Ligands: A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Kinetics: The rate dynamics in chemical or physical systems.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Whales: Large marine mammals of the order CETACEA. In the past, they were commercially valued for whale oil, for their flesh as human food and in ANIMAL FEED and FERTILIZERS, and for baleen. Today, there is a moratorium on most commercial whaling, as all species are either listed as endangered or threatened.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Hydrogen Bonding: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.Atrial Function: The hemodynamic and electrophysiological action of the HEART ATRIA.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Myoglobin: A conjugated protein which is the oxygen-transporting pigment of muscle. It is made up of one globin polypeptide chain and one heme group.Cyclins: A large family of regulatory proteins that function as accessory subunits to a variety of CYCLIN-DEPENDENT KINASES. They generally function as ENZYME ACTIVATORS that drive the CELL CYCLE through transitions between phases. A subset of cyclins may also function as transcriptional regulators.CD40 Ligand: A membrane glycoprotein and differentiation antigen expressed on the surface of T-cells that binds to CD40 ANTIGENS on B-LYMPHOCYTES and induces their proliferation. Mutation of the gene for CD40 ligand is a cause of HYPER-IGM IMMUNODEFICIENCY SYNDROME, TYPE 1.Molecular Conformation: The characteristic three-dimensional shape of a molecule.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.Receptors, Cell Surface: Cell surface proteins that bind signalling molecules external to the cell with high affinity and convert this extracellular event into one or more intracellular signals that alter the behavior of the target cell (From Alberts, Molecular Biology of the Cell, 2nd ed, pp693-5). Cell surface receptors, unlike enzymes, do not chemically alter their ligands.Mathematics: The deductive study of shape, quantity, and dependence. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Fas Ligand Protein: A transmembrane protein belonging to the tumor necrosis factor superfamily that was originally discovered on cells of the lymphoid-myeloid lineage, including activated T-LYMPHOCYTES and NATURAL KILLER CELLS. It plays an important role in immune homeostasis and cell-mediated toxicity by binding to the FAS RECEPTOR and triggering APOPTOSIS.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Nuclear Magnetic Resonance, Biomolecular: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Heme: The color-furnishing portion of hemoglobin. It is found free in tissues and as the prosthetic group in many hemeproteins.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Endocytosis: Cellular uptake of extracellular materials within membrane-limited vacuoles or microvesicles. ENDOSOMES play a central role in endocytosis.Solubility: The ability of a substance to be dissolved, i.e. to form a solution with another substance. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.RANK Ligand: A transmembrane protein belonging to the tumor necrosis factor superfamily that specifically binds RECEPTOR ACTIVATOR OF NUCLEAR FACTOR-KAPPA B and OSTEOPROTEGERIN. It plays an important role in regulating OSTEOCLAST differentiation and activation.Membrane Glycoproteins: Glycoproteins found on the membrane or surface of cells.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.TNF-Related Apoptosis-Inducing Ligand: A transmembrane-protein belonging to the TNF family of intercellular signaling proteins. It is a widely expressed ligand that activates APOPTOSIS by binding to TNF-RELATED APOPTOSIS-INDUCING LIGAND RECEPTORS. The membrane-bound form of the protein can be cleaved by specific CYSTEINE ENDOPEPTIDASES to form a soluble ligand form.CD30 Ligand: A membrane-bound tumor necrosis family member found primarily on activated T-LYMPHOCYTES that binds specifically to CD30 ANTIGEN. It may play a role in INFLAMMATION and immune regulation.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.OX40 Ligand: A membrane-bound tumor necrosis family member that is expressed on activated antigen-presenting cells such as B-LYMPHOCYTES and MACROPHAGES. It signals T-LYMPHOCYTES by binding the OX40 RECEPTOR.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Antibodies, Monoclonal: Antibodies produced by a single clone of cells.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.CHO Cells: CELL LINE derived from the ovary of the Chinese hamster, Cricetulus griseus (CRICETULUS). The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems for the study of genetic alterations in cultured mammalian cells.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Mice, Inbred C57BLPeptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.4-1BB Ligand: A membrane bound member of the TNF superfamily that is expressed on activated B-LYMPHOCYTES; MACROPHAGES; and DENDRITIC CELLS. The ligand is specific for the 4-1BB RECEPTOR and may play a role in inducing the proliferation of activated peripheral blood T-LYMPHOCYTES.Receptors, Immunologic: Cell surface molecules on cells of the immune system that specifically bind surface molecules or messenger molecules and trigger changes in the behavior of cells. Although these receptors were first identified in the immune system, many have important functions elsewhere.Radioligand Assay: Quantitative determination of receptor (binding) proteins in body fluids or tissue using radioactively labeled binding reagents (e.g., antibodies, intracellular receptors, plasma binders).DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).AmputeesTranscription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Bacterial Proteins: Proteins found in any species of bacterium.Cell Adhesion: Adherence of cells to surfaces or to other cells.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Cell Line, Tumor: A cell line derived from cultured tumor cells.Antigens, CD95: A tumor necrosis factor receptor subtype found in a variety of tissues and on activated LYMPHOCYTES. It has specificity for FAS LIGAND and plays a role in regulation of peripheral immune responses and APOPTOSIS. Multiple isoforms of the protein exist due to multiple ALTERNATIVE SPLICING. The activated receptor signals via a conserved death domain that associates with specific TNF RECEPTOR-ASSOCIATED FACTORS in the CYTOPLASM.Chromatography, Affinity: A chromatographic technique that utilizes the ability of biological molecules to bind to certain ligands specifically and reversibly. It is used in protein biochemistry. