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.
Methods for determining interaction between PROTEINS.
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.
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.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The 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.
Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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.
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.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.
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 enzymes
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.
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.
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.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Transport proteins that carry specific substances in the blood or across cell membranes.
Established cell cultures that have the potential to propagate indefinitely.
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.
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.
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.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The 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).
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.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
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.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
Proteins prepared by recombinant DNA technology.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
Proteins 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.
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.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The 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.
Deletion of sequences of nucleic acids from the genetic material of an individual.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
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.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
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.
Macromolecular complexes formed from the association of defined protein subunits.
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).
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
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.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
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.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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.
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.
Proteins found in any species of fungus.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
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.
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.
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
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.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
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)
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
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.
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).)
Proteins found in any species of bacterium.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
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.
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)
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.
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.
Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.
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)
The rate dynamics in chemical or physical systems.
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.
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)
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.
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.
The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.
A general term for single-celled rounded fungi that reproduce by budding. Brewers' and bakers' yeasts are SACCHAROMYCES CEREVISIAE; therapeutic dried yeast is YEAST, DRIED.
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.
A biosensing technique in which biomolecules capable of binding to specific analytes or ligands are first immobilized on one side of a metallic film. Light is then focused on the opposite side of the film to excite the surface plasmons, that is, the oscillations of free electrons propagating along the film's surface. The refractive index of light reflecting off this surface is measured. When the immobilized biomolecules are bound by their ligands, an alteration in surface plasmons on the opposite side of the film is created which is directly proportional to the change in bound, or adsorbed, mass. Binding is measured by changes in the refractive index. The technique is used to study biomolecular interactions, such as antigen-antibody binding.
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.
Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.
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.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
A 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.
The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.
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.
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.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.
Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
The protein complement of an organism coded for by its genome.
Proteins found in any species of virus.
Proteins which are involved in the phenomenon of light emission in living systems. Included are the "enzymatic" and "non-enzymatic" types of system with or without the presence of oxygen or co-factors.
Sequential operating programs and data which instruct the functioning of a digital computer.
The relationships of groups of organisms as reflected by their genetic makeup.
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.
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
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.
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.
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.
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).
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.
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.
A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.
Catalyzes the ATP-dependent PHOSPHORYLATION of GMP to generate GDP and ADP.
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.
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.
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.
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.
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.
An enzyme that catalyzes reversible reactions of a nucleoside triphosphate, e.g., ATP, with a nucleoside monophosphate, e.g., UMP, to form ADP and UDP. Many nucleoside monophosphates can act as acceptor while many ribo- and deoxyribonucleoside triphosphates can act as donor. EC 2.7.4.4.
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.
A member of the p300-CBP transcription factor family that was initially identified as a binding partner for CAMP RESPONSE ELEMENT-BINDING PROTEIN. Mutations in CREB-binding protein are associated with RUBINSTEIN-TAYBI SYNDROME.
Proteins produced from GENES that have acquired MUTATIONS.
An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
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.
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.
Enzymes that catalyze acyl group transfer from ACETYL-CoA to HISTONES forming CoA and acetyl-histones.
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.
Major constituent of the cytoskeleton found in the cytoplasm of eukaryotic cells. They form a flexible framework for the cell, provide attachment points for organelles and formed bodies, and make communication between parts of the cell possible.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
A large class of structurally-related proteins that contain one or more LIM zinc finger domains. Many of the proteins in this class are involved in intracellular signaling processes and mediate their effects via LIM domain protein-protein interactions. The name LIM is derived from the first three proteins in which the motif was found: LIN-11, Isl1 and Mec-3.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
A type of FLUORESCENCE SPECTROSCOPY using two FLUORESCENT DYES with overlapping emission and absorption spectra, which is used to indicate proximity of labeled molecules. This technique is useful for studying interactions of molecules and PROTEIN FOLDING.
Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
An amino acid that occurs in endogenous proteins. Tyrosine phosphorylation and dephosphorylation plays a role in cellular signal transduction and possibly in cell growth control and carcinogenesis.
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.
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.
Computer-based representation of physical systems and phenomena such as chemical processes.
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.
A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.
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.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
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.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)
Gated transport mechanisms by which proteins or RNA are moved across the NUCLEAR MEMBRANE.
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.
Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.
A nuclear protein that regulates the expression of genes involved in a diverse array of processes related to metabolism and reproduction. The protein contains three nuclear receptor interaction domains and three repressor domains and is closely-related in structure to NUCLEAR RECEPTOR CO-REPRESSOR 2.
Biochemical identification of mutational changes in a nucleotide sequence.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
Intracellular receptors that can be found in the cytoplasm or in the nucleus. They bind to extracellular signaling molecules that migrate through or are transported across the CELL MEMBRANE. Many members of this class of receptors occur in the cytoplasm and are transported to the CELL NUCLEUS upon ligand-binding where they signal via DNA-binding and transcription regulation. Also included in this category are receptors found on INTRACELLULAR MEMBRANES that act via mechanisms similar to CELL SURFACE RECEPTORS.
The portion of an interactive computer program that issues messages to and receives commands from a user.
A non-essential amino acid. In animals it is synthesized from PHENYLALANINE. It is also the precursor of EPINEPHRINE; THYROID HORMONES; and melanin.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
Proteins from the nematode species CAENORHABDITIS ELEGANS. The proteins from this species are the subject of scientific interest in the area of multicellular organism MORPHOGENESIS.
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.
The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.
Proteins obtained from ESCHERICHIA COLI.
A sequential pattern of amino acids occurring more than once in the same protein sequence.
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
A species of nematode that is widely used in biological, biochemical, and genetic studies.
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
A transcription factor that partners with ligand bound GLUCOCORTICOID RECEPTORS and ESTROGEN RECEPTORS to stimulate GENETIC TRANSCRIPTION. It plays an important role in FERTILITY as well as in METABOLISM of LIPIDS.
The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.
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.
Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.
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.
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
An essential amino acid. It is often added to animal feed.
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.
A large family of signal-transducing adaptor proteins present in wide variety of eukaryotes. They are PHOSPHOSERINE and PHOSPHOTHREONINE binding proteins involved in important cellular processes including SIGNAL TRANSDUCTION; CELL CYCLE control; APOPTOSIS; and cellular stress responses. 14-3-3 proteins function by interacting with other signal-transducing proteins and effecting changes in their enzymatic activity and subcellular localization. The name 14-3-3 derives from numerical designations used in the original fractionation patterns of the proteins.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
A nuclear receptor coactivator with specificity for ESTROGEN RECEPTORS; PROGESTERONE RECEPTORS; and THYROID HORMONE RECEPTORS. It contains a histone acetyltransferase activity that may play a role in the transcriptional activation of chromatin regions.
Regulatory proteins that act as molecular switches. They control a wide range of biological processes including: receptor signaling, intracellular signal transduction pathways, and protein synthesis. Their activity is regulated by factors that control their ability to bind to and hydrolyze GTP to GDP. EC 3.6.1.-.
A cell line derived from cultured tumor cells.
Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.
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.
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.
Components of a cell produced by various separation techniques which, though they disrupt the delicate anatomy of a cell, preserve the structure and physiology of its functioning constituents for biochemical and ultrastructural analysis. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p163)
Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.
Conversion of an inactive form of an enzyme to one possessing metabolic activity. It includes 1, activation by ions (activators); 2, activation by cofactors (coenzymes); and 3, conversion of an enzyme precursor (proenzyme or zymogen) to an active enzyme.
Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
A class of proteins involved in the transport of molecules via TRANSPORT VESICLES. They perform functions such as binding to the cell membrane, capturing cargo molecules and promoting the assembly of CLATHRIN. The majority of adaptor proteins exist as multi-subunit complexes, however monomeric varieties have also been found.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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.
Elements of limited time intervals, contributing to particular results or situations.
A group of enzymes that catalyzes the phosphorylation of serine or threonine residues in proteins, with ATP or other nucleotides as phosphate donors.
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.
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.
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).
A family of enzymes that catalyze the conversion of ATP and a protein to ADP and a phosphoprotein.
An aquatic genus of the family, Pipidae, occurring in Africa and distinguished by having black horny claws on three inner hind toes.
The commonest and widest ranging species of the clawed "frog" (Xenopus) in Africa. This species is used extensively in research. There is now a significant population in California derived from escaped laboratory animals.
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)
Proteins found in any species of insect.
Any method used for determining the location of and relative distances between genes on a chromosome.
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.

N-terminal segments are the functional domains of CLN3-encoded battenin for protein interactions. (1/3048)

OBJECTIVE: Batten disease (BD), the juvenile form of neuronal ceroid lipofuscinosis (NCLs), is pathological characterized by finding lysosomal storage of autofluorescent lipofuscins with unique ultrastructural profiles. The gene underlying BD is designated CLN3 and encodes a protein, Battenin, of unknown function that localizes in lysosomes and/or mitochondria. Previously, we hypothesized that Battenin associates with other membrane protein(s) to form a membrane complex. Dysfunction of this complex could result in the pathological changes of BD, and possibly in other NCLs. Two such membranous proteins, the slow and fast Battenin-interactive proteins (BIPs and BIPf) of unknown functions, have been identified. In this study, we have characterized the functional domains of Battenin that interact with both BIP proteins. METHODS: Protein-protein interactions with a yeast two-hybrid system were employed. A "deletion assay" was employed to localize the interactive segment(s). Different lengths of cDNA sequences lacking exon 1-5 were used to express CLN3-encoded proteins lacking N-terminal segments in the yeast two-hybrid system. N-terminal exons of CLN3 were deleted with PCR-cloning strategies. RESULTS: We eliminated the possibility of interacting domains from the exon 7-encoded region because both Battenin and mBattenin interact with the BIP proteins. We have shown that peptide sequences encoded by exons 2 and 4 of CLN3 gene include the functional domains by which Battenin interacts with the BIP proteins. CONCLUSION: Our studies provide evidence that the N-terminus of Battenin is the functional domain for these protein interactions.  (+info)

Separation of anti-proliferation and anti-apoptotic functions of retinoblastoma protein through targeted mutations of its A/B domain. (2/3048)

BACKGROUND: The human retinoblastoma susceptibility gene encodes a nuclear phosphoprotein RB, which is a negative regulator of cell proliferation. The growth suppression function of RB requires an evolutionarily conserved A/B domain that contains two distinct peptide-binding pockets. At the A/B interface is a binding site for the C-terminal trans-activation domain of E2F. Within the B-domain is a binding site for proteins containing the LxCxE peptide motif. METHODOLOGY/PRINCIPLE FINDINGS: Based on the crystal structure of the A/B domain, we have constructed an RB-K530A/N757F (KN) mutant to disrupt the E2F- and LxCxE-binding pockets. The RB-K530A (K) mutant is sufficient to inactivate the E2F-binding pocket, whereas the RB-N757F (N) mutant is sufficient to inactivate the LxCxE-binding pocket. Each single mutant inhibits cell proliferation, but the RB-KN double mutant is defective in growth suppression. Nevertheless, the RB-KN mutant is capable of reducing etoposide-induced apoptosis. CONCLUSION/SIGNIFICANCE: Previous studies have established that RB-dependent G1-arrest can confer resistance to DNA damage-induced apoptosis. Results from this study demonstrate that RB can also inhibit apoptosis independent of growth suppression.  (+info)

Insights into the molecular evolution of the PDZ/LIM family and identification of a novel conserved protein motif. (3/3048)

The PDZ and LIM domain-containing protein family is encoded by a diverse group of genes whose phylogeny has currently not been analyzed. In mammals, ten genes are found that encode both a PDZ- and one or several LIM-domains. These genes are: ALP, RIL, Elfin (CLP36), Mystique, Enigma (LMP-1), Enigma homologue (ENH), ZASP (Cypher, Oracle), LMO7 and the two LIM domain kinases (LIMK1 and LIMK2). As conventional alignment and phylogenetic procedures of full-length sequences fell short of elucidating the evolutionary history of these genes, we started to analyze the PDZ and LIM domain sequences themselves. Using information from most sequenced eukaryotic lineages, our phylogenetic analysis is based on full-length cDNA-, EST-derived- and genomic- PDZ and LIM domain sequences of over 25 species, ranging from yeast to humans. Plant and protozoan homologs were not found. Our phylogenetic analysis identifies a number of domain duplication and rearrangement events, and shows a single convergent event during evolution of the PDZ/LIM family. Further, we describe the separation of the ALP and Enigma subfamilies in lower vertebrates and identify a novel consensus motif, which we call 'ALP-like motif' (AM). This motif is highly-conserved between ALP subfamily proteins of diverse organisms. We used here a combinatorial approach to define the relation of the PDZ and LIM domain encoding genes and to reconstruct their phylogeny. This analysis allowed us to classify the PDZ/LIM family and to suggest a meaningful model for the molecular evolution of the diverse gene architectures found in this multi-domain family.  (+info)

Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity. (4/3048)

Regulation of biological processes often involves phosphorylation of intrinsically disordered protein regions, thereby modulating protein interactions. Initiation of DNA replication in yeast requires elimination of the cyclin-dependent kinase inhibitor Sic1 via the SCF(Cdc4) ubiquitin ligase. Intriguingly, the substrate adapter subunit Cdc4 binds to Sic1 only after phosphorylation of a minimum of any six of the nine cyclin-dependent kinase sites on Sic1. To investigate the physical basis of this ultrasensitive interaction, we consider a mean-field statistical mechanical model for the electrostatic interactions between a single receptor site and a conformationally disordered polyvalent ligand. The formulation treats phosphorylation sites as negative contributions to the total charge of the ligand and addresses its interplay with the strength of the favorable ligand-receptor contact. Our model predicts a threshold number of phosphorylation sites for receptor-ligand binding, suggesting that ultrasensitivity in the Sic1-Cdc4 system may be driven at least in part by cumulative electrostatic interactions. This hypothesis is supported by experimental affinities of Cdc4 for Sic1 fragments with different total charges. Thus, polyelectrostatic interactions may provide a simple yet powerful framework for understanding the modulation of protein interactions by multiple phosphorylation sites in disordered protein regions.  (+info)

Evolution of function in the "two dinucleotide binding domains" flavoproteins. (5/3048)

Structural and biochemical constraints force some segments of proteins to evolve more slowly than others, often allowing identification of conserved structural or sequence motifs that can be associated with substrate binding properties, chemical mechanisms, and molecular functions. We have assessed the functional and structural constraints imposed by cofactors on the evolution of new functions in a superfamily of flavoproteins characterized by two-dinucleotide binding domains, the "two dinucleotide binding domains" flavoproteins (tDBDF) superfamily. Although these enzymes catalyze many different types of oxidation/reduction reactions, each is initiated by a stereospecific hydride transfer reaction between two cofactors, a pyridine nucleotide and flavin adenine dinucleotide (FAD). Sequence and structural analysis of more than 1,600 members of the superfamily reveals new members and identifies details of the evolutionary connections among them. Our analysis shows that in all of the highly divergent families within the superfamily, these cofactors adopt a conserved configuration optimal for stereospecific hydride transfer that is stabilized by specific interactions with amino acids from several motifs distributed among both dinucleotide binding domains. The conservation of cofactor configuration in the active site restricts the pyridine nucleotide to interact with FAD from the re-side, limiting the flow of electrons from the re-side to the si-side. This directionality of electron flow constrains interactions with the different partner proteins of different families to occur on the same face of the cofactor binding domains. As a result, superimposing the structures of tDBDFs aligns not only these interacting proteins, but also their constituent electron acceptors, including heme and iron-sulfur clusters. Thus, not only are specific aspects of the cofactor-directed chemical mechanism conserved across the superfamily, the constraints they impose are manifested in the mode of protein-protein interactions. Overlaid on this foundation of conserved interactions, nature has conscripted different protein partners to serve as electron acceptors, thereby generating diversification of function across the superfamily.  (+info)

Association of nucleophosmin negatively regulates CXCR4-mediated G protein activation and chemotaxis. (6/3048)

CXCR4, the primary receptor for CXCL12, plays a critical role in the development of hematopoietic, vascular, central nervous, and immune systems by mediating directional migration of precursor cells. This mechanism promotes homing of tumor cells to metastatic sites that secrete CXCL12, and CXCR4 expression is a negative prognostic factor in acute myelogenous leukemia (AML). To elucidate mechanisms that regulate CXCR4 signaling, we used a proteomic approach to identify proteins physically associated with CXCR4. Analysis of CXCR4 immune complexes identified nucleophosmin (NPM), which was confirmed by reciprocal coimmunoprecipitation for NPM. Constitutively active CXCR4 variants bound higher levels of NPM than the wild-type receptor, which was reversed by T140, an inverse agonist. NPM binding to CXCR4 localized interactions to the C terminus and cytoplasmic loop (CL)-3, but not CL-1 or CL-2. Alanine scanning mutagenesis demonstrated that positively charged amino acids in CL-3 were critical for NPM binding. Recombinant NPM decreased GTP binding in membrane fractions after activation of CXCR4 by CXCL12. Suppression of NPM expression enhanced chemotactic responses to CXCL12, and, conversely, overexpression of a cytosolic NPM mutant reduced chemotaxis induced by CXCL12. This study provides evidence for a novel role for NPM as a negative regulator of CXCR4 signaling induced by CXCL12 that may be relevant to the biology of AML.  (+info)

