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.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.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.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.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.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.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.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.Nucleotide Motifs: Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.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.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.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.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.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.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.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).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).Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.Protein Interaction Domains and Motifs: Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.Helix-Turn-Helix Motifs: The first DNA-binding protein motif to be recognized. Helix-turn-helix motifs were originally identified in bacterial proteins but have since been found in hundreds of DNA-BINDING PROTEINS from both eukaryotes and prokaryotes. They are constructed from two alpha helices connected by a short extended chain of amino acids, which constitute the "turn." The two helices are held at a fixed angle, primarily through interactions between the two helices. (From Alberts et al., Molecular Biology of the Cell, 3d ed, p408-9)Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.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.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.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.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Helix-Loop-Helix Motifs: Recurring supersecondary structures characterized by 20 amino acids folding into two alpha helices connected by a non-helical "loop" segment. They are found in many sequence-specific DNA-BINDING PROTEINS and in CALCIUM-BINDING PROTEINS.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.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.EF Hand Motifs: Calcium-binding motifs composed of two helices (E and F) joined by a loop. Calcium is bound by the loop region. These motifs are found in many proteins that are regulated by calcium.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.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).)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.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Bacterial Proteins: Proteins found in any species of bacterium.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.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.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Protein Transport: The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.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.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.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.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.Two-Hybrid System Techniques: Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.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.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.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.Leucine Zippers: DNA-binding motifs formed from two alpha-helixes which intertwine for about eight turns into a coiled coil and then bifurcate to form Y shaped structures. Leucines occurring in heptad repeats end up on the same sides of the helixes and are adjacent to each other in the stem of the Y (the "zipper" region). The DNA-binding residues are located in the bifurcated region of the Y.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.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.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)Repetitive Sequences, Amino Acid: A sequential pattern of amino acids occurring more than once in the same protein sequence.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.AT-Hook Motifs: DNA-binding motifs, first described in one of the HMGA PROTEINS: HMG-I(Y) PROTEIN. They consist of positively charged sequences of nine amino acids centered on the invariant tripeptide glycine-arginine-proline. They act to fasten the protein to an AT RICH SEQUENCE in the DNA.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)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.Cercopithecus aethiops: A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.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).Cytoplasm: The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)Kinetics: The rate dynamics in chemical or physical systems.Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.Protein Sorting Signals: Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.PhosphoproteinsCell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Adaptor Proteins, Signal Transducing: A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymesFungal Proteins: Proteins found in any species of fungus.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.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.Leucine: An essential branched-chain amino acid important for hemoglobin formation.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Nuclear Magnetic Resonance, Biomolecular: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Tyrosine: A non-essential amino acid. In animals it is synthesized from PHENYLALANINE. It is also the precursor of EPINEPHRINE; THYROID HORMONES; and melanin.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Endocytosis: Cellular uptake of extracellular materials within membrane-limited vacuoles or microvesicles. ENDOSOMES play a central role in endocytosis.Ligands: A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)src Homology Domains: Regions of AMINO ACID SEQUENCE similarity in the SRC-FAMILY TYROSINE KINASES that fold into specific functional tertiary structures. The SH1 domain is a CATALYTIC DOMAIN. SH2 and SH3 domains are protein interaction domains. SH2 usually binds PHOSPHOTYROSINE-containing proteins and SH3 interacts with CYTOSKELETAL PROTEINS.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).Position-Specific Scoring Matrices: Tabular numerical representations of sequence motifs displaying their variability as likelihood values for each possible residue at each position in a sequence. Position-specific scoring matrices (PSSMs) are calculated from position frequency matrices.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.HEK293 Cells: A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.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.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.Viral Proteins: Proteins found in any species of virus.Adaptor Protein Complex 2: An adaptor protein complex primarily involved in the formation of clathrin-related endocytotic vesicles (ENDOSOMES) at the CELL MEMBRANE.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.Glutathione Transferase: A transferase that catalyzes the addition of aliphatic, aromatic, or heterocyclic FREE RADICALS as well as EPOXIDES and arene oxides to GLUTATHIONE. Addition takes place at the SULFUR. It also catalyzes the reduction of polyol nitrate by glutathione to polyol and nitrite.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.