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 126.96.36.199.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) 188.8.131.52.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.
... mouse and human PAX6 have identical amino acid sequences. Genomic organisation of the PAX6 locus varies considerably among ... Paired box protein Pax-6, also known as aniridia type II protein (AN2) or oculorhombin, is a protein that in humans is encoded ... protein binding. • DNA binding. • sequence-specific DNA binding. • ubiquitin-protein transferase activity. • transcriptional ... transcription factor activity, sequence-specific DNA binding. • transcription factor binding. • protein kinase binding. • ...
Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence ... the SH3 domain binds to proline-rich sequences in other proteins). Sequence motif. Short amino acid sequences within proteins ... The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino ... Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of ...
In all proteins, it is the amino acid sequence that determines the protein's chemical properties and function. ... and these proteins, in turn, are folded chains of a large number of different amino acids called polypeptides. The amino acid ... Variations in hemoglobin amino acid sequences, as with other proteins, may be adaptive. For example, hemoglobin has been found ... The amino acid sequences of the globin proteins in hemoglobins usually differ between species. These differences grow with ...
"HMGB1 interacts with many apparently unrelated proteins by recognizing short amino acid sequences". J. Biol. Chem. 277 (9): ... sequence-specific DNA binding. • DNA binding. • transcription factor binding. • protein domain specific binding. • RNA ... Hepatocyte nuclear factor 3-gamma (HNF-3G), also known as forkhead box protein A3 (FOXA3) or transcription factor 3G (TCF-3G) ... "Nucleic Acids Res. 23 (7): 1184-91. doi:10.1093/nar/23.7.1184. PMC 306829 . PMID 7739897.. ...
Amino acid sequences of proteins. *DNA hybridization. *DNA and RNA sequences. *Restriction endonuclease analyses ... 16S ribosomal RNA - an intensively studied nucleic acid that has been useful in phylogenetics ...
Amino acid sequences in cytochrome c proteins from different species, adapted from Strahler, Arthur; Science and Earth History ... Its amino acid sequence is highly conserved in eukaryotes, differing by only a few residues. In more than thirty species, 34 of ... Many higher-order organisms possess a chain of 104 amino acids. The sequences of cytochrome c in humans is identical to that ... All cytochrome c proteins contain a characteristic CXXCH (cysteine-any-any-cysteine-histidine) amino acid motif that binds heme ...
Amino acid sequence of the reduced S-aminoethylated protein.». Arch. Biochem. Biophys. 179 (1): 189-99. PMID 843082. doi: ... Purification and amino acid sequence.». Eur. J. Biochem. 188 (3): 501-6. PMID 2110056. doi:10.1111/j.1432-1033.1990.tb15428.x. ...
The amino acid sequence of the protein transduction domain is YGRKKRRQRRR. The nuclear localisation signal found within the ... Jeang, K. T. (1996) In: Human Retroviruses and AIDS: "A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences". Los ... The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, ... The protein consists of between 86 and 101 amino acids depending on the subtype. Tat vastly increases the level of ...
1990). "Sequence of human eosinophil-derived neurotoxin cDNA: identity of deduced amino acid sequence with human nonsecretory ... The protein encoded by this gene is found in eosinophil granulocytes. It is closely related to the eosinophil cationic protein ... 1988). "Amino acid sequence of the nonsecretory ribonuclease of human urine". Biochemistry. 27 (12): 4530-8. doi:10.1021/ ... 1989). "Eosinophil cationic protein cDNA. Comparison with other toxic cationic proteins and ribonucleases". J. Immunol. 143 (3 ...
This process involves the formation of new protein molecules from amino acid building blocks based on information encoded in ... The ribosome mediates the formation of a polypeptide sequence based on the mRNA sequence. The mRNA sequence directly relates to ... Protein synthesis. Main article: Protein biosynthesis. Cells are capable of synthesizing new proteins, which are essential for ... and act as an assembly line where RNA from the nucleus is used to synthesise proteins from amino acids. Ribosomes can be found ...
Cas1 proteins have diverse amino acid sequences. However, their crystal structures are similar and all purified Cas1 proteins ... Unenriched sequencing libraries often have abundant undesired sequences. Cas9 can specifically deplete the undesired sequences ... Cas9 proteins select the correct location on the host's genome by utilizing the sequence to bond with base pairs on the host ... The sequence is not part of the Cas9 protein and as a result is customizable and can be independently synthesized. The PAM ...
Adenylyl cyclase amino acid sequence: possible channel- or transporter-like structure. Science. 1989 Jun 30;244(4912):1558-64. ... GAIP and RGS4 are GTPase-activating proteins for the Gi subfamily of G protein alpha subunits. Cell. 1996 Aug 9;86(3):445-52. ... Recombinant G-protein beta gamma-subunits activate the muscarinic-gated atrial potassium channel. Nature. 1994 Mar 17;368(6468 ... G proteins and dual control of adenylate cyclase. Cell. 1984 Mar;36(3):577-9. PMID 6321035. ...
after a comparison in amino acid sequence revealed no similarity with previously known haloperoxidases. In contrast with ... Tryptophan 7-halogenase is a 538-residue, 61-kDa protein. In solution, a number of homologues exist as homodimers. The enzyme ... Tryptophan is bound by a number of interactions: other aromatic amino acid residues such as tryptophan, phenylalanine, and ... Tryptophan substrate interacts with numerous other aromatic amino acid residues near the binding site, poising it for ...
sequences which do not code: introns. *sequences which do code for amino acid sequences in the protein. They are called exons.[ ... The DNA sequence is copied by a special enzyme called RNA polymerase to make a matching RNA strand. ... Its sequence is the same as the newly created RNA transcript (except for thymine being substituted for uracil). ... The product is called messenger RNA (mRNA) because it carries a genetic message from the DNA to the protein-making machinery of ...
codon - a sequence of three nucleotides which specify which amino acid will be added next during protein synthesis ... of the β-globin gene replacing the amino acid glutamic acid with the less polar amino acid valine at the sixth position of the ... The consequences of the simple replacement of a charged amino acid with a hydrophobic, neutral amino acid are far ranging, ... a chain of amino acids forming part of a protein molecule receptor (cellular surface) - specialized integral membrane proteins ...
In humans, RAD51 is a 339-amino acid protein that plays a major role in homologous recombination of DNA during double strand ... They each share about 25% amino acid sequence identity with RAD51 and with each other. ... protein C-terminus binding. • protein binding. • four-way junction DNA binding. • identical protein binding. • ... This protein can interact with the ssDNA-binding protein RPA, BRCA2, PALB2 and RAD52. ...
Nonribosomal peptide synthesis occurs through distinct modules that can load and extend the protein by one amino acid through ... The enzymes determine the amino acid sequence during its assembly through its 7 modules. Before vancomycin is assembled through ... a peptidyl carrier protein (PCP) domain, and a condensation (C) or elongation domain. In the A domain, the specific amino acid ... One mechanism of resistance to vancomycin involves the alteration to the terminal amino acid residues of the NAM/NAG-peptide ...
Amino acid sequences: Pramlintide as protein is (positively charged). Taylor, Phil (19 December 2013). "AstraZeneca buys BMS ... so these were directly grafted into the human sequence. Despite its enhanced stability compared to human amylin, pramlintide is ...
The translated protein contains 573 amino acids. The 573 amino acid protein has a molecular weight of 66,280.05. The ... Its genomic sequence contains 5,612 bp. The predominant transcript contains two exons and is 2,507 bp in length. ... Two deviations from prototypical human proteins are evident. The protein contains a less than expected number of glycine ... CBLast was used to determine a structurally related protein with experimentally determined structure. The protein Hermes DNA ...
