adbe85a661aec1b8f89d4008031f04570ac2615d&keytype2=tf_ipsecsha

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

We present a new framework for global and localalignment of amino acid sequences based on hierarchicalmotif vectors that ... sequence alignment; amino acid sequence analysis;physico-chemical profiles; motif vectors; waveletdecomposition. ... for global and local alignment of amino acid sequences based on hierarchical motif vectors that characterize local amino acid ... We then formulate different schemes for aligning amino acid sequences based on their respective motif vectors globally as well ...
more infohttp://actapress.com/Abstract.aspx?paperId=45053

The amino acid sequence of dog (Canis familiaris) hemoglobin.  - PubMed - NCBIThe amino acid sequence of dog (Canis familiaris) hemoglobin. - PubMed - NCBI

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. ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/864726

What is the amino acid sequence Trypsin-ultra? | NEBWhat is the amino acid sequence Trypsin-ultra? | NEB

What is the amino acid sequence Trypsin-ultra? FAQ: What is the amino acid sequence Trypsin-ultra?. The amino acid sequence of ... Monarch Nucleic Acid Purification Kits are optimized for maximum performance and minimal environmental impact. Kits are ... Monarch Nucleic Acid Purification Kits are optimized for maximum performance and minimal environmental impact. Kits are ... DNA Library Prep Kit with novel fragmentation reagent meets the dual challenge of generating high quality next gen sequencing ...
more infohttps://www.neb.com/faqs/2011/07/06/what-is-the-sequence-for-this-trypsin

Viral Amino acid sequence - Biology-OnlineViral Amino acid sequence - Biology-Online

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 ... How can a viral amino acid sequence be used to identify a virus? ... Viral Amino acid sequence. * Quote Post by Layd33foxx » Tue Mar ... Protein sequences are not so well used for organism identification, since you cannot multiply them. Nucleic acids are better ...
more infohttps://www.biology-online.org/biology-forum/viewtopic.php?p=140577

2422-Nucleotide and/or Amino Acid Sequence Disclosures in Patent Applications2422-Nucleotide and/or Amino Acid Sequence Disclosures in Patent Applications

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 ...
more infohttps://www.uspto.gov/web/offices/pac/mpep/s2422.html

AC: A Compression Tool for Amino Acid Sequences.AC: A Compression Tool for Amino Acid Sequences.

Advancement of protein sequencing technologies has led to the production of a huge volume of data that needs to be stored and ... Specific amino acid sequences present in the primary amino acid sequence of proteins which mediate their export from the CELL ... Consensus Sequence. A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is ... Sequence Alignment. The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as ...
more infohttps://www.bioportfolio.com/resources/pmarticle/2280904/AC-A-Compression-Tool-for-Amino-Acid-Sequences.html

Amino Acid Sequence Homology - Medical Dictionary online-medical-dictionary.orgAmino Acid Sequence Homology - Medical Dictionary online-medical-dictionary.org

Amino Acid Sequence Homology. The degree of similarity between sequences of Amino Acids. This information is useful for the ...
more infohttp://www.online-medical-dictionary.org/definitions-a/amino-acid-sequence-homology.html

Biology-Online • View topic - Viral Amino acid sequenceBiology-Online • View topic - Viral Amino acid sequence

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 ...
more infohttp://www.biology-online.org/biology-forum/post-140539.html

A conserved amino acid sequence directing intracellular type III secretion by Salmonella typhimurium | PNASA conserved amino acid sequence directing intracellular type III secretion by Salmonella typhimurium | PNAS

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 ...
more infohttps://www.pnas.org/content/97/13/7539?ijkey=bf31572186d4cc8ae13bf8f0bcb1fd9a9e593729&keytype2=tf_ipsecsha

Amino acid sequence | definition of amino acid sequence by Medical dictionaryAmino acid sequence | definition of amino acid sequence by Medical dictionary

... 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 ...
more infohttps://medical-dictionary.thefreedictionary.com/amino+acid+sequence

Grazing Molecule Excitation as a Tool to Analyse the Amino Acid Sequence in OligopeptidesGrazing Molecule Excitation as a Tool to Analyse the Amino Acid Sequence in Oligopeptides

A novel mass spectrometric method to analyse the sequence of amino acid residues in oligopeptides is proposed. Amino acid ... Grazing Molecule Excitation as a Tool to Analyse the Amino Acid Sequence in Oligopeptides. H. Jungclas,1 L. Schmidt,1 V. V. ... This specific property of GMD offers the possibility to determine the amino acid sequence of oligopeptides. ... fragment ion spectra of oligopeptides must contain a peak of high abundance corresponding to the N-terminal amino acid. ...
more infohttps://www.hindawi.com/archive/2011/356589/abs/

Determining mutated, mRNA, Amino Acid sequence | Physics Forums - The Fusion of Science and CommunityDetermining mutated, mRNA, Amino Acid sequence | Physics Forums - The Fusion of Science and Community

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) ...
more infohttps://www.physicsforums.com/threads/determining-mutated-mrna-amino-acid-sequence.395384/

A new method of inference of ancestral nucleotide and amino acid sequences. | GeneticsA new method of inference of ancestral nucleotide and amino acid sequences. | Genetics

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 ...
more infohttps://www.genetics.org/content/141/4/1641.short

KDEL (amino acid sequence) - WikipediaKDEL (amino acid sequence) - Wikipedia

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 ...
more infohttps://en.wikipedia.org/wiki/KDEL_(amino_acid_sequence)

KKXX (amino acid sequence) - WikipediaKKXX (amino acid sequence) - Wikipedia

... 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 ...
more infohttps://en.wikipedia.org/wiki/KKXX_(amino_acid_sequence)

Synthesis of a fragment of bovine fibrinopeptide B with the amino acid sequence 12-21 | SpringerLinkSynthesis of a fragment of bovine fibrinopeptide B with the amino acid sequence 12-21 | SpringerLink

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. ...
more infohttps://link.springer.com/article/10.1007/BF00565798

Amino acid sequence of rabbit muscle aldolase and the structure of the active center.Amino acid sequence of rabbit muscle aldolase and the structure of the active center.