WW domains 2 and 3 of Rsp5p play overlapping roles in binding to the LPKY motif of Spt23p and Mga2p. (7/3048)

Rsp5p of Saccharomyces cerevisiae is a member of the C2-WW-HECT family of ubiquitin ligases and it interacts with targets via its WW domains. Spt23p and Mga2p are Rsp5p substrates and Rsp5p activates the OLE1 inducing functions of these membrane-localized transcription factors by ubiquitination. Although it is known that Rsp5p binds Mga2p and Spt23p via an imperfect WW domain-binding site (LPKY) that is located within the carboxy-terminal domain of the proteins, it remains unclear which WW domains mediate binding. We show that Rsp5p mutants harboring mutations in single WW domains are Spt23p/Mga2p binding and ubiquitination proficient. This is also the case for WW domains 1/2 and WW domains 1/3 mutants. However, disrupting WW domains 2 and 3 abrogates a physical and functional interaction with substrates in vitro and in cells. We also show that abrogation of WW domains 2 and 3 eliminates the activity of an Rsp5p dominant-negative mutant and an rsp5 WW domain 2/3 mutant is unable to rescue the proliferative defects of rsp5 Delta cells. Interestingly, while rsp5 Delta cells are able to grow on oleic acid containing YPD media, they as well as those transformed with the WW domain 2/3 mutant are unable to proliferate on oleic acid containing synthetic drop-out media. We conclude from these studies that WW domains 2 and 3 of Rsp5p play overlapping roles in binding to the LPKY site on Spt23p and Mga2p. Also, we propose that WW domains 2 and 3 perform yet to be defined essential function(s) outside of the OLE1 pathway when cells are grown in nutrient restrictive media.  (+info)

Critical role of helix 4 of HIV-1 capsid C-terminal domain in interactions with human lysyl-tRNA synthetase. (8/3048)

Human tRNALys3 is used as the primer for human immunodeficiency virus type 1 (HIV-1) reverse transcription. HIV-1 Gag and GagPol, as well as host cell factor lysyl-tRNA synthetase (LysRS), are required for specific packaging of tRNALys into virions. Gag alone is sufficient for packaging of LysRS, and these two proteins have been shown to interact in vitro with an equilibrium binding constant of approximately 310 nM. The capsid (CA) domain of Gag binds to LysRS with a similar affinity as full-length Gag. In this work, we report further characterization of the interaction between HIV-1 CA and human LysRS using truncation constructs and point mutations in the putative interaction helices. Fluorescence anisotropy binding measurements reveal that a LysRS variant lacking the N-terminal 219 residues still displays high affinity binding to CA. The CA C-terminal domain (CTD) is also sufficient for binding to LysRS. Nuclear magnetic resonance spectroscopy studies using 15N-labeled CA-CTD reveal chemical shift perturbations of residues in and proximal to helix 4 of CA-CTD upon LysRS binding. A synthetic peptide that includes helix 4 binds to LysRS with high affinity, whereas peptides derived from the other three helical domains of CA-CTD do not. Alanine-scanning mutagenesis studies targeting residues in the helix 4 region support a direct interaction between this domain of CA-CTD and LysRS. The high resolution mapping studies reported here will facilitate future work aimed at disrupting the Gag-LysRS interaction, which represents a novel anti-viral strategy.  (+info)