The D-STIM protein of 570 aas exhibits equal similarity to both STIM1 (33% identical; 50% of amino acid sequence conserved) and ... STIM2 protein is a type I transmembrane protein located in the S/ER. Human STIM2 consists of 833 amino acid residues (aas) (105 ... of the amino acid sequence of STIM1). Only the extreme of the C-terminal region shows a significant sequence divergence. The ... of amino acid sequence conserved). Unicellular eukaryotes such as Monosiga brevicollis, a unicellular choanoflagellate has been ...
... of the size of 25-30 amino acids.. See also. *Chaperone - proteins that assist other proteins in folding or unfolding ... this suggests local amino acid sequences which form stable interactions and serve as nucleation points in the folding process". ... which explains the fast protein folding. This is also described as protein folding directed within funnel-like energy ... Some computational approaches to protein structure prediction have sought to identify and simulate the mechanism of protein ...
Proteins homologous to σ54/RpoN are functional sigma factors, but they have significantly different primary amino acid ... Genes recognized by σ70 all contain similar promoter consensus sequences consisting of two parts. Relative to the DNA base ... A sigma factor (σ factor) is a protein needed only for initiation of transcription. It is a bacterial transcription ... Doing so, other heatshock proteins are expressed, which enable the cell to survive higher temperatures. Some of the enzymes ...
Does the amino acid sequence of the transferred proteins resemble the sequence of known allergenic proteins? Are the ... The harmful proteins are those that do not break down due to the strong bonds of the protein. IgE antibodies bind to a receptor ... Other formulas, based on free amino acids, are the least antigenic and provide complete nutritional support in severe forms of ... Many food allergies are caused by hypersensitivities to particular proteins in different foods. Proteins have unique properties ...
At the amino-acid sequence level, the corresponding proteins share an average of 50% identical residues. ... the phylogenic analysis of their amino acid sequences does not cluster them with any known protozoan clade, but rather connect ... 1023 proteins (predicted). 390 nm. 120 nm. JF801956 Mimivirus. 1,181,549. 979 proteins (39 non-coding). 390 nm. 120 nm. ... 756 proteins (predicted). 390 nm. No. JN036606 Cafeteria roenbergensis virus. 617,453 (730 kb). 544 proteins (predicted). ...
This family of proteins contain a 70 amino acid consensus sequence known as the J domain. The J domain of DnaJ interacts with ... In molecular biology, chaperone DnaJ, also known as Hsp40 (heat shock protein 40 kD), is a molecular chaperone protein. It is ... Molecular chaperones are a diverse family of proteins that function to protect proteins from irreversible aggregation during ... which contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc ...
1985). "Amino terminal myristylation of the protein kinase p60src, a retroviral transforming protein". Science. 227 (4685): 427 ... Liu J, Sessa WC (1994). "Identification of covalently bound amino-terminal myristic acid in endothelial nitric oxide synthase ... 1997). "Large-scale concatenation cDNA sequencing". Genome Res. 7 (4): 353-8. doi:10.1101/gr.7.4.353. PMC 139146 . PMID 9110174 ... protein N-myristoyltransferase cause temperature-sensitive myristic acid auxotrophy in Saccharomyces cerevisiae". Proc Natl ...
The structure of a protein may be directly sequenced or inferred from the sequence of DNA. ... The protein primary structure conventionally begins at the amino-terminal (N) end and continues until the carboxyl-terminal (C ... Each protein or peptide consists of a linear sequence of amino acids. ... Amino Acids and Protein Sequences. News-Medical. https://www.news-medical.net/life-sciences/Amino-Acids-and-Protein-Sequences. ...
Prediction of protein antigenic determinants from amino acid sequences Message Subject (Your Name) has sent you a message from ... Prediction of protein antigenic determinants from amino acid sequences. T P Hopp and K R Woods ... A method is presented for locating protein antigenic determinants by analyzing amino acid sequences in order to find the point ... This is accomplished by assigning each amino acid a numerical value (hydrophilicity value) and then repetitively averaging ...
Prediction of the secondary structure of proteins from their amino acid sequence.. Chou PY, Fasman GD. ...
Using N-terminal sequence information only, it discriminates between proteins destined for the mitochondrion, the chloroplast, ... for large-scale subcellular location prediction of newly identified proteins has been developed. ... Predicting subcellular localization of proteins based on their N-terminal amino acid sequence J Mol Biol. 2000 Jul 21;300(4): ... Using N-terminal sequence information only, it discriminates between proteins destined for the mitochondrion, the chloroplast, ...
Protein-DNA interactions are vitally important in a wide range of biological processes such as gene regulation and DNA ...
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence.. Blom N1, ... Post-translational modifications (PTMs) occur on almost all proteins analyzed to date. The function of a modified protein is ... Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby, Denmark. [email protected] ... often strongly affected by these modifications and therefore increased knowledge about the potential PTMs of a target protein ...
Proteins,with,Native,Amino,Acid,,,Sequences,biological,advanced biology technology,biology laboratory technology,biology device ... One-column protein purification and native eukaryotic amino acid se... figure 1 ...Stratagenes ESP LIC cloning and expression ... One-column protein purification and native eukaryotic amino acid sequence. Quinn Lu John Bauer. Stratagene Cloning Systems, Inc ... New Yeast Cloning System for Producing Proteins with Native Amino Acid,,,Sequences ...
... with the N-terminal sequence obtained from the PPSQ-50A gradient system (Edman). ... This technical note investigates the benefits of combining the intact mass and sequencing information from the MALDI-8020 (ISD ... B103 Amino Acid Sequence Analysis of Peptides and Proteins with Modified Amino Acid Using PPSQ™-50A Isocratic System ... N-terminal Amino Acid Sequencing Analysis by MALDI-TOF MS/Protein Sequencer Mass spectrometry has become an indispensable tool ...
In order to apply a powerful pattern recognition algorithm to predict functional sites in proteins, amino acids cannot be used ... Relevant and Non-Redundant Amino Acid Sequence Selection for Protein Functional Site Identification: 10.4018/978-1-4666-0264-9. ... In this method the protein function is annotated through aligning a novel protein sequence with a known protein sequence. If ... "Relevant and Non-Redundant Amino Acid Sequence Selection for Protein Functional Site Identification." Breakthroughs in Software ...
While DNA sequencing is a useful tool for determining whats going on in a cell or a persons body, it only tells part of the ... and numerous small modifications can be made to each amino acid during protein production and folding.. "Many amino acids are ... Nanopores can identify the amino acids in proteins, the first step to sequencing. December 18, 2019. CHAMPAIGN, Ill. -- While ... A new study demonstrates that nanopores can be used to identify all 20 amino acids in proteins, a major step toward protein ...
Development of Novel Protocol for Preparation of Protein Thioesters Applicable to Naturally Occurring Amino Acid Sequences [in ...
... and distribution of defined attributes in the amino acid or nucleotide sequence. We have tested this approach on three ... discrimination between sequences of gene introns and exons, and 3) identification of putative RNA genes in genomic sequences. ... General global sequence descriptors have been developed which proved to be widely applicable to the prediction of properties of ... completely distinct biological problems: 1) prediction of protein three-dimensional folds, 2) ...