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Oligopeptides: Peptides composed of between two and twelve amino acids.Receptors, Cytoplasmic and Nuclear: 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.Molecular Weight: The sum of the weight of all the atoms in a molecule.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Programmed Cell Death 1 Ligand 2 Protein: A costimulatory B7 antigen that has specificity for the T-CELL receptor PROGRAMMED CELL DEATH 1 RECEPTOR. It is closely-related to CD274 antigen; however, its expression is restricted to DENDRITIC CELLS and activated MACROPHAGES.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.Receptors, TNF-Related Apoptosis-Inducing Ligand: Tumor necrosis factor receptor family members that are widely expressed and play a role in regulation of peripheral immune responses and APOPTOSIS. The receptors are specific for TNF-RELATED APOPTOSIS-INDUCING LIGAND and signal via conserved death domains that associate with specific TNF RECEPTOR-ASSOCIATED FACTORS in the CYTOPLASM.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Flow Cytometry: Technique using an instrument system for making, processing, and displaying one or more measurements on individual cells obtained from a cell suspension. Cells are usually stained with one or more fluorescent dyes specific to cell components of interest, e.g., DNA, and fluorescence of each cell is measured as it rapidly transverses the excitation beam (laser or mercury arc lamp). Fluorescence provides a quantitative measure of various biochemical and biophysical properties of the cell, as well as a basis for cell sorting. Other measurable optical parameters include light absorption and light scattering, the latter being applicable to the measurement of cell size, shape, density, granularity, and stain uptake.Dose-Response Relationship, Drug: The relationship between the dose of an administered drug and the response of the organism to the drug.Receptors, G-Protein-Coupled: The largest family of cell surface receptors involved in SIGNAL TRANSDUCTION. They share a common structure and signal through HETEROTRIMERIC G-PROTEINS.Surface Plasmon Resonance: 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.COS Cells: CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)Antigens, CD: Differentiation antigens residing on mammalian leukocytes. CD stands for cluster of differentiation, which refers to groups of monoclonal antibodies that show similar reactivity with certain subpopulations of antigens of a particular lineage or differentiation stage. The subpopulations of antigens are also known by the same CD designation.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.T-Lymphocytes: Lymphocytes responsible for cell-mediated immunity. Two types have been identified - cytotoxic (T-LYMPHOCYTES, CYTOTOXIC) and helper T-lymphocytes (T-LYMPHOCYTES, HELPER-INDUCER). They are formed when lymphocytes circulate through the THYMUS GLAND and differentiate to thymocytes. When exposed to an antigen, they divide rapidly and produce large numbers of new T cells sensitized to that antigen.Glycoproteins: Conjugated protein-carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins.Rabbits: The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Drug Design: The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Lymphocyte Activation: Morphologic alteration of small B LYMPHOCYTES or T LYMPHOCYTES in culture into large blast-like cells able to synthesize DNA and RNA and to divide mitotically. It is induced by INTERLEUKINS; MITOGENS such as PHYTOHEMAGGLUTININS, and by specific ANTIGENS. It may also occur in vivo as in GRAFT REJECTION.Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).Amino Acid Substitution: The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.Intercellular Signaling Peptides and Proteins: Regulatory proteins and peptides that are signaling molecules involved in the process of PARACRINE COMMUNICATION. They are generally considered factors that are expressed by one cell and are responded to by receptors on another nearby cell. They are distinguished from HORMONES in that their actions are local rather than distal.Allosteric Regulation: The modification of the reactivity of ENZYMES by the binding of effectors to sites (ALLOSTERIC SITES) on the enzymes other than the substrate BINDING SITES.Mice, Inbred BALB CCalcium: A basic element found in nearly all organized tissues. It is a member of the alkaline earth family of metals with the atomic symbol Ca, atomic number 20, and atomic weight 40. Calcium is the most abundant mineral in the body and combines with phosphorus to form calcium phosphate in the bones and teeth. It is essential for the normal functioning of nerves and muscles and plays a role in blood coagulation (as factor IV) and in many enzymatic processes.Lectins: Proteins that share the common characteristic of binding to carbohydrates. Some ANTIBODIES and carbohydrate-metabolizing proteins (ENZYMES) also bind to carbohydrates, however they are not considered lectins. PLANT LECTINS are carbohydrate-binding proteins that have been primarily identified by their hemagglutinating activity (HEMAGGLUTININS). However, a variety of lectins occur in animal species where they serve diverse array of functions through specific carbohydrate recognition.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).Receptors, sigma: A class of cell surface receptors recognized by its pharmacological profile. Sigma receptors were originally considered to be opioid receptors because they bind certain synthetic opioids. However they also interact with a variety of other psychoactive drugs, and their endogenous ligand is not known (although they can react to certain endogenous steroids). Sigma receptors are found in the immune, endocrine, and nervous systems, and in some peripheral tissues.Spectrophotometry: The art or process of comparing photometrically the relative intensities of the light in different parts of the spectrum.Histidine: An essential amino acid that is required for the production of HISTAMINE.Epitopes: Sites on an antigen that interact with specific antibodies.Stereoisomerism: The phenomenon whereby compounds whose molecules have the same number and kind of atoms and the same atomic arrangement, but differ in their spatial relationships. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)Iodine Radioisotopes: Unstable isotopes of iodine that decay or disintegrate emitting radiation. I atoms with atomic weights 117-139, except I 127, are radioactive iodine isotopes.Cricetulus: A genus of the family Muridae consisting of eleven species. C. migratorius, the grey or Armenian hamster, and C. griseus, the Chinese hamster, are the two species used in biomedical research.Enzyme Activation: 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.Peptide Library: A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Cross-Linking Reagents: 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.