... 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 ...
more infohttps://www.uniprot.org/citations/4812352
  • an amino acid sequence, into parts at the cleavage sites specified by a peptide pattern and position. (mathworks.com)
  • Any peptide or protein that can be expressed as a sequence using the symbols in WIPO Standard ST.25 (1998), Appendix 2, Table 3 in conjunction with a description in the Feature section to describe, for example, modified linkages, cross links and end caps, non-peptidyl bonds, etc., is embraced by this definition. (uspto.gov)
  • 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)
  • Such Ts mutants of Gal4 can be used for conditional expression of a variety of genes by using the well characterized upstream-activating-sequence-Gal4 system. (pnas.org)
  • These data demonstrate that the 15-amino acid sequence of NFATx1 is a major transactivation sequence required for induction of genes by NFATx1 in T cells and possibly regulates NFAT activity through tissue-specific alternative splicing. (jimmunol.org)
  • Explanations of these results have included accelerated evolution in the snake lineage, paralogy rather than orthology, and faulty determination of the sequence, and the rattlesnake is now often omitted from cytochrome c phylogenetic trees. (biochemj.org)
  • The manual sequencing of the tryptic peptic from the alpha and beta chains of dog hemoglobin is described, including evidence for the existence of two alphaT-13 peptides and thus 2 alpha chains, one with threonine and one with alanine at position 130. (nih.gov)
  • Although the actual sequence was published in 1970, the evidence on which it was based has not previously appeared. (nih.gov)
  • Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50162 (16 pages) at the British Library Document Supply Centre, Boston Spa. (biochemj.org)
  • Here we provide evidence showing that 15 amino acids in the carboxyl-terminal end of NFATx1 are required for its maximum transactivation activity in Jurkat T cells. (jimmunol.org)
  • On the other hand, the amino-terminal region of NFAT1(NFATp) and NFATx/NFAT4 is important and sufficient for binding to calcineurin and seems to regulate nuclear translocation ( 16 , 17 , 18 ). (jimmunol.org)
  • Relevant and Non-Redundant Amino Acid Sequence Selection for Protein Functional Site Identification. (igi-global.com)
  • 37 CFR 1.821 Nucleotide and/or amino acid sequence disclosures in patent applications. (uspto.gov)
  • 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)
  • 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)
  • c) Patent applications which contain disclosures of nucleotide and/or amino acid sequences must contain, as a separate part of the disclosure, a paper copy disclosing the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of §§ 1.822 and 1.823 . (uspto.gov)
  • The probability that the amino acids for all interior nodes at a site reconstructed by the new method are correct was calculated to be 0.91, 0.86, and 0.73 for all, variable, and parsimony-informative sites, respectively, whereas the corresponding probabilities for the parsimony method were 0.84, 0.76, and 0.51, respectively. (genetics.org)
  • 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)
  • This transactivation sequence is altered by tissue-specific alternative splicing in newly isolated NFATx isoforms, resulting in lower transactivation activity in Jurkat T cells. (jimmunol.org)
  • We have re-investigated the sequence of the snake protein, and believe that the correct sequence differs in nine places from that used for evolutionary theorizing since 1965. (biochemj.org)
  • The contradiction can be resolved by assuming sufficiently large degeneracy of the information contents of amino acid sequences with respect to function. (springer.com)
  • 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)
  • Amino acid sequence of rabbit muscle aldolase and the structure of the active center. (uniprot.org)
  • Each beat corresponds to one amino acid, and the piece is in 3/4 time, so each six measures would correspond to five turns around the alpha structure. (stephan-zielinski.com)
  • Atlas of Protein Sequence and Structure, Vol. 5 , Silver Spring: Natl. (springer.com)
  • A fusion between these 15 amino acids and the GAL4 DNA binding domain was capable of transactivating reporters driven by the GAL4 DNA binding site. (jimmunol.org)
  • The motif vectors are constructed by carrying out wavelet decomposition on numeric property sequences obtained by replacing each amino acid in a sequence with their respective properties, and concatenating such profiles obtained for a large number of physico-chemical properties into a single column vector. (actapress.com)
  • Values of two sequence based parameters, the average hydrophobicity, and the hydrophobic moment were used for the prediction. (pnas.org)
  • Amino acids with side chains that are neither aromatic not aliphatic control the piano and organ: the nine non-hydrophobics the piano, and the four hydrophobics the organ. (stephan-zielinski.com)
  • The three amino acids with aliphatic side chains control the low synthesizer, while the four with aromatics control the percussion. (stephan-zielinski.com)
  • Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches. (nih.gov)
  • One of the most difficult steps in protein crystallography is model-building, which consists of constructing a backbone and then amino acid side chains into an electron density map. (ebscohost.com)
  • on the average, at each position of the chain a choice of 1 out of 5 or less amino acids, and not a choice of 1 out of 20 is necessary for constructing a protein with a specified function. (springer.com)
  • Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and transposases of an unusual family of insertion elements. (asm.org)
  • If no sequence is present for a sequence identifier, the code "000" shall be used in place of the sequence. (uspto.gov)
  • shall include the total number of SEQ ID NOs, whether followed by a sequence or by the code "000. (uspto.gov)
  • 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)
  • three bases provide the code for each amino acid. (thefreedictionary.com)
  • Accordingly, isolated DNA sequences (SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7) are provided which code for the expression of 1-deoxyxylulose-5-phosphate synthase from plants. (osti.gov)