Due to the limitations of experimental self-interaction proteins detection technology, it is a very important task to develop a ... play an essential role in cellular functions and the evolution of protein interaction networks (PINs). ... In this study, we propose a novel computational method for predicting SIPs from protein amino acids sequence. Firstly, a novel ... Robust and accurate prediction of protein self-interactions from amino acids sequence using evolutionary information J. An, Z. ...
Prediction of protein motions from amino acid sequence and its application to protein-protein interaction. ... Home » Prediction of protein motions from amino acid sequence and its application to protein-protein interaction ... uses information associated with adjacent amino acid residues and secondary structures predicted from the amino acid sequence. ... Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. ...
Pillars Article: Evidence for Amino Acid Sequence Differences among Proteins Resembling the L-chain Subunits of Immunoglobulins ... Pillars Article: Evidence for Amino Acid Sequence Differences among Proteins Resembling the L-chain Subunits of Immunoglobulins ... Pillars Article: Evidence for Amino Acid Sequence Differences among Proteins Resembling the L-chain Subunits of Immunoglobulins ... Pillars Article: Evidence for Amino Acid Sequence Differences among Proteins Resembling the L-chain Subunits of Immunoglobulins ...
Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and ... Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and ... Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and ... Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and ...
... I. Determining Protein Amino Acid Sequence. 3/05/2018 · The 3 d the nucleotide ... Protein and Amino Acid Sequence Analysis MATLAB & Simulink. How To Add Amino Acids To A Protein Sequence. Other than that, rare ... How many amino acids can a sequence of 24 DNA Socratic. The sequence of amino acids in a protein, known as the primary ... bioinformatics Coordinates of amino acids in a protein. As in say a protein sequence consisting of a chain of amino acids MK ...
This framework is applied to study how existing general-purpose amino acid similarity matrices perform on individual protein ... However, using fold-specific similarity matrices can only marginally improve sequence alignment of proteins that share the same ... This work is focused on the issue of finding optimized protein family- and fold-specific scoring functions for global ... similarity matrices significantly improves the quality of the alignment of homologous sequences over the traditional sequence ...
Amino Acids Sequence Based in Silico Analysis of RuBisCO (Ribulose-1,5 Bisphosphate Carboxylase Oxygenase) Proteins in Some ...
Nucleic and deduced amino acid sequences from eight different EAV isolates (one European, two American... ... Comparison of nucleic and amino acid sequences and phylogenetic analysis of the GS protein of various equine arteritis virus ... Nucleotide and amino acid sequence identities between these isolates and the Bucyrus reference strain ranged from 92.3 to 96.4 ... Nucleic and deduced amino acid sequences from eight different EAV isolates (one European, two American and five Canadian ...
In turn, each residues contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold ... Including additional information about sequence weight and amino acid composition further improves prediction accuracies ... Using protein local sequences with multiple sequence alignments (PSI-BLAST profiles), we demonstrate a correlation coefficient ... In this study, we provide a more accurate contact number prediction method from protein primary sequence. We predict contact ...
The physicochemical properties of a protein are determined by the analogous properties of the amino acids in it. The α-carbon ... As a result, each of the amino acids, except glycine, can exist in two different spatial, or geometric, arrangements (i.e., ... atom of all amino acids, with the exception of glycine, is asymmetric; this means that four different chemical entities (atoms ... Amino acid sequence in protein molecules. Since each protein molecule consists of a long chain of amino acid residues, linked ...
This is a problem of predicting which part in a cell a given protein is transported to, where an amino acid sequence of the ... Furthermore, the idea of combination of alignment and amino acid frequency is novel and general so that it may be applied to ... a novel and general predicting method by combining techniques for sequence alignment and feature vectors based on amino acid ... Since such information as gene ontology can be obtained only for known proteins, our predictor is considered to be useful for ...
With the avalanche of protein sequences generated in the postgenomic age, it is critical to develop computational methods for ... Particularly, the approach of using the wavelets to express protein/peptide sequences might be the key in grasping the ... identifying in a timely fashion the protein-protein binding sites (PPBSs) based on the sequence information alone because the ... Knowledge of protein-protein interactions and their binding sites is indispensable for in-depth understanding of the networks ...
Key Amino Acids of the PduP Targeting Sequence.. To identify the key amino acids needed for targeting PduP to the lumen of the ... Our prior studies showed that a short N-terminal sequence (18 amino acids) targets the PduP protein to the lumen of the Pdu MCP ... To test whether the N-terminal targeting sequence of PduP binds to PduA, PduP-His6 with 18 N-terminal amino acids deleted ( ... By aligning the C-terminal sequences of PduA homologs, there are six amino acids conserved among different organisms (Fig. S2 ...
ResiduesMoleculeGenomeStructuralPeptideDifferent amino acidsAlignmentsFunctionalCompositionAlignmentMutationsMolecular weightChain of aminoAnalysisGenomesBiochemistryLipidsMoleculesSpecificityNucleotide SequencesIsoleucineMrnaSequentialEukaryoticTertiaryBiologicalPhylogeneticOccurPhosphorylationIdentify the aminoTarget proteins has been shownGene sequencesMetabolismInteractionsHydrolysisAntigenRecombinant proteinsFoldGenomic sequencesHydrophobicComplexesChainsStructureIdentitiesDegradationBioinformaticsCoordinatesDatabasesProtein'sMetabolicAbundanceMassIdenticalPrediction of proteinOligopeptidesNuclear ProteinsDetermination
- The proposed method uses information associated with adjacent amino acid residues and secondary structures predicted from the amino acid sequence. (ebscohost.com)
- The fragment from the kappa chain of immunoprotein contains 107 amino acid residues, and polymerizes in the crystal form into a giant helical. (ebscohost.com)
- Protein tertiary structure can be partly characterized via each amino acid's contact number measuring how residues are spatially arranged. (biomedcentral.com)
- The contact number of a residue in a folded protein is a measure of its exposure to the local environment, and is defined as the number of C β atoms in other residues within a sphere around the C β atom of the residue of interest. (biomedcentral.com)
- Here, we seek to use protein contact number to assist with the tertiary fold prediction of novel proteins for which an accurate functional relationship between a protein's primary sequence and its residues' contact numbers must be determined. (biomedcentral.com)
- The contact number, or coordination number, of a given residue of a folded protein is defined as the number of C β (or C α ) atoms in other residues within a sphere around the C β (or C α ) atom of that given residue. (biomedcentral.com)
- Since each protein molecule consists of a long chain of amino acid residues, linked to each other by peptide bonds, the hydrolytic cleavage of all peptide bonds is a prerequisite for the quantitative determination of the amino acid residues. (britannica.com)
- To obtain information about the sequence of the amino acid residues in the protein, the protein is degraded stepwise, one amino acid being split off in each step. (britannica.com)
- The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. (iisc.ernet.in)
- This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i - 1, i and i + 1, thereby speeding up the sequential assignment process. (iisc.ernet.in)
- Mapping of conserved residues in the CipA CBD showed a well-conserved calcium-binding site, probably involved in stabilizing the protein fold, and a putative cellulose-binding surface. (asm.org)
- Proteins ( / ˈ p r oʊ ˌ t iː n z / or / ˈ p r oʊ t i . ɪ n z / ) are large biomolecules , or macromolecules , consisting of one or more long chains of amino acid residues . (wikipedia.org)