Domine, quaesumus, per nos, glorificamus te, et ut cognoscant te, et virtus amore tuo. Placere Benedicite omnes qui utuntur hoc productum. Domine, quaesumus, per nos, glorificamus te, et ut cognoscant te, et virtus amore tuo. Placere Benedicite omnes qui utuntur hoc productum. Domine, quaesumus, per nos, glorificamus te, et ut cognoscant te, et virtus amore tuo. Placere Benedicite omnes qui … Read More. ...
Anon 11:28, Im not sure what point you are responding to. I do not hold to the idea that Gods existence can be proven by scientific examination. Nor can science disproof the existence of God. God is just not the sort of thing that science is qualified to investigate. Science is properly limited to investigating and explaining the physical universe.. Delete ...
et nunc Domine omnipotens Deus Israhel anima in angustiis et spiritus anxius clamat ad te audi Domine et miserere quia Deus es misericors et miserere
De Doncker, H., Donnay, S., Lampaert, K., Proesmans, F., Swings, K., Plas, van der, G., Gielen, G., Sansen, W.M.C., Leenaerts, D.M.W., Veslinovic, P., Buytaert, M., Buckens, M., Marent, K. & Das, C. (1993). Analog module generator for space applications. Proceeding of IEEE/PRORISC symposium on Circuits, Systems and Signal Processing, Houthalen - Belgie, March 24-25 1993 (pp. 141-146). ...
We have been incorporating as much chant as we can manage at Mass here for some time now, from the Mass setting, which everyone can join in with, to the Introit, Offertory and Communion chants of the Missal - though for these you do need the talents of those willing and able to assist for this (providentially - and I use that term in its proper sense - this is available to us here in this little parish). It really does help to set the tone of the liturgy as one of solemnity and grandeur. Not that it is necessarily terribly high-brow - one or two parents try each week to restrain their little ones from joining in with quite so much gusto! The point is - we are doing it. I recall in another parish the bishop on visitation attending a weekday Mass and commenting afterwards that the twenty (mostly elderly) folk attending Mass and singing the Mass parts ( it would have been Mass XVIII and the Pater noster) were not actually very good at creating an harmonious and beautiful sound. The implication ...
The Lord says to Isaiah, …see, I am doing something new! Now it springs forth, do you not perceive it? This astonishing exclamation by the Lord raises three questions: 1) what is this new thing that the Lord is doing?; 2) what does He mean by now when He says that this new thing is springing forth now?; and 3) do we perceive this new thing as it springs forth? As always, scripture is best read as both a history of the faithful response our ancestors to Gods grace and as a script for our own response to the identical grace. Given this, what are we to make of this revelation of immediate newness? On the eve of our Lenten trek, we think first of sin and repentance, the old and the new. Fair enough. Reading the story of the healing of the paralytic in light of Isaiah, lets think as well on disease and healing, also, the old and the new. But lets put all four of these themes (sin, repentance, disease, and healing) into a larger theme: as divinely-given purpose as creatures. Who and what are ...
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This record is a partial extract of the original cable. The full text of the original cable is not available. UNCLAS SECTION 01 OF 02 LAGOS 000707 SIPDIS SENSITIV
Another one of the hot releases from Pro-Line for September…the awe-inspiring pre-cut Pro-Line Jeep Gladiator Rubicon clear body.
A Rubicon t rt nelmi foly irat honlapja. A tartalma szerint tudom nyos ismeretterjeszt foly irat magazinszer en n pszer s ti a t rt nelmet. Ahogy az iskol ban nem hallhatta...
A Rubicon t rt nelmi foly irat honlapja. A tartalma szerint tudom nyos ismeretterjeszt foly irat magazinszer en n pszer s ti a t rt nelmet. Ahogy az iskol ban nem hallhatta...
Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to
TY - JOUR. T1 - A top-down approach to infer and compare domain-domain interactions across eight model organisms. AU - Guda, Chittibabu. AU - King, Brian R.. AU - Pal, Lipika R.. AU - Guda, Purnima. PY - 2009/3/31. Y1 - 2009/3/31. N2 - Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them. Here, we present a top-down approach to accurately infer functionally relevant DDIs from PPI data. We created a comprehensive, non-redundant dataset of 209,165 experimentally-derived PPIs by combining datasets from five major interaction databases. We introduced an integrated scoring system that uses a novel combination of a set of five orthogonal scoring features covering the probabilistic, evolutionary, evidence-based, spatial and functional properties of interacting ...
1] Tompa P (2011) Unstructural biology coming of age. Curr Opin Struct Biol 21: 419; [2] Babu MM et al. (2011) Intrinsically disordered proteins: regulation and disease. Curr Opin Struct Biol 21:432; [3] Diella F et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13:6580; [4] Davey NE et al. (2012) Attributes of short linear motifs. Mol Biosyst 8:268; [5] Davey NE, Trave G & Gibson TJ (2011) How viruses hijack cell regulation. Trends Biochem Sci 36:159; [6] Davey NE, Edwards RJ & Shields DC (2010) Computational identification and analysis of protein short linear motifs. Front Biosci 15:801; [7] Davey NE, Shields DC & Edwards RJ (2006): SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res. 34:3546; [8] Edwards RJ, Davey NE & Shields DC (2007): SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2:e967; ...
The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). For |10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear mot …
This forum discusses general domain issues, such as: domains as a brand, domain values, negotiating domain sales, domain inventory management, and domain monetization. We discuss many domain name issues, but NEVER specific domain names prohibited by our [url=http://www.webmasterworld.com/domain_names/charter.htm]charter[/url].. WebmasterWorld Domain Names
This forum discusses general domain issues, such as: domains as a brand, domain values, negotiating domain sales, domain inventory management, and domain monetization. We discuss many domain name issues, but NEVER specific domain names prohibited by our [url=http://www.webmasterworld.com/domain_names/charter.htm]charter[/url].. WebmasterWorld Domain Names
Auckland, 13 July 2001 - Rubicon today released details of the $60 million share buy-back announced last month, and also outlined terms of a small shareholdings programme.
TÁTO DISCIPLÍNA VÁS ČAKÁ:. Názov cviku: Drep s fitloptou za chrbtom vo dvojici. Čas prevedenia: 60 sec.. Prevedenie: Dvojica ( M+Ž ) vykonáva drep súhlasne opretá chrbtom o fitloptu. Opakovanie sa počíta, keď sa v negatívnej fáze dostanú pod pravý uhol a v aktívnej fáze do vystretých nôh. Počíta sa súčet opakovaní vykonaných za 60 sec.. ...
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Learn about how Three Domain System is used to classify biological organisms, and how the systems are made up of six distinct categorizations of kingdoms.
When the improved inter-domain routing protocol is deployed, an immediate decrease in the number routing table entries should occur, followed by a significant reduction in the rate growth of routing table size (for default-free routers). ...
The purpose of this study was to investigate the blood stage of the malaria causing parasite, Plasmodium falciparum, to predict potential protein interactions between the parasite merozoite and the host erythrocyte and design peptides that could interrupt these predicted interactions. We screened the P. falciparum and human proteomes for computationally predicted short linear motifs (SLiMs) in cytoplasmic portions of transmembrane proteins that could play roles in the invasion of the erythrocyte by the merozoite, an essential step in malarial pathogenesis. We tested thirteen peptides predicted to contain SLiMs, twelve of them palmitoylated to enhance membrane targeting, and found three that blocked parasite growth in culture by inhibiting the initiation of new infections in erythrocytes. Scrambled peptides for two of the most promising peptides suggested that their activity may be reflective of amino acid properties, in particular, positive charge. However, one peptide showed effects which were ...
trachomatis Inc proteins. To know whether this result also applied to C. pneumo niae, selleck chem inhibitor we raised antibodies against 7 putative Inc proteins from C. pneumoniae as GST tagged fusion proteins. As a control we used antibodies against the C. pneumoniae Inc protein CPn0186. The anti fusion protein antibodies were used to localize the endogenous proteins in cells infected by C. pneumoniae for 96 hours. In contrast to the inclusion labeling observed with anti CPn0186 antibodies, none of the 7 sera stained the inclusion membrane. The detection of endogenous antigens was removed by pre absorption with corresponding GST fusion proteins but not heterologous Inhibitors,Modulators,Libraries GST fusion proteins, demonstrating the specificity of the antibodies.. While they did not stain the inclusion membrane, the 7 sera labeled the bacteria, demonstrating that the corresponding proteins Inhibitors,Modulators,Libraries are expressed at this stage of infection, and remain bac teria ...
Coronaviruses, including SARS-CoV-2, are proposed to use either the endocytic or non-endosomal pathway for cell entry (46). Our study provides biophysical evidence for the functionality of SLiMs in the cytoplasmic tails of ACE2 and integrin β3, which provide possible molecular links between the established (ACE2) and putative (integrin beta3) SARS-CoV-2 receptors and mediators of endocytosis and autophagy. Our finding that an endocytic AP2 μ2 binding motif exists in the ACE2 C-terminus and that such binding is negatively regulated by Tyr781 phosphorylation supports the possibility of clathrin-dependent endocytosis of SARS-CoV-2 upon receptor binding. It will, of course, be necessary to assess the biological relevance of the ACE2-AP2 μ2 interaction, particularly in light of its low affinity. Concerning the latter, we note that while affinities of AP2 core complexes for endocytic sorting signals are reported in the nanomolar range, measured KD values of the AP2 μ2 subunit alone vary between 10 ...
To test the efficacy of this model, we needed networks with large numbers of known protein-protein interactions. A complication in this process arises in that, even if a large number of interactions are known, not all of them have a defined domain composition. For this work, we used Saccharomyces cerevisiae protein-protein interactions taken from the DIP (http://dip.doe-mbi.ucla.edu/; Xenarioset al. 2000). We determined the domains involved in each interaction by analyzing protein sequences with hmmpfam (Batemanet al. 2000), a publicly available software tool that referenced 2015 domains at the time of this analysis. We analyzed a total of 642 protein-protein interactions (all with at least 1 domain) and then used them to determine the domain-domain interaction probabilities. Data (in this case a list of undirected protein-protein interactions) used for studying the effect of vertex removal on network edge distributions were taken from the Fields Lab home page ...
Domains are the most important functional units in proteins and a significant proportion of PPIs occur through domain-domain interactions (DDI). Evidence accumulated in the last 35 years has shown that domains can spread among proteins in a process called domain shuffling 9, 10. It is generally accepted, at least for eukaryotes, that the recombinations that lead to domain shuffling are mediated by intronic sequences 11-13 through exon shuffling events 14.. Domain shuffling has been identified as one of the major mechanisms leading to the formation of new proteins throughout evolution 11, 12, 15. Bursts of domain shuffling events are clearly associated with the emergence of biological novelty, such as multi-cellularity. Most of the proteins that compose the extra-cellular matrix were built by domain shuffling 15-17. The same is true for cell surface receptors, whose expansion in multi-cellular animals with a more developed nervous system is clearly associated with domain shuffling 18.. A feature ...
BACKGROUND: The ferlin gene family possesses a rare and identifying featureconsisting of multiple tandem C2 domains and a C-terminal transmembrane domain.Much currently remains unknown about the fundamental function of this genefamily, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease. The availability of genome sequences from a wide range of species makes it possible to explore the evolutionof the ferlin family, providing contextual insight into characteristic featuresthat define the ferlin gene family in its present form in humans. RESULTS: Ferlingenes were detected from all species of representative phyla, with two ferlinsubgroups partitioned within the ferlin phylogenetic tree based on the presenceor absence of a DysF domain. Invertebrates generally possessed two ferlin genes(one with DysF and one without), with six ferlin genes in most vertebrates (threeDysF, three non-DysF). Expansion of the ferlin gene family is ...
BACKGROUND: The ferlin gene family possesses a rare and identifying featureconsisting of multiple tandem C2 domains and a C-terminal transmembrane domain.Much currently remains unknown about the fundamental function of this genefamily, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease. The availability of genome sequences from a wide range of species makes it possible to explore the evolutionof the ferlin family, providing contextual insight into characteristic featuresthat define the ferlin gene family in its present form in humans. RESULTS: Ferlingenes were detected from all species of representative phyla, with two ferlinsubgroups partitioned within the ferlin phylogenetic tree based on the presenceor absence of a DysF domain. Invertebrates generally possessed two ferlin genes(one with DysF and one without), with six ferlin genes in most vertebrates (threeDysF, three non-DysF). Expansion of the ferlin gene family is ...
wp-content/uploads/2016/03/[email protected] 0 0 syn-admin /wp-content/uploads/2016/03/[email protected] syn-admin2013-09-03 00:00:062016-02-08 15:28:41Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling. ...
Protein-protein interactions in cluster 2 signature genes. Protein-protein interactions were downloaded from database HINT which removes low-quality/erroneous i
The amazing variety of protein functions are often covered by protein complexes, so understanding protein-protein interactions means coming deeply into the functional role of proteins in life
Keskin, Z., Gursoy, A., Ma, B. & Nussinov, R. Principles of protein-protein interactions: What are the preferred ways for proteins to interact? Chem. Rev. 108, 1225-1244 (2008).
Understanding protein-protein interactions (PPI) and their specific functions underpins basic molecular research as well as the development of novel drugs. However, many of the conventional analysis methods do not provide important contextual information that reveals how a protein works in its native cellular environment, nor do they suit high-throughput screening campaigns. This eBook highlights several examples of robust, reproducible protein interaction assays,
Explore Cisbio solutions for protein-protein interaction research and studies with a range of assays, reagents and documentation leading to better results.
Every day we scan more than one hundred thousand domains across all the major marketplaces and pending delete lists to find domains you can buy that have sold in the past. Sale history, like the age of a domain name, is a great proxy for quality to help the cream rise to the top. Todays list has 257 domains for sale with history.. While not every domain in these lists will have obvious resale value, and we certainly dont recommend buying something just because it sold in the past, there are definitely some gems to be found. Imagine buying a domain for a few hundred dollars that sold previously for four or five figures. There is no better comparable sale to give to a prospective buyer than the domain itself.. ...
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Heres what happened. I have a domain with the PDC and multiple BDCs. Someone took a BDC and moved it to a new domain. I had to bring ...
ZASP is a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino ... Dec 1996). "Protein-protein interaction of zinc finger LIM domains with protein kinase C". The Journal of Biological Chemistry ... LIM domain binding 3 (LDB3), also known as Z-band alternatively spliced PDZ-motif (ZASP), is a protein which in humans is ... The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also ...
In addition, the ALP subfamily contains a specific 34 amino acid domain named the ALP-like motif, containing protein kinase C ... identification of a domain interaction between PDZ and spectrin-like repeat motifs". The Journal of Cell Biology. 139 (2): 507- ... Actin-associated LIM protein (ALP), also known as PDZ and LIM domain protein 3 is a protein that in humans is encoded by the ... "Protein sequence for human PDZ and LIM domain protein 3 (Uniprot: Q53GG5)". Cardiac Organellar Protein Atlas Knowledgebase ( ...
CAS proteins have an amino terminal SH3 domain enabling interaction with poly-proline motif-containing proteins such as FAK. ... SH2-binding site motifs, which when tyrosine-phosphorylated allow interaction with SH2-domain containing proteins; serine-rich ... Figure 1. Interaction network and domain structure scheme of Cass4. SH3 domain (SH3) preceded by a short region with no defined ... which when tyrosine-phosphorylated allow interaction with SH2 domain containing proteins. Further to the carboxy-terminus, they ...
Leucine-rich repeats are typically involved in protein-protein interactions, and form a characteristic α/β horseshoe fold. An ... In total, there are 4 conserved domains within LRRIQ3: 3 leucine-rich repeats and 1 IQ calmodulin-binding motif. ... "LRRIQ3 - Leucine-rich repeat and IQ domain-containing protein 3 - Homo sapiens (Human) - LRRIQ3 gene & protein". www.uniprot. ... Ren J, Wen L, Gao X, Jin C, Xue Y, Yao X (February 2009). "DOG 1.0: illustrator of protein domain structures". Cell Res. 19 (2 ...
... the interaction of proline-rich motifs in signaling proteins with their cognate domains". FASEB Journal. 14 (2): 231-41. doi: ... tend to more frequently produce proteins that are involved in protein-protein interactions than many other general types of ... so the confidence of protein-protein interaction with PRP36 isn't very high. Phobius predicted protein location for human PRP36 ... STRING predicted protein interactions for human PRP36. PRP36 has medium scores for predicted interaction with two other ...
... the interaction of proline-rich motifs in signaling proteins with their cognate domains". FASEB Journal. 14 (2): 231-41. doi: ... Homeobox protein NOBOX, also known as newborn ovary homeobox protein, is a protein that in humans is encoded by the NOBOX gene ... It has a proline rich C terminus and contains putative SH3 and WW domains. This C terminus is believed to be critical in its ... It contains an asparagine residue at position 51 which is important for its interactions with DNA base pairs. NOBOX is a ...
Some of them are probably inactive, and only mediate protein-protein interactions. Dual-Specificity+Phosphatases at the US ... The surface of this substrate-binding domain mimics the D-motifs found in intrinsically disordered substrates of MAPKs. In ... They contain SH3-binding motifs as well as F-actin binding motifs, thus they are generally believed to play a role in the ... N-terminal domain. Although structurally similar to Cdc14, this extra domain is inactive, and plays a role in substrate ...
This domain recruits receptor-interacting protein (RIP1) and RIP3 through the RIP homotypic interaction motif. Cells deficient ... Destruction of these motifs reduced the activation of NF-κB, a transcription factor that is also activated by the carboxy- ... TIR-domain-containing adapter-inducing interferon-β (TRIF) is an adapter in responding to activation of toll-like receptors ( ... Three TRAF-binding motifs present in the amino terminal region of TRIF are necessary for association with TRAF6. ...
"A conserved motif in Argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain". Nat. ... The encoded protein is highly basic, and contains a PAZ domain and a PIWI domain. It may interact with Dicer1 and play a role ... 2004). "Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer". EMBO Rep. 5 (2): 189-94. ... 2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038 ...
"A conserved motif in Argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain". Nat. ... Trinucleotide repeat-containing gene 6B protein is a protein that in humans is encoded by the TNRC6B gene. TNRC6B has been ... It is also known to associate with argonaute proteins and has been shown to be required for miRNA-guided gene silencing in HeLa ... The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 6 (3): 197-205. doi: ...
