Protein interaction domains and motifs. Medical search

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)

There are many different types of diseases, ranging from acute and short-term conditions such as the common cold or flu, to chronic and long-term conditions such as diabetes, heart disease, or cancer. Some diseases are infectious, meaning they can be transmitted from one person to another through contact with a contaminated surface or exchange of bodily fluids. Other diseases are non-infectious, meaning they are not transmitted from person to person and are typically caused by genetic mutations or environmental factors.

The diagnosis and treatment of disease is the focus of the medical field, and doctors and other healthcare professionals use a variety of tools and techniques to identify and manage diseases. These may include physical exams, laboratory tests, imaging studies, and medications. In some cases, surgery or other procedures may be necessary to treat a disease.

Some common examples of diseases include:

1. Heart disease: A condition that affects the heart and blood vessels, often caused by high blood pressure, high cholesterol, or smoking.
2. Diabetes: A condition in which the body is unable to properly regulate blood sugar levels, often caused by genetics or obesity.
3. Cancer: A condition in which abnormal cells grow and multiply, often causing damage to surrounding tissues.
4. Inflammatory diseases: Conditions such as arthritis, where the body's immune system causes inflammation and pain in the joints.
5. Neurological diseases: Conditions that affect the brain and nervous system, such as Alzheimer's disease, Parkinson's disease, or multiple sclerosis.
6. Infectious diseases: Conditions caused by the presence of pathogens such as bacteria, viruses, or fungi, including the common cold, flu, and tuberculosis.
7. Genetic diseases: Conditions that are caused by changes in DNA, such as sickle cell anemia or cystic fibrosis.
8. Autoimmune diseases: Conditions where the body's immune system attacks healthy cells and tissues, such as rheumatoid arthritis or lupus.
9. Pulmonary diseases: Conditions that affect the lungs, such as asthma, chronic obstructive pulmonary disease (COPD), or lung cancer.
10. Gastrointestinal diseases: Conditions that affect the digestive system, such as inflammatory bowel disease (IBD) or irritable bowel syndrome (IBS).

These are just a few examples of the many different types of diseases that exist. Diseases can be caused by a wide range of factors, including genetics, lifestyle choices, and environmental factors. Understanding the causes and symptoms of different diseases is important for developing effective treatments and improving patient outcomes.

The signs and symptoms of Liddle syndrome usually become apparent during infancy or early childhood and may include:

* Seizures: Seizures are the most common symptom of Liddle syndrome and can range from mild to severe. They can occur at any time, but are often triggered by fever, stress, or other infections.
* Poor muscle tone: Children with Liddle syndrome may have low muscle tone, which can make it difficult for them to sit up, walk, or perform other physical activities.
* Learning difficulties: Children with Liddle syndrome may experience learning difficulties, such as difficulty with speech, language, and cognitive skills.
* Developmental delays: Children with Liddle syndrome may experience developmental delays, such as delayed sitting, standing, or walking.
* Vision problems: Some children with Liddle syndrome may experience vision problems, such as blurred vision or difficulty seeing objects in the distance.

Liddle syndrome is usually diagnosed through a combination of clinical evaluation and genetic testing. Genetic testing can help identify mutations in the SCN1A gene that are associated with the condition. Imaging studies, such as electroencephalograms (EEGs) or magnetic resonance imaging (MRI), may also be used to rule out other conditions and confirm the diagnosis.

There is no cure for Liddle syndrome, but various treatments can help manage the symptoms. Anticonvulsant medications, such as sodium channel blockers, can help reduce the frequency and severity of seizures. Physical therapy and occupational therapy can help improve muscle tone and motor skills. Speech and language therapy may be helpful for children with learning difficulties or speech problems. In some cases, surgery may be necessary to treat related conditions, such as scoliosis or other spinal deformities.

The prognosis for children with Liddle syndrome varies depending on the severity of the condition and the presence of other health issues. With proper management, many children with Liddle syndrome can lead active, productive lives. However, some individuals may experience ongoing seizures or other health problems that can impact their quality of life. Regular follow-up appointments with a healthcare provider are important to monitor the condition and adjust treatment as needed.

In conclusion, Liddle syndrome is a rare genetic disorder that affects the nervous system and can cause a range of symptoms, including seizures, developmental delays, and vision problems. While there is no cure for the condition, various treatments can help manage the symptoms and improve the prognosis. Early diagnosis and ongoing medical care are essential to ensure the best possible outcome for individuals with Liddle syndrome.

Rubulavirus infections are a type of viral infection caused by the rubulavirus, which is a member of the Paramyxoviridae family. The virus primarily affects the respiratory and gastrointestinal tracts and can cause a range of symptoms, including fever, cough, sore throat, runny nose, and diarrhea.

Rubulavirus infections are most commonly seen in young children and can be severe in some cases, particularly in those with underlying medical conditions such as asthma or heart disease. In rare cases, the virus can also cause more serious complications such as pneumonia or encephalitis.

There is no specific treatment for rubulavirus infections, and treatment is primarily focused on managing symptoms and supporting the body's immune system. Over-the-counter medications such as acetaminophen or ibuprofen may be used to help manage fever and pain, while antiviral medications may be prescribed in severe cases.

Prevention is key to managing rubulavirus infections, and this includes practicing good hygiene, avoiding close contact with people who are sick, and getting vaccinated against the virus. Vaccination is particularly important for children and individuals who work with young children, as they are at higher risk of contracting the virus.

In conclusion, rubulavirus infections can cause a range of symptoms and can be severe in some cases, particularly in young children and those with underlying medical conditions. Prevention and good hygiene practices are key to managing these infections, and treatment is focused on supporting the body's immune system and managing symptoms.

Neoplasm refers to an abnormal growth of cells that can be benign (non-cancerous) or malignant (cancerous). Neoplasms can occur in any part of the body and can affect various organs and tissues. The term "neoplasm" is often used interchangeably with "tumor," but while all tumors are neoplasms, not all neoplasms are tumors.

Types of Neoplasms

There are many different types of neoplasms, including:

1. Carcinomas: These are malignant tumors that arise in the epithelial cells lining organs and glands. Examples include breast cancer, lung cancer, and colon cancer.
2. Sarcomas: These are malignant tumors that arise in connective tissue, such as bone, cartilage, and fat. Examples include osteosarcoma (bone cancer) and soft tissue sarcoma.
3. Lymphomas: These are cancers of the immune system, specifically affecting the lymph nodes and other lymphoid tissues. Examples include Hodgkin lymphoma and non-Hodgkin lymphoma.
4. Leukemias: These are cancers of the blood and bone marrow that affect the white blood cells. Examples include acute myeloid leukemia (AML) and chronic lymphocytic leukemia (CLL).
5. Melanomas: These are malignant tumors that arise in the pigment-producing cells called melanocytes. Examples include skin melanoma and eye melanoma.

Causes and Risk Factors of Neoplasms

The exact causes of neoplasms are not fully understood, but there are several known risk factors that can increase the likelihood of developing a neoplasm. These include:

1. Genetic predisposition: Some people may be born with genetic mutations that increase their risk of developing certain types of neoplasms.
2. Environmental factors: Exposure to certain environmental toxins, such as radiation and certain chemicals, can increase the risk of developing a neoplasm.
3. Infection: Some neoplasms are caused by viruses or bacteria. For example, human papillomavirus (HPV) is a common cause of cervical cancer.
4. Lifestyle factors: Factors such as smoking, excessive alcohol consumption, and a poor diet can increase the risk of developing certain types of neoplasms.
5. Family history: A person's risk of developing a neoplasm may be higher if they have a family history of the condition.

Signs and Symptoms of Neoplasms

The signs and symptoms of neoplasms can vary depending on the type of cancer and where it is located in the body. Some common signs and symptoms include:

1. Unusual lumps or swelling
2. Pain
3. Fatigue
4. Weight loss
5. Change in bowel or bladder habits
6. Unexplained bleeding
7. Coughing up blood
8. Hoarseness or a persistent cough
9. Changes in appetite or digestion
10. Skin changes, such as a new mole or a change in the size or color of an existing mole.

Diagnosis and Treatment of Neoplasms

The diagnosis of a neoplasm usually involves a combination of physical examination, imaging tests (such as X-rays, CT scans, or MRI scans), and biopsy. A biopsy involves removing a small sample of tissue from the suspected tumor and examining it under a microscope for cancer cells.

The treatment of neoplasms depends on the type, size, location, and stage of the cancer, as well as the patient's overall health. Some common treatments include:

1. Surgery: Removing the tumor and surrounding tissue can be an effective way to treat many types of cancer.
2. Chemotherapy: Using drugs to kill cancer cells can be effective for some types of cancer, especially if the cancer has spread to other parts of the body.
3. Radiation therapy: Using high-energy radiation to kill cancer cells can be effective for some types of cancer, especially if the cancer is located in a specific area of the body.
4. Immunotherapy: Boosting the body's immune system to fight cancer can be an effective treatment for some types of cancer.
5. Targeted therapy: Using drugs or other substances to target specific molecules on cancer cells can be an effective treatment for some types of cancer.

Prevention of Neoplasms

While it is not always possible to prevent neoplasms, there are several steps that can reduce the risk of developing cancer. These include:

1. Avoiding exposure to known carcinogens (such as tobacco smoke and radiation)
2. Maintaining a healthy diet and lifestyle
3. Getting regular exercise
4. Not smoking or using tobacco products
5. Limiting alcohol consumption
6. Getting vaccinated against certain viruses that are associated with cancer (such as human papillomavirus, or HPV)
7. Participating in screening programs for early detection of cancer (such as mammograms for breast cancer and colonoscopies for colon cancer)
8. Avoiding excessive exposure to sunlight and using protective measures such as sunscreen and hats to prevent skin cancer.