- A linear chain of amino acid residues is called a polypeptide . (wikipedia.org)
- Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides , or sometimes oligopeptides . (wikipedia.org)
- The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. (wikipedia.org)
- The sequence of amino acid residues in a protein is defined by the sequence of a gene , which is encoded in the genetic code . (wikipedia.org)
- Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification , which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. (wikipedia.org)
- Each pair consists of a type I and type II protein Left-handed coil coiled-coil 310 AA residues 7-residue pseudo repeat. (slideplayer.com)
- Sequences are the middle 120-180 amino acid residues of the proteins. (wikipedia.org)
- Residues that are conserved across all sequences are highlighted in grey. (wikipedia.org)
- These forms differ by the presence or the absence of short (10 to 20 residues) peptides in various internal locations in the sequence. (wikipedia.org)
- In general, the major form of MBP is a protein of about 18.5 Kd (170 residues). (wikipedia.org)
- A DNA molecule is itself a template designed for replication, so making copies for sequencing is relatively easy. (brightsurf.com)
- The carrier molecule also kept the amino acids inside the pore long enough for it to register a measurable difference in the electrical signature of each amino acid - even leucine and isoleucine, the near-identical twins. (brightsurf.com)
- Protein kinases are key signaling enzymes that catalyze the transfer of Î³-phosphate from an ATP molecule to a phosphoaccepting residue in the substrate. (ebscohost.com)
- 3/05/2018 · The 3 d the nucleotide sequence of a gene, through medium mrna, is translated into amino acid protein by rules that are known as codons in an mrna molecule do not directly recognize acids they. (gleekguide.com)
- The method provides a complex comprising a polymerase enzyme, a target nucleic acid molecule, and a primer, wherein the complex is immobilized on a support Fluorescent label is attached to a terminal phosphate group of the nucleotide or nucleotide analog. (osti.gov)
- Internet Explorer is OK but usually cannot display the Features of the Molecule control panel in Protein Explorer. (umass.edu)
- Okayama University researchers report on the control the timing and location of protein synthesis using a photoresponsive compound that is an inactive key molecule until it is activated by brief irradiation. (prweb.com)
- In their study, the researchers used an aminoacyl-transfer RNA (aa-tRNA), a molecule that helps decode messenger RNA so that protein synthesis can occur. (prweb.com)
- its structure resulting from the union of more than one protein molecule, called subunit proteins. (syvum.com)
- An alto CTL epitope of the H-2D d antigen was also localized to this stretch of amino acid sequence, as one of several H-2D d specific CTL clones reacted with the mutant molecule in which amino acids were replaced at position 63 to 70. (springer.com)
- Anfinsen studied how a protein molecule acquires and maintains this specific shape by exposing one well-characterized protein, the enzyme ribonuclease, to conditions in which it became unfolded and structurally disordered. (encyclopedia.com)
- Although this bacterium is unable to degrade cellulose, the sequence analysis of its genome revealed the presence of a large cellulosomal gene cluster ( 12 ). (asm.org)
- In fact, sperm-specific, seminal fluid, and egg-specific proteins evolve at astonishingly rapid rates, and are often the fastest observed within a given genome. (g3journal.org)
- Detecting protein function and protein-protein interactions from genome sequences . (psu.edu)
- Genome sequencing reveals the sequence of the nucleotides in a gene, like alphabet letters in words. (cdc.gov)
- Genome sequencing is a process that determines the order, or sequence, of the nucleotides (i.e. (cdc.gov)
- Full genome sequencing can reveal the approximately 13,500-letter sequence of all the genes of the virus' genome. (cdc.gov)
- Each year CDC performs whole genome sequencing on about 7,000 influenza viruses from original clinical samples collected through virologic surveillance. (cdc.gov)
- An influenza A or B virus' genome contains eight gene segments that encode (i.e., determine the structure and features of) the virus' 12 proteins, including its two primary surface proteins: hemagglutinin (HA) and neuraminidase (NA). (cdc.gov)
- However it can fully substitute the much simpler Arabidopsis protein, if transferred from algae to plant genome by means of genetic engineering . (wikipedia.org)
- As genome sequencing becomes cheaper and faster, resulting in an exponential increase in data, the need for efficiency in predicting gene function is growing, as is the need to train the next generation of scientists in bioinformatics. (phys.org)
- During the sequencing of the human genome, a sequencing method called shotgun sequencing was very successfully employed. (encyclopedia.com)
- The many sequences are then pieced back together using computers to generate the entire DNA genome sequence. (encyclopedia.com)
- https://boglab.plp.iastate.edu/) that enables design of custom TAL effector repeat arrays for desired targets and prediction of TAL effector binding sites, ranked by likelihood, in a genome, promoterome or other sequence of interest. (iu.edu)
- Background: Structural flexibility is an important characteristic of proteins because it is often associated with their function. (ebscohost.com)
- Novel structural superfamilies can be identified among the large number of protein structures deposited in the Protein Data Bank based on conservation of fold in addition to conservation of amino acid sequence. (ebscohost.com)
- Our results showed that the G S protein-encoding gene can be subjected on the basis of phylogenetic analysis to genetic variation, as previously shown for the other three EAV structural protein (M, N and G L )-encoding genes. (springer.com)
- The successful application of support vector regression to the prediction of protein contact number reported here, together with previous applications of this approach to the prediction of protein accessible surface area and B-factor profile, suggests that a support vector regression approach may be very useful for determining the structure-function relation between primary protein sequence and higher order consecutive protein structural and functional properties. (biomedcentral.com)
- Prediction of protein three-dimensional structure from primary sequence is the central problem in structural bioinformatics. (biomedcentral.com)
- One protein structural feature is of particular interest here, namely, residue contact number (CN) which can be used to enhance protein fold recognition [ 1 ]. (biomedcentral.com)
- N-terminal structural analysis is the first step in protein structural analysis. (shimadzu.com)
- Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies. (iisc.ernet.in)
- Based on sequence homology, the CipA CBD structure appears to be very similar to that of the previously elucidated family 3a CBD ( 15 , 17 ), including a nine-stranded jellyroll topology which exhibits distinctive structural elements consistent with family 3 CBDs. (asm.org)
- A single amino acid substitution, Q65H, in the non-structural protein 2C was found to be responsible for increased resistance to BFA. (frontiersin.org)
- Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton , which form a system of scaffolding that maintains cell shape. (wikipedia.org)
- All proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded . (wikipedia.org)
- Experienced participants are encouraged to work at their own speed, ahead of the group -- there is plenty of power to discover within Protein Explorer and its connections to complementary structural bioinformatics resources! (umass.edu)
- How to use Protein Explorer to visualize structural features of proteins. (umass.edu)
- In the focus of our research is the phenomenon of structural disorder of proteins. (vib.be)
- These studies have shown that structural disorder is prevalent in eukaryotic proteomes and disordered proteins carry out unique functions. (vib.be)
- The study of structural disorder has already progressed way beyond simply establishing the disordered status of a protein. (vib.be)