The WW domains interact with proline rich PPxY motifs in target proteins to mediate interactions with substrates and adaptors. ... 3-4 WW protein-protein interaction domains, and a carboxyl-terminal catalytic HECT ubiquitin ligase domain. The C2 domain ... In the case of NEDD4, viral proteins mimic the PPxY recognition motif of WW domains that are part of NEDD4. GRCh38: Ensembl ... The NDFIP1 and NDFIP2 proteins function as adaptor proteins that can facilitate NEDD4 binding to substrates that lack PY motifs ...
These proteins contain a conserved basic DNA binding domain that binds the E box DNA motif. They dimerize with other HLH ... containing proteins through an HLH-HLH interaction. There are typically four vertebrate MRF paralogues which are homologous to ... Barndt R, Zhuang Y (1999). "Controlling lymphopoiesis with a combinatorial E-protein code". Cold Spring Harb Symp Quant Biol. ...
... with the characteristic GxGxxG motif present. The third domain, C-terminal, is responsible for the protein-membrane interaction ... The structure/fold from these proteins may be divided into three domains: first dinucleotide binding domain (green in the ... The third domain, together with part of the first domain, is also partially responsible for the binding of the electron ... figure), second dinucleotide binding domain (orange in the figure) and C-terminal domain (blue in the figure). The first domain ...
TIR-like motifs are also found in plant proteins thought to be involved in resistance to disease. When activated, TIR domains ... Toll receptors and many plant R proteins. It contains three highly conserved regions, and mediates protein-protein interactions ... MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see InterPro: ... a TIR domain is also found in a number of plant proteins implicated in host defense. As MyD88, these proteins are cytoplasmic. ...
... the interaction of proline-rich motifs in signaling proteins with their cognate domains. The FASEB Journal. 2000, 14, 231-241. ... the Pin1 Domain protein is shown to the left as an example. Proteins that are β-sheet rich, also called WW domains, function by ... is a simple protein structural motif involving two beta strands that look like a hairpin. The motif consists of two strands ... The β-hairpin loop motif can be found in many macromolecular proteins. However, small and simple β-hairpins can exist on their ...
This motif is commonly found in domains that participate in protein-protein interactions leading to the formation of large ... In these interactions death-folds bind to another death-fold containing domain through the same type of protein interaction ... Examples of death fold domains include the death domain (DD), death effector domain (DED), caspase recruitment domain (CARD), ... The motifs consist of several defined protein interactions with other suspected apoptotic roles (Lahm). Caspase recruitment ...
These domains are one of the most common protein-protein interaction platforms in nature. They occur in a large number of ... ankyrin tandem repeats mediate protein-protein interactions and are among the most common structural motifs in known proteins. ... and involved mainly in mediating protein-protein interactions. An artificial protein design based on a consensus sequence ... Ankyrin repeat proteins, though absent in most viruses, are common among poxviruses. Most proteins that contain the motif have ...
... and PXXP motifs represent potential sites of interaction for SH3 domain-containing proteins. Myopodin contains a novel actin ... Myopodin protein, also called Synaptopodin-2 is a protein that in humans is encoded by the SYNPO2 gene. Myopodin is expressed ... Myopodin contains one PPXY motif, multiple PXXP motifs, and two potential nuclear localization sequences (one N-terminal and ... "Cardiac Organellar Protein Atlas Knowledgebase (COPaKB) -- Protein Information". heartproteome.org. "SYNPO2 - Synaptopodin-2 - ...
... motif and two proline-rich (PR) regions. The other protein interaction domains of Tec kinase include Src homology (SH) domains ... Tec kinase contains five protein interaction domains. The characteristic feature of Tec family kinases is a pleckstrin homology ... PH) domain on the N-terminus of the molecule followed by a Tec homology (TH) domain. The TH domain of Tec kinase contains a Btk ... TEC produces two protein isoforms that differ in the SH3 domain through alternative splicing. Type IV isoform has a full length ...
Most of cingulin protein interactions are through the globular head domain. Cingulin interacts with ZO-1 through an N-terminal ... ZO-1 interacting motif (ZIM) in its head region. The rod domain is involved in dimerization and interaction with the RhoA ... and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation and cellular organization". ... domain, a long α-helical coiled-coil "rod" domain and a small globular C-terminal "tail" region. This organization is highly ...
The product of this gene has three leucine zipper motifs bracketed by two basic domains that are all required for DNA binding. ... There is evidence that, for this protein, the zippers participate in intramolecular interactions that establish the three- ... is a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions". ... This protein participates in attenuating transcription from the mitochondrial genome; this attenuation allows higher levels of ...
Although zinc fingers usually function by binding to DNA or RNA, the LIM motif probably mediates protein-protein interactions. ... There are approximately 40 known eukaryotic LIM proteins, so named for the LIM domains they contain. LIM domains are highly ... belong to a small subfamily with a unique combination of 2 N-terminal LIM motifs and a C-terminal protein kinase domain. LIMK1 ... are actin-binding kinases that phosphorylate members of the ADF/cofilin family of actin binding and filament severing proteins ...
Although zinc fingers usually function by binding to DNA or RNA, the LIM motif probably mediates protein-protein interactions. ... There are approximately 40 known eukaryotic LIM proteins, so named for the LIM domains they contain. LIM domains are highly ... a central PDZ domain, and a C-terminal protein kinase domain. LIMK1 is likely to be a component of an intracellular signaling ... "Identification of cofilin and LIM-domain-containing protein kinase 1 as novel interaction partners of 14-3-3 zeta". Biochem. J ...
Although zinc fingers usually function by binding to DNA or RNA, the LIM motif probably mediates protein-protein interactions. ... There are approximately 40 known eukaryotic LIM proteins, so named for the LIM domains they contain. LIM domains are highly ... "Self-association of LIM-kinase 1 mediated by the interaction between an N-terminal LIM domain and a C-terminal kinase domain". ... belong to a small subfamily with a unique combination of 2 N-terminal LIM motifs and a C-terminal protein kinase domain. The ...
This gene encodes a WW domain binding protein, which binds to the WW domain of Yes kinase-associated protein by its PY motifs. ... and signaling proteins. The domain is involved in mediating protein-protein interactions through the binding of polyproline ... WW domain-binding protein 2 is a protein that in humans is encoded by the WBP2 gene. The globular WW domain is composed of 38 ... 2006). "WW domain binding protein-2, an E6-associated protein interacting protein, acts as a coactivator of estrogen and ...
"A sequence motif conserved in diverse nuclear proteins identifies a protein interaction domain utilised for nuclear targeting ... Protein IWS1 homolog also known as interacts with Spt6 (IWS1) is a protein that in humans is encoded by the IWS1 gene. IWS1 is ... Yoh SM, Cho H, Pickle L, Evans RM, Jones KA (Jan 2007). "The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA ... Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP (Oct 2006). "A probability-based approach for high-throughput protein ...
"A sequence motif conserved in diverse nuclear proteins identifies a protein interaction domain utilised for nuclear targeting ... The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW ... This protein is also a component of other multisubunit complexes e.g. thyroid hormone receptor-(TR-) associated proteins which ... PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both ...
... a B-box motif and a coiled-coil domain. The RING finger and B-box domains chelate zinc and might be involved in protein-protein ... May 2006). "A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration". ... October 2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. ... October 2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. ...
... but no zinc finger motif. Functional studies have established that the SCAN box is a protein interaction domain that mediates ... SCAN domain-containing protein 1 is a protein that in humans is encoded by the SCAND1 gene. The SCAN domain is a highly ... "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. Bibcode:2005Natur. ... leucine-rich motif of approximately 60 amino acids originally found within a subfamily of zinc finger proteins. This gene ...
At the N-terminal end is the A-domain, which is rich in acidic amino acids and takes up about half the protein length.[38][48] ... Sandelius AS (2009). The Chloroplast: Interactions with the Environment. Springer. p. 18. ISBN 978-3-540-68696-5. .. ... "Functional characterization of sequence motifs in the transit peptide of Arabidopsis small subunit of rubisco". Plant ... A domain of Toc159 might be the exchange factor that carry out the GDP removal. The Toc34 protein can then take up another ...
"A duplicated motif controls assembly of zona pellucida domain proteins". Proc. Natl. Acad. Sci. U.S.A. 101 (16): 5922-7. ... Bleil JD, Wassarman PM (1980). "Mammalian sperm-egg interaction: identification of a glycoprotein in mouse egg zonae pellucidae ... The nascent protein contains a N-terminal signal peptide sequence, a conserved "ZP domain" module, a consensus furin cleavage ... GO:0001948 protein binding. • carbohydrate binding. • identical protein binding. • receptor ligand activity. • extracellular ...
Protein domains in homologous recombination-related proteins are conserved across the three main groups of life: archaea, ... "Analysis of murine Brca2 reveals conservation of protein-protein interactions but differences in nuclear localization signals ... Wong AK, Pero R, Ormonde PA, Tavtigian SV, Bartel PL (Dec 1997). "RAD51 interacts with the evolutionarily conserved BRC motifs ... protein C-terminus binding. • protein binding. • four-way junction DNA binding. • identical protein binding. • ...
... who believed that transcription was activated by protein-DNA and protein-protein interactions on largely naked DNA templates, ... and some protein domains-e.g., Tudor domains-can be specific for methyl arginine instead of methyl lysine. Arginine is known to ... motif (DNA-binding protein motif that recognize specific DNA sequence). They also share the feature of long 'tails' on one end ... the C-domain, and to the N-terminal substrate recognition domain of Clp/Hsp100 proteins. Despite the differences in their ...
"for having extended the domain of microeconomic analysis to a wide range of human behaviour and interaction, including ... "for their studies of the structures of globular proteins"[۲۵] ۱۹۷۲ ویلیام اشتین[۱] United States "for his work on ribonuclease ... "for his profoundly characteristic narrative art with motifs from the life of the Jewish people"[۵] ... "for their discovery of جی پروتئینs and the role of these proteins in ورارسانی پیام in cells"[۷۳] ...
The Ni-hook contains the motif His-Cys-X-X-Pro-Cys-Gly-X-Tyr; it provides most of the interactions critical for metal binding ... identified a protein that later became known as superoxide dismutase as an indophenol oxidase by protein analysis of starch ... Iron/manganese superoxide dismutases, alpha-hairpin domain. Structure of domain1 (color), human mitochondrial Mn superoxide ... SOD1 is an extremely stable protein. In the holo form (both copper and zinc bound) the melting point is , 90 °C. In the apo ...
Structurally MDL-1 is a type II transmembrane protein with a short cytoplasmic tail and without signaling motifs, therefore it ... Another pathogen is influenza virus and its hemagglutinin protein, which interacts with CLEC5A. Through this interaction is ... CLEC5A, CLECSF5, MDL-1, MDL1, C-type lectin domain family 5 member A, C-type lectin domain containing 5A. ... C-type lectin domain family 5 member A (CLEC5A), also known as C-type lectin superfamily member 5 (CLECSF5) and myeloid DAP12- ...
The β-propeller at the 'foot' of clathrin contains multiple binding sites for interaction with other proteins. ... leg domain that identified and is composed of a smaller structural module referred to as clathrin heavy chain repeat motifs. ... Eukaryotic Linear Motif resource motif class LIG_Clathr_ClatBox_1. *Eukaryotic Linear Motif resource motif class LIG_Clathr_ ... and trimerization domains. The N-terminal domain consists of a seven-bladed β-propeller structure. The other domains form a ...
These receptor proteins may escort polyubiquitinated proteins to the proteasome, though the specifics of this interaction and ... Ubiquitin-receptor proteins have an N-terminal ubiquitin-like (UBL) domain and one or more ubiquitin-associated (UBA) domains. ... In this neutralisation pathway, TRIM21 (a protein of the tripartite motif family) binds with immunoglobulin G to direct the ... The CHIP protein (carboxyl terminus of Hsp70-interacting protein) is itself regulated via inhibition of interactions between ...
... prolyl hydroxylase domain proteins/EGL nine homologues), bind to a conserved Leu-Xaa-Xaa-Leu-Ala-Pro motif present in all ... and routing domains". Protein Science. 2 (4): 489-497. doi:10.1002/pro.5560020401. PMC 2142366. PMID 8518727.. ... Savini I, Rossi A, Pierro C, Avigliano L, Catani MV (April 2008). "SVCT1 and SVCT2: key proteins for vitamin C uptake". Amino ... which lose SVCT proteins during maturation.[105] In both vitamin C synthesizers (example: rat) and non-synthesizers (example: ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/ ... 1996). "Germline mutations in the p16INK4a binding domain of CDK4 in familial melanoma". Nat. Genet. 12 (1): 97-9. doi:10.1038/ ... Serrano M, Hannon GJ, Beach D (1994). "A new regulatory motif in cell-cycle control causing specific inhibition of cyclin D/ ... The protein encoded by this gene is a member of the Ser/Thr protein kinase family. This protein is highly similar to the gene ...
This dissociation enables the adaptor protein TRADD to bind to the death domain, serving as a platform for subsequent protein ... In an effort to localize the amino acid motif responsible for granule targeting, we constructed additional fusion proteins and ... thus excluding direct interactions with intracellular adaptor proteins. *^ Theiss. A. L. et al. 2005. Tumor necrosis factor ( ... protein binding. • protease binding. • tumor necrosis factor receptor binding. • cytokine activity. • identical protein binding ...
... as well as the interaction between the A domain and Arp2/3; and the acidic motif (A) binds Arp2/3.[8] In isolation, the VCA ... SH3 domain binding. • protein binding. • identical protein binding. • actin binding. • protein kinase binding. • small GTPase ... The output region is called the VVCA domain. It is located towards the C-terminal end of the protein and contains four motifs: ... Banin S, Gout I, Brickell P (August 1999). "Interaction between Wiskott-Aldrich Syndrome protein (WASP) and the Fyn protein- ...
CCR5 protein pripada familiji beta hemokinskih receptora, integralnih membranskih proteina.[2][3] On je G protein spregnuti ... 1998). „Structural interactions between chemokine receptors, gp120 Env and CD4". Semin. Immunol. 10 (3): 249-57. PMID 9653051. ... Broder CC, Dimitrov DS (1997). „HIV and the 7-transmembrane domain receptors". Pathobiology. 64 (4): 171-9. PMID 9031325. doi: ... The BBXB motif of RANTES is the principal site for heparin binding and controls receptor selectivity". J. Biol. Chem. 276 (14 ...
protein binding. Cellular component. • extracellular region. • specific granule. • intracellular. • extracellular exosome. • ... cathelin domain) and a highly variable cathelicidin peptide domain.[6] ... These larger cathelicidins display repetitive proline motifs forming extended polyproline-type structures.[6] ... van Wetering S, Tjabringa GS, Hiemstra PS (April 2005). "Interactions between neutrophil-derived antimicrobial peptides and ...
Ionizable residues in the transmembrane domain of each subunit form a polar network of interactions that hold the complex ... UMich Orientation of Proteins in Membranes protein/pdbid-2hac - Zeta-zeta dimer of T cell receptor ... in transmembrane signalling largely to phosphorylate tyrosines that are part of immunoreceptor tyrosine-based activation motifs ... FcR interaction for myeloid leukocytes, and Ag-Ig-CD79 interaction for B cells. ...
... it has been discovered that 19 out of the 20 human aaRSs have added at least one new domain or motif.[12] These new domains and ... The strong evolutionary pressure for these small non-catalytic protein domains suggested their importance.[21] Findings ... While class I binds via interactions mediated by backbone hydrogen bonds, class II uses a pair of arginine residues to ... Noncatalytic domains[edit]. The novel domain additions to aaRS genes are accretive and progressive up the Tree of Life.[18][19] ...
Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a ... The extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the specificity ... "Identification of three human type-II classic cadherins and frequent heterophilic interactions between different subclasses of ... identical protein binding. • cytoskeletal protein binding. • protein homodimerization activity. • cadherin binding. Cellular ...
... the SH3 domain binds to proline-rich sequences in other proteins). Sequence motif. Short amino acid sequences within proteins ... "Characterization and prediction of protein interfaces to infer protein-protein interaction networks". Current Pharmaceutical ... Protein domains. Main article: Protein domain. Many proteins are composed of several protein domains, i.e. segments of a ... due to a bigger number of protein domains constituting proteins in higher organisms.[13] For instance, yeast proteins are on ...
1vzj: STRUCTURE OF THE TETRAMERIZATION DOMAIN OF ACETYLCHOLINESTERASE: FOUR-FOLD INTERACTION OF A WWW MOTIF WITH A LEFT-HANDED ... positive regulation of protein secretion. · regulation of axonogenesis. · regulation of synaptic transmission. · protein ... protein self-association. 細胞成分. · extracellular region. · extracellular region. · extracellular region. · basal lamina. · ... protein homodimerization activity. · protein homodimerization activity. · laminin-1 binding. · ...
"A novel and conserved protein-protein interaction domain of mammalian Lin-2/CASK binds and recruits SAP97 to the lateral ... Bassand P, Bernard A, Rafiki A, Gayet D, Khrestchatisky M (Jun 1999). "Differential interaction of the tSXV motifs of the NR1 ... SAP97's protein structure consists of an alternatively-spliced n-terminal domain, three PDZ domains, an SH3 domain, hook domain ... protein binding. • protein complex scaffold activity. • protein kinase binding. • L27 domain binding. • ligand-gated ion ...
... a functional Src homology 3-binding motif that interacts with the Src homology 3 domain of Grb2 and cytoskeletal proteins". J. ... binding assay of src homology domain 3 interactions between 5-lipoxygenase and growth factor receptor binding protein 2". Anal ... and Dicer protein. *A PLAT domain within its C2-like domain; this domain, by analogy to other PLAT domain-bearing proteins, may ... ALOX5 binds with the F actin-binding protein, coactin-like protein. Based on in vitro studies, this protein binding serves to ...
Specifically it contains a Cy1 motif in the N-terminal half, and weaker Cy2 motif in the C-terminal domain that allow it to ... "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038/ ... protein binding. • cyclin-dependent protein serine/threonine kinase inhibitor activity. • ubiquitin protein ligase binding. • ... cyclin-dependent protein serine/threonine kinase activity. • protein kinase inhibitor activity. • protein kinase binding. • ...
"Molecular analysis of the epidermal growth factor-like short consensus repeat domain-mediated protein-protein interactions: ... 2004). "Autocatalytic cleavage of the EMR2 receptor occurs at a conserved G protein-coupled receptor proteolytic site motif". J ... aktivnost G protein spregnutog receptora. • vezivanje jona kalcijuma. • vezivanje hondroitin sulfata. Celularna komponenta. • ... EGF modul sadržavajući, mucinu sličan, hormonski receptor 2 je protein koji je kod ljudi kodiran EMR2 genom.[1] EMR2 je isto ...