It's important to note that not all cancers can be prevented, and some may be caused by factors that are not yet understood or cannot be controlled. However, by taking these steps, individuals can reduce their risk of developing cancer and improve their overall health and well-being.

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 ...

https://en.wikipedia.org/wiki/LDB3

THOC 3 and 6 both contains WD40 repeat motifs that allow interaction with other THO proteins. THOC5 and THOC7 binds tightly and ... is a multi-domain protein composed of one conserved N-terminal RNA recognition and four leucine-rich repeat motifs, a central ... and a C-terminal ubiquitin associated domain that mediates interactions with nucleoporins. The NTF2-like domain is able to form ... The N and C-termini of ALYREF both contain UAP56-bonding motifs (UBMs), which are necessary for its interaction with UAP56. ...

https://en.wikipedia.org/wiki/TREX_Complex

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. ...

https://en.wikipedia.org/wiki/TRIF

"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. Bibcode: ...

https://en.wikipedia.org/wiki/EIF2C2

"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: ...

https://en.wikipedia.org/wiki/TNRC6B

... 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 ...

https://en.wikipedia.org/wiki/PRP36

... 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 ...

https://en.wikipedia.org/wiki/NOBOX

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. ...

https://en.wikipedia.org/wiki/Myogenic_regulatory_factors

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 ( ...

https://en.wikipedia.org/wiki/PDLIM3

... 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 ...

https://en.wikipedia.org/wiki/TEC_(gene)

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 ...

https://en.wikipedia.org/wiki/Cingulin

A conserved protein motif, termed the Kruppel-associated box (KRAB) domain, mediates protein-protein interactions (Eichler et ... Zinc finger protein 208 is a protein that in humans is encoded by the ZNF208 gene. Zinc finger proteins (ZNFs), such as ZNF208 ... This article incorporates text from the United States National Library of Medicine, which is in the public domain. v t e ( ... Most ZNFs contain conserved C2H2 motifs and are classified as Kruppel-type zinc fingers. ...

https://en.wikipedia.org/wiki/Zinc_finger_protein_208

January 2008). "PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains". ... linear motifs or minimotifs are short stretches of protein sequence that mediate protein-protein interaction. The first ... Protein structural motifs, Protein domains, Short linear motifs). ... Linear motif mediated protein-protein interactions have shown promise in recent years as novel drug targets. Success stories ...

https://en.wikipedia.org/wiki/Short_linear_motif

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 ...

https://en.wikipedia.org/wiki/NEDD4

CAS proteins have an amino terminal SH3 domain enabling interaction with poly-proline motif-containing proteins such as FAK. ... which when tyrosine-phosphorylated allow interaction with SH2 domain containing proteins. Further to the carboxy-terminus, they ... this motif is conserved among the other three CAS family proteins and is an important binding site for the Src SH2 domain. ... Using a yeast two-hybrid approach, the CASS4 protein SH3 domain was shown to interact with the FAK C-terminus, despite the ...

https://en.wikipedia.org/wiki/CASS4

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 ...

https://en.wikipedia.org/wiki/LRRIQ3

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 ...

https://en.wikipedia.org/wiki/Lim_kinase

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 ...

https://en.wikipedia.org/wiki/LIMK1

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 ...

https://en.wikipedia.org/wiki/LIMK2

... 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 ...

https://en.wikipedia.org/wiki/Beta_hairpin

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 ...

https://en.wikipedia.org/wiki/WBP2

"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 ...

https://en.wikipedia.org/wiki/IWS1

The 119 amino-terminal cytoplasmic domain of LMP2A has several motifs that mediate interactions between proteins, including ... "The Epstein-Barr virus latent membrane protein 2A PY motif recruits WW domain-containing ubiquitin-protein ligases". Virology. ... Epstein-Barr virus (EBV) latent membrane protein 2 (LMP2) are two viral proteins of the Epstein-Barr virus. LMP2A/LMP2B are ... The N-terminus domain of LMP2A is tyrosine phosphorylated and associates with Src family protein tyrosine kinases (PTKs) as ...

https://en.wikipedia.org/wiki/Epstein–Barr_virus_latent_membrane_protein_2

"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 ...

https://en.wikipedia.org/wiki/MED26

... 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 ...

https://en.wikipedia.org/wiki/NDH-2

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 ...

https://en.wikipedia.org/wiki/Ankyrin_repeat

... residues of the core motif and additional arginine and lysine residues of the WRKY domain are responsible for interaction with ... The WRKY protein domain is 60 to 70 amino acids long type of DNA binding domain. The domain is characterized by a highly ... The WRKY protein domain is a globular shape composed of five anti-parallel β-strands. The core WRKYGQK motif is found on the ... Eighteen amino acids are highly conserved in the WRKY protein domain, including the core motif, zinc-finger binding cysteines ...

https://en.wikipedia.org/wiki/WRKY_protein_domain

... which can mediate interactions with other proteins. P1 motif is the most important among them, because it is crucial for ... CSK binds two prolin-rich motifs (P1 and P2) in the structure of PTPN22 through its SH3 domain and the P1 motif is more ... is a cytoplasmatic protein encoded by gene PTPN22 and a member of PEST family of protein tyrosine phosphatases. This protein is ... Another interaction partner of the PTPN22 is TRAF3. This protein bind the PTPN22 and regulate its translocalization to a plasma ...

https://en.wikipedia.org/wiki/PTPN22

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 ...

https://en.wikipedia.org/wiki/Death_fold

Both motif types rely upon interactions with SH2 domain-containing proteins to transduce signals upon binding to an IgG immune ... CD32 receptors bind to the lower hinge region of IgG via an extracellular domain. Additionally, all CD32 subtypes readily bind ... CD32 is a type I transmembrane protein with a helical transmembrane region. Whereas the extracellular region consists of three ... When an ITIM is phosphorylated, it activates effector proteins that dephosphorylate the downstream targets of the ITAM signal ...

https://en.wikipedia.org/wiki/CD32

... is a laboratory technique for the study of protein-protein, protein-peptide, and protein-DNA interactions that ... The N2 domain binds to the F pilus during virion infection freeing the N1 domain which then interacts with a TolA protein on ... "Comparison of bacterial and phage display peptide libraries in search of target-binding motif". Appl. Biochem. Biotechnol. 127 ... characterize small molecules-protein interactions and map protein-protein interactions. Users can use three dimensional ...

https://en.wikipedia.org/wiki/Phage_display

In addition to its interactions with RNA, N forms protein-protein interactions with the coronavirus membrane protein (M) during ... The N-terminal domain - sometimes known as the RNA-binding domain, though other parts of the protein also interact with RNA - ... Parts of the IDR, particularly a conserved sequence motif rich in serine and arginine residues (the SR-rich region), may also ... Like the other structural proteins, the gene encoding the N protein is located toward the 3' end of the genome. N protein is ...

https://en.wikipedia.org/wiki/Coronavirus_nucleocapsid_protein

2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. Bibcode: ... The CLINT1 protein binds to the terminal domain of the clathrin heavy chain and stimulates clathrin cage vesicle assembly. ... 2004). "Characterization of a gamma-adaptin ear-binding motif in enthoprotin". FEBS Lett. 555 (3): 437-42. doi:10.1016/S0014- ... Kalthoff C, Groos S, Kohl R, Mahrhold S, Ungewickell EJ (November 2002). "Clint: a novel clathrin-binding ENTH-domain protein ...

https://en.wikipedia.org/wiki/CLINT1

... is a neuronal protein with a novel type of heparin-binding domain". Journal of Cell Science. 112 (Pt 12): 2019-32. doi:10.1242/ ... consists of two proline-rich regions in the half closest to the transmembrane domain, two EF-hand-like motifs near the centre, ... This interaction facilitates neurite outgrowth and the adhesion strength needed to stop outgrowth. The dimerisation of the ... The NHL domain on the extracellular domain of teneurins acts as a homophilic recognition site to mediate this specific binding ...

https://en.wikipedia.org/wiki/TENM3

Protein Science. 13 (10): 2819-24. doi:10.1110/ps.04682504. PMC 2286551. PMID 15340161. LILRA3+protein,+human at the US ... This article incorporates text from the United States National Library of Medicine, which is in the public domain. v t e v t e ... the LILRA3 might impair interactions of membrane-bound LILRs (such as LILRB1, an inhibitory receptor expressed on effector and ... identification of a novel family of human Ig superfamily members that possess immunoreceptor tyrosine-based inhibition motifs ...

https://en.wikipedia.org/wiki/LILRA3

WD repeat domain phosphoinositide-interacting protein 2 is a protein that in humans is encoded by the WIPI2 gene. WD40 repeat ... have a 7-bladed propeller structure and contain a conserved motif for interaction with phospholipids. WIPI2 is the mammalian ... 2001). "Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs ... of multiprotein complexes by presenting a beta-propeller platform for simultaneous and reversible protein-protein interactions ...