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.Oligopeptides: Peptides composed of between two and twelve amino acids.Intracellular Signaling Peptides and Proteins: Proteins and peptides that are involved in SIGNAL TRANSDUCTION within the cell. Included here are peptides and proteins that regulate the activity of TRANSCRIPTION FACTORS and cellular processes in response to signals from CELL SURFACE RECEPTORS. Intracellular signaling peptide and proteins may be part of an enzymatic signaling cascade or act through binding to and modifying the action of other signaling factors.Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.PDZ Domains: Protein interaction domains of about 70-90 amino acid residues, named after a common structure found in PSD-95, Discs Large, and Zona Occludens 1 proteins. PDZ domains are involved in the recruitment and interaction of proteins, and aid the formation of protein scaffolds and signaling networks. This is achieved by sequence-specific binding between a PDZ domain in one protein and a PDZ motif in another protein.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.Peptide Library: A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.Protein Isoforms: Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.Ubiquitin-Protein Ligases: A diverse class of enzymes that interact with UBIQUITIN-CONJUGATING ENZYMES and ubiquitination-specific protein substrates. Each member of this enzyme group has its own distinct specificity for a substrate and ubiquitin-conjugating enzyme. Ubiquitin-protein ligases exist as both monomeric proteins multiprotein complexes.Adenosine Triphosphatases: A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.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)CHO Cells: CELL LINE derived from the ovary of the Chinese hamster, Cricetulus griseus (CRICETULUS). The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems for the study of genetic alterations in cultured mammalian cells.Zinc: A metallic element of atomic number 30 and atomic weight 65.38. It is a necessary trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Zinc deficiency is associated with ANEMIA, short stature, HYPOGONADISM, impaired WOUND HEALING, and geophagia. It is known by the symbol Zn.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Hydrophobic and Hydrophilic Interactions: The thermodynamic interaction between a substance and WATER.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.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Precipitin Tests: Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.Endosomal Sorting Complexes Required for Transport: A set of protein subcomplexes involved in PROTEIN SORTING of UBIQUITINATED PROTEINS into intraluminal vesicles of MULTIVESICULAR BODIES and in membrane scission during formation of intraluminal vesicles, during the final step of CYTOKINESIS, and during the budding of enveloped viruses. The ESCRT machinery is comprised of the protein products of Class E vacuolar protein sorting genes.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Mutant Proteins: Proteins produced from GENES that have acquired MUTATIONS.Green Fluorescent Proteins: Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.Nuclear Localization Signals: Short, predominantly basic amino acid sequences identified as nuclear import signals for some proteins. These sequences are believed to interact with specific receptors at the NUCLEAR PORE.Immunoprecipitation: The aggregation of soluble ANTIGENS with ANTIBODIES, alone or with antibody binding factors such as ANTI-ANTIBODIES or STAPHYLOCOCCAL PROTEIN A, into complexes large enough to fall out of solution.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.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Nerve Tissue ProteinsDNA Footprinting: A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.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.Hydrogen Bonding: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.Protein Subunits: Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly.3T3 Cells: Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.Response Elements: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.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.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Microscopy, Fluorescence: Microscopy of specimens stained with fluorescent dye (usually fluorescein isothiocyanate) or of naturally fluorescent materials, which emit light when exposed to ultraviolet or blue light. Immunofluorescence microscopy utilizes antibodies that are labeled with fluorescent dye.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Protein-Serine-Threonine Kinases: A group of enzymes that catalyzes the phosphorylation of serine or threonine residues in proteins, with ATP or other nucleotides as phosphate donors.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)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.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.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.Lysine: An essential amino acid. It is often added to animal feed.Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Endoplasmic Reticulum: A system of cisternae in the CYTOPLASM of many cells. In places the endoplasmic reticulum is continuous with the plasma membrane (CELL MEMBRANE) or outer membrane of the nuclear envelope. If the outer surfaces of the endoplasmic reticulum membranes are coated with ribosomes, the endoplasmic reticulum is said to be rough-surfaced (ENDOPLASMIC RETICULUM, ROUGH); otherwise it is said to be smooth-surfaced (ENDOPLASMIC RETICULUM, SMOOTH). (King & Stansfield, A Dictionary of Genetics, 4th ed)3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.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.Arginine: An essential amino acid that is physiologically active in the L-form.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Ubiquitin: A highly conserved 76-amino acid peptide universally found in eukaryotic cells that functions as a marker for intracellular PROTEIN TRANSPORT and degradation. Ubiquitin becomes activated through a series of complicated steps and forms an isopeptide bond to lysine residues of specific proteins within the cell. These "ubiquitinated" proteins can be recognized and degraded by proteosomes or be transported to specific compartments within the cell.Cell Line, Tumor: A cell line derived from cultured tumor cells.Structural Homology, Protein: The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Calcium-Binding Proteins: Proteins to which calcium ions are bound. They can act as transport proteins, regulator proteins, or activator proteins. They typically contain EF HAND MOTIFS.Cell Cycle Proteins: Proteins that control the CELL DIVISION CYCLE. This family of proteins includes a wide variety of classes, including CYCLIN-DEPENDENT KINASES, mitogen-activated kinases, CYCLINS, and PHOSPHOPROTEIN PHOSPHATASES as well as their putative substrates such as chromatin-associated proteins, CYTOSKELETAL PROTEINS, and TRANSCRIPTION FACTORS.Multiprotein Complexes: Macromolecular complexes formed from the association of defined protein subunits.Histidine: An essential amino acid that is required for the production of HISTAMINE.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
Important motifs included animal friezes, symposia and komasts. Mythological imagery is quite rare; when it occurs, it usually ... There was also some experimentation with added colours, mainly red and white, and also, to some extent, with figural motifs ( ... As in Athens, kalos inscriptions occurred. Boeotian potters had a predilection to produce plastic vessels, also kantharoi with ... The paintings style often appears comical; komasts and satyrs were preferred motifs. Boeotian red-figure vase painting ...