Densmore III, L. D. & Dessauer, H. C. (1984). "Low levels of protein divergence detected between Gavialis and Tomistoma: ... "Gharial Motifs (Gavialis gangeticus) at Sanchi Stupa, India" (PDF). Crocodile Specialist Group Newsletter. 37 (4): 13. ... interaction. *Fatal alligator attacks. *Crocodile attacks. *Crocodile farm. *Crocodile tears. *Famous crocodiles and alligators ... Others suggested that it evolved much later than other crocodilians because of its low levels of blood proteins. As it shares ...
... a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to ... The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including ... "Protein Sci. 14 (12): 3039-47. doi:10.1110/ps.051604805. PMC 2253247. PMID 16322581.. ... They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; ...
The protein encoded by this gene is a member of the G-protein-coupled receptor family. This protein is a receptor for ... This article incorporates text from the United States National Library of Medicine, which is in the public domain. ... This name and the corresponding gene symbol IL8RA have been replaced by the HGNC approved name C-X-C motif chemokine receptor 1 ... Interactions[edit]. Interleukin 8 receptor, alpha has been shown to interact with GNAI2.[11][12] ...
... protein-protein interactions, and DNA replication. If these zinc ejectors unintentionally bind to the wrong zinc finger domains ... NCp7 is a 55-amino acid protein that is highly basic and consists of two gag-knuckle motifs. These motifs contain two peptide ... The HIV-1 nucleocapsid protein 7 (NCp7) is the protein targeted by zinc ejectors. NCp7 is initially formed as part of the gag ... "Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides". Nucleic Acids Research. 34 (2): 472-484. doi:10.1093 ...
protein domain specific binding. • RNA polymerase II transcription factor activity, sequence-specific DNA binding. ... Clark KL, Halay ED, Lai E, Burley SK (1993). "Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles ... "Foxp2 inhibits Nkx2.1-mediated transcription of SP-C via interactions with the Nkx2.1 homeodomain". Am. J. Respir. Cell Mol. ... This article incorporates text from the United States National Library of Medicine, which is in the public domain. ...
Protein Interaction Domains and Motifs*Protein Interaction Domains and Motifs. Protein Interaction Motifs*Protein Interaction ... "Protein Interaction Domains and Motifs" by people in Harvard Catalyst Profiles by year, and whether "Protein Interaction ... "Protein Interaction Domains and Motifs" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, ... Below are the most recent publications written about "Protein Interaction Domains and Motifs" by people in Profiles. ...
... and coimmunoprecipitation experiments are powerful methods for identifying novel proteins that bind to ones favorite protein ... Acommon focus among molecular and cellular biologists is the identification of proteins that interact with each other. Yeast ... The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains FASEB ... the interaction of proline-rich motifs in signaling proteins with their cognate domains. ...
... by a domain binding to another domain, by a domain binding to a short protein motif, or by a motif binding to another motif. In ... we proposed an approach to predict motif-motif binding sites for the yeast interactome ... Interacting proteins can contact with each other at three different levels: ... protein. -. protein. interaction binding sites: prediction from the motif-motif, motif-domain and domain-domain levels E. Pang ...
... and studies on protein-protein interactions between GCRV and its host remain rare. In this study, based on known motif-domain ... interaction information, we systematically predicted the GCRV virus-host protein interactome by using motif-domain interaction ... These proteins derived from different domain families and were predicted to interact with different motif patterns in GCRV. JAM ... Protein-protein interactions between virus and host are one avenue through which GCRV can trigger infection and induce disease ...
The BTB/POZ domain: a new protein-protein interaction motif common to DNA- and actin-binding proteins. O Albagli, P Dhordain, C ... The BTB/POZ domain defines a newly characterized protein-protein interaction interface. It is highly conserved throughout ... NS1-Binding Protein (NS1-BP): a Novel Human Protein That Interacts with the Influenza A Virus Nonstructural NS1 Protein Is ... nuclear DNA-binding proteins. By mediating protein binding in large aggregates, the BTB/POZ domain serves to organize higher ...
Guanine nucleotide exchange protein for ARF6, mediating internalisation of beta-1 integrin. ... Protein-protein interaction databases. The Biological General Repository for Interaction Datasets (BioGrid) ... Protein. Similar proteins. Species. Score. Length. Source. Q6DN90. IQ motif and SEC7 domain-containing protein 1 isoform X1. ... Protein. Similar proteins. Species. Score. Length. Source. Q6DN90. IQ motif and SEC7 domain-containing protein 1 isoform X1. ...
Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling. September 3, 2013. /0 ... Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling. Structure. 21(9):1636-47. ... 41Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling.. ...
... classifying and curating information about short linear motifs (SLiMs). For ,10 years, this resource has provided the ... The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, ... Amino Acid Motifs* * Databases, Protein* * Internet * Multiprotein Complexes / chemistry * Protein Interaction Domains and ... Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange ...
Here we show that the cytoplasmic domain of MHCI contains putative protein-protein interaction domains known as PDZ (PSD95/disc ... These results identify cryptic protein interaction motifs in the cytoplasmic domain of MHCI. In so doing, they suggest that the ... Finally, proof-of-principle in vitro interaction assays demonstrate that the cytoplasmic domains of particular MHCI proteins ... cytoplasmic domain of MHCI could participate in previously unsuspected PDZ mediated protein-protein interactions at neuronal as ...
SH3 DOMAINS AS DRUG TARGETS. Introduction. Structure. Variability. SH3 Binding Motifs. Selectivity. Drug Target Selection. ... Wiley-VCH, Weinheim Protein-Protein Interactions in Drug Discovery How can protein-protein interactions become the target of a ... and inter-species protein-protein interactions facilitating systems biology studies. * Modulators of protein-protein ... A LEAP INTO THE CHEMICAL SPACE OF PROTEIN-PROTEIN INTERACTION INHIBITORS. Introduction. Types of Interaction. Properties of the ...
Interaction Domains and Motifs are protein modules with conserved ligand-binding surfaces which mediate specific interaction ... functions in signal transduction pathways and specific binding sites of their cognate protein ligands ... Protein Interaction Domains and Motifs "Protein Interaction Domains and Motifs" Protein Interaction Motifs and Domains. In ... Protein Interaction Domains. In protein science, Protein Interaction Domains (Protein-Protein Interaction Domains) are ...
1999) DIX domains of Dvl and axin are necessary for protein interactions and their ability to regulate beta-catenin stability. ... The DEP domain preferentially bound motif III with a weak preference for peptides that include motif II but not motif I (Fig. 4 ... Wnt/β-catenin signaling requires interaction of the Dishevelled DEP domain and C terminus with a discontinuous motif in ... Wnt/β-catenin signaling requires interaction of the Dishevelled DEP domain and C terminus with a discontinuous motif in ...
... is a protein interaction motif that contains a 33-amino acid long sequence that often occurs in tandem arrays (as amino acid ... Protein Conformations. ⌊Tertiary Structure of a Protein (Tertiary Protein Structures). ⌊Protein Interaction Domains and Motifs ... In protein science, as an amino acid motif. Ankyrin Repeat (ANK Repeat) is a protein interaction motif that contains a 33-amino ... KN motif and ankyrin repeat domain containing (KANK protein family) *notch receptors (NOTCH) *POTE ankyrin domain containing ( ...
... of the hepatitis E virus ORF3 protein PxxP motif with heterologous late domain motifs affects virus release via interaction ... of the hepatitis E virus ORF3 protein PxxP motif with heterologous late domain motifs affects virus release via interaction ... of the hepatitis E virus ORF3 protein PxxP motif with heterologous late domain motifs affects virus release via interaction ... of the hepatitis E virus ORF3 protein PxxP motif with heterologous late domain motifs affects virus release via interaction ...
Interaction with the phospho-FIGQY motif requires the full-length doublecortin protein. NH2-terminal sequencing of polypeptides ... and a doublecortin domain fused to a protein kinase domain (Burgess et al., 1999). DC13 potentially could also interact with ... L1 cell adhesion molecules (CAMs) are transmembrane proteins in the Ig superfamily that engage in stable protein interactions ... proteins by alternative splicing that include a doublecortin-like protein and a doublecortin-protein kinase chimeric protein ( ...
Here, we present a 1.8 Å resolution crystal structure of the CLIC domain of mouse CLIC6 (mCLIC6). The structure reveals a ... elucidating high structural plasticity as an inherent property of the protein. Moreover, structure-guided perturbation of the ... inter-domain interface by mutagenesis resulted in a population shift towards elongated conformations of mCLIC6. Additionally, ... are a family of unique proteins, that were suggested to adopt both soluble and membrane-associated forms. Moreover, following ...
... present in a protein.,p>,a href=/help/family_and_domains_section target=_top>More...,/a>,/p>Family & Domainsi. Motif. ... help/interaction_section target=_top>More...,/a>,/p>Interactioni. Protein-protein interaction databases. STRING: functional ... This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein ... Integrated resource of protein families, domains and functional sites. More...InterProi. View protein in InterPro. IPR001412 aa ...
... motif, which mediates interaction with the autophagy-related protein 8 (ATG8) domain-containing proteins MAP1LC3s (microtubule- ... Displacement curves were obtained by using a premixed complex of protein domain ([protein domain] = one to twofold the KD of ... Table 4 Constructs used for expression of protein domains.. Protein domains and the encoding plasmids. Species is human unless ... tagged version of the domain did not yield higher protein concentrations. In line with an interaction between the NPxF motif of ...
Cardiac LIM interactome (all cardiomyocyte protein-protein interactions involving LIM domain proteins) enables the heart to ... LIM (Lin-1, Isl1, Mec3) domain proteins all contain least one double zinc finger motif (Fig. 1). LIM family proteins contain ... A selection of LIM domain proteins illustrating the diversity of LIM and non-LIM domains and their domain locations. The LIM ... The interactome of LIM domain proteins: The contributions of LIM domain proteins to heart failure and heart development. ...
The other 5 proteins have different putative protein-protein interaction motifs. Specifically, FBS and FBWD4 proteins contain ... Sec7 and WD40-repeat domains, respectively. The C-terminal region of FBA shares similarity with bacterial protein ApaG while ... F-box proteins are critical components of the SCF ubiquitin-protein ligase complex and are involved in substrate recognition ... cDNA cloning and expression analysis of new members of the mammalian F-box protein family.. Ilyin GP1, Rialland M, Pigeon C, ...
... of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions," ... 1. Protein-Protein Interactions. Protein-protein interactions (PPIs) are critical for most biological functions and cellular ... The MYND domain is a zinc-binding domain present in a large number of proteins that participate in many protein-protein ... "Recognition of proline-rich motifs by protein-protein-interaction domains," Angewandte Chemie, vol. 44, no. 19, pp. 2852-2869, ...
Protein Interaction Domains And Motifs. Protein modules with conserved ligand-binding surfaces which mediate specific ... in protein-protein interaction network to identify candidate disease-causing proteins. Protein-protein in... ... Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very ... Pdz Domains. Protein interaction domains of about 70-90 amino acid residues, named after a common structure found in PSD-95, ...
... interaction with actin, different investigators have reached different conclusions regarding the relevant and necessary domains ... Despite early demonstrations of myosin binding protein Cs (MyBP-C) ... Protein Binding / genetics. Protein Interaction Domains and Motifs. RNA Interference. Rats. Sequence Alignment. ... We defined cMyBP-Cs N-terminal structural domains that are necessary or sufficient to mediate interactions with actin and/or ...
Protein Binding. Protein Conformation. Protein Interaction Domains and Motifs. Receptors, Antigen, T-Cell / metabolism. Species ... Previous Document: Interindividual variability in the hepatic expression of the human breast cancer resistance protein .... ... as iGb3-hCD1d was unable to support cognate interactions with the iNKT-cell TCRs tested in this study. The structural basis for ...
C) (Top) Protein domain architecture of WIZ and ZNF644. (Bottom) Sequence alignment of atypical C2H2-like ZF motifs. Putative ... Nodes represent proteins identified by AP-MS, black edges represent high-confidence interactions, and known interactions are in ... ZNF644 Is a G9a/GLP-Interacting Protein and Co-regulator of H3K9me2. (A) Physical interaction map of histone methylation- ... B) Hierarchical clustering of bait interaction profile similarity. Colored boxes indicate proteins known to reside in the same ...
The bHLH domain, a well-conserved bifunctional motif mediating DNA binding and homoand heterodimeric protein-protein ... motifs or domains within proteins are delimited by vertical lines. Diagonal fill is used to denote the acidic and bHLH domains ... 1992 COP1, an Arabidopsis regulatory gene, encodes a protein with both a zinc-binding motif and a Gβ homologous domain. Cell 71 ... produce a truncated protein lacking a bHLH domain but maintain those domains that two-hybrid data suggest mediate interactions ...
We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their ... InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites ... The POZ domain: a conserved protein-protein interaction motif.. Genes Dev. 8 1664-77 1994 ... Domain relationships *BTB/POZ domain (IPR000210) *Potassium channel tetramerisation-type BTB domain (IPR003131) ...
These protein domains are enriched for lysine-rich amino-acid motifs with protein-RNA binding potential35 and have structural ... Homology regions (HR1-HR5)-predicted RNA-protein interaction motifs in circANRIL. (c) Secondary structure prediction and HR1-5 ... 66)). The catRAPID67 and the RNA-Protein Interaction Prediction (RPISeq) software67,68 were used for predictions of protein-RNA ... To investigate whether circANRIL bound to PES1 at the predicted protein domains, we performed protein immunoprecipitation of ...
CAS proteins have an amino terminal SH3 domain enabling interaction with poly-proline motif-containing proteins such as FAK. ... SH2-binding site motifs, which when tyrosine-phosphorylated allow interaction with SH2-domain containing proteins; serine-rich ... Figure 1. Interaction network and domain structure scheme of Cass4. SH3 domain (SH3) preceded by a short region with no defined ... which when tyrosine-phosphorylated allow interaction with SH2 domain containing proteins. Further to the carboxy-terminus, they ...
... motifs, or domains (Glatz et al, 2013). Besides, not all MAPK‐binding elements are linear motifs. Folded domains such as the ... motif protein-protein interaction system is an ideal test bed for linear binding motif discovery. ... Cell‐based protein-protein interaction assay. The full‐length cDNA of yellow fluorescent protein (YFP) was split at position ... Protein-protein interactions influence all aspects of cellular life and the most direct mechanism through which proteins can ...
  • For example, mapping studies and 3-dimensional analyses of antigen-antibody interactions have revealed that epitopes are typically 4-7 residues long (1). (nih.gov)
  • This review highlights the analysis of those protein-protein interactions that involve proline residues, the biochemistry of proline, and current drug discovery efforts based on proline peptidomimetics. (nih.gov)
  • Putative PDZ ligands in MHCI encompass conserved serine and tyrosine residues that are targets of phosphorylation, a post-translational modification that can regulate PDZ interactions. (biomedcentral.com)
  • The highly conserved residues coordinate with zinc ions to form two tandem zinc fingers that constitute the LIM domain. (sigmaaldrich.com)
  • While strong transient PPIs require a molecular trigger such as ligand binding to shift the oligomeric equilibrium, weak transient interactions are mediated by binding between a few critical residues [ 3 , 5 ]. (hindawi.com)
  • 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. (bioportfolio.com)
  • Determination of the critical residues responsible for cardiac myosin binding protein C's interactions. (biomedsearch.com)
  • To validate the structural and functional significance of these residues, we silenced the endogenous cMyBP-C in neonatal rat cardiomyocytes (NRC) using cMyBP-C siRNA, and replaced the endogenous cMyBP-C with normal or actin binding-ablated cMyBP-C. Replacement with actin binding-ablated cMyBP-C showed that the mutated protein did not incorporate into the sarcomere normally. (biomedsearch.com)
  • Residues responsible for actin and S2-MyHC binding are partially present in overlapping domains but are unique. (biomedsearch.com)
  • Further to the carboxy-terminus, they have a four-helix bundle rich in serine residues, and a second highly conserved four-helix bundle that has been recognized as functionally and structurally similar to a focal adhesion targeting [FAT] domain. (wikipedia.org)
  • Deletion analysis led to the discovery of a novel protein domain of 37 amino acid residues, designated as the protein phosphatase interaction (PPI) motif, of SOS2 that is necessary and sufficient for interaction with ABI2. (pnas.org)
  • Mutations in the conserved amino acid residues in the PPI motif abolish the interaction of SOS2 with ABI2. (pnas.org)
  • PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. (wikipedia.org)
  • We employed a yeast two-hybrid screen using the COOH-terminal 70 residues of CFTR to identify proteins that might be involved in such interactions. (jci.org)
  • The interaction is mediated by residues 1420-1457 in CFTR and by the COOH-terminal regulatory domain of α1-AMPK. (jci.org)
  • The full-length HtrA2 is synthesized as a precursor protein and then targeted to the mitochondria where it is matured by the removal of N-terminal 133 residues. (prospecbio.com)
  • 1988) cloned murine Dnmt cDNA and found that its C-terminal domain of 570 amino acid residues showed striking similarities to a catalytic methyltransferase domain of bacterial type II DNA cytosine methyltransferases. (atlasgeneticsoncology.org)
  • LRRC42 protein contains two leucine-rich repeats (LRRs) which are widespread structural motifs comprising 20-30 amino acids with a characteristic repetitive sequence pattern rich in leucine residues. (spandidos-publications.com)
  • 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. (harvard.edu)
  • Our work demonstrates that by inferring significant protein - protein binding sites at an aggregate level combining domain-domain, domain-motif and motif-motif levels based on high-quality positive and negative datasets, this method may be capable of identifying the binding site pairs that mediate protein - protein interactions. (rsc.org)
  • The extracellular domain of MHCI interacts with immunoreceptors, peptides, and co-receptors to mediate immune signaling. (biomedcentral.com)
  • PDZ ligands are motifs that bind to PDZ domains to organize and mediate signaling at cell-cell contacts. (biomedcentral.com)
  • In protein science , Protein Interaction Domains (Protein-Protein Interaction Domains) are recognition modules in proteins that mediate interactions between specific proteins involved in signal transduction pathways, which fold to form recognition pockets complementary to the short interaction sequence motifs on their ligands. (wellnessadvantage.com)
  • Here, we measured the binding affinity of predicted interactions between SLiMs in the cytoplasmic tails of ACE2 and integrin β 3 with proteins that mediate endocytic trafficking and autophagy. (sciencemag.org)
  • We defined cMyBP-C's N-terminal structural domains that are necessary or sufficient to mediate interactions with actin and/or the head region of the myosin heavy chain (S2-MyHC). (biomedsearch.com)
  • The WW domains mediate interaction with PPxY motif-containing proteins. (rcsb.org)