https://en.wikipedia.org/wiki/WIPI2

The structure of Φ29 is composed of seven main proteins: the terminal protein (p3), the head or capsid protein (p8), the head ... Specifically, the functional domains of pRNA bind to the gp16 packaging enzyme and the structural connector molecule to aid in ... Guo, Peixuan; Zhang, Chunlin; Chen, Chaoping; Garver, Kyle; Trottier, Mark (1998-07-01). "Inter-RNA Interaction of Phage φ29 ... end of the genome that uses a repeating TTT motif to move the replication complex backward without altering the template ...

https://en.wikipedia.org/wiki/Bacillus_virus_phi29

2007). "The conserved CPH domains of Cul7 and PARC are protein-protein interaction modules that bind the tetramerization domain ... "The ubiquitin-conjugating enzymes UbcH7 and UbcH8 interact with RING finger/IBR motif-containing domains of HHARI and H7-AP1". ... Nakayama M, Kikuno R, Ohara O (2003). "Protein-Protein Interactions Between Large Proteins: Two-Hybrid Screening Using a ... Cullin-9 is a protein that in humans is encoded by the CUL9 gene. PARC (gene) has been shown to interact with P53. GRCh38: ...

https://en.wikipedia.org/wiki/PARC_(gene)

... inferring associations between ontology terms and protein domains or combinations of domains from the existing gene/protein- ... ORFs and their localization gene structure coding regions location of regulatory motifs Functional annotation consists of ... biochemical function biological function involved regulation and interactions expression These steps may involve both ... Genome annotation consists of three main steps:. identifying portions of the genome that do not code for proteins identifying ...

https://en.wikipedia.org/wiki/DNA_annotation

Activity of ABL1 protein is negatively regulated by its SH3 domain, and deletion of the SH3 domain turns ABL1 into an oncogene ... Cao C, Leng Y, Li C, Kufe D (April 2003). "Functional interaction between the c-Abl and Arg protein-tyrosine kinases in the ... and gamma subunit immunoreceptor tyrosine-based activation motif in signaling of myeloid high affinity Fc receptor for IgG (Fc ... Welch PJ, Wang JY (November 1993). "A C-terminal protein-binding domain in the retinoblastoma protein regulates nuclear c-Abl ...

https://en.wikipedia.org/wiki/ABL_(gene)

The main functional part of the voltage-sensitive protein domain of these channels generally contains a region composed of S3b ... Alabi AA, Bahamonde MI, Jung HJ, Kim JI, Swartz KJ (November 2007). "Portability of paddle motif function and pharmacology in ... interactions between P-segment motions and inactivation". The Journal of Neuroscience. 19 (5): 1577-85. doi:10.1523/JNEUROSCI. ... Na+, K+, and Ca2+ channels are composed of four transmembrane domains arranged around a central pore; these four domains are ...

https://en.wikipedia.org/wiki/Voltage-gated_ion_channel

The protein encoded by this gene has four repeats of quasi-RNA recognition motif (RRM) domains that bind RNAs. This protein ... Kim JH, Hahm B, Kim YK, Choi M, Jang SK (May 2000). "Protein-protein interaction among hnRNPs shuttling between nucleus and ... Kim JH, Hahm B, Kim YK, Choi M, Jang SK (May 2000). "Protein-protein interaction among hnRNPs shuttling between nucleus and ... Polypyrimidine tract-binding protein 1 is a protein that in humans is encoded by the PTBP1 gene. This gene belongs to the ...

https://en.wikipedia.org/wiki/PTBP1

Many viroporins also have additional effects on cellular metabolism and homeostasis mediated by protein-protein interactions ... "Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers". Nature Structural & ... Class II viroporins possess a helix-turn-helix motif with both helices crossing the membrane; in class IIA both termini are ... Some viroporins have established functional effects exerted through protein-protein interactions. For example, the HIV-1 ...

https://en.wikipedia.org/wiki/Viroporin

... subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit". Genes ... with one member of the dimer anchored to its binding motif on the enhancer and the other member anchored to its binding motif ... A connector protein dimer (e.g. CTCF or YY1) stabilizes the loop by anchoring one member on the enhancer and the other on the ... Many other elements/motifs may be present. There is no such thing as a set of "universal elements" found in every core promoter ...

https://en.wikipedia.org/wiki/Promoter_(genetics)

Blatch GL, Lässle M (November 1999). "The tetratricopeptide repeat: a structural motif mediating protein-protein interactions ... The TPR domains are found in many proteins that facilitate specific interactions with a partner protein. Three-dimensional ... 2 domain at their C-terminus, which also has an unknown function. Another conserved domain in the TTC39B protein is the TPR_12 ... and protein transport complexes. Two more TPR domains are found in the TTC39B protein: TPR1 which spans from amino acids 393 to ...

https://en.wikipedia.org/wiki/Tetratricopeptide_repeat_protein_39B

Lin KT, Lu RM, Tarn WY (October 2004). "The WW domain-containing proteins interact with the early spliceosome and participate ... Banerjee H, Rahn A, Gawande B, Guth S, Valcarcel J, Singh R (February 2004). "The conserved RNA recognition motif 3 of U2 snRNA ... Gozani O, Potashkin J, Reed R (August 1998). "A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the ... "Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein". The ...

https://en.wikipedia.org/wiki/SF3B1

... into DNA and integrated into the genome based on the sequence-motifs recognized by the protein's endonuclease domain. LINE-1 ( ... on the chromosome through interaction facilitated by different proteins and elements. Non-coding RNAs such as short- ... Furthermore, SINEs frequently contain motifs for YY1 polycomb proteins. YY1 is a zinc-finger protein that acts as a ... Thereafter, one of the strands is incorporated into a multi-protein RNA-induced silencing complex (RISC). Among these proteins ...

https://en.wikipedia.org/wiki/Short_interspersed_nuclear_element

... and may be proteolytically processed to release the UBL domain or may function as protein-protein interaction domains. UBL ... UBLs that are capable of conjugation (sometimes known as Type I) have a characteristic sequence motif consisting of one to two ... UBLs that do not exhibit covalent conjugation (Type II) often occur as protein domains genetically fused to other domains in a ... Ubiquitin-like proteins (UBLs) are a family of small proteins involved in post-translational modification of other proteins in ...

https://en.wikipedia.org/wiki/Ubiquitin-like_protein

UniProt entry on Cholesterol-24 hydroxylase HMDB Database entry RCSB Protein Data Bank Entry Review on Cholesterol-24 ... a structural motif absent in all other related cytochrome p450 enzymes. While the exact function of these proline residues ... with the aliphatic tail of the cholesterol held in place by interactions with the following hydrophobic residues: Phe-121, Val- ... the conserved stretch of 23 hydrophobic residues in the N-terminus that make up a transmembrane-anchoring domain (residues 3-27 ...

https://en.wikipedia.org/wiki/Cholesterol_24-hydroxylase

MHC-β is a 223 kDa protein composed of 1935 amino acids. MHC-β is a hexameric, asymmetric motor forming the bulk of the thick ... McKillop DF, Geeves MA (August 1993). "Regulation of the interaction between actin and myosin subfragment 1: evidence for three ... about the converter domain and drives actin filaments towards the M-line. Several mutations in MYH7 have been associated with ... that dimerize and multimerize into a coiled-coil motif to form the light meromyosin (LMM), thick filament rod. The 9 nm alpha- ...

https://en.wikipedia.org/wiki/MYH7

These motifs contain conserved H-C links. Gli family zinc finger proteins are mediators of Sonic hedgehog (Shh) signaling and ... Gli2beta is an isoform spliced at the first splicing site which contains a repression domain and consists of an intact ... Litingtung Y, Chiang C (October 2000). "Specification of ventral neuron types is mediated by an antagonistic interaction ... Zinc finger protein GLI2 also known as GLI family zinc finger 2 is a protein that in humans is encoded by the GLI2 gene. The ...

https://en.wikipedia.org/wiki/GLI2

... binding is important for many protein-protein interactions and even for interactions between the domains of a single protein. ... Articles with short description, Short description matches Wikidata, Protein structural motifs, Helices). ... Some proteins, such as the antifreeze protein of Hypogastrura harveyi consist of bundles of glycine-rich polyglycine II helices ... A polyproline helix is a type of protein secondary structure which occurs in proteins comprising repeating proline residues. A ...

https://en.wikipedia.org/wiki/Polyproline_helix

... due to its characteristics this ncRNA resembles previous regulatory motifs called riboswitches, icd-II ncRNA motif has been ... It is a homodimer in which each subunit has a Rossmann fold, and a common top domain of interlocking β sheets. Mtb ICDH-1 is ... The metal-ion forms a little complex through ionic interactions with the oxygen atoms on the fourth and fifth carbons (also ... Portal: Biology (Articles with short description, Short description matches Wikidata, Genes on human chromosome 2, Protein ...

https://en.wikipedia.org/wiki/Isocitrate_dehydrogenase

Inhibitor of growth protein 5 (ING5), Thioredoxin domain-containing protein 9 (TXNDC9), and MORF4-family associated proteins ( ... There are no known transmembrane domains for C3orf62. C3orf62 has a KKXX-like motif in the C-terminus meaning C3orf62 may be ... "C3orf62". STRING Interaction Network. Retrieved 7 May 2017. "C3orf62". BioGRID. Retrieved 7 May 2017. "C3orf62". InAct. ... The unmodified C3orf62 protein is a "glycine depleted protein" relative to amounts of glycine in proteins in the rest of the ...