Supernovas occur when stars explode and contain an extraordinary amount of energy. In the fifth part of Universe Symphony, the ... This movement is represented by rhythmic motifs. In the final part of Universe, the composer creates a contrast by using major ...
Mythological imagery is rare, but of outstanding quality when it occurs. Only 30 vases with mythological motifs are known. They ... Horsemen, animal friezes, heraldic images or groups of humans occur. A large lotus-palmette cross is also often included. ... Lekanes and Etruscan-style cups occur exceptionally. The construction of the vases is straightforward and simple. A typical ...
It occurs in ten steps and proves that phosphorylation is a much required and necessary step to attain the end products. ... This reveals interesting recurring patterns of interactions - network motifs. Computational methods have been developed to ... This activity occurs only in situations wherein the cell is damaged or physiology is disturbed in normal healthy individuals. ... This reaction occurs due to the enzyme hexokinase, an enzyme that helps phosphorylate many six-membered ring structures. ...
The tetrahedrane motif occurs broadly in chemistry. White phosphorus (P4) and yellow arsenic (As4) are examples. Several types ...
Such short motifs (e.g., GC-box) often occur by chance in nonfunctional sequences and detecting these motifs can be challenging ... The motif might have appeared in different species by chance. These motifs could be detected if sequences from more organisms ... A slower rate of change occurs in TFBS than in other, less critical, parts of the non-coding genome. Phylogenetic footprinting ... Because of the variable internal sequence, the motif cannot be detected. However, if we could use a program to search for ...
Jars with black-on-red exterior designs also occur. Agua Fria Glaze-on-red occurs throughout the Rio Grande Glaze Ware area. It ... The upper exteriors sometimes have slashes, crosses, or similar isolated motifs. ... San Clemente Polychrome occurs from Albuquerque south. Honea (1966) has described a variant on San Clemente Glaze Polychrome, ... it occurs with other rim forms (Franklin 2007). Carlson, Roy L., 1970, White Mountain Red Ware: A Pottery Tradition of East- ...
This domain has a highly conserved motif that is common to all members of the PARP family. PAR polymer can reach lengths of up ... Cleavage occurs at aspartic acid 214 and glycine 215, separating PARP into a 24kDA and 89kDA segment. The smaller moiety ... The DNA-binding domain is composed of two zinc finger motifs. In the presence of damaged DNA (base pair-excised), the DNA- ... It has been shown that this binding occurs independent of the other domains. This is integral in a programmed cell death model ...
This motif occurs 37 times in the database. This would suggest that the linear amino acid sequence may not be an underlying ... For example, the QKRAA sequence is an amino acid motif in the third hypervariable region of HLA-DRB1*0401. This motif is also ... The probability of finding a perfect match with a motif of 5 amino acids in length is 1 in 3.7 X 10−7 (0.055). Therefore, ... B cell tolerance then must occur within the periphery after the induction of B cell tolerance within the thymus as a more ...
This motif occurs only in the K'axob vessels. They have not been seen in any other Late Formative period villages. This motif ... Vessel painting did not occur until the Classical period. In the Middle Formative period, some of the slipped vessels were ... A particular design that appears on K'axob potteries is the cross motif. ... which occurred in the Terminal Classic period. Standing at 13 meters tall, this pyramid has since been heavily eroded and ...
These compounds are now known to also have regulatory roles, and to occur in representatives of all kingdoms of living ... This motif represents crosslinking of the linear polymer. Crosslinked polyphosphates adopt the sheet-structure Phyllosilicates ... 6.6 Further protonation occurs at lower pH values. ATP forms chelate complexes with metal ions. The stability constant for the ... refers to the fact that it is high relative to the amount of energy released in the organic chemical reactions that can occur ...