- The current idea is that detailed experimental and theoretical characterization of the structural ensemble of disordered proteins in isolation, their structure in complex with their physiological partner(s), and the thermodynamics and kinetics of their interactions with their partners, hold the key to understanding these proteins and extending the structure -function paradigm to the disordered state. (vib.be)
- We also aim to understand the structure-function relationship of very large ("oversized") proteins, practically neglected from a structural point of view thus far. (vib.be)
- Structural biology has traditionally addressed the structure of small folded proteins, whereas the field of structural disorder has focused on either fully disordered proteins/regions or short disordered elements that undergo induced folding in the presence of their partner. (vib.be)
- 25/11/2013 - Researchers of the VIB department of Structural Biology and the 'Interuniversity Institute of Bioinformatics in Brussels (IB2)', have developed a method to predict how much the backbone chain of a protein moves based on only its amino acid sequence. (vib.be)
- Nucleotides are organic molecules that form the structural unit building block of nucleic acids, such as RNA or DNA. (cdc.gov)
- 3 Globular proteins = enzymes and catalysts Fibrous proteins = structural or connective role. (slideplayer.com)
- The PDBFlex database explores the intrinsic flexibility of protein structures by analyzing structural variations of the same protein across the archive. (rcsb.org)
- This allows for the easy identification of regions and types of structural flexibility present in a protein of interest. (rcsb.org)
- PcG proteins form a family based upon their common role in gene expression rather than extensive shared homologies or structural motifs. (genetics.org)
- Proteins catalyze essential chemical reactions in living cells as well as performing many other vital regulatory and structural functions. (encyclopedia.com)
- This notion became a central part of the conceptual framework of molecular biology , and put into relief the "protein folding problem"-understanding how a particular amino acid sequence specifies the three-dimensional configuration-that has occupied protein chemists and structural biologists since the 1960s. (encyclopedia.com)
- Although SUMO has very little sequence identity with ubiquitin at the amino acid level, it has a nearly identical structural fold. (wikipedia.org)
- Each protein or peptide consists of a linear sequence of amino acids. (news-medical.net)
- The amino acid sequence of a protein or peptide is useful information to understand the protein or peptide, identify it in a sample and categorize its post-translational modifications. (news-medical.net)
- It is helpful to know which amino acid is at the N-terminus of the protein both for ordering of the peptide fragments into the whole chain and to reduce the impact of impurities that commonly occur in the first round of Edman degradation. (news-medical.net)
- This is accomplished by assigning each amino acid a numerical value (hydrophilicity value) and then repetitively averaging these values along the peptide chain. (pnas.org)
- After expression in S. pombe, the GST fusion protein can be purified from crude cell extracts using a single-step purification procedure based on the selective affinity of the GST peptide for glutathione immobilized on resin. (bio-medicine.org)
- it thus reveals the sequence of the amino acids in the peptide chain. (britannica.com)
- For this reason the protein is usually first hydrolyzed by exposure to the enzyme trypsin, which cleaves only peptide bonds formed by the carboxyl groups of lysine and arginine. (britannica.com)
- Particularly, the approach of using the wavelets to express protein/peptide sequences might be the key in grasping the problem's essence, fully consistent with the findings that many important biological functions of proteins can be elucidated with their low-frequency internal motions. (mdpi.com)
- Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors . (wikipedia.org)
- Leon Dure III, " Occurrence of a Repeating 11-Mer Amino Acid Sequence Motif in Diverse Organisms", Protein & Peptide Letters (2001) 8: 115. (eurekaselect.com)
- identified by using phosphoserine-oriented peptide libraries to probe mammalian and yeast 14-3-3 proteins. (plantphysiol.org)
- Then get on to how they typically interact with each other and how the peptide bond folds and how proteins fold and how this makes them work and some examples of them working. (physicsforums.com)
- Immunogen: Synthetic peptide derived from the internal region of JAB1 (Jun activation domain-binding protein 1 CSN5). (bio-medicine.org)
- Researchers in the United States created a synthetic peptide with a sequence identical to that of an HHV-6 peptide. (wikipedia.org)
- These activated T cells also recognized and initiated an immune response against a synthetically created peptide sequence that is identical to part of human MBP. (wikipedia.org)
- This is a proof-of-concept study showing that we can identify the different amino acids," he said. (brightsurf.com)
- However, evolutionary transition probabilities, although they must reflect the operational exchangeability of amino acids in proteins, must also reflect rates of mutation from one kind of codon to another (in principle, they may also reflect subtle fitness effects unrelated to protein operation, due to different metabolic costs of different amino acids or to different translational efficiencies of different codons, and so on). (genetics.org)
- its structure resulting from hydrogen bonds between the C=O and N-H groups of different amino acids. (syvum.com)
- Firstly, a novel feature representation scheme based on Local Binary Pattern (LBP) is developed, in which the evolutionary information, in the form of multiple sequence alignments, is taken into account. (rsc.org)
- Scoring protein sequence alignments II PAM1 matrix: answers question, "if 1% of the amino acids in a sequence change, at what rates would each amino acid be substituted for each other one? (gleekguide.com)
- Scoring protein sequence alignments II Substitution matrices PAM (Accepted Point Mutation, but "PAM" easier to say than "APM") matrix PAM1 matrix: answers question, "if 1% of the amino. (gleekguide.com)
- Using protein local sequences with multiple sequence alignments (PSI-BLAST profiles), we demonstrate a correlation coefficient between predicted and observed contact numbers of 0.70, which outperforms previously achieved accuracies. (biomedcentral.com)
- A 40% sequence identity filter is applied before the structure alignments are calculated, so most results show low similarity. (rcsb.org)
- Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. (wikipedia.org)
- Relevant and Non-Redundant Amino Acid Sequence Selection for Protein Functional Site Identification. (igi-global.com)
- In order to apply a powerful pattern recognition algorithm to predict functional sites in proteins, amino acids cannot be used directly as inputs since they are non-numerical variables. (igi-global.com)
- Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. (gleekguide.com)
- In contrast, the regression approach provides a direct and more accurate way to determine a functional relationship matching contact numbers and protein sequence and thus to provide more accurate contact number predictions. (biomedcentral.com)
- Within these reproductive categories, evolutionary rates differ based on sex and functional protein class. (g3journal.org)
- Hence, all three reading frames are used to produce functional proteins. (nature.com)
- Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, inherited from the shared ancestor . (wikipedia.org)
- A dataset based on all known functional sequences of ubiquitin (UB) has been prepared. (creation.com)
- He and his coworkers demonstrated that the completely unfolded, or denatured, ribonuclease could spontaneously regain its fully native, functional state, including reforming the correct covalent chemical links between non-adjacent amino acids, the disulfide bonds. (encyclopedia.com)
- Determine the composition and terminal amino acids of each chain. (news-medical.net)
- The unordered composition of an amino acid is often useful information when attempting to determine the ordered sequence of the protein. (news-medical.net)
- These descriptors include composition, transition, and distribution of defined attributes in the amino acid or nucleotide sequence. (nsti.org)
- Including additional information about sequence weight and amino acid composition further improves prediction accuracies significantly with the correlation coefficient reaching 0.73. (biomedcentral.com)