https://en.wikipedia.org/wiki/C3orf62

A and protein kinase C phosphorylation sites and modulates Ca2+-dependent cleavage of spectrin and protein-protein interaction ... Hirai H, Matsuda S (September 1999). "Interaction of the C-terminal domain of delta glutamate receptor with spectrin in the ... Fourthly, a six amino acid insert in the twenty-first spectrin motif with unknown function has been reported. Alpha II-spectrin ... Frappier T, Stetzkowski-Marden F, Pradel LA (1991). "Interaction domains of neurofilament light chain and brain spectrin". ...

https://en.wikipedia.org/wiki/SPTAN1

The protein contains basic helix-loop-helix (bHLH) structural motif. This gene is a proto-oncogene and encodes a nuclear ... Feng XH, Liang YY, Liang M, Zhai W, Lin X (January 2002). "Direct interaction of c-Myc with Smad2 and Smad3 to inhibit TGF-beta ... v t e This article incorporates text from the United States National Library of Medicine, which is in the public domain. ( ... The encoded protein forms a heterodimer with the related transcription factor MAX. This complex binds to the E box DNA ...

https://en.wikipedia.org/wiki/MYC

... like domain and the RNP consensus sub-motif RNP2. In vitro the BZIP-like domain mediates homodimerization and stable binding to ... "Specific interactions of the autoantigen L7 with multi-zinc finger protein ZNF7 and ribosomal protein S7". The Journal of ... "Specific interactions of the autoantigen L7 with multi-zinc finger protein ZNF7 and ribosomal protein S7". The Journal of ... 60S ribosomal protein L7 is a protein that in humans is encoded by the RPL7 gene. Ribosomes, the organelles that catalyze ...

https://en.wikipedia.org/wiki/60S_ribosomal_protein_L7

"Interaction between the amino-terminal SH3 domain of CRK and its natural target proteins". J. Biol. Chem. 271 (24): 14468-72. ... 1995). "The SH3 domain of Crk binds specifically to a conserved proline-rich motif in Eps15 and Eps15R". J. Biol. Chem. 270 (25 ... This protein has several SH2 and SH3 domains (src-homology domains) and is involved in several signaling pathways, recruiting ... The N-terminal SH2 domain of this protein functions as a positive regulator of transformation whereas the C-terminal SH3 domain ...

https://en.wikipedia.org/wiki/Adapter_molecule_crk

At the N-terminus of the protein, SH2 domain is formed. This domain is important for the interaction of SHIP1 with the ... but contains a proline-rich region that forms the motif for binding SH3 domain and also contains sequence containing tyrosine ... Highly conserved phosphatase domain is in central part of the protein. This catalytic domain is flanked on the N-terminal side ... independently on its catalytic activity by serving as a bridge for other proteins thereby regulate protein-protein interactions ...

https://en.wikipedia.org/wiki/INPP5D

2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3: 89. doi: ... Serrano M, Hannon GJ, Beach D (December 1993). "A new regulatory motif in cell-cycle control causing specific inhibition of ... Clark PA, Llanos S, Peters G (July 2002). "Multiple interacting domains contribute to p14ARF mediated inhibition of MDM2". ... PRC1 and PRC2 are two protein complexes that modify the expression of p16 through the interaction of various transcription ...

https://en.wikipedia.org/wiki/P16

title = "The POZ domain: A conserved protein-protein interaction motif",. abstract = "We describe a novel zinc finger protein, ... The POZ domain acts as a specific protein-protein interaction domain: The POZ domains of ZID and Ttk can interact with ... The POZ domain acts as a specific protein-protein interaction domain: The POZ domains of ZID and Ttk can interact with ... The POZ domain acts as a specific protein-protein interaction domain: The POZ domains of ZID and Ttk can interact with ...

https://experts.umn.edu/en/publications/the-poz-domain-a-conserved-protein-protein-interaction-motif

... protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used ... Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral ... Identification of motif-based interactions between SARS-CoV-2 protein domains and human pe ... Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 ...

https://pesquisa.bvsalud.org/portal/resource/pt/mdl-37704626

Protein interactions between a pathogen and its host are fundamental in the establishment of the pathogen and underline the ... Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions. Zhang A, He L, Wang Y. Zhang A ... on the identification of structural descriptors from motif-domain interactions of protein complexes deposited in the Protein ... Figure 1. Protocol for the prediction of the viral-human interactome based on structural motif-domain interactions. Figure 2. ...

https://www.ncbi.nlm.nih.gov/pubmed/23951184

Protein Interaction Domains and Motifs * Protein Transport * Reactive Oxygen Species / metabolism * Saccharomyces cerevisiae / ... Intramolecular interactions control Vms1 translocation to damaged mitochondria Mol Biol Cell. 2013 May;24(9):1263-73. doi: ... the mitochondrial targeting domain [MTD]). Of interest, MTD-mediated mitochondrial targeting of Vms1 is negatively regulated by ... is a component of a mitochondrial surveillance system that mediates the stress-responsive degradation of mitochondrial proteins ...

https://pubmed.ncbi.nlm.nih.gov/23468520/

G protein-coupled receptor hetero-oligomerization is a dynamic process, which depends on the relative … ... Protein Interaction Domains and Motifs Actions. * Search in PubMed * Search in MeSH ... Keywords: C‐X‐C motif chemokine ligand 11; C‐X‐C motif chemokine ligand 12; adrenergic receptor; alpha; blood pressure; ... C-X-C motif) Receptor 4 in Vascular Smooth Muscle Cells Lauren J Albee 1 , Jonathan M Eby 1 , Abhishek Tripathi 1 , Heather M ...

https://pubmed.ncbi.nlm.nih.gov/28862946/

Protein Interaction Domains and Motifs; Recombinant Proteins/biosynthesis; Recombinant Proteins/chemistry; Recombinant Proteins ... Abstract: Protein·protein interactions, which often involve interactions among an acyl carrier protein (ACP) and ACP partner ... Title: Probing the selectivity and protein·protein interactions of a nonreducing fungal polyketide synthase using mechanism- ... Here, we employ mechanism-based crosslinkers to successfully probe ACP and ketosynthase (KS) domain interactions in NR-PKSs. We ...

https://tools.niehs.nih.gov/portfolio/index.cfm?do=portfolio.publicationDetail&id=2041957

LIM domains: double zinc finger motifs involved in protein-protein interactions].. Mizuno K; Higuchi O. Tanpakushitsu Kakusan ... 3. Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins.. Agulnick AD; Taira M; Breen JJ; Tanaka T ... Drosophila genes that encode LIM-domain containing proteins: their organization, functions, and interactions].. Gubenko IS. ... 1. LIM domain proteins.. Dawid IB; Toyama R; Taira M. C R Acad Sci III; 1995 Mar; 318(3):295-306. PubMed ID: 7788499. [TBL] ...

https://pubmedhh.nlm.nih.gov/biomarkers/search.php?id=7788499&mod=related&page=1&outid=&proj=

LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have ... LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have ... mRNA and Protein(s) * NM_001289934.2 → NP_001276863.1 leucine-rich repeat and calponin homology domain-containing protein 4 ... mRNA and Protein(s) * XM_047420389.1 → XP_047276345.1 leucine-rich repeat and calponin homology domain-containing protein 4 ...

https://www.ncbi.nlm.nih.gov/gene/4034

Knockout Tested Rabbit recombinant monoclonal Amyloid Precursor Protein antibody [EPR5118-34]. Validated in WB, IHC, Flow Cyt ( ... The PID domain-containing proteins which bind APP require the YENPTY motif for full interaction. These interactions are ... The NPXY sequence motif found in many tyrosine-phosphorylated proteins is required for the specific binding of the PID domain. ... Involved in cell mobility and transcription regulation through protein-protein interactions. Can promote transcription ...

https://www.abcam.com/products/primary-antibodies/amyloid-precursor-protein-antibody-epr5118-34-ab126732.html

The chromatin remodelling protein CHR2 interacts with Serrate in Arabidopsis to regulate microRNA biogenesis. ... Direct interaction with SE is required for post-transcriptional inhibition of miRNA accumulation by CHR2 but not for its ... The red, blue and cyan arrows indicate the interaction domains of the indicated proteins. d, RT-PCR shows that all genes are ... dsRNA-binding domain 2 (RBD2) in HYL1 interacts with the N-terminal and mid domains (N+Mid) of the SE core19. The DESRM motif ...

https://www.nature.com/articles/s41586-018-0135-x?error=cookies_not_supported&code=92a2259d-9258-4bdb-89d4-bdf898485873

Protein Interaction Binding Motifs Protein Interaction Domains Protein Interaction Motifs Protein-Protein Interaction Domains ... Proline-Rich Protein Domains [G02.111.570.820.709.275.750.485] * Protein Interaction Domains and Motifs [G02.111.570.820. ... Protein Interaction Domains and Motifs Preferred Concept UI. M0509370. Scope Note. Protein modules with conserved ligand- ... Protein Interaction Domains and Motifs Preferred Term Term UI T696769. Date05/03/2007. LexicalTag NON. ThesaurusID NLM (2008). ...

https://meshb.nlm.nih.gov/record/ui?ui=D054730

Auxilin shares a number of protein-protein interaction motifs with other endocytic proteins, including AP180. We demonstrate ... Uncoating of clathrin-coated vesicles requires the J-domain protein auxilin for targeting hsc70 to the clathrin coats and for ... In contrast, the two DLL motifs within the clathrin-binding domain were exclusively involved in clathrin binding. Surprisingly ... they interacted not only with the N-terminal domain of the heavy chain, but also with the distal domain. Moreover, both DLL ...