Small molecule effector binding occurs in the cleft between these subdomains. Binding to phosphorylated Hpr/Crh occurs along ... The LacI/GalR subfamily can be functionally subdivided based on the presence or absence of a "YxxPxxxAxxL" motif in the liker ... sequence; CcpA belongs to the subdivision containing this motif. The regulatory domain is further subdivided into a N-terminal ...
It often contains mythological scenes, but the first erotic motifs in Attic vase painting also occur here. Unique motifs ...
I saw the apple orchard and the garage and the Legion." Surprisingly, Ruby's vision actually occurs. One night, Miss Stairs ... The Town that Drowned portrays many different motifs and symbols. The author, Riel Nason, shows these throughout the story ... through the characters and significant events that occur. These are very relatable to modern everyday life, as they portray ...
Mythological motifs occur more rarely, but are already created with great care. By this time, Etruscan vase painting had begun ... Instead, the vase bodies were now mostly covered with ornamental and floral motifs. Larger compositions now only occurred in ... Chiusi became especially important through the Tondo Group, which produced drinking cups with mostly dionysiac motifs on the ... sometimes also with Etruscan motifs. The Phantom Group mostly painted cloaked figures in combination with compositions of plant ...
... s occur widely as minerals, comprising major sources of all cobalt compounds. Binary cobalt sulfide minerals ... adopts the spinel motif. The Co9S8 compound is known as a very rare cobaltpentlandite (the Co analogue of pentlandite). Mixed ...
... occurs naturally as the very rare anhydrous mineral tolbachite and the dihydrate eriochalcite. Both are ... In this motif, the copper centers are octahedral. Most copper(II) compounds exhibit distortions from idealized octahedral ... Both the anhydrous and the dihydrate forms occur naturally as the very rare minerals tolbachite and eriochalcite, respectively ...
The motif becomes heavily phosphorylated at the serine residue; if this phosphorylation occurs the variant becomes γH2A.X. ... The C-terminal of H2A.X contains an additional motif compared to H2A. The motif that is added is Ser-Gln-(Glu/Asp)- ( ... Resistance to nucleosomes occurs in H2A.Z by binding to H1 factor. H2A.Z gene is an essential gene in yeast and it is denoted ... Core formation first occurs through the interaction of two H2A molecules. Then, H2A forms a dimer with H2B; the core molecule ...
Herakles generally occurs frequently, e.g. with Nessos, Acheloos, the Nemean Lion, Alkyoneus or Pholos. Hermes is depicted ... Some vases show rare motifs, e.g. Keto accompanied by a white seal. In once case, both painters collaborated on a single vase. ... The ornamentation is a major constituent of the hydriai, it is not upstaged by the figural motifs. Stencild were used to create ... They were especially interested in mythological motifs, usually indicating an eastern influence. On the name vase of the ...
It is based on the motif of human sacrifice. The events described in the poem allegedly occurred at the beginning of the 14th ... The same motif is described in poetry composed in some other languages. The version in Serbian is considered as the major South ... For example, "The Building of Skadar" (Vuk II, 25) is based on the motif of a blood sacrifice being required to make a building ... "The Building of Skadar" is an old epic, the events of which are reported to have occurred during the first half of the ...
Asx and ST turns both occur frequently at the N-termini of α-helices, as part of asx motifs or ST motifs, with the asx, serine ... Similar motifs occur with aspartate or asparagine as residue i, called asx turn. Four types of asx turn and ST turn can be ... A proportion of ST turns are accompanied by a mainchain-mainchain hydrogen bond that qualifies them as ST motifs. Duddy, WJ; ... Golovin, A; Henrick K (2008). "MSDmotif: exploring protein sites and motifs". BMC Bioinformatics. 9: 312. doi:10.1186/1471-2105 ...
The decorative motifs of this region's clothing are zoological, botanical and geometrical. The motif of the snake, rooster, and ... Triangles, rhombuses, circles and crosses occur frequently,and they are known as symbols of health and fertility. Chromatically ... It did not have a collar, and its motifs were solar and lunar. The material which was used to knit these vests was known as ... The motifs and patterns on these garments can be explained by prehistoric religion. ...
These also may occur in the intron (intronic splicing enhancers, ISE) or exon (exonic splicing enhancers, ESE). Most of the ... Such proteins contain RNA recognition motifs and arginine and serine-rich (RS) domains. In general, the determinants of ... Two normally occurring isoforms in humans are produced by an exon-skipping mechanism. An mRNA including exon 6 encodes the ... Alternative splicing occurs as a normal phenomenon in eukaryotes, where it greatly increases the biodiversity of proteins that ...