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Adenosine Triphosphate: An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.Receptors, Notch: A family of conserved cell surface receptors that contain EPIDERMAL GROWTH FACTOR repeats in their extracellular domain and ANKYRIN repeats in their cytoplasmic domains. The cytoplasmic domain of notch receptors is released upon ligand binding and translocates to the CELL NUCLEUS where it acts as transcription factor.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Calorimetry: The measurement of the quantity of heat involved in various processes, such as chemical reactions, changes of state, and formations of solutions, or in the determination of the heat capacities of substances. The fundamental unit of measurement is the joule or the calorie (4.184 joules). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Zinc: A metallic element of atomic number 30 and atomic weight 65.38. It is a necessary trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Zinc deficiency is associated with ANEMIA, short stature, HYPOGONADISM, impaired WOUND HEALING, and geophagia. It is known by the symbol Zn.Receptors, Tumor Necrosis Factor: Cell surface receptors that bind TUMOR NECROSIS FACTORS and trigger changes which influence the behavior of cells.Bacterial Vaccines: Suspensions of attenuated or killed bacteria administered for the prevention or treatment of infectious bacterial disease.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Organometallic Compounds: A class of compounds of the type R-M, where a C atom is joined directly to any other element except H, C, N, O, F, Cl, Br, I, or At. (Grant & Hackh's Chemical Dictionary, 5th ed)HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Integrins: A family of transmembrane glycoproteins (MEMBRANE GLYCOPROTEINS) consisting of noncovalent heterodimers. They interact with a wide variety of ligands including EXTRACELLULAR MATRIX PROTEINS; COMPLEMENT, and other cells, while their intracellular domains interact with the CYTOSKELETON. The integrins consist of at least three identified families: the cytoadhesin receptors(RECEPTORS, CYTOADHESIN), the leukocyte adhesion receptors (RECEPTORS, LEUKOCYTE ADHESION), and the VERY LATE ANTIGEN RECEPTORS. Each family contains a common beta-subunit (INTEGRIN BETA CHAINS) combined with one or more distinct alpha-subunits (INTEGRIN ALPHA CHAINS). These receptors participate in cell-matrix and cell-cell adhesion in many physiologically important processes, including embryological development; HEMOSTASIS; THROMBOSIS; WOUND HEALING; immune and nonimmune defense mechanisms; and oncogenic transformation.Coordination Complexes: Neutral or negatively charged ligands bonded to metal cations or neutral atoms. The number of ligand atoms to which the metal center is directly bonded is the metal cation's coordination number, and this number is always greater than the regular valence or oxidation number of the metal. A coordination complex can be negative, neutral, or positively charged.Fluorescent Dyes: Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.Cell Movement: The movement of cells from one location to another. Distinguish from CYTOKINESIS which is the process of dividing the CYTOPLASM of a cell.HEK293 Cells: A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.Molecular Dynamics Simulation: A computer simulation developed to study the motion of molecules over a period of time.Apoptosis Regulatory Proteins: A large group of proteins that control APOPTOSIS. This family of proteins includes many ONCOGENE PROTEINS as well as a wide variety of classes of INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS such as CASPASES.Butyrylcholinesterase: An aspect of cholinesterase (EC 184.108.40.206).Tumor Necrosis Factor-alpha: Serum glycoprotein produced by activated MACROPHAGES and other mammalian MONONUCLEAR LEUKOCYTES. It has necrotizing activity against tumor cell lines and increases ability to reject tumor transplants. Also known as TNF-alpha, it is only 30% homologous to TNF-beta (LYMPHOTOXIN), but they share TNF RECEPTORS.Enzyme-Linked Immunosorbent Assay: An immunoassay utilizing an antibody labeled with an enzyme marker such as horseradish peroxidase. While either the enzyme or the antibody is bound to an immunosorbent substrate, they both retain their biologic activity; the change in enzyme activity as a result of the enzyme-antibody-antigen reaction is proportional to the concentration of the antigen and can be measured spectrophotometrically or with the naked eye. Many variations of the method have been developed.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Iron: A metallic element with atomic symbol Fe, atomic number 26, and atomic weight 55.85. It is an essential constituent of HEMOGLOBINS; CYTOCHROMES; and IRON-BINDING PROTEINS. It plays a role in cellular redox reactions and in the transport of OXYGEN.Chromatography, Gel: Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.Magnesium: A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.Spectrum Analysis: The measurement of the amplitude of the components of a complex waveform throughout the frequency range of the waveform. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Cell Adhesion Molecules: Surface ligands, usually glycoproteins, that mediate cell-to-cell adhesion. Their functions include the assembly and interconnection of various vertebrate systems, as well as maintenance of tissue integration, wound healing, morphogenic movements, cellular migrations, and metastasis.Binding Sites, Antibody: Local surface sites on antibodies which react with antigen determinant sites on antigens (EPITOPES.) They are formed from parts of the variable regions of FAB FRAGMENTS.Dendritic Cells: Specialized cells of the hematopoietic system that have branch-like extensions. They are found throughout the lymphatic system, and in non-lymphoid tissues such as SKIN and the epithelia of the intestinal, respiratory, and reproductive tracts. They trap and process ANTIGENS, and present them to T-CELLS, thereby stimulating CELL-MEDIATED IMMUNITY. They are different from the non-hematopoietic FOLLICULAR DENDRITIC CELLS, which have a similar morphology and immune system function, but with respect to humoral immunity (ANTIBODY PRODUCTION).Crystallization: The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Hemeproteins: Proteins that contain an iron-porphyrin, or heme, prosthetic group resembling that of hemoglobin. (From Lehninger, Principles of Biochemistry, 1982, p480)Enterococcus