https://www.wikigenes.org/e/ref/e/12732633.html

CD2BP2-GYF domain in complex with proline-rich CD2 tail segment peptide ... Intracellular protein interaction domains are essential for eukaryotic signaling. In T cells, the CD2BP2 adaptor binds two ... In T cells, the CD2BP2 adaptor binds two membrane-proximal proline-rich motifs in the CD2 cytoplasmic tail via its GYF domain, ... Intracellular protein interaction domains are essential for eukaryotic signaling. ...

https://www.rcsb.org/structure/1L2Z

The GW182 proteins have been shown to bind to Ago PIWI domain by multiple GW motifs which fit into two tryptophan-binding ... A sub-micromolar dissociation constant is on par with GW182 and Tudor domain-containing proteins interaction with human Ago and ... The fact that the PIWI domains in both Ago and PIWI proteins are used to engage with downstream processes suggests that protein ... Proteomic analysis of the PIWI protein PRG-1 revealed an interaction with the constitutive P granule protein DEPS-1. ...

https://www.biorxiv.org/content/10.1101/580043v1.full

The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains.. Kay ... Group I WW domains bind proteins containing the PPXY motif, while group II recognize the PPLP motif. Group III recognise PPR ... WW are small modular domains of 38-40 residues long that mediate protein-protein interaction through binding of short proline- ... It is a multidomain protein contains a WW domain and PPIase domain and both domains work together to target the p(S/T)P ...

http://elm.eu.org/elms/LIG_WW_1

... dystroglycans WW domain-binding motif PPPY appears to be the most crucial in disrupting the interaction. Therefore the j3- ... Various methods were used to investigate the protein:protein interactions of 0- dystroglycan. In a yeast two-hybrid assay f3- ... protein interactions within this complex. However, the proteins are ideally placed to transduce signals from the extracellular ... Dystrophin associates with a group of membrane-associated proteins called the dystrophin-associated protein complex (DAPC) via ...

https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.669280

We show that these DDIs occur frequently in protein complexes and that homotypic interactions (of a domain with itself) are ... to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs. Here we map ... suggesting that the functionality of many domain pairs in mediating protein interactions is maintained in evolution. ... of different organisms and demonstrate that there is a catalog of domain pairs that is used to mediate various interactions in ...

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-12-r125

... of the catalytic domain of human atypical protein kinase C-iota reveals interaction mode of phosphorylation site in turn motif ... Contribution of globular death domains and unstructured linkers to MyD88(.)IRAK-4 heterodimer formation: An explanation for the ...

https://www.biochem.mpg.de/publication-search/6335774?person=%2Fpersons%2Fresource%2Fpersons78826

... protein interactions, protein stability, and protein conformation. This process is regulated by palmitoyl acyltransferases that ... protein interactions, protein stability, and protein conformation. This process is regulated by palmitoyl acyltransferases that ... In this review, we will explore the recent findings on protein S-acylation, the enzymatic regulation of this process, and ... In this review, we will explore the recent findings on protein S-acylation, the enzymatic regulation of this process, and ...

https://www.frontiersin.org/articles/10.3389/fmolb.2021.656440/full

... and C-terminal domains of the molecule. The structure consists of four EF-hand motifs although only the first three EF hands ... Structure of the neuronal protein calexcitin suggests a mode of interaction in signalling pathways of learning and memory ... Structure of the neuronal protein calexcitin suggests a mode of interaction in signalling pathways of learning and memory ... Structure of the neuronal protein calexcitin suggests a mode of interaction in signalling pathways of learning and memory ...

https://eprints.soton.ac.uk/35533/

Many RGS proteins possess additional C- and N-terminal modular protein-binding domains and motifs. The presence of these ... that RGS proteins inhibit G protein-mediated signaling at the level of the receptor-G protein interaction or the G protein ... This domain is found in regulation of G-protein signalling (RGS) proteins, as well as other related proteins, including:. * ... GTPase-activating proteins for heterotrimeric G proteins: regulators of G protein signaling (RGS) and RGS-like proteins. ...

https://smart.embl.de/smart/do_annotation.pl?DOMAIN=RGS&START=845&END=973&E_VALUE=3.15e-2&TYPE=SMART&BLAST=TFTDLLNNKLEFEHFRQFLESHSSSLDLMCWIDIEQFRRIIFKDQKQREEKSIYIKNKYLNKKYFFGPRSPASLHQQNQIMLLSGGWGRILHEQLDASVLVEIQKHVLNRLENVWLPLFLSSEQFASRQ

Interaction networks (from direct experimentation, text-mining, co-expression, protein homology, gene neighborhood etc.) ... functional domains and motifs *copy number variation *gene-gene relationships *knock out and transgenic phenotypes ... For the human ABC proteins, 49 genes have been reported and organized into 7 sequence and domain homology subfamilies ii,iii. ... For the human ABC proteins, 49 genes have been reported and organized into 7 sequence and domain homology subfamilies [i],[ii ...

https://grants.nih.gov/grants/guide/notice-files/NOT-OD-21-148.html

We further constructed the mutant variants of ERp44 and found the interaction domain with ACLY. The promotion of ERp44 on cell ... The endoplasmic reticulum (ER) resident protein 44 is a UPR-induced ER protein of the protein disulphide isomerase (PDI) family ... Furthermore, we successfully constructed the mutant variants of ERp44 and found the interaction domain with ATP citrate lyase( ... More importantly, we also observed that the interaction of ERp44 with ACLY, especially the thioredoxin region in ERp44 play a ...

https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-020-02694-1

Evaluating caveolin interactions: do proteins interact with the caveolin scaffolding domain through a widespread aromatic ... residue-rich motif? PLoS One. 2012; 7:e44879.. 13. Patel HH, Murray F, Insel PA. Caveolae as organizers of pharmacologically ... inhibit the interaction of the proteins and Cav-1, and re-store the functions of Cav-1 binding proteins. Heme oxygenase-1 (HO-1 ... Regulation of cAMP-mediated signal transduction via interaction of caveolins with the catalytic subunit of protein kinase A. J ...

https://www.oncotarget.com/article/16676/text/

For adenoviruses that contain an integrin-binding RGD motif in the penton base proteins, an initial virus-cell interaction ... The E3 CR1 proteins possess a single putative transmembrane domain near their C-termini and are likely to have arisen by gene ... The fiber knob domain mediates the initial virus-cell interaction by binding to a cellular receptor. A phylogenetic tree ... However, all members of SAdV-A and SAdV-B contain the RGD motif in the penton base protein, which suggests that the short fiber ...

https://wwwnc.cdc.gov/eid/article/18/7/11-1665

This PTP contains a C-terminal PEST motif, which serves as a protein-protein interaction domain, and may be related to protein ... The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling ... The immunogen recognized by this antibody maps to a region between residue 760 and 780 of human protein tyrosine phosphatase, ...

https://www.novusbio.com/products/ptpn12-antibody_nb100-60666

https://meshb-prev.nlm.nih.gov/record/ui?ui=D054730

It is now widely accepted that lipid rafts actively participate in the processing of amyloid precursor protein to generate ... and to support additional protein-protein interactions [47]. In the case of flotillins, an evolutionarily conserved domain ... the presence of caveolin-binding motifs in many raft proteins allow them to bind to the scaffolding domain of caveolin, which ... Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions" [1]. ...

https://www.intechopen.com/chapters/74235

... formed through phase separation and that multivalent interactions in disordered proteins and through domain-motif interactions ... Our laboratory has shown that a low-complexity domain (LCD) within the RNA-binding protein hnRNPA1 undergoes reversible phase ... Speckle-type POZ protein localization in biomolecular condensates. The speckle-type POZ protein (SPOP) is a tumor suppressor ... Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation Martin EW et al. ...

https://www.stjude.org/research/labs/mittag-lab.html

... isolating neurotransmitter receptor-associated proteins, and (3) determining the role of protein-protein interactions in ... defining sorting motifs present in neurotransmitter receptor cytosolic domains, (2) isolating neurotransmitter receptor- ... associated proteins, and (3) determining the role of protein-protein interactions in trafficking and specific synapse ... defining sorting motifs present in neurotransmitter receptor cytosolic domains, (2) ...

https://videocast.nih.gov/watch=10753

38. Physiological levels of calcitonin regulate the mouse osteoclast calcitonin receptor by a protein kinase Alpha-mediated mechanism. (nih.gov)
39. Tight junction protein ZO-1 controls organic cation/carnitine transporter OCTN2 (SLC22A5) in a protein kinase C-dependent way. (nih.gov)
NMR analysis shows that the Fyn but not the Lck tyrosine kinase SH3 domain competes with CD2BP2 GYF-domain binding to the same CD2 proline-rich sequence in vitro. (rcsb.org)
However it is noted that the kinases inhibitors may not selectively differentiate kinases since a large number of protein kinase enzymes share a common cofactor and similar three-dimensional structure of the catalytic site. (iscb.org)
LIM kinase-1 and LIM kinase-2 belong to a small subfamily with a unique combination of 2 N-terminal LIM motifs and a C-terminal protein kinase domain. (nih.gov)
11/05/2007) TOTAL 2008 NEW DESCRIPTORS = 456 MH - A Kinase Anchor Proteins UI - D054758 MN - D12.644.360.24.65 MN - D12.776.157.57.01 MN - D12.776.476.24.69 MS - A structurally-diverse family of intracellular-signaling adaptor proteins that selectively tether specific protein kinase A subtypes to distinct subcellular sites. (nih.gov)
They play a role in focusing the PROTEIN KINASE A activity toward relevant substrates. (nih.gov)
Over fifty members of this family exist, most of which bind specifically to regulatory subunits of CYCLIC-AMP-DEPENDENT PROTEIN KINASE TYPE II such as CAMP PROTEIN KINASE RIIALPHA or CAMP PROTEIN KINASE RIIBETA. (nih.gov)
Ataxia telangiectasia mutant protein activates c-Abl tyrosine kinase in response to ionizing radiation. (nih.gov)
Inhibition of DNA binding by the phosphorylation of poly ADP-ribose polymerase protein catalysed by protein kinase C. Biochem Biophys Res Commun 187 , 730-736. (nih.gov)
Single-stranded-DNA binding alters human replication protein A structure and facilitates interaction with DNA-dependent protein kinase. (nih.gov)