In this motif, the two tetrahedra share a common edge. The inorganic polymer silicon disulfide features an infinite chain of ... Inversion of tetrahedral occurs widely in organic and main group chemistry. The so-called Walden inversion illustrates the ...
"Identification of high-molecular-weight proteins with multiple EGF-like motifs by motif-trap screening". Genomics. 51 (1): 27- ... The beta-folded sheets occur at many of the key domains, including the EGF-domains, kelch domains, and EGF-laminin domains. ... Leucine Zipper: A motif found in regulatory proteins, as predicted by PSORT II Laminin EGF-like domain: laminins are the major ... Each of the seven blades are made up of a four stranded beta-folded motifs. It is also important to note that although many ...
... the offbeat/onbeat motif method is much more common."[61] With this type of guajeo motif, the three-side of clave is expressed ... For cultural insiders, identifying the... 'dance feet' occurs instinctively and spontaneously. Those not familiar with the ... Clave motif[edit]. A chord progression can begin on either side of the clave. One can, therefore, be on either the three-side ... Offbeat/onbeat motif[edit]. Moore: "By the 1940s [there was] a trend toward the use of what Peñalosa calls the 'offbeat/onbeat ...
O-GlcNAc modification at a conserved residue in rat (Ser1009) and human (Ser1011) IRS-1 is adjacent to a putative binding motif ... O-GlcNAc modification did not occur at any known or newly identified Ser/Thr phosphorylation sites and in most cases occurred ... Modification of Insulin Receptor Substrate-1 Occurs in Close Proximity to Multiple SH2 Domain Binding Motifs. Amanda L. Klein, ... O-Linked N-Acetylglucosamine Modification of Insulin Receptor Substrate-1 Occurs in Close Proximity to Multiple SH2 Domain ...
A Cancer-Associated Mutation in Atypical Protein Kinase Cι Occurs in a Substrate-Specific Recruitment Motif ... A Cancer-Associated Mutation in Atypical Protein Kinase Cι Occurs in a Substrate-Specific Recruitment Motif ... A Cancer-Associated Mutation in Atypical Protein Kinase Cι Occurs in a Substrate-Specific Recruitment Motif ... A Cancer-Associated Mutation in Atypical Protein Kinase Cι Occurs in a Substrate-Specific Recruitment Motif ...
Naturally occurring germline and tumor-associated mutations within the ATP-binding motifs of PTEN lead to oxidative damage of ... Recent identification of naturally occurring cancer and germline mutations within the ATP-binding motifs of PTEN (heretofore ... ATP-binding motif mutants abrogate PTENs tumor-suppressive capabilities on cell signaling pathways. To determine the relative ... 2). In contrast, K62R and Y65C, both located within the ATP-binding motif A (residues 60-73), appear to behave more similar to ...
TAG motif only represents 2% of the cases (Fig. 2B). Hence, some of the MEF2 motifs occur very frequently in Arabidopsis ... and the y axis the percentage of the motifs that occur in a given distance interval. The total number of motifs of each type is ... we investigated whether these motifs occur with comparable frequencies in Arabidopsis promoters, or whether some of them occur ... Some MEF2 Motifs Occur More Frequently in Promoters. Because AtMIKC* protein complexes are able to discriminate between the 16 ...
Here we employ computational modeling to study neuronal dynamics on small subgraphs - or motifs - across a hierarchy of spatial ... Indeed, the corresponding motif occurs disproportionally in mammalian cortex (Fig. 1), hence being embedded in many cortical ... Dynamics of common driving motif (M3) versus common driving motifs with resonant sources (M6, M9 and M3+1) in motifs of ... Perhaps the archetypal motif in this family is M9 (see Fig. 1) also known as the dynamical relaying motif [24]-[27], [33]-[38] ...
Hence, binding must occur at a different residue.. The G-G/F-XXXG Motif Can Be Used to Rewire Other Transporters.. Finally, we ... a full G-G/F-XXXG motif, (ii) a related S-G-XXXG motif, (iii) a motif unrelated to the glycine-rich motif, and (iv) the lack of ... this work describes the discovery of a conserved G-G/F-XXXG motif and an engineering approach to modify this motif. This motif ... The native motif within S. cerevisiae HXT7 is G36G37F38V39F40G41. We initially evaluated two double mutations to this motif: ...
5, the p-value of two motifs co-occurring on j sequences is the sum of probabilities that two motifs co-occurring on more than ... when the adjusted p-value of two co-occurring motifs less than 0.05, it shows the observation of co-occurring motifs on j ... Detection of co-occurring motifs. In case one motif may include two separate complementary regions, we designed a post-analysis ... In our study, a pair of motifs were considered as the possible co-occurring motifs if they had over 0.8 normalized mutual ...