faecalis: A species of gram-positive, coccoid bacteria commonly isolated from clinical specimens and the human intestinal tract. Most strains are nonhemolytic.Microscopy, Fluorescence: Microscopy of specimens stained with fluorescent dye (usually fluorescein isothiocyanate) or of naturally fluorescent materials, which emit light when exposed to ultraviolet or blue light. Immunofluorescence microscopy utilizes antibodies that are labeled with fluorescent dye.Antigens, CD40: A member of the tumor necrosis factor receptor superfamily with specificity for CD40 LIGAND. It is found on mature B-LYMPHOCYTES and some EPITHELIAL CELLS, lymphoid DENDRITIC CELLS. Evidence suggests that CD40-dependent activation of B-cells is important for generation of memory B-cells within the germinal centers. Mutations of the gene for CD40 antigen result in HYPER-IGM IMMUNODEFICIENCY SYNDROME, TYPE 3. Signaling of the receptor occurs through its association with TNF RECEPTOR-ASSOCIATED FACTORS.Cercopithecus aethiops: A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.NK Cell Lectin-Like Receptor Subfamily K: An activating NK cell lectin-like receptor subfamily that regulates immune responses to INFECTION and NEOPLASMS. Members of this subfamily generally occur as homodimers.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Jurkat Cells: A CELL LINE derived from human T-CELL LEUKEMIA and used to determine the mechanism of differential susceptibility to anti-cancer drugs and radiation.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Copper: A heavy metal trace element with the atomic symbol Cu, atomic number 29, and atomic weight 63.55.Receptor Protein-Tyrosine Kinases: A class of cellular receptors that have an intrinsic PROTEIN-TYROSINE KINASE activity.Diffusion of Innovation: The broad dissemination of new ideas, procedures, techniques, materials, and devices and the degree to which these are accepted and used.Intracellular Signaling Peptides and Proteins: Proteins and peptides that are involved in SIGNAL TRANSDUCTION within the cell. Included here are peptides and proteins that regulate the activity of TRANSCRIPTION FACTORS and cellular processes in response to signals from CELL SURFACE RECEPTORS. Intracellular signaling peptide and proteins may be part of an enzymatic signaling cascade or act through binding to and modifying the action of other signaling factors.Immunoglobulin G: The major immunoglobulin isotype class in normal human serum. There are several isotype subclasses of IgG, for example, IgG1, IgG2A, and IgG2B.Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Cytokines: Non-antibody proteins secreted by inflammatory leukocytes and some non-leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.Oligosaccharides: Carbohydrates consisting of between two (DISACCHARIDES) and ten MONOSACCHARIDES connected by either an alpha- or beta-glycosidic link. They are found throughout nature in both the free and bound form.Static Electricity: The accumulation of an electric charge on a objectMacrophages: The relatively long-lived phagocytic cell of mammalian tissues that are derived from blood MONOCYTES. Main types are PERITONEAL MACROPHAGES; ALVEOLAR MACROPHAGES; HISTIOCYTES; KUPFFER CELLS of the liver; and OSTEOCLASTS. They may further differentiate within chronic inflammatory lesions to EPITHELIOID CELLS or may fuse to form FOREIGN BODY GIANT CELLS or LANGHANS GIANT CELLS. (from The Dictionary of Cell Biology, Lackie and Dow, 3rd ed.)Killer Cells, Natural: Bone marrow-derived lymphocytes that possess cytotoxic properties, classically directed against transformed and virus-infected cells. Unlike T CELLS; and B CELLS; NK CELLS are not antigen specific. The cytotoxicity of natural killer cells is determined by the collective signaling of an array of inhibitory and stimulatory CELL SURFACE RECEPTORS. A subset of T-LYMPHOCYTES referred to as NATURAL KILLER T CELLS shares some of the properties of this cell type.Enteropathy-Associated T-Cell Lymphoma: A primary peripheral T-cell lymphoma in the gastrointestinal tract, most often in the jejunum, associated with a history of CELIAC DISEASE or other gastrointestinal diseases.Affinity Labels: Analogs of those substrates or compounds which bind naturally at the active sites of proteins, enzymes, antibodies, steroids, or physiological receptors. These analogs form a stable covalent bond at the binding site, thereby acting as inhibitors of the proteins or steroids.Water: A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Carbon Monoxide: Carbon monoxide (CO). A poisonous colorless, odorless, tasteless gas. It combines with hemoglobin to form carboxyhemoglobin, which has no oxygen carrying capacity. The resultant oxygen deprivation causes headache, dizziness, decreased pulse and respiratory rates, unconsciousness, and death. (From Merck Index, 11th ed)B-Lymphocytes: Lymphoid cells concerned with humoral immunity. They are short-lived cells resembling bursa-derived lymphocytes of birds in their production of immunoglobulin upon appropriate stimulation.Tissue Distribution: Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Cell Division: The fission of a CELL. It includes CYTOKINESIS, when the CYTOPLASM of a cell is divided, and CELL NUCLEUS DIVISION.Protein Isoforms: Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.Spectrum Analysis, Raman: Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light.Allosteric Site: A site on an enzyme which upon binding of a modulator, causes the enzyme to undergo a conformational change that may alter its catalytic or binding properties.Calcium-Binding Proteins: Proteins to which calcium ions are bound. They can act as transport proteins, regulator proteins, or activator proteins. They typically contain EF HAND MOTIFS.Receptor Activator of Nuclear Factor-kappa B: A tumor necrosis factor receptor family member that is specific for RANK LIGAND and plays a role in bone homeostasis by regulating osteoclastogenesis. It is also expressed on DENDRITIC CELLS where it plays a role in regulating dendritic cell survival. Signaling by the activated receptor occurs through its association with TNF RECEPTOR-ASSOCIATED FACTORS.Protein Transport: The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.Apoproteins: The protein components of a number of complexes, such as enzymes (APOENZYMES), ferritin (APOFERRITINS), or lipoproteins (APOLIPOPROTEINS).Adenosine Diphosphate: Adenosine 5'-(trihydrogen diphosphate). An adenine nucleotide containing two phosphate groups esterified to the sugar moiety at the 5'-position.Tyrosine: A non-essential amino acid. In animals it is synthesized from PHENYLALANINE. It is also the precursor of EPINEPHRINE; THYROID HORMONES; and melanin.