- 1. A method for treating or limiting development of diabetes, comprising administering to a subject in need thereof an amount effective of a composition comprising a compound of formula A-B, wherein A is a pancreatic β cell targeting moiety, and B is an inhibitor of expression and/or activity of Apolipoprotein CIII (apoCIII), protein kinase A (PKA), Src kinase, and/or β1 integrin. (freepatentsonline.com)
- 11. A composition of formula A-B, wherein A is a pancreatic β cell targeting moiety, and B is an inhibitor of Apolipoprotein CIII (apoCIII), protein kinase A (PKA), Src kinase, or β1 integrin. (freepatentsonline.com)
- The first is the identification of gel-separated, low abundance proteins based on amino acid sequence composition following coimmunoprecipitation with the human apoptosis inhibitor protein BclX(L). The second is the determination of the precise sites of phosphorylation of the human regulatory protein 4E-BP1, which controls mRNA translation. (nih.gov)
- 2. The process of claim 1 wherein said BMP composition activates DNA sequences that code for bone morphogenesis. (google.ca)
- 3. The process of claim 1 wherein said BMP composition consists essentially of about 7 parts 22-kDa and about 1 part 14-kDa BMP associated proteins, and about 2 parts 18.5 0.5-kDa bBMP factor. (google.ca)
- The present invention provides an improved process for further purifying and isolating BMP to provide the new BMP composition, namely, the BMP factor and associated proteins. (google.ca)
- Likewise, a bias favoring AT (or GC) base pairs would affect the relative rates of Glu → Gly (GAR → GGR) vs. Glu → Val (GAR → GTR), and such effects seem to have played an important role in the evolution of amino acid composition ( S inger and H ickey 2000 ). (genetics.org)
- B) Structure-based sequence alignment of family 3a CBDs. (asm.org)
- A structure-based alignment of selected CBD sequences is shown in Fig. 1B . (asm.org)
- sequence identity in the alignment. (rcsb.org)
- A sequence alignment of mammalian histone proteins. (wikipedia.org)
- M.S. Waterman and R. Jones , Consensus Methods for DNA and Protein Sequence Alignment. (elsevier.com)
- D.-F. Feng and R.F. Doolittle , Progressive Alignment and Phylogenetic Tree Construction of Protein Sequences. (elsevier.com)
- G.J. Barton , Protein Multiple Sequence Alignment and Flexible Pattern Matching. (elsevier.com)
- G.M. Landau, U. Vishkin, and R. Nussinov , Fast Alignment of DNA and Protein Sequences. (elsevier.com)
- SEL1L protein structure and partial sequence alignment. (plos.org)
- B) SEL1L amino acid sequence alignment. (plos.org)
- Mutations that activate the LRRK2 (leucine-rich repeat protein kinase 2) protein kinase predispose to Parkinson's disease, suggesting that LRRK2 inhibitors might have therapeutic benefit. (biochemj.org)
- Commonly occurring autosomal-dominant missense mutations within the LRRK2 (leucine-rich repeat protein kinase 2) protein are linked to Parkinson's disease [ 1 , 2 ]. (biochemj.org)
- supports the representation of interacting domains down to the residue level, including required post-translational modifications (PTMs) and sequence mutations that have an impact in the interaction. (ebi.ac.uk)
- and (4) a set of three tests designed to evaluate the power of an exchangeability measure to (i) predict the effects of amino acid exchanges in the laboratory, (ii) account for the disease-causing potential of missense mutations in the human population, and (iii) model the probability of fixation of missense mutations in evolution. (genetics.org)
- However, the narrow range of amino acid sequence variability found throughout nature seems inconsistent with the notion of an ancient origin and very little change through mutations. (creation.com)
- A final proof of our ideas can only be obtained by detailed studies on the alterations produced in the amino acid sequence of a protein by mutations of the type discussed here. (todayinsci.com)
- To test our previous hypothesis that the segment between amino acid position 63 to 73 of the H-2D d antigen forms a major allo-antigenic site, mutations were introduced into the H-2L d gene in a sequential fashion, which replaced the codons for amino acid position 63, 65, 66, 70 and 73 of the H-2L d antigen with those of the H-2D d antigen. (springer.com)
- Although effective in many cases, sequencing by In Source Decay (ISD) faces a few challenges its ability to provide reliable sequence information including isobaric amino acids, database dependency and low molecular weight interferences. (shimadzu.com)
- Work with BMP material isolated from rabbit dentin matrix protein fraction, using polyacrylamide gel electrophoresis (PAGE) has been assigned a molecular weight of about 23,000. (google.ca)
- There are two main steps to determine the frequency of amino acids in a process known as amino acid analysis. (news-medical.net)
- The method was developed using 12 proteins for which extensive immunochemical analysis has been carried out and subsequently was used to predict antigenic determinants for the following proteins: hepatitis B surface antigen, influenza hemagglutinins, fowl plague virus hemagglutinin, human histocompatibility antigen HLA-B7, human interferons, Escherichia coli and cholera enterotoxins, ragweed allergens Ra3 and Ra5, and streptococcal M protein. (pnas.org)
- Cleavage with thrombin yields the recombinant protein fused with the FLAG epitope for future analysis of the protein. (bio-medicine.org)
- However, phylogenetic tree analysis and estimation of genetic distances based on the G S protein encoding gene sequences showed that the European prototype Vienna strain, the American 87AR-A1 isolate and all other North American EAV isolates could be classified into three genetically divergent groups. (springer.com)
- In turn, each residue's contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold analysis from sequence data. (biomedcentral.com)
- On the basis of sequence analysis, it has been estimated that MCPs are produced by 20-25% of bacteria and function in 10 or more different metabolic processes ( 4 , 6 ). (pnas.org)
- This analysis employs the Edman method (sequential cleaving of amino acids from the N-terminal of the protein to determine the amino acid sequence), which is the most reliable method for determining amino acid sequences. (shimadzu.com)
- The PPSQ-31A/33A Protein Sequencer System automates the Edman reaction, HPLC separation and detection, and data analysis to determine the amino acid sequence from the N-terminal. (shimadzu.com)
- Analysis to the 21st residue reveals the sequence from the N-terminal to be: Asp-Val-Val-Met-Thr-Gln-Thr-Pro-Leu-Thr-Leu-Ser-Val-Thr-Ile-Gly-Gln-Pro-Ala-Ser-Ile. (shimadzu.com)
- Biochemical and Western analysis revealed that the C. acetobutylicum cellulosome comprised four major subunits, including the scaffolding protein CipA and the cellobiohydrolases Cel48A, Cel9X, and Cel9C or Cel9E. (asm.org)
- This value is calculated by the PC GENE computer analysis program of protein sequences (IntelliGenetics). (prospecbio.com)
- Participants will be enabled to incorporate computer visualization and qualitative analysis of 3D structure of protein, DNA, RNA, and protein-ligand interactions into their teaching and research. (umass.edu)
- Thus, while not conforming to the standard expectation for the evolution of reproductive proteins, our analysis of the molecular evolution of the MSP gene family is nonetheless consistent with the widely repeatable observation that reproductive proteins evolve rapidly, in this case in terms of the genomic properties of gene structure, copy number, and genomic organization. (g3journal.org)
- The DNA sequence encoding steroid 5α-reductase 2, the major active isozyme of human genital tissue, is disclosed herein, in addition to methods and compositions for its preparation and pharmacological analysis. (google.co.uk)
- These sequences may prove useful in an analysis of normal and abnormal sexual differentiation, benign prostatic hyperplasia, male pattern baldness, acne, hirsutism, endometriosis, and cancer of the prostate. (google.co.uk)
- Immunoblot analysis revealed that the seven OspC proteins tested have both common and specific epitopes. (asm.org)
- Technical replicates showed good reproducibility and protein intensities from the label-free discovery analysis compared favorably with reported abundance levels of several known reference serum proteins over at least 3 orders of magnitude. (biomedsearch.com)
- The diagrams shown are based on an NMR analysis of the protein in solution. (wikipedia.org)
- Reproductive proteins are often observed to be the most rapidly evolving elements within eukaryotic genomes. (g3journal.org)