We find that the proteins in our set are covered to a substantial extent by the recurrent non-contiguous structural motifs, ... The non-alanine amino acids that are most common in the recurrent structural motifs, i.e., phenylalanine, isoleucine, leucine, ... In view of their properties, such structural motifs are potentially useful for inter-residue contact prediction and protein ... This indicates that the recurrent structural motifs, as we define them, describe recurrent structural patterns that are ...
Buy your own T-Shirt with a funny motifs: the fat-sucker design at Spreadshirt, your custom t-shirt printing platform! ... This funny motifs: the fat-sucker T-Shirt is printed on a T-Shirt and designed by Vektorschmiede. Available in many sizes and ... An error has occurred. The given e-mail address is either wrong, or already exists within our system. ... From our collection of funny motifs: The mosquito. Tags: wing, mosquito, sting, mosquito, mediterranean, disease, flying, devil ...
funny clown plants fruits vegetables kids motifs Baby Bib ✓ Unlimited options to combine colours, sizes & styles ✓ Discover ... An error has occurred. The given e-mail address is either wrong, or already exists within our system. ...
... occur in only a single motif, and an additional 13% of groups occur in only two motifs. These groups are probably examples of ... which occurs commonly when motifs are generated manually. Overfitting occurs when a motif is designed to cover all variability ... This generates a second motif, which in conjunction with the first motif, covers more of the training set than the first motif ... The motifs occur in vertical lines because coverage is an integer quantity. The lower curve is the Pareto-optimal curve, which ...
The structural modification includes addition or deletion of a leucine-based motif or parts thereof. In one embodiment, methods ... The "neurotoxin" may be naturally occurring or man-made.. "Modified neurotoxin" means a neurotoxin which includes a structural ... Leucine-based motif and clostridial neurotoxins. US7691974. Mar 25, 2008. Apr 6, 2010. Allergan, Inc.. Leucine-based motif and ... Leucine-based motif and clostridial neurotoxins. US7705125. Mar 27, 2008. Apr 27, 2010. Allergan, Inc.. Leucine-based motif and ...
No programming is required for this course although some command line work (though within a web browser) occurs in the 5th ... This, the second part, Bioinformatic Methods II, will cover motif searching, protein-protein interactions, structural ...
A straight-forward and robust method to identify potential regulatory motifs in co-regulated genes is presented. SCOPE does not ... will improve the motif score. This can occur through over-representation or motif position preference. Working with partial ... Clicking on a colored box next to a motif will toggle the display of that motif on or off in the motif map. In addition to a ... The user is not required to guess at the size of the motif or the number of occurrences of the motif as many other motif ...
Secondary Structure and Motifs. The secondary structure of proteins is due to foldings that occur within their structure. These ... The helix-loop-helix motif is a knobby structure, and the zinc finger projects outward like its name. These last two motifs ... Combinations of secondary structure form "motifs." A coiled-coil motif is common among proteins that associate with the DNA ... This occurs because the codon for valine, GUG, has replaced the codon for glutamic acid, GAG. This change from acidic to basic ...
... a significant proportion of Asx motifs occur at the N-terminus of an alpha helix with the Asx as the N cap residue. Asx motifs ... The Asx motif is a commonly occurring feature in proteins and polypeptides. It consists of four or five amino acid residues ... A related motif is the ST motif which has serine or threonine as the first residue. Wan, WY; Milner-White EJ (1999). "A natural ... Asx motifs occur commonly in proteins and polypeptides. When one of the hydrogen bonds is between the main chain oxygen of ...
In spite of overall low sequence similarity among IGYPs; they showed conserved N- and C-terminal motifs and a unified gene ... IGYP homologues were also found in 25 other Dikarya fungal species, all of which shared conserved motifs and the same gene ... Y/F/WxC motifs are not restricted to the N-terminal regions and occur at high frequency in non-secreted proteins of other fungi ... motifs. RF motifs were not obvious, but in the middle of IGYP homologues there was a conserved 5-amino acid KxWxP motif (x is ...
... certain motifs might only occur at one spatial scale or for a certain age range. Third, regions of interest which show one ... Third, regions of interest which show one motif at a lower resolution may show a range of motifs at a higher resolution which ... motif at a lower resolution may show a range of motifs at a higher resolution which may or may not include the original motif ... certain motifs might only occur at one spatial scale or for a certain age range. ...