An antibody's binding affinity to its target is extraordinarily high.. Many ligand transport proteins bind particular small ... The canonical example of a ligand-binding protein is haemoglobin, which transports oxygen from the lungs to other organs and ... These proteins must have a high binding affinity when their ligand is present in high concentrations, but must also release the ... Proteins can bind to other proteins as well as to small-molecule substrates. When proteins bind specifically to other copies of ...
Upon binding, the receptor often undergoes a conformational change and may bind further signaling ligands in order to activate ... Intrinsic transcriptional involves the three following domains: transcription-activating, DNA-binding, and ligand-binding. ... "Ligand Binding Domain". www.ks.uiuc.edu. Retrieved 2017-04-06. "Cell signalling". OpenLearn. Retrieved 2017-04-06. Stockert, R ... Problems with nuclear receptor binding as a result of shortages of ligand or receptors can have drastic effects on the cell. ...
Identification by ligand binding". The Journal of Biological Chemistry. 257 (19): 11416-23. PMID 6288684. Manning, DR; Gilman, ... In 1980, he succeeded in identifying and isolating the new protein, which he named G protein, as it specifically bind GTP ... Gilman, AG (1970). "A protein binding assay for adenosine 3':5'-cyclic monophosphate". Proceedings of the National Academy of ... A family of structurally homologous guanine nucleotide-binding proteins". The Journal of Biological Chemistry. 258 (11): 7059- ...
Plow, Edward F.; Haas, Thomas A.; Zhang, Li; Loftus, Joseph; Smith, Jeffrey W. (2000-07-21). "Ligand Binding to Integrins". ... Fluciclatide, an (18)F-labeled small peptide that binds to integrin αVβ3 and integrin αVβ5, is being tested as a tool to ... The RGD motif is presented in a slightly different ways in different proteins, making it possible for the many RGD-binding ... Pierschbacher, M. D.; Ruoslahti, E. (1987-12-25). "Influence of stereochemistry of the sequence Arg-Gly-Asp-Xaa on binding ...
Ligand-dependent corepressor is a protein that in humans is encoded by the LCOR gene. LCOR is a transcriptional corepressor ... White JH, Fernandes I, Mader S, Yang XJ (Jun 2004). "Corepressor recruitment by agonist-bound nuclear receptors". Vitam Horm. ... "Entrez Gene: LCOR ligand dependent nuclear receptor corepressor". Nagase T, Nakayama M, Nakajima D, et al. (2001). "Prediction ... "Ligand-dependent nuclear receptor corepressor LCoR functions by histone deacetylase-dependent and -independent mechanisms". Mol ...
Researchers have created an avidin with reversible binding characteristics through nitration or iodination of the binding site ... Oligosaccharide side chain not required for ligand association". The Biochemical Journal. 248 (1): 167-71. PMC 1148514 . PMID ... "that the binding site of avidin is destroyed on heat denaturation". The biotin-binding properties of avidin were exploited ... A 1992 study found that thermal inactivation of the biotin binding activity of avidin was described by D121 °C = 25 min and z ...
Vaughan RA, Kuhar MJ (1996). "Dopamine transporter ligand binding domains. Structural and functional properties revealed by ... sodium ions must bind to the extracellular domain of the transporter before dopamine can bind. Once dopamine binds, the protein ... Once inside, it binds to TAAR1 or enters synaptic vesicles through VMAT2. When amphetamine binds to TAAR1, it reduces the ... The human dopamine transporter (hDAT) contains a high affinity extracellular zinc binding site which, upon zinc binding, ...
CXCR6 binds the ligand CXCL16. However, CXCR6 is more closely related in structure to CC chemokine receptors than to other CXC ... Its principle ligand is CXCL13 (or BLC). CXCR6 was formerly called three different names (STRL33, BONZO, and TYMSTR) before ... There are two isoforms, CXCR3-A and CXCR3-B. It has three highly related ligands in mammals, CXCL9, CXCL10 and CXCL11. CXCR4 ( ... The CXCR3 binding chemokine IP-10/CXCL10: structure and receptor interactions. Biochemistry 41: 10418-10425, 2002. Legler D.F ...
Cortajarena AL, Regan L (May 2006). "Ligand binding by TPR domains". Protein Science. 15 (5): 1193-8. doi:10.1110/ps.062092506 ... of which the concave face is usually involved in ligand binding. In terms of sequence, a TPR possesses a mixture of small and ... The binding of the Rac GTPase is a key step into the assembly of the complex and the TPRs in the phox unit mediate the assembly ... Its TPR1 domain is known to recognize the C-terminal of Hsp70 while TPR2 binds to the C-terminal of Hsp90. Both C-terminal ...