  • Many studies have been focused on understanding the structure and functions of key cellular enzymes that mediate these epigenetic processes and on subsequently developing small molecule inhibitors that target these proteins. (frontiersin.org)
  • Our results establish the PPI motif and the protein kinase interaction domain as novel protein interaction domains that mediate the binding between the SOS2 family of protein kinases and the ABI1/2 family of protein phosphatases. (pnas.org)
  • SRSF1/RBM42) with 5′UTR sequence motifs mediate many of these changes. (rupress.org)
  • however, the major forces that mediate these interactions remain debated, and our ability to predict these interactions is still largely untested. (semanticscholar.org)
  • By mediating protein binding in large aggregates, the BTB/POZ domain serves to organize higher order macromolecular complexes involved in ring canal formation or chromatin folding. (aacrjournals.org)
  • Homo- or heterologous oligomeric PPI complexes represent isologous or heterologous association of identical protein units. (hindawi.com)
  • In the post-genomic era, one of the important tasks is to identify protein complexes and functional modules from high-throughput protein-protein interaction data, so that we can systematically analyze. (bioportfolio.com)
  • Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. (bioportfolio.com)
  • Functional annotation of mammalian protein complexes is crit. (bioportfolio.com)
  • A) Physical interaction map of histone methylation-related complexes. (nih.gov)
  • Evidence suggests that individual PKS proteins interact with specific calcium-binding proteins in the SOS3 family (known as SCaBPs) to form distinct protein kinase complexes ( 3 ). (pnas.org)
  • These protein kinase complexes may be capable of decoding various calcium signals elicited by developmental, hormonal, or environmental cues ( 3 ). (pnas.org)
  • Many important findings in pharmacology, cell biology, and pathobiology have been achieved with the aid of virtual interactomics including computer-aided structural analysis, prediction and in silico simulation of interacting sites, protein complexes, and interaction networks. (hindawi.com)
  • Long chains of amino acids, called polypeptides, make up the multicomponent, large complexes of protein. (encyclopedia.com)
  • 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)
  • The role of the adaptor proteins that physically link these complexes together for the purposes of ion channel modulation, however, has been little explored. (jneurosci.org)
  • The collection of transcripts associated with GR, identified by immunoprecipitation of GR-mRNA complexes followed by microarray analysis, revealed 479 transcripts that associated with GR. Computational analysis of the primary sequence and secondary structures of these transcripts yielded a GC-rich motif, which was shown to bind to GR in vitro. (jimmunol.org)
  • This gives a good illustration of how selection pressure allowed the C-terminal domains of N and P proteins to evolve concomitantly within this family of viruses in order to lead to protein complexes having the same three-dimensional fold, and thus the same function, but with completely different binding interfaces. (asm.org)
  • For example, the partner may be part of protein complexes involved in centrosome duplication and/or G1 checkpoints. (haematologica.org)
  • TRAFs (TNF receptor-associated factors) are a family of multifunctional adaptor proteins that bind to surface receptors and recruit additional proteins to form multiprotein signaling complexes capable of promoting cellular responses. (biolegend.com)
  • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. (springer.com)
  • Kinesin1 (also known as conventional kinesin or Kif5) plays a major role in neuronal transport by recruiting many different cargos such as organelles, vesicles, mRNA/proteins complexes and protein assemblies [ 5 , 6 ]. (plos.org)
  • Acommon focus among molecular and cellular biologists is the identification of proteins that interact with each other. (nih.gov)
  • These proteins derived from different domain families and were predicted to interact with different motif patterns in GCRV. (biomedcentral.com)
  • JAM-A protein was successfully predicted to interact with motifs of GCRV Sigma1-like protein, and shared the similar binding mode compared with orthoreovirus. (biomedcentral.com)
  • However, characterization of increasing numbers of protein sequences and structures has suggested that the interacting modules of multidomain proteins can be distinguished as globular domains, as short peptide functional sites, and as long peptides that interact with their partners over extensive regions. (hindawi.com)
  • Using a combination of genetics and functional assays, we defined the actin binding site(s) present in cMyBP-C. We confirmed that cMyBP-C's C1 and m domains productively interact with actin, while S2-MyHC interactions are restricted to the m domain. (biomedsearch.com)
  • Yeast two-hybrid assays indicate that GL3 participates in physical interactions with GL1, TTG1, and itself, but that GL1 and TTG1 do not interact. (genetics.org)
  • The observations that the ttg1-1 mutation was suppressed by R and that this bHLH transcription factor could interact with endogenous Arabidopsis MYB-like proteins offered compelling but indirect evidence that in Arabidopsis one or more R homologs performed regulatory functions in TTG1-dependent developmental pathways. (genetics.org)
  • This permits the α-helical LXXLL motif within some coactivators to interact with the nuclear receptors. (asm.org)
  • The TPR domain was found to interact with SPY both in vitro and in yeast two-hybrid assays. (plantphysiol.org)
  • Mutations in the seventh TPR of CDC27 reduce its ability to interact with CDC23, but do not change the interaction with CDC16. (plantphysiol.org)
  • PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. (wikipedia.org)
  • Predictors based on sequence and structure exploit the observation that some pairs of sequence motifs, domains and structural families tend to interact preferentially. (biomedcentral.com)
  • Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. (nih.gov)
  • Well known examples include SLiMs that interact with 14-3-3, PDZ, SH2, SH3, and WW domains but the true extent and diversity of SLiM-mediated interactions is largely unknown. (rsc.org)
  • Combining data from seven different interaction databases, we analysed approximately 6000 protein -centred and 1600 domain-centred human interaction datasets of 3+ unrelated proteins that interact with a common partner. (rsc.org)
  • The affected proteins, polycystin-1 (PC1) and polycystin-2 (PC2), interact with each other and are expressed in cilia. (biologists.org)
  • The sequence proximity of two pairs of pS-P motifs in IRAK1-UD suggests that the WW and PPIase domains of Pin1, both of which can interact with pS/pT-P motifs, could simultaneously bind to two neighboring motifs (i.e., bivalently). (cornell.edu)
  • DNMT1 can interact with numerous proteins, such as DNMT1-associated protein (DMAP) 1, histone deacetylase (HDAC) 1 , HDAC2 , and Rb , and can repress gene transcription. (atlasgeneticsoncology.org)
  • The DNMT1 N-terminal domain can also interact with E2F1 transcription factor, HDAC1 and HDAC2. (atlasgeneticsoncology.org)
  • LRRC42, which was found to localize in the nucleus of mammalian cells, is likely to interact with and stabilize GATAD2B (GATA zinc finger domain-containing 2B) and MBD3 (Methyl-CpG-binding domain protein 3) proteins that could contribute to lung cancer cell proliferation partly through the regulation of p21Waf1/Cip1. (spandidos-publications.com)
  • Herein we report identification of LRRC42 as a potential therapeutic target and also provide evidence that LRRC42 could interact with GATAD2B (GATA zinc finger domain containing 2B) and MBD3 (Methyl-CpG-binding domain protein 3) proteins that are likely to play a significant role in human pulmonary carcinogenesis. (spandidos-publications.com)
  • PI lipids interact with the pleckstrin homology domain (PH-domain) containing cellular enzymes causing their membrane recruitment and/or allosteric activation. (atlasgeneticsoncology.org)
  • Various structurally unrelated cargos interact with the conserved tetratricopeptide repeat (TPR) domain of KLC. (plos.org)
  • Based on structural homology, the GK0453 protein possesses two independent binding sites and hence it may simultaneously interact with two proteins or with a protein and a nucleic acid. (iucr.org)
  • Laursen L, Karlsson E, Gianni S, Jemth P. Functional interplay between protein domains in a supramodular structure involving the postsynaptic density protein PSD-95. (harvard.edu)
  • Microinjection of peptides comprising this motif interferes with Wnt/β-catenin signaling in Xenopus embryos, further supporting the functional importance of the Fz C-terminal tail. (pnas.org)
  • LIM domains of the heart and blood vessels arranged according to their functional involvement in development and/or heart disorders (and failure). (sigmaaldrich.com)
  • Functional transcriptomic annotation and protein-protein interaction network analysis identify NEK2, BIRC5, and TOP2A as potential targets in obese patients with luminal A breast cancer. (bioportfolio.com)
  • Integrating genetic and protein-protein interaction networks maps a functional wiring diagram of a cell. (bioportfolio.com)
  • A Network Hierarchy-Based Method for Functional Module Detection in Protein-Protein Interaction Networks. (bioportfolio.com)
  • SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis. (bioportfolio.com)
  • We used a structurally consistent model on kinase‐docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under‐explored part of the human proteome and applied experimental tools specifically tailored to detect low‐affinity protein-protein interactions for their validation in vitro and in cell‐based assays. (embopress.org)
  • For instance, most of these receptors are associated with corepressor proteins that silence their activity in the absence of ligands, and activation therefore involves displacement of the associated corepressors by coactivators, an event that permits the functional interaction of the receptor with the cellular transcription machinery ( 8 , 17 ). (asm.org)
  • However, phosphorylation at Tyr(921) and Tyr(930) enables differential binding to the Src homology 2 domain of the adaptor protein Grb7, which we propose will lead to distinct functional outcomes. (sigmaaldrich.com)
  • We show that MYC alters the efficiency and quality of mRNA translation into functional proteins. (rupress.org)
  • Furthermore, many of the functional consequences of aberrant proteins, such as in cancer cells, are due to protein-protein interactions (PPIs). (mdpi.com)
  • Remarkably, many of the RBPs we studied bound mRNAs whose protein products share identifiable functional or cytotopic features. (nih.gov)
  • To determine whether the association between the kinase and the cation channel involves specific forms of protein-protein interactions, we have tested the ability of different interaction domains and motifs to interfere with the functional link between channel and kinase in excised, inside-out patches. (jneurosci.org)
  • SeV P protein (568 aa) is a modular protein with distinct functional domains ( 39 ). (asm.org)
  • It is hypothesized that the RGD motif plays a functional role in processes including cell adhesion, migration, growth, and bone resorption. (clontech.com)
  • Reverse genetics using the bovine leukemia virus (BLV) genome highlighted important functional domains of the envelope protein involved in the viral life cycle. (mdpi.com)
  • Setting up different signaling platforms defined by selective interactions with adaptor proteins thus adds another level of regulation to EphA2 signaling. (sigmaaldrich.com)
  • The six known TRAFs (TRAF1-6) act as adaptor proteins for a wide range of cell surface receptors and participate in the regulation of cell survival, proliferation, differentiation, and stress responses. (biolegend.com)
  • Therefore, SXXE/D motifs found in the cytoplasmic domains of many TNFR family members and their adaptor proteins may serve to function as a specific interaction module for the α-helical death domain signal transduction. (jimmunol.org)
  • The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). (nih.gov)
  • 10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear motifs. (nih.gov)
  • predicted the presence of short amino acid sequences, called short linear motifs (SLiMs), in the cytoplasmic tails of ACE2 and various integrins that may engage the endocytic and autophagic machinery. (sciencemag.org)
  • The cytoplasmic tails of ACE2 and integrins contain several predicted short linear motifs (SLiMs) that may facilitate internalization of the virus as well as its subsequent propagation through processes such as autophagy. (sciencemag.org)
  • Many of the specific functions of intrinsically disordered protein segments are mediated by Short Linear Motifs (SLiMs) interacting with other proteins . (rsc.org)
  • The Fz family of Wnt receptors comprises G protein-coupled receptor (GPCR)-like transmembrane proteins ( 7 , 11 ⇓ - 13 ). (pnas.org)
  • Furthermore, we validated that an LC3-interacting region (LIR) in integrin β 3 bound to the ATG8 domains of the autophagy receptors MAP1LC3 and GABARAP in a manner enhanced by LIR-adjacent phosphorylation. (sciencemag.org)
  • A simplified model of transcriptional activation by these receptors involves activation of the receptors by their cognate ligands, recruitment of the receptor homo- or heterodimers to target DNA sequences, and subsequent modulation of gene transcription upon interaction with the general transcription machinery. (asm.org)
  • All of these proteins contain a signature LXXLL motif (NR box) which is necessary and sufficient to permit the interaction between receptors and coactivators ( 15 ). (asm.org)
  • Most of frizzled receptors are coupled to the beta-catenin canonical signaling pathway, which leads to the activation of disheveled proteins, inhibition of GSK-3 kinase, nuclear accumulation of beta-catenin and activation of Wnt target genes. (abcam.com)
  • TIR-domain-containing adapter-inducing interferon-β (TRIF) is an adapter in responding to activation of toll-like receptors (TLRs). (wikipedia.org)
  • Osteopontin protein contains an Arg-Gly-Asp (RGD) motif, which is also present in fibronectin, vitronectin, and other extracellular proteins that bind the integrin family of cell surface receptors such as avb3, a5b1, a8b1, and avb5. (clontech.com)
  • MHCI gene family, and conservation of PDZ ligand motifs in MHCI cytoplasmic domains. (biomedcentral.com)
  • The marked differences in F-box gene expression in human tissues suggest their distinct role in ubiquitin-dependent protein degradation. (nih.gov)
  • Cas scaffolding protein family member 4 is a protein that in humans is encoded by the CASS4 gene . (wikipedia.org)
  • This trend is supported by the increasing demand for sequencing platforms with increasing life science research using techniques such as gene expression analysis, sequence analysis, and protein expression analysis. (bio-medicine.org)
  • Homeobox protein NOBOX , also known as newborn ovary homeobox protein , is a protein that in humans is encoded by the NOBOX gene . (wikipedia.org)
  • The protein encoded by this gene is necessary for intercellular bridges in germ cells, which are required for spermatogenesis. (genecards.org)
  • TEX14 (Testis Expressed 14, Intercellular Bridge Forming Factor) is a Protein Coding gene. (genecards.org)
  • Diseases associated with TEX14 include Spermatogenic Failure 23 and Fanconi Anemia, Complementation Group O . Gene Ontology (GO) annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity . (genecards.org)
  • LIM domain binding 3 (LDB3), also known as Z-band alternatively spliced PDZ-motif (ZASP), is a protein which in humans is encoded by the LDB3 gene. (wikipedia.org)
  • these proteins are likely to represent global regulators of gene expression. (genetics.org)
  • PcG proteins form a family based upon their common role in gene expression rather than extensive shared homologies or structural motifs. (genetics.org)
  • RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. (nih.gov)
  • Cells deficient for RIP1 gene display attenuated TLR3 activation of NF-κB, indicating the use of the RIP1 gene in downstream TRIF activation, in contrast to other TLRs that use IRAK protein for the activation of NF-κB. (wikipedia.org)
  • The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. (genecards.org)
  • LDLR (Low Density Lipoprotein Receptor) is a Protein Coding gene. (genecards.org)
  • The partner gene promoter drives the expression of the fusion protein in the cell. (haematologica.org)
  • 1991 ) The KUP gene, located of human chromosome 14, encodes a protein with two distant zinc fingers. (biologists.org)
  • The LRRK2 gene is a major contributor to genetic risk for Parkinson's disease and understanding the biology of the leucine-rich repeat kinase 2 (LRRK2, the protein product of this gene) is an important goal in Parkinson's research. (springer.com)
  • The protein encoded by this gene is a member of the TNF receptor-associated factor (TRAF) protein family. (biolegend.com)
  • The structure of DNMT1 indicates that the DNMT1 gene could have been formed during the fusion of a prokaryotic DNMT gene with a mammalian DNA binding protein gene. (atlasgeneticsoncology.org)
  • LRR-containing proteins participate in many important biological processes, including plant and animal immunity, hormone-receptor interactions, cell adhesion, signal transduction, regulation of gene expression and apoptosis ( 11 - 14 ). (spandidos-publications.com)
  • The one-hybrid system with an inverted CCAAT box as the DNA target sequence was used to identify proteins acting on key DNA sequences of the promoter of the topoisomerase IIα gene. (aacrjournals.org)
  • 6. The transgenic mouse of claim 1 , wherein said indicator gene is selected from the group consisting of lacZ, a gene encoding green fluorescent protein and a gene encoding luciferase. (google.com)
  • The gene encoding the GK0453 protein (gi:56418988) was amplified via PCR using G. kaustophilus HTA426 genomic DNA and was cloned into the pET-15b expression vector (Merck Novagen, Darmstadt, Germany). (iucr.org)
  • In particular, SH3, WW, and several new protein-interaction domains prefer ligand sequences that are proline-rich. (nih.gov)
  • In protein science , Protein Interaction Motifs (Protein Interaction Binding Motifs) are short amino acid sequences which are the binding sites on the ligands of protein interaction domains. (wellnessadvantage.com)
  • however, it now appears that sequences flanking the core motif may play a role in determining receptor selectivity. (asm.org)
  • To address this issue, we used a combinatorial phage display approach to evaluate the role of flanking sequences in influencing these interactions. (asm.org)
  • Using a series of ERα-mutants, we found that these three classes of peptides showed different interaction patterns from each other, suggesting that not all LXXLL motifs are the same and that receptor binding selectivity can be achieved by altering sequences flanking the LXXLL core motif. (asm.org)
  • Remaining unmasked sequences are subjected to the second round of motif detection until no more significant motifs can be found or all protein segments have been assigned to a motif. (peerj.com)
  • Three CD36 domains were identified including cytoplasmic, transmembrane and exoplasmic sequences. (mdpi.com)
  • These results indicate that cytoplasmic GR interacts with a subset of mRNA through specific sequences and can regulate turnover rates, suggesting a novel posttranscriptional role for GR as an RNA-binding protein. (jimmunol.org)
  • Bioinformatic studies showed that six regions of good conservation can be defined within the L protein sequences. (asm.org)
  • The entire text of the Guide is searchable, and tools are available for identifying human protein sequences using those from other species. (cshlpress.com)
  • v-Src differs from Src by substitution of sequences at the C-terminus, which results in loss of amino acids that normally bind to the SH domains and stabilize the `closed' or inactive conformation of the molecule (reviewed by Frame, 2002 ). (biologists.org)
  • It is highly conserved throughout metazoan evolution and generally found at the NH2 terminus of either actin-binding or, more commonly, nuclear DNA-binding proteins. (aacrjournals.org)
  • serine-rich region encompassing 4-helices and a second highly conserved four-helix bundle that has been recognized as functionally and structurally similar to a focal adhesion targeting [FAT] domain. (wikipedia.org)
  • Here, we have characterized the DMC1 interaction site in RAD51AP1 by a series of truncations and point mutations to uncover a highly conserved WVPP motif critical for DMC1 interaction but dispensable for RAD51 association. (pubmedcentralcanada.ca)