A. A. Adzhubei and M. J. E. Sternberg, "Left-handed polyproline II helices commonly occur in globular proteins," Journal of ... Table 2: The proline-rich motif (PRM) and the proline-rich motif binding (PRB) domain in immune-related proteins. ... This concomitant binding of p300 to a relatively ubiquitous proline repeat motif and the classic hydrophobic LXXLL motif of the ... and a basic motif connected through a central region to a WH-2 motif that binds the actin nucleating complex [80, 82]. Most ...
Cytosine rich DNA sequences can fold into a structure called an i-motif. These structures typically appear in non-coding or ... The intercalation in i-motifs can occur in different ways leading to formation of two form;s R- and S-forms. ... Structure of the i-motif. The i-motif is a tetrameric or four stranded structure consisting of two parallel duplexes (double ... Fundamental aspects of the nucleic acid i-motif structures.. *i-Motif DNA: Structure, stability and targeting with ligands. ...
Cleavage within the hyalectans occurs at Glu-Xaa recognition motifs. Plays a role in embryonic development, including limb and ... conserved sequence motif of biological significance.,p>,a href=/help/motif target=_top>More...,/a>,/p>Motifi. 207 - 214. ... Cleavage within the hyalectans occurs at Glu-Xaa recognition motifs. Plays a role in embryonic development, including limb and ... Motif. Feature key. Position(s). DescriptionActions. Graphical view. Length. ,p>This subsection of the Family and Domains ...
Within individual proteins the motif occurs multiple times. For example, the motif appears 6 times in Drosophila egg-chamber ... The Kelch motif is a region of protein sequence found widely in proteins from bacteria and eukaryotes. This sequence motif is ... Eukaryotic Linear Motif resource motif class LIG_HCF-1_HBM_1 This article incorporates text from the public domain Pfam and ... The motif is also found in mouse protein MIPP and in a number of poxviruses. In addition, kelch repeats have been recognised in ...
We show the cleavage occurs at Leu517-Ser518 and is independent of the transmembrane domains. The non-covalent association of ... The GPS motif is necessary, but not sufficient for receptor cleavage, which requires the entire extracellular stalk. Thus, an ... Proteolytic cleavage of the EMR2 receptor requires both the extracellular stalk and the GPS motif.. Chang GW1, Stacey M, ...
Active Motif offers research kits, assays and biocomputing systems that help researchers study the function, regulation and ... Naturally occurring phenolic antioxidant. Displays anti-tumor and anti-platelet effects (ref 1). Activates SIRT1 and increases ...
An exception occurs when the input is (1, 1, 1, 1, 1) and concentrations of and (similarly and ) are both over 0.9. Thus, both ... 2. Simple DNA Gate Motif, Seesaw Gate. In this section, we introduce a simple DNA gate motif, "seesaw" gate, which is an enzyme ... Therefore, an exception must occur somewhere. To determine where the exception occurs, we debug the circuit with the above ... Figure 1 shows a simple DNA gate motif, seesaw gate. In the top left corner, it is abstract diagram for a seesaw gate and a ...
  • Results from cocrystallization studies of LXXLL-containing peptides with the ligand-activated hormone binding domains (HBD) of ER and PPARγ demonstrated that these motifs fit into a groove formed by helices 3, 4, 5, and 12 on the receptor ( 26 , 41 ). (asm.org)
  • A somatic mutation of the dibasic motif (R471C) was the most frequent mutation of PKCι in human cancer, and the intact dibasic motif was required for normal polarized epithelial morphogenesis in three-dimensional cysts. (sciencemag.org)
  • Our data, thus, reveal a novel mechanism of tumorigenesis in patients with germline or somatic mutations affecting PTEN ATP-binding motifs, i.e. qualitative and quantitative impairment of PTEN due to the loss of its phosphatase activity, and nuclear mislocalization, resulting in rapid PTEN protein degradation, suppression of p53-mediated transcriptional activity, loss of protection against oxidative stress as well as accumulation of spontaneous DNA DSBs. (pubmedcentralcanada.ca)
  • In contrast, we identified that both ATP depletion and germline or somatic mutations in PTEN 's ATP-binding motifs (which we will heretofore refer to as PTEN ATP-binding mutations) result in PTEN subcellular mislocalization which we hypothesized results in defects in its nuclear export ( 9 , 10 ). (pubmedcentralcanada.ca)
  • Statistically significant trends that were common to both IgV H 4.21 and 251 were used to deduce motifs that bias somatic hypermutation. (jimmunol.org)
  • Using the thermophilic orthologs as the positive set and the mesophilic orthologs as the negative set, discriminative motif discovery can be used to find motifs that are indicative of a high-temperature environment. (biomedcentral.com)
  • Studies have investigated the relative presence of tetraplex structures (i-motifs and G-quadraplex) and Watson-Crick duplexes. (news-medical.net)