Besides the oxygen ligand, which binds to hemoglobin in a cooperative manner, hemoglobin ligands also include competitive ... Protons bind at various places on the protein, while carbon dioxide binds at the α-amino group. Carbon dioxide binds to ... completing the octahedral group of six ligands. Oxygen binds in an "end-on bent" geometry where one oxygen atom binds to Fe and ... NO binds reversibly to a specific cysteine residue in globin; the binding depends on the state (R or T) of the hemoglobin. The ...
"The Binding of Benzoarylsulfonamide Ligands to Human Carbonic Anhydrase is Insensitive to Formal Fluorination of the Ligand". ... "The Binding of Benzoarylsulfonamide Ligands to Human Carbonic Anhydrase is Insensitive to Formal Fluorination of the Ligand". ... Phys., 2011, 13, 10136-10146 Binding of Small-Molecule Ligands to Proteins: "What You See" Is Not Always "What You Get", ... "Water Networks Contribute to Enthalpy/Entropy Compensation in Protein-Ligand Binding". J. Am. Chem. Soc. 135 (41): 15579-15584 ...
Alter substrate or ligand binding. Circularly permuting a protein can result in the loss of substrate binding, but can ... These are membrane-bound enzymes that catalyze the transfer of a hydride ion between NAD(H) and NADP(H) in a reaction that is ... occasionally lead to novel ligand binding activity or altered substrate specificity. Improve thermostability. Making proteins ... Hatefi, Y.; Yamaguchi, M. (1996). "Nicotinamide nucleotide transhydrogenase: A model for utilization of substrate binding ...
... is a ligand bound to transition metals. These are formed by oxidation peroxide oxidation of a disulfur ... Excessive oxygen can yield a dioxygendisulfur ligand, which can be reduced in turn with triphenylphosphine. Examples are: [Ir( ...
Lu XJ, Shakked Z, Olson WK (July 2000). "A-form conformational motifs in ligand-bound DNA structures". Journal of Molecular ... A distinct group of DNA-binding proteins is the DNA-binding proteins that specifically bind single-stranded DNA. In humans, ... Other non-specific DNA-binding proteins in chromatin include the high-mobility group proteins, which bind to bent or distorted ... Enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication ...
... its binding affinity and dissociation constants, and number of binding sites, TNP-ATP can also be used in ligand binding ... Then, ligand is added to displace the bound analog. This is measured by decreases in fluorescence. One can also do this by ... Using either experiment will allow the binding affinity of the ligand to protein to be measured. TNP-ATP is also valuable ... This produces a saturation curve from which the binding affinity can be determined. The number of binding sites may also be ...
Binding of antagonist ligands to nuclear receptors in contrast induces a conformation of the receptor that preferentially binds ... The N-terminal (A/B), DNA-binding (C), and ligand binding (E) domains are independently well folded and structurally stable ... Thus, this provided an example of how an ancestral ligand-dependent receptor could lose its ability to bind ligands. A ... In the absence of ligand, type II nuclear receptors are often complexed with corepressor proteins. Ligand binding to the ...
"Mapping ligand binding domains in chimeric fibroblast growth factor receptor molecules. Multiple regions determine ligand ... "Insights into the molecular basis for fibroblast growth factor receptor autoinhibition and ligand-binding promiscuity". ... This particular family member binds both acidic and basic fibroblast growth factor and plays a role in bone development and ... FGFR family members differ from one another in their ligand affinities and tissue distribution. A full-length representative ...
"Mapping ligand binding domains in chimeric fibroblast growth factor receptor molecules. Multiple regions determine ligand ... Naruo K, Seko C, Kuroshima K, Matsutani E, Sasada R, Kondo T, Kurokawa T (February 1993). "Novel secretory heparin-binding ... and heparin-binding interfaces". Acta Crystallographica Section D. 57 (Pt 3): 378-84. doi:10.1107/S0907444900020813. PMID ... "Human RPE cells express the FGFR2IIIc and FGFR3IIIc splice variants and FGF9 as a potential high affinity ligand". Experimental ...
"Mapping ligand binding domains in chimeric fibroblast growth factor receptor molecules. Multiple regions determine ligand ... binding specificity". J. Biol. Chem. 274 (49): 34785-94. doi:10.1074/jbc.274.49.34785. PMID 10574949. Loo BB, Darwish KK, ...
The cytC' are capable of binding such ligands as CO, NO or CN(-), albeit with rate and equilibrium constants 100 to 1,000,000- ... The Chromatium vinosum cytC' exhibits dimer dissociation upon ligand binding. Class III comprises the low redox potential ... Kassner RJ (May 1991). "Ligand binding properties of cytochromes c'". Biochim. Biophys. Acta. 1058 (1): 8-12. doi:10.1016/s0005 ... Cytochromes c (cytC) are electron-transfer proteins having one or several heme c groups, bound to the protein by one or, more ...
Andi B; Xu H; Cook PF; West AH (2007). "Crystal structures of ligand-bound saccharopine dehydrogenase from Saccharomyces ... One domain is a Rossmann fold that binds NAD+/NADH, and the other is relatively similar. Both domains contain a six-stranded ...
Xu LZ, Sánchez R, Sali A, Heintz N (Oct 1996). "Ligand specificity of brain lipid-binding protein". The Journal of Biological ... Xu LZ, Sánchez R, Sali A, Heintz N (Oct 1996). "Ligand specificity of brain lipid-binding protein". The Journal of Biological ... Fatty acid binding protein 7, brain (FABP7; also brain lipid binding protein, BLBP), is a human gene. The protein encoded by ... Fatty acid binding proteins (FABPs) are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty ...