The first intracellular domain modulates ligand binding and signal transduction. (nih.gov)
Intracellular protein interaction domains are essential for eukaryotic signaling. (rcsb.org)
This PTP contains a C-terminal PEST motif, which serves as a protein-protein interaction domain, and may be related to protein intracellular half-life. (novusbio.com)
SLC proteins transport the widest variety of molecules across the plasma membrane and intracellular membranes by facilitated diffusion (e.g. (nih.gov)
Nedd8, a ubiquitin-like protein that regulates RING-domain E3 ubiquitin ligases, promoted Î´ENaC ubiquitination, decreased both the intracellular and cell surface Î´ENaC populations, and decreased Î´ßÎ³ENaC amiloride-sensitive short circuit current (Isc -amiloride) in a mammalian epithelium. (bvsalud.org)
Protein palmitoylation is catalyzed by members of the DHHC family of eukaryotic integral membrane enzymes so called because of the catalytic Asp-His-His-Cys motif in a cysteine rich domain (CRD) that resides in an intracellular loop. (nih.gov)

We previously demonstrated that VCP/Cdc48-associated mitochondrial stress responsive 1 (Vms1) is a component of a mitochondrial surveillance system that mediates the stress-responsive degradation of mitochondrial proteins by the proteasome. (nih.gov)
We further identified positively charged surface residues by KS mutagenesis, which mediates key interactions with the negatively charged ACP surface. (nih.gov)
Although zinc fingers usually function by binding to DNA or RNA, the LIM motif probably mediates protein-protein interactions. (nih.gov)

36. Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins. (nih.gov)
In T cells, the CD2BP2 adaptor binds two membrane-proximal proline-rich motifs in the CD2 cytoplasmic tail via its GYF domain, thereby regulating interleukin-2 production. (rcsb.org)

RBBP6 interacts with multifunctional protein YB-1 through its RING finger domain, leading to ubiquitination and proteosomal degradation of YB-1. (nih.gov)
The CUE domain was first described as a region of homology between the yeast Cue1 (coupling of ubiquitin to ER degradation) and human Tollip proteins. (cellsignal.com)
The domain is approximately 40 amino acids in length and is found in proteins that have a variety of functions, including the degradation of misfolded proteins in the endoplasmic reticulum and protein sorting. (cellsignal.com)
Although physico-chemically it amounts to attachment of a mere "hydrophobic stick", protein lipidation can modulate protein function by altering structure, folding, interaction with other proteins, degradation and importantly, attachment to membranes. (nih.gov)

Protein lipidation is the co-translational or post-translational covalent addition of a variety of lipids to target proteins. (frontiersin.org)
Our current view of cell membranes is far from the historical view of a being floating mixture of lipids and proteins mixed uniformly in the form of bilayers. (intechopen.com)
Covalent attachment of lipids is one of the most prevalent forms of post translational protein modification. (nih.gov)

Rev has been reported to interact with many host proteins including importin-ß, histone chaperons (Nap1 and B23), and tubulin through its ARM domain. (nih.gov)
Displays serine/threonine-specific phosphorylation of myelin basic protein and histone (MBP) in vitro. (nih.gov)
Retinoblastoma protein recruits histone deacetylase to repress transcription. (nih.gov)

24. The LIM domain protein FHL1C interacts with tight junction protein ZO-1 contributing to the epithelial-mesenchymal transition (EMT) of a breast adenocarcinoma cell line. (nih.gov)
25. TAZ interacts with zonula occludens-1 and -2 proteins in a PDZ-1 dependent manner. (nih.gov)
26. SARS-CoV-2 Envelope (E) protein interacts with PDZ-domain-2 of host tight junction protein ZO1. (nih.gov)
Furthermore we identified a novel motif on DEPS-1, PBS, which interacts directly with the Piwi domain of PRG-1. (biorxiv.org)
This protein interacts strongly with caspase 2 and weakly with caspase 9. (nih.gov)
Rev interacts with Crm1 through a leucine-rich nuclear export signal located in its C-terminus, and with RRE through an Arginine rich motif (ARM) located in the N-terminal region. (nih.gov)

Impact of Escherichia coli K12 and O18:K1 on human platelets: Differential effects on platelet activation, RNAs and proteins. (nih.gov)
mRNAs are targeted for silencing by small RNAs based on Watson-Crick base-pair complementarity in complex with members of the Argnonaute (Ago) protein family ( Meister, 2013 ). (biorxiv.org)
Building upon this understanding, we are now exploring how the architecture of the RNA-binding domains - as well as the specific composition and sequence patterns of the LCD - may promote dynamic compartmentalization of hnRNPA1, other RNA-binding proteins, and RNAs into RNP granules. (stjude.org)
Bioinformation related to transporter genes, messenger RNAs and their protein products are annotations often found in gene/protein databases such as genecards.org and NCBI . (nih.gov)

The proteins of interest for this RFI are largely the product the products of two large gene families, the Solute Carrier (SLC) and ATP-Binding Cassette (ABC) family of genes. (nih.gov)
Most new protein-coding genes originate from old genes by duplication and domain shuffling. (iscb.org)
Yet de novo protein-coding genes - derived from intergenic DNA - were recently found in multiple species. (iscb.org)
These genes are of particular interest as they alone can invent novel protein structures. (iscb.org)
We asked how often de novo genes appear, how many exist in any genome and what proteins they make. (iscb.org)
The name MADS-box is derived from the four first letters of MCM1 from Saccharomyces cerevisiae , AGAMOUS from Arabidopsis , DEFICIENS from snapdragon and SRF4 from humans, and the proteins encoded by these genes contain a highly conserved region called the MADS-box that is approximately 60 amino acid residues in length ( Messenguy & Dubois, 2003 ). (peerj.com)
Structurally, almost all MADS-box genes contain a conserved MADS domain consisting of 60 amino acid residues at the N- terminus, and this domain is responsible for binding the CArG-box (CC(A/T) 6 GG) in the regulatory region of target genes ( Messenguy & Dubois, 2003 ). (peerj.com)
The main difference between plant type I and type II MADS-box genes is whether they contain a K domain. (peerj.com)
Type I MADS-box genes contain only one highly conserved MADS domain with no or few introns, and their abundance is lower at the transcriptional level. (peerj.com)
Type II MADS-box genes have a multi-intron structure with the exception of the highly conserved MADS domain. (peerj.com)
This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. (thebiogrid.org)
These novel composite genes were likely advantageous for their hosts, since they show significant residence times in haloarchaeal genomes-consistent with a long phylogenetic history involving vertical descent and lateral gene transfer-and encode proteins with optimized isoelectric points. (biomedcentral.com)
There are a range of different mechanisms that can produce novel genes, including de novo genes, synthesized either partly or completely from non-coding DNA [ 12 ], from the divergence of an existing protein-coding sequence beyond the point at which it is recognizable as a homologue (e.g. following gene duplication events), or by fusion or fission of existing protein-coding sequences [ 13 ]. (biomedcentral.com)

There are approximately 40 known eukaryotic LIM proteins, so named for the LIM domains they contain. (nih.gov)

The POZ domain acts as a specific protein-protein interaction domain: The POZ domains of ZID and Ttk can interact with themselves but not with each other, POZ domains from ZF5, or the viral protein SalF17R. (umn.edu)
In the present work, we developed a single predictive model for building a host-viral interactome based on the identification of structural descriptors from motif-domain interactions of protein complexes deposited in the Protein Data Bank (PDB). (nih.gov)
therefore, viral and human proteins sharing a descriptor were predicted as interacting proteins. (nih.gov)
The analysis of the host-viral interactome allowed to identify a set of new interactions that further explain molecular mechanism associated with viral infections and showed that it was able to capture human proteins already associated to viral infections (human infectome) and non-infectious diseases (human diseasome). (nih.gov)
The analysis of human proteins targeted by viral proteins in the context of a human interactome showed that their neighbors are enriched in proteins reported with differential expression under infection and disease conditions. (nih.gov)
She currently studies the underlying mechanisms of viral pathogenesis, viral protein-host protein interactions, and the potential use of humanized scFvs and nanobodies for treatment. (nih.gov)
The HIV-1 Rev protein is a key regulatory factor that is essential for both early and late phases of viral replication cycles, and therefore represents an important viral target for drug development. (nih.gov)

Skp1 connects cell cycle regulation to the ubiquitin proteolysis machinery through a novel motif, the F-box. (nih.gov)