  • This tool allows the systematic searching of all catalogued three-dimensional nucleic acid PDB structures that contain secondary structure motifs such as mismatches, (a)symmetric internal loops, hairpin loops, and bulge loops. (rcsb.org)
  • Thus, tertiary structures can be seen as a combination of basic building block motifs implying that all complex protein structures have evolved from the assembly of small independently folding super secondary structures. (omicsonline.org)
  • The success of designing super secondary motifs that fold in isolation underscores the prospects of designing and or identification of independently folding motifs from the existing protein structures. (omicsonline.org)
  • Dans les structures cristallines obtenues, des interactions non-covalentes entre groupements nitro démontrent leur potentiel en chimie supramoléculaire. (umontreal.ca)
  • Cytotoxicity and cytokine production triggered by DNAM-1 were mediated via a conserved tyrosine- and asparagine-based motif in the cytoplasmic domain of DNAM-1. (rupress.org)
  • Proteolytic cleavage of the EMR2 receptor requires both the extracellular stalk and the GPS motif. (nih.gov)
  • The GPS motif is necessary, but not sufficient for receptor cleavage, which requires the entire extracellular stalk. (nih.gov)
  • We sampled more than 10 8 variations of the core LXXLL motif with estradiol-activated estrogen receptor alpha (ERα) as a target and found three different classes of peptides. (asm.org)
  • In conclusion, using a combinatorial approach to define cofactor-receptor interactions, we have clearly been able to demonstrate that not all LXXLL motifs are functionally equivalent, a finding which suggests that it may be possible to target receptor-LXXLL interactions to develop receptor-specific antagonists. (asm.org)
  • Together, these findings suggest that agrin-induced phosphorylation of the β subunit motif increases the stoichiometry of rapsyn binding to the AChR, thereby helping to stably cluster the receptor and anchor it at high density in the postsynaptic membrane. (jneurosci.org)
  • Here, we combine comprehensive mass spectrometric glycan sequencing and molecular dynamics simulations to elucidate the substitution pattern in softwood xylans and to investigate the effect of distinct intramolecular motifs on xylan conformation and on the interaction with cellulose surfaces in Norway spruce (Picea abies). (diva-portal.org)
  • We therefore compared the properties of wild-type (WT) p28 and IL-27 with those of mutants lacking the poly-E acidic motif. (jimmunol.org)
  • The C-D loop acidic motif could therefore confer IL-27-specific pharmacological properties beneficial for therapeutic applications targeting osteoclasts, stem or immune cells residing at the endosteal surface of bone marrow. (jimmunol.org)
  • In lab experiments, it seemed that this DNA origami could occur only under acidic conditions that did not exist inside a cell. (latimes.com)
  • For example, researchers showed that an i-motif shape could form in an environment that was extremely crowded, even if it wasn't so acidic. (latimes.com)
  • Here we employ computational modeling to study neuronal dynamics on small subgraphs - or motifs - across a hierarchy of spatial scales. (plos.org)
  • The majority of these motif classes, however, were also found to be significantly enriched in one or more randomised datasets. (rsc.org)
  • A detailed investigation of cytosine methylation levels showed that it gradually decreased within ~2Kb of the motifs and was lowest at sites where crossover occurred. (weizmann.ac.il)
  • Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these, the phenomenon of "dynamical relaying" - a mechanism that relies on a specific network motif - has proven to be the most robust with respect to parameter mismatch and system noise. (plos.org)
  • Highly specific motifs are well suited for searching entire proteomes, while generating very few false predictions. (pnas.org)
  • Thus, emotif can generate extremely specific motifs that will produce fewer than one expected false prediction per 10 10 tests, as well as more sensitive motifs that cover all members of a family. (pnas.org)
  • emotif also can be used to find several highly specific motifs that characterize different subsets of a protein family. (pnas.org)
  • By combining these highly specific motifs together in a disjunction, we can potentially describe a protein family with both high specificity and sensitivity. (pnas.org)
  • Analysis of epigenetic modifications around the motifs showed, in most cases, a specific epigenetic architecture. (weizmann.ac.il)
  • We identified a protein interaction surface containing a dibasic motif (RIPR) that bound a distinct subset of PKCι substrates including lethal giant larvae 2 (LLGL2) and myosin X, but not other substrates such as Par3. (sciencemag.org)
  • Upon phosphorylation by Src kinases, this motif enabled binding of DNAM-1 to adaptor Grb2, leading to activation of enzymes Vav-1, phosphatidylinositol 3′ kinase, and phospholipase C-γ1. (rupress.org)