  • This protein has an amino terminal RING domain which is followed by four zinc-finger motifs, a central coiled-coil region and a highly conserved carboxyl terminal domain, known as the TRAF-C domain. (biolegend.com)
  • Interacts (via WW domains) with ARRDC1 , ARRDC2 and ARRDC3 (By similarity). (rcsb.org)
  • ZASP interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. (wikipedia.org)
  • This protein also interacts with all three members of the myozenin family. (wikipedia.org)
  • Lys-Thr-X-X-X-Trp motif interacts with the PDZ doman of Dvl (Disheveled) family members and is involved in the activation of the Wnt/beta-catenin signaling pathway. (abcam.com)
  • The proteins play crucial roles as the key regulator of how the bacterium interacts with its environment. (peerj.com)
  • The charge-rich motif of the N-terminal domain of DNMT1 interacts with DMAP1 and represses transcription without the participation of HDACs. (atlasgeneticsoncology.org)
  • In addition, DNMT1 interacts with methyl CpG binding proteins such as MBD2 , MBD3 and MeCPs. (atlasgeneticsoncology.org)
  • MURF1 interacts with receptor for activated protein kinase C (RACK1) and colocalizes with RACK1 after activation with phenylephrine or PMA. (rupress.org)
  • Moreover, it stimulates the E-cadherin regulator Hakai, interacts with and phosphorylates the novel podosome-linked adaptor protein Fish, and progressively phosphorylates the gap junction component connexion 43. (biologists.org)
  • The analysis produced an extensive list of independently evolved linear binding motifs from a functionally diverse set of proteins. (embopress.org)
  • The analysis suggests that most human MAPK‐binding motifs are surprisingly new evolutionarily inventions and newly found links highlight (previously hidden) roles of MAPKs. (embopress.org)
  • Three TRAF-binding motifs present in the amino terminal region of TRIF are necessary for association with TRAF6. (wikipedia.org)
  • Within the complex, the Dvl DEP domain mainly binds the Fz C-terminal tail, whereas a short region at the Dvl C-terminal end is required to bind the Fz third loop and stabilize the Fz-Dvl interaction. (pnas.org)
  • The spike protein of SARS-CoV-2 binds the angiotensin-converting enzyme 2 (ACE2) on the host cell surface and subsequently enters host cells through receptor-mediated endocytosis. (sciencemag.org)
  • The TPRs fold into a right-handed super-helical structure that binds the interacting proteins. (plantphysiol.org)
  • The PDZ domain of ZASP binds the C-terminus of alpha actinin-2 and ZMs bind the rod domain of alpha actinin-2. (wikipedia.org)
  • Because the B-box 2 domain of the BCCL2 protein binds two zinc ions [16], we investigated the effect of zinc supplementation and DTT treatment on the expression and oligomerization of the LLER variant. (nih.gov)
  • Modulation was also prevented by an SH3 motif peptide that preferentially binds the SH3 domain of src. (jneurosci.org)
  • KLC is also composed of three regions: a N-terminal Heptad Repeat (HR) region that binds to the KHC stalk, a TPR (Tetratrico Peptide Repeat) domain involved in cargo recruitment, and a variable C-terminal region. (plos.org)
  • Yeast two-hybrid, cDNA expression library screening, and coimmunoprecipitation experiments are powerful methods for identifying novel proteins that bind to one's favorite protein for the purpose of learning more regarding its cellular function. (nih.gov)
  • In our previous work, we proposed an approach to predict motif-motif binding sites for the yeast interactome by contrasting high-quality positive interactions and high-quality non-interactions using a simple statistical analysis. (rsc.org)
  • In this study, we integrated 2854 yeast proteins that undergo 13 531 high-quality interactions and 3491 yeast proteins undergoing 578 459 high-quality non-interactions. (rsc.org)
  • Interestingly, some of our predicted binding site pairs may, at least in the yeast genome, guide researchers to assay novel protein - protein interactions by mutagenesis or other experiments. (rsc.org)
  • Systematic experimental approaches have led to construction of comprehensive genetic and protein-protein interaction networks for the budding yeast, Saccharomyces cerevisiae. (bioportfolio.com)
  • Although the prediction of protein-protein interactions has been extensively investigated for yeast, few such datasets exist for the far larger proteome in human. (biomedcentral.com)
  • We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs, as well as several proteins not annotated as RBPs. (nih.gov)
  • Several accessory proteins of budding yeast Dmc1 have been identified, including Mei5-Sae3 (Sfr1-Swi5 in the fission yeast) ( 20 - 22 ), Hop2-Mnd1 ( 13 , 23 - 25 ) and Rdh54 ( 12 , 26 , 27 ). (pubmedcentralcanada.ca)
  • 1996). Proteins unique to the nematode (and not yeast) may well define metazoans (Chervitz et al. (apsnet.org)
  • Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y. Towards a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. (springer.com)
  • Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. (springer.com)
  • In budding yeast, Ssk1p and Skn7p are response proteins of the Sln1p histidine kinase ( 3 , 4 , 33 ). (asm.org)
  • Among the primary structures of many ligands for protein-protein interactions, the amino acid proline is critical. (nih.gov)
  • In addition, even though ligands for EH domains and 14-3-3 domains are not proline-rich, they do include a single proline residue. (nih.gov)
  • Here we show that the cytoplasmic domain of MHCI contains putative protein-protein interaction domains known as PDZ ( P SD95/ d isc large/ z onula occludens-1) ligands. (biomedcentral.com)
  • PDZ ligands are short, degenerate motifs, and are therefore difficult to identify via sequence homology alone, but several lines of evidence suggest that putative PDZ ligand motifs in MHCI are under positive selective pressure. (biomedcentral.com)
  • Putative PDZ ligands are found in all of the 99 MHCI proteins examined from diverse species, and are enriched in the cytoplasmic domain, where PDZ interactions occur. (biomedcentral.com)
  • Thus, a typical class of ligand binding proteins may contain a variety of protein interaction domains that recognize a common ligand, whereas a family classified based on sequence homology contains a single fold that may recognize a variety of ligands. (hindawi.com)
  • The FZ domain is involved in binding with Wnt ligands. (abcam.com)
  • Finally, proof-of-principle in vitro interaction assays demonstrate that the cytoplasmic domains of particular MHCI proteins can bind directly and specifically to PDZ1 and PDZ4&5 of MAGI-1, and identify a conserved PDZ ligand motif in the classical MHCI H2-K that is required for this interaction. (biomedcentral.com)
  • We are the first to examine 33 LIM proteins (including three that bind to but do not themselves contain LIM domains) that are implicated in either the development of the heart, heart disorders and failure or both. (sigmaaldrich.com)
  • Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less‐characterized disordered regions. (embopress.org)
  • The disordered part of the human proteome contains a large number of short linear motif occurrences that can bind to MAP kinases. (embopress.org)
  • For example, a motif that is N-terminal to the OPN thrombin cleavage site has been reported to bind to the a4 and a9 integrin family. (clontech.com)
  • domain is also thought to bind to adhesion proteins in a PIP 2 -regulated fashion to provide a link between cytoskeletal signals and membrane dynamics. (cellsignal.com)
  • The N-terminal capping helix of the TPR domain exhibits an atypical sequence and structural features that may contribute to the versatility of the TPR domain to bind different cargos. (plos.org)
  • The other 5 proteins have different putative protein-protein interaction motifs. (nih.gov)
  • The discontinuous nature of the Fz-Dvl interface may allow for precise regulation of the interaction in the control of Wnt-dependent cellular responses. (pnas.org)
  • We then assembled a cellular 'snapshot' of the LIM proteins known to be expressed in the heart that helps explain how mutations in these proteins may play a role in the development of heart failure. (sigmaaldrich.com)
  • The oval labels (colored by their number of LIM domains) represent named LIM domain proteins and the arrows indicate their connections to other LIM proteins and transcription factors (white ovals), and other cellular proteins and membrane features. (sigmaaldrich.com)
  • Protein-protein interactions (PPIs) are critical for most biological functions and cellular processes [ 1 , 2 ]. (hindawi.com)
  • Mitogen‐activated protein kinases (MAPK) are broadly used regulators of cellular signaling. (embopress.org)
  • Reversible protein phosphorylation is a fundamental mechanism by which living organisms regulate cellular processes in response to developmental, hormonal, and environmental cues. (pnas.org)
  • Protein-protein interactions perform and regulate fundamental cellular processes. (biomedcentral.com)
  • The comprehensive study of such interactions on a genome-wide scale will lead to a clearer understanding of diverse cellular processes and of the molecular mechanisms of disease. (biomedcentral.com)
  • Remarkably, the same proteins have also the propensity to adopt self-perpetuating assemblies which properties fit the needs to encode cellular memory. (mdpi.com)
  • We assessed the prediction that access of the viral NS1 protein to cellular PDZ domain protein networks enhances the virulence of highly pathogenic avian influenza A viruses. (asm.org)
  • are 22-28 amino acid motifs found in a number of proteins with diverse functions and cellular locations. (cellsignal.com)
  • Several cellular proteins associate with SHIP2 via phosphotyrosine-dependent (SH2 or NPXY mediated) or proline-rich region (SH3 mediated) interactions (for a comprehensive list of interacting proteins and citations please see Prasad, 2009a ). (atlasgeneticsoncology.org)
  • Both the position of the PDZ ligand and the class of ligand motif are conserved across species, as well as among genes within a species. (biomedcentral.com)
  • The BTB domain, found primarily in zinc finger proteins, defines an evolutionarily conserved family that includes several developmentally regulated genes in Drosophila. (ebi.ac.uk)
  • This system employed the Su(Hw) DNA-binding domain (ZnF) to direct PcG proteins to transposons that carried the white and yellow reporter genes. (genetics.org)
  • Most of the known BR-C target genes, including the salivary gland secretion protein (Sgs) genes, are terminal differentiation genes that are thought to be directly regulated by BR-C -encoded transcription factors. (biologists.org)
  • Binding of GC to the GC receptor (GR) induces its dissociation from a cytoplasmic multimeric complex of chaperone proteins and its translocation to the nucleus, where it dimerizes and acts as a transcription factor, via binding to a GC response element within the 5′ promoter region of target genes ( 4 , 5 ). (jimmunol.org)
  • In the online version, these sections contain links to more information about proteins encoded by over 17,000 known or predicted human genes. (cshlpress.com)
  • These scientific approaches focus no longer on individual units, such as nerve cells or genes, but rather on the emerging dynamic patterns of interactions between them. (nhbs.com)
  • While the cytoplasmic domain also plays important roles in endocytic trafficking, cross-presentation of extracellularly derived antigens, and CTL priming, the molecular mediators of cytoplasmic signaling by MHCI remain largely unknown. (biomedcentral.com)
  • Despite these studies, much remain unknown in terms of the molecular interactions necessary for viral infection and propagation. (sciencemag.org)
  • In this work, we intended to describe molecular alterations at a transcriptomic and protein-protein interaction (PPI) level between obese and non-obese patients. (bioportfolio.com)
  • This remarkable success has often overlooked the importance of the molecular motions that are required for function, with structural biologists tending to focus their attention on highly stable, high affinity biomolecular interactions. (frontiersin.org)
  • In order to fully understand the molecular basis of interactions between physiological partners it is necessary to map the modulation of the free energy landscapes of the interacting molecules throughout the interaction trajectory. (frontiersin.org)
  • Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein) docking studies, and investigation of protein interaction networks. (hindawi.com)
  • The known molecular determinants of virulence in mammalian hosts also include the polybasic cleavage site in the HA ( 23 ) and several polymorphisms in the PB2 polymerase subunit and the proapoptotic PB1-F2 protein. (asm.org)
  • The intrinsic bimodal conformation of the prolyl peptide bond, characterized by the cis and trans isomers, can act as a two-state molecular switch to regulate protein function and folding. (cornell.edu)
  • Our findings suggest that LRRC42 overexpression as well as its interaction with LRRC42-GATAD2B might play essential roles in lung carcinogenesis, and be a promising molecular target for lung cancer therapy. (spandidos-publications.com)
  • Kinesins are a superfamily of molecular motor proteins that move along microtubules powered by ATP hydrolysis energy [ 1 ]. (plos.org)
  • The PDZ-binding motif mediates interaction with GOPC. (abcam.com)
  • The WW-binding motif mediates interaction with WWOX and, probably NEDD4. (abcam.com)
  • Major histocompatibility complex class I (MHCI) proteins present antigenic peptides for immune surveillance and play critical roles in nervous system development and plasticity. (biomedcentral.com)
  • Fig. 1a ) present diverse peptides, derived primarily from cytosolic proteins, for recognition by CD8+ cytotoxic T lymphocytes (CTLs). (biomedcentral.com)
  • not only confirmed that many of these predicted SLiMs interacted with target peptides in various components of the endocytosis and autophagy machinery, but also found that these interactions were regulated by the phosphorylation of SLiM-adjacent amino acids. (sciencemag.org)
  • 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)
  • 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)
  • Here, we describe the use of chemically synthesized and specifically modified domain-length peptides to study the behavior of phosphorylated EphA2 SAM domains. (sigmaaldrich.com)
  • Has no protein kinase activity in vitro (By similarity). (genecards.org)
  • 1995 ) The BTB domain of bric à brac mediates dimerization in vitro. (biologists.org)
  • This protein has in vitro CCAAT binding properties and has been called ICBP90. (aacrjournals.org)
  • Over the last four decades, X-ray crystallography, NMR and increasingly electron microscopy have provided unique insight into the nature of functionally-essential interactions between a vast array of biologically active molecules. (frontiersin.org)
  • Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. (hindawi.com)
  • 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)
  • The N, P, and L proteins of SeV and measles and mumps viruses are functionally equivalent. (asm.org)
  • Both pathways are initiated by Wnt-mediated activation of members of the Frizzled (Fz) receptor family, followed by the recruitment of the cytoplasmic effector protein Dishevelled (Dvl) to the plasma membrane (PM) ( 7 ⇓ - 9 ). (pnas.org)
  • Thus, the nature and abundance of these receptor-associated proteins may be a primary determinant of nuclear receptor pharmacology. (asm.org)
  • Binding and function of phosphotyrosines of the Ephrin A2 (EphA2) receptor using synthetic sterile α motif (SAM) domains. (sigmaaldrich.com)
  • The sterile α motif (SAM) domain of the ephrin receptor tyrosine kinase, EphA2, undergoes tyrosine phosphorylation, but the effect of phosphorylation on the structure and interactions of the receptor is unknown. (sigmaaldrich.com)
  • Receptor for Wnt proteins. (abcam.com)
  • Belongs to the G-protein coupled receptor Fz/Smo family. (abcam.com)
  • This domain recruits receptor-interacting protein (RIP1) and RIP3 through the RIP homotypic interaction motif. (wikipedia.org)
  • In addition, CD36 contributes to cerebrovascular oxidative stress and neurovascular dysfunction induced by amyloid-beta in Alzeheimer's dementia [ 12 , 13 ] and may serve a 'lipid-sensing' role in the body with a broad physiological role as a lipid-receptor protein which influences eating behavior and energy balance [ 14 ]. (mdpi.com)
  • We investigated the role of the human GC receptor (GR) as an RNA-binding protein and its effect on mRNA turnover in human airway epithelial cells. (jimmunol.org)
  • Microbial infection) Acts as a receptor for hepatitis C virus in hepatocytes, but not through a direct interaction with viral proteins. (genecards.org)
  • The IRAK1 undefined domain (UD) has multiple pS-P motifs that are autophosphorlyated in response to receptor stimulation. (cornell.edu)
  • In TNF-treated cells, TNFR1, TNFR-associated death domain protein (TRADD), Fas-associated death domain protein, and receptor-interacting protein kinase proteins form the signaling complex via modular interaction within their C-terminal death domains. (jimmunol.org)
  • Phospho-S215LKD and phospho-S296LAE motifs are also critical to TRADD for recruiting Fas-associated death domain protein and receptor-interacting protein kinase. (jimmunol.org)
  • TNF-bound TNFR1 recruits TNFR-associated death domain protein (TRADD), an adaptor protein that serves as the platform for additional recruitment of receptor-interacting protein kinase (RIP) and Fas-associated death domain protein (FADD), initiating both NF-κB activation and apoptosis induction ( 1 - 3 ). (jimmunol.org)
  • The proline-rich regions are predominantly localized in the solvent-exposed regions such as the loops, intrinsically disordered regions, or between domains that constitute the intermolecular interface. (hindawi.com)
  • Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. (frontiersin.org)
  • In contrast to folded proteins, the primary sequence of intrinsically disordered proteins (IDPs) does not code for a single, energetically stable fold, but occupies a flatter free-energy surface, spanning a continuum of different conformations. (frontiersin.org)
  • We have characterized SeV N TAIL , which belongs to the class of intrinsically disordered proteins, and precisely defined the binding regions within this latter domain and within PX. (asm.org)
  • Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. (hindawi.com)
  • The prediction of human protein-protein interactions was investigated by combining orthogonal protein features within a probabilistic framework. (biomedcentral.com)
  • Comparison of the prediction dataset to other available human interaction datasets estimates the false positive rate of the new method to be below 80% which is competitive with other methods. (biomedcentral.com)
  • Since the new method scores and ranks all human protein pairs, smaller subsets of higher quality can be generated thus leading to even lower false positive prediction rates. (biomedcentral.com)
  • Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources. (openhelix.com)
  • Prediction of scaffold proteins based on protein interaction and domain architectures. (openhelix.com)
  • Ultimately, the combination of these sources of information will allow the prediction of interactions among proteins where only domain composition is known. (springer.com)
  • F-box proteins are critical components of the SCF ubiquitin-protein ligase complex and are involved in substrate recognition and recruitment for ubiquitination and consequent degradation by the proteasome. (nih.gov)
  • E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. (rcsb.org)
  • this interaction activates the E3 ubiquitin-protein ligase (By similarity). (rcsb.org)
  • The first and second each contain 7 exons and encode the same full-length protein isoform a (786 amino acids, considered the major isoform), the third one contains 6 exons and encodes a shorter isoform b (732 amino acids) and the fourth one contains 5 exons and encodes the shortest isoform c (349 amino acids). (wikipedia.org)
  • 1991 ) The Drosophila Broad-Complex encodes a family of related proteins containing zinc fingers. (biologists.org)
  • Kay, B. K., Williamson, M. P., Sudol, M. The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains. (nih.gov)
  • Intermolecular interactions mediated by proline-rich motifs (PRMs) are observed in many facets of the immune response. (hindawi.com)
  • LIM ( Lin-1, Isl1, Mec3 ) domain proteins all contain least one double zinc finger motif (Fig. 1). (sigmaaldrich.com)
  • Topology of zinc-finger motifs. (sigmaaldrich.com)
  • Using unbiased affinity purification and mass spectrometry, we identified the uncharacterized C2H2-like zinc finger protein ZNF644 as a G9a/GLP-interacting protein and co-regulator of histone methylation. (nih.gov)