However, the POZ domain of GAGA can interact efficiently with the POZ domain of Ttk. (umn.edu)
Those RGS proteins that contain GGL domains can interact with G protein beta subunits to form novel dimers that prevent G protein gamma subunit binding and G protein alpha subunit association, thereby preventing heterotrimer formation. (embl.de)
This, along with de novo proteins' propensity to interact, increases the chance that some will use their novel structures (and possibly novel functionalities) to integrate into existing genetic networks and survive for a long evolutionary time. (iscb.org)
A conserved MFP motif in α−helix1 and an LL motif in α−helix 3 interact with the conserved hydrophobic patch of ubiquitin. (cellsignal.com)

Unlike SH3 domains, which use two surface pockets to accommodate proline residues of ligands, the GYF domain employs phylogenetically conserved hydrophobic residues to create a single interaction surface. (rcsb.org)
Protein S-acylation is the reversible addition of fatty acids to the cysteine residues of target proteins. (frontiersin.org)
The removal of fatty acids from acylated cysteine residues is catalyzed by acyl protein thioesterases. (frontiersin.org)
For the rest of this review, we specifically discuss S-acylation, the covalent linkage of various fatty acids (14-20 carbons) via a thioester bond to the cysteine residues of substrate proteins. (frontiersin.org)

LIM domains are highly conserved cysteine-rich structures containing 2 zinc fingers. (nih.gov)

RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits. (embl.de)
RGS proteins markedly reduce the lifespan of GTP-bound alpha subunits by stabilising the G protein transition state. (embl.de)
This RGS domain is necessary for conferring upon RGS proteins the capacity to regulate negatively a variety of Galpha protein subunits. (embl.de)
Previous work found that ENaC gating is regulated by proteases through cleavage of the extracellular domains of the α and Î³ subunits. (bvsalud.org)

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 . (nih.gov)
Recognition modules in proteins that mediate interactions between specific proteins involved in SIGNAL TRANSDUCTION PATHWAYS . (nih.gov)
These sub-organelle ultrastructures depend on the Piwi-interacting motif of DEPS-1 and mediate piRNA function. (biorxiv.org)
We have made critical contributions to the conceptual understanding that biomolecular condensates are formed through phase separation and that multivalent interactions in disordered proteins and through domain-motif interactions mediate this process. (stjude.org)
While the LCD of hnRNPA1 is sufficient to mediate phase separation, its folded RNA-binding domains also contribute to phase separation in the presence of RNA, giving rise to several mechanisms of assembly. (stjude.org)

These studies define cellular and biochemical mechanisms by which Vms1 locali-zation to mitochondria is controlled to enable an efficient protein quality control system. (nih.gov)
The tendency and ability of proteins to change shape dictates how cellular components cluster and how sequence and conformation drive function. (stjude.org)
We have dissected the interaction between HIV-1 Gag and the host cellular ESCRT-associated protein, Alix. (nih.gov)
This occurred through a decrease in ENaC protein at the cell surface and in the total cellular pool, an effect that did not require the catalytic activity of PCSK9. (bvsalud.org)
A global genetic interaction network maps a wiring diagram of cellular function. (thebiogrid.org)
In the cellular milieu, thioesters can be cleaved by thioesterases and thus protein S-acylation is unique in being the only reversible form of protein lipidation. (nih.gov)
These components are then inserted into enzymes and other proteins for use in a wide range of crucial cellular activities like electron transport in respiratory chain complexes, regulatory sensing, photosynthesis, and DNA repair. (nih.gov)

27. Association of ARVCF with zonula occludens (ZO)-1 and ZO-2: binding to PDZ-domain proteins and cell-cell adhesion regulate plasma membrane and nuclear localization of ARVCF. (nih.gov)
Instead, evidence accumulated in the last three decades has revealed that membrane constituents can segregate to form discrete domains. (intechopen.com)
Our research focuses on understanding the molecular interactions underlying the formation of membrane-less organelles or so-called biomolecular condensates and how they give rise to function and disease. (stjude.org)
This study reports the demonstration that localization of Grk protein to the dorsal-anterior region of the oocyte depends on membrane trafficking, differing from the nonmembranous particle transport of its mRNA during this stage. (sdbonline.org)
During her postdoctoral studies at the University of Massachusetts Medical School (UMASS), she focused on the structure and function of outer membrane proteins, mainly Occ-family of porins from P. aeruginosa , and their role in bacterial pathogenesis and antibiotic resistance. (nih.gov)
Three members of the membrane bound O-acyltransferase (MBOAT) family, a distinct family of integral membrane enzymes, also catalyze protein lipidation. (nih.gov)

Short AMINO ACID SEQUENCES which are the BINDING SITES on the LIGANDS of protein interaction domains. (nih.gov)
Noncoding RNA sequences can regulate gene expression via interactions with epigenetic and other control mechanisms. (stanford.edu)
This suggests that new structural information will come from understanding the structures of sequences from combined domains. (nih.gov)

abstract = "We describe a novel zinc finger protein, ZID (zinc finger protein with interaction domain). (umn.edu)

Synthetic peptide within Human Amyloid Precursor Protein aa 50-150 (extracellular). (abcam.com)
It is now widely accepted that lipid rafts actively participate in the processing of amyloid precursor protein to generate amyloid beta peptides, a main component of amyloid plaques. (intechopen.com)

Our study reveals how specific protein-protein interactions drive the spatial organisation and function of small RNA pathways within membraneless organelles. (biorxiv.org)
RGS (Regulator of G Protein Signalling) proteins are multi-functional, GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways. (embl.de)
Such disorders as hay fever, periodontitis, atherosclerosis, rheumatoid arthritis, and even cancer showed the involvement of similar pathways with a range of protein targets engaged in chronic inflammation development. (lifechemicals.com)
This screening set was designed based on published data on protein interaction signaling pathways and the protein structural data availability (RCSB protein data bank) along with active protein inhibitors (ChEMBL DB). (lifechemicals.com)

From NCBI Gene: This gene encodes a member of the Ced-4 family of apoptosis proteins. (nih.gov)

My laboratory characterizes the molecular mechanisms underlying neurotransmitter receptor transport and localization at the synapse using several research strategies which include (1) defining sorting motifs present in neurotransmitter receptor cytosolic domains, (2) isolating neurotransmitter receptor-associated proteins, and (3) determining the role of protein-protein interactions in trafficking and specific synapse localization. (nih.gov)
The localization of grk mRNA and its protein product in the oocyte is crucial for the establishment of both the AP and dorsal-ventral axes. (sdbonline.org)
This finding is based on the study of a newly identified hypomorphic allele of Syx1A whose germ-line clones have defective dorsal follicle-cell specification and abnormal Grk protein localization after stage 7. (sdbonline.org)
Although no defect was detected in Syx1A clones in Grk posterior localization and signaling to activate EGFR in the posterior follicle cells, it cannot be ruled out that that Syx1A has no role in the posterior localization of Grk protein. (sdbonline.org)

Protein·protein interactions, which often involve interactions among an acyl carrier protein (ACP) and ACP partner enzymes, are important for coordinating polyketide biosynthesis. (nih.gov)
What sets these three apart is that each of these three enzymes, Goat, Hhat and Porcupine, has a unique substrate, all secreted signaling proteins and each uses a distinct fatty acyl substrate. (nih.gov)

They fold to form recognition pockets complementary to the short interaction sequence motifs on their LIGANDS . (nih.gov)

Of the different forms of protein lipidation, the most pervasive form is attachment of a fatty acid to internal cysteines through a thioester. (nih.gov)

HN - 2008 BX - Child Abuse, Adult Survivors MH - Agouti Signaling Protein UI - D054366 MN - D12.644.276.49 MN - D12.776.467.49 MN - D23.529.49 MS - A secreted protein of approximately 131 amino acids (depending on species) that regulates the synthesis of eumelanin (brown/black) pigments in MELANOCYTES. (nih.gov)
HN - 2008 (1993) MH - Agouti-Related Protein UI - D054369 MN - D12.644.276.74 MN - D12.776.467.74 MN - D23.529.74 MS - A secreted protein of approximately 131 amino acids that is related to AGOUTI SIGNALING PROTEIN and is also an antagonist of MELANOCORTIN RECEPTOR activity. (nih.gov)

Although they have conserved catalytic cores, DHHC enzymes vary in their protein substrate selection, lipid substrate preference, and regulatory mechanisms. (frontiersin.org)

Of interest, MTD-mediated mitochondrial targeting of Vms1 is negatively regulated by a direct interaction with the Vms1 N-terminus. (nih.gov)

We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. (thebiogrid.org)

Upon activation by GPCRs, heterotrimeric G proteins exchange GDP for GTP, are released from the receptor, and dissociate into free, active GTP-bound alpha subunit and beta-gamma dimer, both of which activate downstream effectors. (embl.de)

28. Domain-swapped dimerization of the second PDZ domain of ZO2 may provide a structural basis for the polymerization of claudins. (nih.gov)
34. Structural Basis of a Key Factor Regulating the Affinity between the Zonula Occludens First PDZ Domain and Claudins. (nih.gov)
Identified structural elements suggest that the encoded protein resembles a receptor. (nih.gov)
This entry represents a structural domain with a multi-helical fold consisting of a 4-helical bundle with a left-handed twist and an up-and-down topology. (embl.de)
In 2015, she joined the Laboratory of Structural Biology Research and the Protein Expression Laboratory at the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS). (nih.gov)
Dr. Eren's research focuses on understanding the structural and mechanistic aspects of Rev-host protein interactions and finding target regions to inhibit Rev activity using antibodies, synthetic peptides, and aptamers. (nih.gov)
Furthermore, Structural Genomics efforts have contributed 40% of known novel domains. (nih.gov)