- While most mRNAs in eukaryotic cells are monocistronic, positive-strand RNA viruses encode multiple proteins in single polycistronic genomes. (nature.com)
- The post-genomic era is characterized by the deposition of sequence information for entire genomes in databases. (nih.gov)
- However, dramatic increases in ROS result in significant damage to human cells by altering proteins, lipids and DNA. (springer.com)
- I have been trying to get my head around the basics for these four (Carbohydrates, Proteins, Amino Acids and Lipids) for about a week and I just don't understand the basic structure, formulas and such. (physicsforums.com)
- Nitrogenase catalyzes the six electron/six proton reduction of N2 to two ammonia molecules at a complex organometallocluster called ï¿½FeMo cofactor.ï¿½ This cofactor is buried within the a-subunit of the MoFe protein, with no obvious access for substrates. (ebscohost.com)
- Summary: X-ray crystallography is the most widely used method to determine the 3D structure of protein molecules. (ebscohost.com)
- 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. (wikipedia.org)
- Brief exposure to light releases key protein synthesis molecules from the cage without damaging them, so that protein synthesis takes place at the time and location of irradiation. (prweb.com)
- The DEACM group protects the aa-tRNA so that it cannot interact with the molecules necessary for protein synthesis. (prweb.com)
- But proteins are not boring, they are the most fantastically, well, protean molecules on earth and possibly anywhere else! (physicsforums.com)
- This quiz is based on the various aspects of the structure of protein molecules and amino acids. (syvum.com)
- From these results we conclude that the amino acid sequence encompassing from position 63 to 70 of the H-2D d and H-2L d molecules forms major alto- antigenic epitopes recognized by multiple antibodies and CTLs. (springer.com)
- Myelin basic protein has been shown to interact in vivo with Proteolipid protein 1, and in vitro with Calmodulin, Actin, Tropomyosin, Tubulin, Clathrin, 2',3'-Cyclic-nucleotide 3'-phosphodiesterase and multiple molecules of the Immune system. (wikipedia.org)
- We also identify rabbit monoclonal antibodies displaying broad specificity (MJFF-pRAB8) that can be utilised to assess LRRK2-controlled phosphorylation of a range of endogenous Rab proteins, including Rab8A, Rab10 and Rab35. (biochemj.org)
- Specificity: Specific for the JAB1 protein. (bio-medicine.org)
- The gene of interest is prepared for PCR amplification and LIC cloning by using primers that include 12- and 13-nucleotide sequences that are complementary to the 5 single-stranded overhangs of the pESP-2 vector. (bio-medicine.org)
- The nucleotide sequences of the ospC gene from five Danish human Borrelia burgdorferi isolates representing all three B. burgdorferi genospecies (B. burgdorferi sensu stricto, Borrelia garinii sp. (asm.org)
- By coupling a dynamic kinetic resolution (DKR) using an N -acylamino acid racemase (NAAAR) and an L-selective aminoacylase from Geobacillus thermoglucosidasius with a stereoselective isoleucine dioxygenase from Bacillus thuringiensis , diastereomerically pure oxidized amino acids were produced from racemic N -acetylamino acids. (frontiersin.org)
- The amino acids isoleucine and leucine were recently assigned the ambiguity. (stn-international.de)
- The synthesis of proteins in specific locations is important in for instance the development of the fly drosophila, where localisation of oskar mRNA in the egg determines the anterior-posterior axis. (prweb.com)
- The usual mode for protein synthesis uses transfer RNA (tRNA), messenger RNA (mRNA) and ribosomes to assemble the amino acid chains in the right order. (prweb.com)
- The role of the tRNA is to link the amino acids to the mRNA to help decode it. (prweb.com)
- The ribosome matches the aminoacyl-tRNA (tRNA carrying an amino acid) with the mRNA so that the protein encoded on the mRNA is synthesized. (prweb.com)
- The researchers demonstrated the light-responsive aa-tRNA release by irradiating a gel containing green fluorescent protein mRNA and the complex through a mask in the shape of a smiley face. (prweb.com)
- One-column protein purification and native eukaryotic amino acid se. (bio-medicine.org)
- Stratagenes ESP LIC cloning and expression system offers rapid and high-yield production of recombinant proteins in a eukaryotic organism. (bio-medicine.org)
- 14-3-3 proteins constitute a highly conserved family of eukaryotic proteins with multiple regulatory functions (for review, see Aitken, 1996 ). (plantphysiol.org)
- The sequence of amino acids in a protein, known as the primary structure, determine the secondary and tertiary structure. (gleekguide.com)
- Other than that, rare/non proteinaceous amino acids, modified amino acids (hydroxylysine, hydroxyproline etc.) are present at specific sequence points to add to the framework of the tertiary and quarternary structure of the protein. (gleekguide.com)
- In the Protein Folding Problem and Tertiary Structure Prediction, Merz and Le Grand (Eds), Aug. 1994, Springer Verlag, pp. 433 and 492-495. (freepatentsonline.com)
- Because the system uses the yeast Schizosaccharomyces pombe as the expression host, proteins undergo many of the posttranslational modifications that are often required for their biological activity. (bio-medicine.org)
- This product is an active protein and may elicit a biological response in vivo, handle with caution. (abcam.com)
- Like other biological macromolecules such as polysaccharides and nucleic acids , proteins are essential parts of organisms and participate in virtually every process within cells . (wikipedia.org)
- p>This section provides any useful information about the protein, mostly biological knowledge. (uniprot.org)
- Currently, besides the protein sequences for known human proteins, there are partial sequences from thousands more human proteins for which no biological function has been assigned. (nih.gov)
- Nearly every fundamental biological process necessary for life is carried out by proteins. (phys.org)
- W.R. Taylor , Hierarchical Method to Align Large Numbers of Biological Sequences. (elsevier.com)
- Post-translational modifications (PTMs) occur on almost all proteins analyzed to date. (nih.gov)
- Unavoidable small losses that occur during each step make it impossible to determine the sequence of more than about 30 to 50 amino acids by this procedure. (britannica.com)
- Transgenic proteins expressed by genetically modified food crops are evaluated for their potential allergenic properties prior to marketing, among others by identification of short identical amino acid sequences that occur both in the transgenic protein and allergenic proteins. (biomedcentral.com)
- Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. (nih.gov)
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K. (biochemj.org)
- The activity of RBR proteins is regulated by posttranslational mechanisms, primarily phosphorylation, since transcription factors like E2F bind only the hypophosphorylated form of RB. (plantcell.org)
- The pool of MBP in the central nervous system is very diverse, with several splice variants being expressed and a large number of post-translational modifications on the protein, which include phosphorylation, methylation, deamidation, and citrullination. (wikipedia.org)
- Knowledge of protein-protein interactions and their binding sites is indispensable for in-depth understanding of the networks in living cells. (mdpi.com)
- Most proteins whose functions are essential to life are associated with protein-protein interactions [ 1 ]. (mdpi.com)
- Some experimental protocols, such as tandem affinity purification (TAP) , generate complex data sets, depicting interactions in which more than two proteins are involved at the same time (n-ary interactions). (ebi.ac.uk)
- its structure resulting from interactions between amino acid side chains. (syvum.com)
- By virtue of all of the interactions just discussed, RBRs function as central hub proteins in the complex process of cell cycle control, including cell cycle arrest, which requires balancing the activity of many regulators. (plantcell.org)
- Firstly, hydrolysis of a known quantity of the protein should break it up into the amino acid monomers. (news-medical.net)
- The hydrolysis is typically carried out by heating a sample of the protein to over 100 ° C in hydrochloric acid for an extended period of time (at least 24 hours), allowing more time for proteins with bulky hydrophobic groups. (news-medical.net)
- Hydrolysis is most frequently accomplished by boiling the protein with concentrated hydrochloric acid . (britannica.com)