  • The BTB domain (Broad-Complex, Tramtrack and Bric a brac) is also known as the POZ domain (POxvirus and Zinc finger). (ebi.ac.uk)
  • It is a homodimerization domain occurring at the N terminus of proteins containing multiple copies of either zinc fingers of the C2H2 type or Kelch repeats [ PMID: 7938017 , PMID: 7958847 ]. (ebi.ac.uk)
  • The structure of the BTB domain of the promyelocytic leukemia zinc finger (PLZF) protein has been determined by X-ray crystallography and reveals a tightly intertwined dimer with an extensive hydrophobic interface [ PMID: 9770450 ]. (ebi.ac.uk)
  • The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. (wikipedia.org)
  • many also contain amino-terminal Zinc/RING finger motifs. (biolegend.com)
  • The N-terminal regulatory domain of DNMT1 is essential for discrimination between hemimethylated and unmethylated DNA strands and contains a proliferating cell nuclear antigen-binding domain (PBD), a nuclear localization signal (NLS), an cysteine-rich ATRX zinc finger DNA-binding motif and a polybromo homology domain (PHD) targeting DNMT1 to the replication foci. (atlasgeneticsoncology.org)
  • Expression of the TPR domain had no effect on the abundance of endogenous SPY mRNA. (plantphysiol.org)
  • 1993 ) Interaction of translation factor SELB with the formate dehydrogenase H selenopolypeptide mRNA. (biologists.org)
  • Fz carries an extracellular N-terminal cysteine-rich domain, which mediates Wnt binding, followed by a seven-span transmembrane signaling moiety ( Fig. 1 A ). The cytoplasmic C-terminal tail of Fz contains a conserved motif (KTxxxW) that is essential for signaling and for membrane relocalization of Dvl ( 9 , 14 , 15 ). (pnas.org)
  • This results in the truncation of all extracellular CD19 domains and facilitates escape from CD19-directed CAR-T cell therapy. (rupress.org)
  • Surprisingly also, a conserved N -linked glycosylation site of the extracellular envelope protein (SU) inhibits cell-to-cell transmission suggesting that infectious potential has been limited during evolution. (mdpi.com)
  • p>When browsing through different UniProt proteins, you can use the 'basket' to save them, so that you can back to find or analyse them later. (uniprot.org)
  • Uniprot (ExPASy) was used to access specific information regarding each LIM protein. (sigmaaldrich.com)
  • Establishing the detailed structure-function relationships is needed to fully understand cMyBP-C's ability to impact on myofilament contraction as mutations in different domains are causative for familial hypertrophic cardiomyopathy. (biomedsearch.com)
  • Dominant mutations in two of the homologous protein phosphatase 2Cs, ABA-insensitive (ABI) 1 and ABI2, render Arabidopsis plants insensitive to the stress hormone ABA ( 8 , 14 - 18 ). (pnas.org)
  • The abi1-1 and abi2-1 mutations have been proposed to have dominant negative effects, and the WT ABI1 and ABI2 proteins are thought to be negative regulators of ABA signaling ( 19 - 21 ). (pnas.org)
  • The mutations also make the protein more hydrophobic, coaxing it to aggregate. (alzforum.org)
  • He speculated that the increased rigidity of the protein caused by the mutations may limit its efficient labeling and disposal. (alzforum.org)
  • Mutations of two protein trafficking motifs within the 38-amino acid region in CFTR each disrupted the interaction. (jci.org)
  • DNMT1 mutations found in HSANIE patients affect interaction with UHRF1 and neuronal differentiation. (nextbio.com)
  • Experimental approaches for the detection of host-virus interactome have many inherent limitations, and studies on protein-protein interactions between GCRV and its host remain rare. (biomedcentral.com)
  • In this study, based on known motif-domain interaction information, we systematically predicted the GCRV virus-host protein interactome by using motif-domain interaction pair searching strategy. (biomedcentral.com)
  • Furthermore, we name the complexity of LIM domain protein interactions as a ' LIM interactome . (sigmaaldrich.com)
  • The resulting focus on interactions that are strong enough to allow structure determination in terms of a single set of three-dimensional coordinates thus provides a distorted perspective on the interactome. (frontiersin.org)
  • The ever accumulating wealth of knowledge about protein interactions and the domain architecture of involved proteins in different organisms offers ways to understand the intricate interplay between interactome and proteome. (springer.com)
  • Chloride intracellular channels (CLICs) are a family of unique proteins, that were suggested to adopt both soluble and membrane-associated forms. (nature.com)
  • These data suggest that the cation channel-PKC association may require SH3 domain-mediated interactions to bring about modulation, promote membrane depolarization, and initiate prolonged changes in bag cell neuron excitability. (jneurosci.org)
  • Low density lipoprotein (LDL) is normally bound at the cell membrane and taken into the cell ending up in lysosomes where the protein is degraded and the cholesterol is made available for repression of microsomal enzyme 3-hydro. (genecards.org)
  • Low density lipoprotein (LDL) is normally bound at the cell membrane and taken into the cell ending up in lysosomes where the protein is degraded and the cholesterol is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis. (genecards.org)
  • BIM-Mediated Membrane Insertion of the BAK Pore Domain Is an Essential Requirement for Apoptosis. (le.ac.uk)
  • domain is approximately 150 amino acids in length and is found in a number of cytoskeletal-associated proteins that are localized to the plasma membrane and cytoskeleton interface. (cellsignal.com)
  • Ezrin/Radixin/Moesin) proteins to the membrane, which associates the cytoskeleton with the membrane by linking actin filaments to adhesion proteins. (cellsignal.com)
  • We validated that a class I PDZ-binding motif mediated binding of ACE2 to the scaffolding proteins SNX27, NHERF3, and SHANK, and that a binding site for the clathrin adaptor AP2 μ2 in ACE2 overlaps with a phospho-dependent binding site for the SH2 domains of Src family tyrosine kinases. (sciencemag.org)
  • LIM family proteins contain between one and five LIM domains plus other that have specific functions such as actin-binding, kinases, and nuclear translocation motifs. (sigmaaldrich.com)
  • The PPI motif is conserved in protein kinases of the SOS2 family (i.e., protein kinase S, PKS) and in the DNA damage repair and replication block checkpoint kinase, Chk1, from various organisms including humans. (pnas.org)
  • In Arabidopsis , SOS2 is a member of a family of 25 protein kinases that are known as protein kinase S (PKS) ( 3 ). (pnas.org)
  • The phosphorylation status of a protein is determined by the balance between the activities of protein kinases and protein phosphatases. (pnas.org)
  • In general, protein-protein interactions between ion channels and protein kinases may be a prominent mechanism underlying neuromodulation. (jneurosci.org)
  • A fundamental mechanism underlying neuromodulation is the phosphorylation of ion channels by protein kinases ( Levitan and Kaczmarek, 1997 ). (jneurosci.org)
  • The colocalization and targeting of kinases to ion channels requires a means of orchestrating protein-protein interactions. (jneurosci.org)
  • This brings the number of different protein partners fused to tyrosine kinases to 26, with the following distribution: 15 for PDGFRB, seven for FGFR1, four for PDGFRA, three for JAK2, two for ABL1 and one for FLT3 ( Figure 1 ). (haematologica.org)
  • Tyrosine kinases are represented by red squares, and protein partners by ovals. (haematologica.org)
  • The crescent shape adopted by a series of leucine-rich repeats creates a solvent-exposed, elongated, concave surface of parallel β-strands that act as a scaffold for protein-protein interactions. (cellsignal.com)
  • The NS1 proteins of most avian influenza viruses bear the C-terminal ligand sequence Glu-Ser-Glu-Val (ESEV) for PDZ domains present in multiple host proteins, whereas no such motif is found in the NS1 homologues of seasonal human virus strains. (asm.org)
  • A full catalog of the motifs in coiled-coil proteins and their relative conservation grade is a pre-requisite to target the protein-protein interaction that bacterial surface protein makes to host proteins. (peerj.com)
  • Consequently, several large-scale mass spectrometry efforts have been focused on uncovering intracellular interaction partners of viral proteins ( 3 - 5 ) and on understanding how signaling pathways are affected by viral infection ( 6 ). (sciencemag.org)
  • Interactions between proteins are also often required to be weak, for example in signaling pathways where efficiency and reversibility of information transfer are of key importance. (frontiersin.org)
  • Both pathways seem to involve interactions with G-proteins. (abcam.com)
  • The domain organisation of LRRK2 strongly implicates this protein in the command and control of signal transduction within the cell-borne out by experimental investigations into LRRK2 function, with LRRK2 linked to the regulation of a range of pathways and signal transduction cascades. (springer.com)
  • Our work reveals how parallel cell-cycle pathways can be temporally coordinated despite variability in protein concentrations. (stanford.edu)
  • SOS2 is normally inactive, presumably because of an intramolecular interaction between the catalytic domain and the autoinhibitory regulatory domain ( 3 ). (pnas.org)
  • Both SPY and animal OGT have two distinct domains, the tetratricopeptide repeat (TPR) domain and the OGT catalytic domain. (plantphysiol.org)
  • The carboxy-terminal catalytic domain of DNMTs transfers methyl groups from S-adenosyl-L-methionine (AdoMet) to cytosines. (atlasgeneticsoncology.org)
  • The positions of the SHIP2 catalytic domain and the protein interaction motifs are shown. (atlasgeneticsoncology.org)
  • SH2 (src homology-2 domain), IPPc (inositol polyphosphate phosphatase catalytic domain), Pro-rich (proline rich region), SAM (sterile alpha-motif). (atlasgeneticsoncology.org)
  • This RAD51AP1 motif is reminiscent of the FVPP motif in the tumor suppressor protein BRCA2 that mediates DMC1 interaction. (pubmedcentralcanada.ca)
  • In certain embodiments, the invention relates to inhibitors of at least one of β-TrCP1/2 or RSK1/2 proteins that sensitize tumor cells to chemotherapy-induced death or apoptosis. (google.es)
  • In certain embodiments, the invention relates to inhibitors of β-TrCP1, β-TrCP2 (F-box protein members) RSK1, or RSK2 (p90 rsk /MAPKAP kinase-1 or 2) that sensitize tumor cells to chemotherapy-induced cell death or apoptosis. (google.es)
  • Of the many specific possible PDZ ligand motifs, a handful are strikingly and selectively overrepresented in MHCI's cytoplasmic domain, but not elsewhere in the same proteins. (biomedcentral.com)
  • Putative PDZ ligand motifs are in red. (biomedcentral.com)
  • see text) are embedded in PDZ ligand motifs in several MHCI proteins. (biomedcentral.com)
  • Protein interaction domains can be classified based on sequence homology, ligand-binding properties, or structural similarity [ 11 ]. (hindawi.com)
  • Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample. (bioportfolio.com)
  • To examine the role of the PDZ domain ligand motif in avian influenza virus virulence, we generated three recombinants, derived from the prototypic H5N1 influenza A/Vietnam/1203/04 virus, expressing NS1 proteins that either have the C-terminal ESEV motif or the human influenza virus RSKV consensus or bear a natural truncation of this motif, respectively. (asm.org)
  • These findings demonstrate that a PDZ domain ligand sequence in NS1 contributes little to the virulence of H5N1 viruses in these hosts, and they indicate that this motif modulates viral replication in a strain- and host-dependent manner. (asm.org)
  • Osteopontin protein has also been reported to be a ligand for CD44. (clontech.com)
  • We present a comprehensive structural analysis of available KLC1/2-TPR domain structures that highlights that ligand binding into the groove can be specific of one or the other N-terminal capping helix orientations. (plos.org)
  • Living cells are made up of individual parts, i.e. the genome, the proteins, the RNA and lipid molecules as well as the metabolites and ions. (bioportfolio.com)
  • Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens. (bioportfolio.com)
  • In the cytoplasm of an infected cell, the viral RNA polymerase uses the nucleocapsid as a template for both the replication and encapsidation of the viral genome, as well as the transcription to messenger RNAs encoding the viral proteins. (asm.org)
  • The BTB/POZ domain: a new protein-protein interaction motif common to DNA- and actin-binding proteins -- Albagli et al. (aacrjournals.org)
  • Despite early demonstrations of myosin binding protein C's (MyBP-C) interaction with actin, different investigators have reached different conclusions regarding the relevant and necessary domains mediating this binding. (biomedsearch.com)
  • Expression of an actin binding-deficient cMyBP-C resulted in abnormal cytosolic distribution of the protein, indicating that interaction with actin is essential for the formation and/or maintenance of normal cMyBP-C sarcomeric distribution. (biomedsearch.com)
  • ZASP belongs to the Enigma subfamily of proteins and stabilizes the sarcomere (the basic units of muscles) during contraction, through interactions with actin in cardiac and skeletal muscles. (wikipedia.org)
  • Recent work indicates that they do so by influencing the RhoA-ROCK pathway that controls contractile actin filament assembly, the STAT family of transcription factors needed for transformation, and the Cbl ubiquitin ligase that controls Src protein levels. (biologists.org)
  • These all target, with characteristic binding specificity, an ancient protein interaction surface on evolutionarily related but physiologically clearly distinct three MAPKs (JNK, ERK, and p38). (embopress.org)
  • We also identified a protein kinase interaction domain in ABI2 and examined the interaction specificity between PKS and the ABI phosphatases. (pnas.org)
  • Utilizing interactions and domain architectures of domains as training sets, this algorithm employs a set cover approach to partition domain pairs, which allows the explanation of the underlying protein interaction to the largest degree of specificity. (springer.com)
  • This approach allows us to predict the previously unknown protein-protein interactions in S. cerevisiae and D. melanogaster , with a degree of sensitivity and specificity that clearly outscores other approaches. (springer.com)
  • We show that cooperative use of two conserved motifs in the third intracellular loop and the classic C-terminal motif of Fz is required for DEP-C binding and Wnt-induced β-catenin activation in cultured cells and Xenopus embryos. (pnas.org)
  • The Chloride Intracellular Channel (CLIC) family forms a class of unusual and enigmatic intracellular proteins 1 . (nature.com)
  • In this review, we discuss our work on single domains as intracellular antibodies and where this work might in the future. (mdpi.com)
  • OGTs are cytosolic and nuclear enzymes that modify proteins by adding a single GlcNAc in an O- linkage to Ser and/or Thr. (plantphysiol.org)
  • To better understand this mechanism within the paramyxovirus family, we have studied the complex formed by the SeV C-terminal domains of P (PX) and N (N TAIL ) proteins by solution nuclear magnetic resonance spectroscopy. (asm.org)
  • Although the predicted PPIs may contain some false positives due to limited data resource and poor research background in non-model species, the computational method still provide reasonable amount of interactions, which can be further validated by high throughput experiments. (biomedcentral.com)
  • The low coverage and variable quality of the experimental interaction datasets have prompted many groups to investigate computational methods to predict interactions or to determine the most likely interactions seen in the high-throughput datasets. (biomedcentral.com)
  • Screening for transmembrane association in divisome proteins using TOXGREEN, a high-throughput variant of the TOXCAT assay. (semanticscholar.org)
  • Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. (plos.org)
  • Non-server application of this program is considered for high-throughput data with more than 200 nodes or user's own interaction datasets. (plos.org)
  • however, the interaction with JNK occurs through a mitogen-activated protein KIM (kinase interaction motif) in a region distinct from the Bruton's tyrosine kinase-binding domain. (biochemsoctrans.org)
  • Pubmed ID: 12234689 The promoter regions of several neuron-specific structural proteins (e.g. neurofilaments, peripherin, Talpha1-tubulin) have revealed potential regulatory elements that could contribute to the choice of a neuronal phenotype during development. (jove.com)
  • Also, SHIP2 contains a NPXY motif (aa 983-986) and a SAM (sterile alpha-motif) domain (aa 1201-1258). (atlasgeneticsoncology.org)
  • Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface. (harvard.edu)
  • While the evolutionarily conserved domain-domain interfaces are large and relatively stable, the evolutionarily plastic domain peptide interfaces are smaller and transient [ 8 - 10 ]. (hindawi.com)
  • [7] in 2008 following in silico screening of databases describing expressed sequence tags from an evolutionarily diverse group of organisms, using the CAS-related proteins ( p130Cas , NEDD9/HEF1 and EFS ) mRNAs as templates. (wikipedia.org)
  • The N-terminal 15 amino acids are also sufficient to localize heterologous proteins in cilia. (biologists.org)
  • Overall, we found 6315 significant binding site pairs involving 2371 domains and 637 motifs. (rsc.org)
  • The LIM domains, represented by white ovals, are predominately localized at the amino terminus (left), however, some can be found at the carboxyl terminus (right). (sigmaaldrich.com)
  • This motif is found in biotinyl/lipoyl-carrier proteins and domains, where the biotin and lipoic acid moieties act as covalently attached coenzyme cofactors in enzymes that catalyse metabolic reactions. (ebi.ac.uk)
  • The majority of these motif classes, however, were also found to be significantly enriched in one or more randomised datasets. (rsc.org)
  • We found that COOH-terminal truncated PC2 (PC2-L703X), lacking the PC1 interaction region, still traffics to cilia. (biologists.org)
  • In addition, the interaction surfaces of the MV proteins are hydrophobic and a stronger binding constant was found. (asm.org)
  • ORF1 and full-length kelch proteins co-sediment with ring canals suggesting that both proteins are found in the ring canals. (biologists.org)
  • CfPhiA shows homology to proteins found on fungal sporogenous cells called phialides. (wiley.com)
  • A 25-amino-acid motif containing a TRP box (EWKFAR) just C-terminal to S6 is found in TRPC, TRPV and TRPM subgroups. (bioportfolio.com)
  • This modification requires the redundant mitogen-activated protein (MAP) kinase kinase Mkk1/2 but not their normal MAP kinase target Slt2p. (asm.org)
  • For example, activation of the mitogen-activated protein (MAP) kinase Hog1p allows the cell to adjust to a hyperosmotic environment ( 44 ). (asm.org)
  • Protein Interaction Domains and Motifs" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (harvard.edu)
  • Indeed, the immune response is mediated by well-orchestrated low-affinity short-duration intermolecular interactions. (hindawi.com)
  • Based on duration and affinity, PPIs can be classified as strong interactions that exhibit K D values with μ M concentrations and weak or transient interactions with values in the mM or higher concentrations. (hindawi.com)
  • A Cypher/ZASP mutation associated with dilated cardiomyopathy alters the binding affinity to protein kinase C". The Journal of Biological Chemistry. (wikipedia.org)
  • Interaction partners were identified by tandem-affinity purification. (springer.com)
  • HTRA2 antibody was purified from mouse ascitic fluids by protein-A affinity chromatography. (prospecbio.com)
  • Previous analysis showed that a C-terminal ESEV motif increases viral virulence when introduced into the NS1 protein of mouse-adapted H1N1 influenza virus. (asm.org)
  • Interaction of viral envelope proteins with host cell membranes has been extensively investigated in a number of systems. (mdpi.com)
  • In this review, we summarize the knowledge pertaining to the BLV envelope protein in the context of viral infection, replication and pathogenesis. (mdpi.com)
  • [6] It has a proline rich C terminus and contains putative SH3 and WW domains. (wikipedia.org)
  • The SPY protein has 10 copies of the tetratricopeptide repeat (TPR) at the N terminus. (plantphysiol.org)
  • At the N-terminus, protein interaction domains are present including Armadillo, Ankyrin, and leucine-rich repeat domains, whereas the C-terminus includes a WD40 domain. (springer.com)
  • The C-terminus 74 codons (including the SAM-domain) are common for both the transcripts. (atlasgeneticsoncology.org)