In general, prenylation is an enzymatically mediated multi-step process that adds hydrophobic prenyl moieties to the C-terminal cysteines of substrate proteins. (frontiersin.org)

CUE domains have been shown to both bind mono and polyubiquitin and some CUE domain-containing proteins are themselves ubiquitinylated in a CUE domain-dependent manner. (cellsignal.com)
Modeling tools have been used to characterize domain families that bind PI. (nih.gov)
Proteins that bind PI typically have two motifs (or multiple motifs) which allow for temporal and spatial separation of binding events. (nih.gov)

The immunogen recognized by this antibody maps to a region between residue 760 and 780 of human protein tyrosine phosphatase, non-receptor type 12 using the numbering given in entry NP_002826.2 (GeneID 5782). (novusbio.com)
Our laboratory is studying these mechanisms, including SPOP's association with the death-domain-associated protein (DAXX) and the androgen receptor. (stjude.org)
Using these cell biological approaches, we hope to elucidate the mechanisms of neurotransmitter receptor trafficking in neurons and the role of accessory proteins at central synapses. (nih.gov)

To understand the complex role of auxilin in uncoating and clathrin assembly in more detail, we analyzed the molecular organization of its clathrin-binding domain (amino acids 547-813). (wikigenes.org)

Protein Engineering Group and Molecular Modeling Group, Forschungsinstitut für Molekulare Pharmakologie and Freie Universität Berlin, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany. (rcsb.org)
However, the molecular mechanisms of how RNA and proteins in these phase separated organelles assemble remain largely unexplored. (biorxiv.org)
Ozdemir ES, Jang H, Gursoy A, Keskin O, Li Z , Sacks DB, Nussinov R. Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2. (nih.gov)

Role of protein-protein interactions in the function of replication protein A (RPA): RPA modulates the activity of DNA polymerase alpha by multiple mechanisms. (nih.gov)
IQGAP1 binds to Yes-associated protein (YAP) and modulates its transcriptional activity. (nih.gov)

We discuss the implications of multimerization for the function of POZ domain proteins. (umn.edu)
RGS proteins can function as effector antagonists, and recent evidence suggests that RGS proteins can have positive effects on signaling as well. (embl.de)
Therefore Î´- and α - ßÎ³ENaC channel function may be influenced by RING-domain E3 ubiquitin ligases. (bvsalud.org)
These interactions were enhanced by Nedd4-2 and were dependent on the catalytic function of Nedd4-2 as well as its WW domains. (bvsalud.org)
Tyrosine phosphorylation of the scaffold protein IQGAP1 in the MET pathway alters function. (nih.gov)

No trend was observed between resistance and antibody interactions. (cdc.gov)

21. The PDZ motif peptide of ZO-1 attenuates Pseudomonas aeruginosa LPS-induced airway inflammation. (nih.gov)

This inhibitory effect is not dependent on interactions with other proteins and does not appear dependent on specific interactions between the POZ domain and the finger region. (umn.edu)
These studies reveal that the Syx1A dependent trafficking of Grk protein is required for efficient EGFR signaling during DV patterning (Tian, 2013). (sdbonline.org)
Interaction between replication protein A and p53 is disrupted after UV damage in a DNA repair-dependent manner. (nih.gov)
Zhang M, Li Z , Jang H, Hedman AC, Sacks DB, Nussinov R. Ca2+-dependent switch of calmodulin interaction mode with tandem IQ motifs in the scaffolding protein IQGAP1. (nih.gov)

Protein interactions between a pathogen and its host are fundamental in the establishment of the pathogen and underline the infection mechanism. (nih.gov)
Probing the selectivity and protein·protein interactions of a nonreducing fungal polyketide synthase using mechanism-based crosslinkers. (nih.gov)
Here, we employ mechanism-based crosslinkers to successfully probe ACP and ketosynthase (KS) domain interactions in NR-PKSs. (nih.gov)
We are further investigating the mechanism of the generation of insoluble protein deposits in persistent stress granules in neurodegenerative disease. (stjude.org)

It is a redundant collection of different structures obtained for the same protein. (iscb.org)

As in the past, topics of gene cloning, gene expression, protein purification and crystallization and rapid NMR structure determination were highlighted in the meeting program. (nih.gov)

Mutation of ENaC PY motifs, responsible for inherited hypertension (Liddle syndrome), decreased Hrs binding to ENaC. (bvsalud.org)

Proteomic analysis of the PIWI protein PRG-1 revealed an interaction with the constitutive P granule protein DEPS-1. (biorxiv.org)

On the other hand, the prolonged assembly of stress granules can result in their maturation and protein aggregation, giving rise to the hallmarks of neurodegenerative diseases such as ALS. (stjude.org)
We found that, compared to ancient proteins, de novo proteins are shorter, more disordered, promiscuous (interacting with more proteins and DNA), vulnerable to proteases, and less prone to aggregation. (iscb.org)

Nedd4-2 bound to Hrs and catalyzed Hrs ubiquitination but did not alter Hrs protein levels. (bvsalud.org)
Ubiquitination of the scaffold protein IQGAP1 diminishes its interaction with and activation of the Rho GTPase CDC42. (nih.gov)

Tyrosine phosphorylation of RNA polymerase II carboxyl-terminal domain by the Abl-related gene product. (nih.gov)
Tyrosine phosphorylation of mammalian RNA polymerase II carboxyterminal domain. (nih.gov)

While the majority of the lipid modifications to proteins are irreversible, S-acylation is reversible and can be highly dynamic. (frontiersin.org)
Our laboratory has shown that a low-complexity domain (LCD) within the RNA-binding protein hnRNPA1 undergoes reversible phase separation into protein-rich droplets. (stjude.org)

The presence of these additional modules within the RGS proteins provides for multiple novel regulatory interactions performed by these molecules. (embl.de)

The protein encoded by this gene is phosphorylated and activated by ROCK, a downstream effector of Rho, and the encoded protein, in turn, phosphorylates cofilin, inhibiting its actin-depolymerizing activity. (nih.gov)

At its amino terminus ZID contains a 120-amino-acid conserved motif present in a large family of proteins that includes both the otherwise unrelated zinc finger proteins, such as Ttk, GAGA, and ZF5, and a group of poxvirus proteins: We therefore refer to this domain as the POZ (poxvirus and zinc finger) domain. (umn.edu)
33. The carboxyl terminus of Neph family members binds to the PDZ domain protein zonula occludens-1. (nih.gov)
LRCH proteins: a novel family of cytoskeletal regulators. (nih.gov)
The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. (novusbio.com)
Ced-family members contain a caspase recruitment domain (CARD) and are known to be key mediators of programmed cell death. (nih.gov)
The HMG-1 box protein family. (nih.gov)

The encoded protein contains a distinct N-terminal pyrin-like motif, which is possibly involved in protein-protein interactions. (nih.gov)

Amino acid optimizations, which lowered the isoelectric point of haloarchaeal proteins, and abundant lateral gene transfers from bacteria have been invoked to explain this deep evolutionary transition. (biomedcentral.com)

It functions as a subunit of a ubiquitin ligase and is important for maintaining appropriate protein levels of many proto-oncogenes. (stjude.org)

Anatomy15

Organisms13

Chemicals and Drugs88

Analytical, Diagnostic and Therapeutic Techniques and Equipment42

Phenomena and Processes88

Disciplines and Occupations4

Information Science15

Health Care2

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

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

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

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

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

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

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

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

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Protein Interaction Domains and Motifs

Protein Interaction Mapping

Protein Binding

Protein Structure, Tertiary

Molecular Sequence Data

Amino Acid Sequence

Two-Hybrid System Techniques

Binding Sites

Amino Acid Motifs

src Homology Domains

Sequence Homology, Amino Acid

Protein Interaction Maps

Adaptor Proteins, Signal Transducing

Nuclear Proteins

DNA-Binding Proteins

Proteins

Models, Molecular

Transcription Factors

Carrier Proteins

Cell Line

Mutation

Signal Transduction

Recombinant Fusion Proteins

Sequence Alignment

Base Sequence

Conserved Sequence

Protein Conformation

PDZ Domains

Mutagenesis, Site-Directed

Saccharomyces cerevisiae

Databases, Protein

Dimerization

Recombinant Proteins

Protein Structure, Secondary

Membrane Proteins

Transfection

Structure-Activity Relationship

Computational Biology

Cloning, Molecular

Sequence Deletion

HeLa Cells

Transcription, Genetic

Repressor Proteins

Models, Biological

Crystallography, X-Ray

Saccharomyces cerevisiae Proteins

Multiprotein Complexes

DNA

Mutagenesis

Glutathione Transferase

Phosphorylation

DNA Primers

Evolution, Molecular

Precipitin Tests

Peptides

Fungal Proteins

Trans-Activators

Immunoprecipitation

Protein Transport

Transcriptional Activation

Escherichia coli

Algorithms

Cell Nucleus

Peptide Fragments

Amino Acid Substitution

Phosphoproteins

COS Cells

Nerve Tissue Proteins

Bacterial Proteins

RNA-Binding Proteins

Plasmids

Ligands

Promoter Regions, Genetic

Drosophila Proteins

Nucleotide Motifs

Cytoplasm

Kinetics

Sequence Analysis, Protein

Helix-Turn-Helix Motifs

Microscopy, Fluorescence