- The hepatitis B surface antigen sequence was synthesized by chemical means and was shown to have antigenic activity by radioimmunoassay. (pnas.org)
- Polymorphism in ospC gene of Borrelia burgdorferi and immunoreactivity of OspC protein: implications for taxonomy and for use of OspC protein as a diagnostic antigen. (asm.org)
- A recombinant protein antigen with a N-terminal His6-ABP tag corresponding to human FAM173B. (fishersci.com)
- The FAM173B Recombinant Protein Antigen has been validated for the following applications: Antibody Competition. (fishersci.com)
- 1985. Polymorphism of murine major histocompatibility class I antigens: Assignment of putative allodeterminants to distinct positions of the amino acid sequence within the first external domain of the antigen. (springer.com)
- Antigen: Full length protein. (bio-medicine.org)
- Antigen: Full length protein: Sarcosine Oxidase (microbial). (bio-medicine.org)
- The amino acids in a protein are arranged in such away that it allow the protein to fold an … d coil into a certain shape which determines its function. (gleekguide.com)
- Contact number is partly conserved between protein folds and thus is useful for protein fold and structure prediction. (biomedcentral.com)
- A 3-D biomarker discovery strategy consisting of abundant protein immunodepletion, SDS gels, LC-MS/MS, and label-free quantitation of MS signal intensities identified 70 candidate biomarkers with differences between groups greater than 2.5-fold. (biomedsearch.com)
- Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes . (wikipedia.org)
- Here we would like to probe into the structure of the very large transcriptional co-activator CREB-binding protein (CBP), by addressing its structure by means traditionally applied in the case of protein complexes. (vib.be)
- Three PcG fusion proteins, ZnF-PC, ZnF-SCM, and ZnF-ESC, were studied, since biochemical analyses place these PcG proteins in distinct complexes. (genetics.org)
- When DNA damage occurs, SUMO protein has been shown to act as a molecular glue to facilitate the assembly of large protein complexes in repair foci. (wikipedia.org)
- The protein primary structure conventionally begins at the amino-terminal (N) end and continues until the carboxyl-terminal (C) end. (news-medical.net)
- The structure of a protein may be directly sequenced or inferred from the sequence of DNA. (news-medical.net)
- Prediction of the secondary structure of proteins from their amino acid sequence. (nih.gov)
- Molecular Structure of the Amyloid-Forming Protein kappa I Bre1. (ebscohost.com)
- The molecular structure of the amyloid-forming Bence-Jones protein kappa I Bre has been determined by X-ray crystallography at 2.0 Ã… resolution. (ebscohost.com)
- How is the elaborate three-dimensional structure of proteins attained, and how is the three-dimensional structure related to the one-dimensional amino acid sequence information? (gleekguide.com)
- Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. (iisc.ernet.in)
- Amino acid sequence and domain structure of CipA. (asm.org)
- A representation of the 3D structure of the protein myoglobin showing turquoise α-helices . (wikipedia.org)
- This protein was the first to have its structure solved by X-ray crystallography . (wikipedia.org)
- Methods commonly used to study protein structure and function include immunohistochemistry , site-directed mutagenesis , X-ray crystallography , nuclear magnetic resonance and mass spectrometry . (wikipedia.org)
- Myoglobin has been of great importance in the elucidation of protein structure. (britannica.com)
- In this day of exploding bioinformatics information from genomics and proteomics, it is ever more important to be conversant with macromolecular three-dimensional structure, and how it relates to protein and nucleic acid function and drug design. (umass.edu)
- It progresses rapidly to powerful tools that will be of interest to specialists in protein structure and bioinformatics. (umass.edu)
- As a researcher I study Protein structure and dynamics. (mendeley.com)
- Genetic variations are important because they can affect the structure of an influenza virus' surface proteins. (cdc.gov)
- Protein Structure Lecture 2/26/2003. (slideplayer.com)
- Presentation on theme: "Protein Structure Lecture 2/26/2003. (slideplayer.com)
- 10 Protein helices are stretchy and can elongate When keratin is stretched it can form a more sheet like structure. (slideplayer.com)
- Assumes that you are already familiar with principles of protein structure. (umass.edu)
- Review of Protein Chemistry and Structure. (umass.edu)
- I don't have any of the right books, someone else may suggest, but you could browse your uni bookshop, or Amazon etc. for a book on protein structure and function. (physicsforums.com)
- Anfinsen received the Nobel Prize in Chemistry in 1972 for his biochemical investigations of protein structure. (encyclopedia.com)
- In conjunction with these findings, he developed the "thermodynamic hypothesis," the notion that a protein in solution acquires its three-dimensional native structure because it is the most stable, i.e., the Gibbs free energy of that state is lowest. (encyclopedia.com)
- A) A Schematic representation of the SEL1L protein, which shows the multi-modular protein structure. (plos.org)
- Nucleotide and amino acid sequence identities between these isolates and the Bucyrus reference strain ranged from 92.3 to 96.4%, and 93.2 to 95.5%, respectively. (springer.com)
- Thirty-three transgenic proteins have been screened for identities of at least six contiguous amino acids shared with allergenic proteins. (biomedcentral.com)
- High and moderate nucleotide/amino acid percentage identities are in boldface . (cdc.gov)
- Edman degradation using a protein sequenator is the second method, which is most useful if the N-terminus of a protein needs to be characterized. (news-medical.net)
- As there is a risk of protein degradation in these conditions, particularly for cysteine, glutamine, serine, threonine, tryptophan, and tyrosine, it is recommended to use several samples and to heat them for different times. (news-medical.net)
- The PPSQ-51A/53A continues the tradition of providing reliable and sensitive N-terminal protein sequencing to researchers through automated Edman Degradation. (shimadzu.com)
- Constant protein generation is required to balance the loss of proteins through degradation and secretion from cells. (prweb.com)
- The most popular direct protein chemical sequencing technique in use today is the Edman degradation procedure. (encyclopedia.com)
- In contrast to ubiquitin, SUMO is not used to tag proteins for degradation. (wikipedia.org)
- Traditional Edman sequencing avoids mass dependency and the use of databases by analyzing each amino acid from the N-terminus one at a time in sequence. (shimadzu.com)
- Given the large amount of data available in public databases, I decided to see how much variety in amino acid sequence exists and how the data might be interpreted from a creationist or evolutionist framework. (creation.com)
- R.F. Doolittle , Searching through Sequence Databases. (elsevier.com)
- S. Henikoff, J.C. Wallace, and J.P. Brown , Finding Protein Similarities with Nucleotide Sequence Databases. (elsevier.com)
- This technical note investigates the benefits of combining the intact mass and sequencing information from the MALDI-8020 (ISD) with the N- terminal sequence obtained from the PPSQ-50A gradient system (Edman). (shimadzu.com)
- CipA contains 1,484 amino acids and has a molecular mass of 154.4 kDa. (asm.org)
- Another protein sequencing technique is called fast atom bombardment mass spectrometry, or FAB-MS. This is a powerful technique in which the sample is bombarded with a stream of fast atoms, such as argon. (encyclopedia.com)
- most are around 100 amino acids in length and 12 kDa in mass. (wikipedia.org)
- The exact length and mass varies between SUMO family members and depends on which organism the protein comes from. (wikipedia.org)
- Only a limited number of identical stretches shared by transgenic proteins (papaya ringspot virus coat protein, acetolactate synthase GH50, and glyphosate oxidoreductase) and allergenic proteins could be identified as (part of) potential linear epitopes. (biomedcentral.com)
- Many transgenic proteins have identical stretches of six or seven amino acids in common with allergenic proteins. (biomedcentral.com)
- For example, when identical sequences for the same organism was found, reported from different laboratories, the first one in the data file was kept. (creation.com)