... the above-mentioned meta-analysis uses results from 10 different ligands. Exaggerated ligand binding results such as SDZ GLC ... Monomer-dimer equilibrium coupled to ligand binding. Biochemistry. 1974;13(25):5214-9. doi:10.1021/bi00722a026. PMID 4433518. ... Since then another study has shown such elevated percentages in D2 receptors is brain-wide (using a different ligand, which did ... The link was strengthened by experiments in the 1970s which suggested that the binding affinity of antipsychotic drugs for D2 ...
... an extracellular N-terminal ligand-binding domain with cysteine-rich repeats (also called ligand-binding repeats), an epidermal ... THBS1 binds VLDLR and blocks ligand binding. This plays an important role in the reelin pathway, as THBS1 can block the ... VLDLR binds compounds containing apolipoprotein E (apoE). These ligands attach to the cysteine binding repeats in the N- ... VLDLR-III lacks exon 4 that encodes the third ligand-binding repeat. Finally, VLDLR-IV transcripts lack both exon 16 and exon 4 ...
... residues in ligand binding and receptor activation. A second rhodopsin based structural model of the H4 receptor was ... "Mapping histamine H4 receptor-ligand binding modes". MedChemComm. 4: 193-204. doi:10.1039/C2MD20212C. Nijmeijer S, Engelhardt H ... "Discovery of novel human histamine H4 receptor ligands by large-scale structure-based virtual screening". J. Med. Chem. 51 (11 ... "Molecular modeling and site-specific mutagenesis of the histamine-binding site of the histamine H4 receptor". Mol. Pharmacol. ...
Protein binding. 60%. Metabolism. Hepatic via CYP3A4. Elimination half-life. 1.8 ± 0.4 hours. ...
Cavy Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand 3 ELISA Kit-NP_001177872.1 (MBS019114) product datasheet at ... Molecular Function: protein binding; metal ion binding; cytokine activity; tumor necrosis factor receptor binding; receptor ... tumor necrosis factor ligand superfamily member 10; Apo-2 ligand; TNF-related apoptosis inducing ligand TRAIL; tumor necrosis ... Tumor necrosis factor ligand superfamily member 10 UniProt Synonym Protein Names Apo-2 ligand; Apo-2L; TNF-related apoptosis- ...
GAD 65-ligand binding assay ... estradiol at final ligand concentrations of 0.1 nM (hER) and ...
... Dr E. Buxbaum EB15 at le.ac.uk Mon Mar 2 13:22:52 EST 1998 *Previous message: Algal Biliproteins ... Louis Hom wrote: , , Basic question: , Is there an activation energy associated with ligand binding? Yes, there is, and it is ...
FLOWER-SPECIFIC DEFENSIN(4r)-2-Methylpentane-2,4-DiolDioctanoyl L-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphateSulfate Ion[(2r)-2-Octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-Tris(Oxidanyl)-4,5-Diphosphonooxy-Cyclohexyl]oxy-Phosphoryl]oxy-Propyl]octanoate
Ligand binding assays (LBA) is an assay, or an analytic procedure, whose procedure or method relies on the binding of ligand ... Many ligand binding assays require a filtration step to separate bound and unbound ligands before screening. A method called ... Specific binding types to ligand and receptor interactions: Technologies for ligand binding assay continue to advance related ... There are numerous types of ligand binding assays, both radioactive and non-radioactive. As such, ligand binding assays are a ...
... software for analysis of ligand binding , data - Scatchard plots, Kas etc etc. Only one I have heard is LIGAND written , 1980 ... ligand binding analysis software Dr. Larry Mahan lcmahan at helix.nih.gov Tue Nov 29 11:53:17 EST 1994 *Previous message: ... I believe that Peter Munson, one of the original authors of LIGAND has rewritten the software for MACs and PCs. He is still ... Another good program for analysis of pharmacological binding assays is PRISM (DOS name: GraphPad InPlot) from GraphPad, Inc. in ...
Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport ... Literature: Receptor, ligand binding region (IPR001828). References used in this entry. The following publications were ... X-ray structures of the leucine-binding protein illustrate conformational changes and the basis of ligand specificity.. ... Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both ...
Such problems arise in the spectral analysis of ligand binding to macromolecule. Here, we present a spectral data analysis ... This methodology does not require prior knowledge of ligand molar extinction coefficients (free and bound), which potentially ... limits binding analysis. Data are acquired simply by reconstructing the experimental data and by adjusting the product of ... method using SVD (SVD analysis) and nonlinear fitting to determine the binding characteristics of intercalating drugs to DNA. ...
... Jochen M. Schwenk,1,2 Oliver Poetz,1 Robert Zeillinger,3 and Thomas O. Joos1 ... Forty-seven breast cancer tissue samples were available with EGFR values previously determined in radio-ligand binding assays. ...
Recognition and biochemical processing of DNA requires that proteins and other ligands are able to distinguish their DNA ... binding sites from other parts of the molecule. In addition to the direct recognition elements embedded in the linear sequence ... A-form conformational motifs in ligand-bound DNA structures J Mol Biol. 2000 Jul 21;300(4):819-40. doi: 10.1006/jmbi.2000.3690 ... Our analysis pinpoints ligand-induced conformational changes that are difficult to detect from the global perspective used in ...
3D View: Structure , Electron Density , Ligand Interaction. Global Symmetry: Cyclic - C2 (3D View). Global Stoichiometry: Homo ... 3D View: Structure , Electron Density , Ligand Interaction. Global Symmetry: Cyclic - C2 (3D View). Global Stoichiometry: Homo ... 3D View: Structure , Electron Density , Ligand Interaction. Global Symmetry: Cyclic - C2 (3D View). Global Stoichiometry: Homo ... 3D View: Structure , Electron Density , Ligand Interaction. Global Symmetry: Cyclic - C2 (3D View). Global Stoichiometry: Homo ...
Protein interactions and ligand binding: From protein subfamilies to functional specificity. Antonio Rausell, David Juan, ... Protein interactions and ligand binding: From protein subfamilies to functional specificity. Antonio Rausell, David Juan, ... Protein interactions and ligand binding: From protein subfamilies to functional specificity Message Subject (Your Name) has ... Protein interactions and ligand binding: From protein subfamilies to functional specificity. Antonio Rausell, David Juan, ...
... ligand-binding sites of small molecules and (ii) protein interaction sites. Ligand-binding sites are conceptually associated to ... ligand-binding residues and protein binding sites) is projected on it. ... Protein interactions and ligand binding: From protein subfamilies to functional specificity. Antonio Rausell, David Juan, ... Protein interactions and ligand binding: From protein subfamilies to functional specificity. Antonio Rausell, David Juan, ...
Proteins matched: Nuclear hormone receptor, ligand-binding domain (IPR000536) This domain is found in the following proteins: ...
AF-1: Activation Function-1; DBD: DNA binding domain; NLS: Nuclear localizing signal; LBD: Ligand binding domain; AF-2: ... ESR1 ligand-binding domain mutations in hormone-resistant breast cancer.. Toy W1, Shen Y, Won H, Green B, Sakr RA, Will M, Li Z ... two independent cohorts of metastatic ER-positive breast tumors and identified mutations in ESR1 affecting the ligand-binding ...
A D Podjarny; Annick P Dejaegere; Bruno Kieffer;] -- The binding of small ligands to biological molecules is central to most ... Biophysical approaches determining ligand binding to biomolecular targets. [ ... Ligand binding (Biochemistry) a schema:Intangible ;. schema:name "Ligand binding (Biochemistry)"@en ;. . ... Biophysical approaches determining ligand binding to biomolecular targets. Author:. A D Podjarny; Annick P Dejaegere; Bruno ...
Although a significant amount of information is available with respect to the planar aromatic hydrocarbon AhR ligands, the ... is a ligand-dependent transcription factor that can be activated by structurally diverse synthetic and naturally-occurring ... Ligand binding and activation of the Ah receptor Chem Biol Interact. 2002 Sep 20;141(1-2):3-24. doi: 10.1016/s0009-2797(02) ... In addition, the lack of information regarding the actual three-dimensional structure of the AhR ligand binding domain (LBD) ...
Novel compounds show high affinity for specific cocainereceptors in the brain, particularly dopamine transporter sites,and have the formula ##STR1## Wherein Y=CH.sub.2 R.sub.3, CO.sub.2R.sub.2 or ##STR2## R.sub.1 =hydrogen, C.sub.1-5 alkyl, R.sub.2=hydrogen, C.sub.1-6 alkyl, C.sub.3-8 cycloalkyl, C.sub.1-4 alkoxy,C.sub.1-6 alkynyl, halogen or amine, R.sub.3 =OH,
The invention relates to novel compounds which show highaffinity for cocaine receptors in the brain, particularly dopamineand serotonin transporter sites. The compounds may be used asimaging or pharmaceutical agents, in the diagnosis and treatment ofdrug addiction, depression, anorexia and neurodegenerativediseases.
Thus, the prediction of reliable binding poses of candidate ligands, through... ... Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection. ... Thus, the prediction of reliable binding poses of candidate ligands, through molecular docking simulations, represents a key ... Ballante F. (2018) Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection. In: Mavromoustakos ...
There is a substantial amount of historical ligand binding data available from site-directed mutagenesis (SDM) studies of many ... GPCRs Adenosine receptors Homology modeling Ligand binding Binding kinetics Receptor Site-directed mutagenesis ... This information was generated prior to the wave of GPCR crystal structure, in an effort to understand ligand binding with a ... There is a substantial amount of historical ligand binding data available from site-directed mutagenesis (SDM) studies of many ...
HORMONE-BOUND HUMAN PROGESTERONE RECEPTOR LIGAND-BINDING DOMAIN. *DOI: 10.2210/pdb1A28/pdb ... Here we report the 1.8 A crystal structure of a progesterone-bound ligand-binding domain of the human progesterone receptor. ... A hormone-induced stabilization of the carboxy-terminal secondary structure of the ligand-binding domain of the progesterone ... 3D View: Structure , Electron Density , Ligand Interaction. Global Symmetry: Asymmetric - C1 Global Stoichiometry: Monomer - A1 ...
PR ligand, such as progesterone, induces conformation changes in PR ligand binding domain (LBD), thus mediates subsequent gene ... However, no apo-form (non-ligand bound) of PR LBD model has been proposed either by experiments or computational methods so far ... the structural dynamics of PR LBD using molecular dynamics simulations and advanced sampling tools in both ligand-bound and the ... PR LBD may adopt different conformations upon an agonist or an antagonist binding. These different conformations would trigger ...
Ligand-binding assays are the most commonly used platform ... Ligand-binding assays are the most commonly used platform in ... Ligand-binding assays are frequently designed to detect appropriate analytes in complex biological matrices with limited or no ... 17493687 - Binding of mouse mannan-binding lectins to different bacterial pathogens of mice.. 2852987 - A comparative ... ligand-binding assays are often subjected to various degrees of matrix interferences that lead to an erroneous under- or over- ...
... is modulated by ligand binding. In the absence of bound ligands, DHFR extends at very low forces, averaging 27 pN, without any ... Ligand binding modulates the mechanical stability of dihydrofolate reductase.. [Sri Rama Koti Ainavarapu, Lewyn Li, Carmen L ... Our results explain the large reduction in the degradation rate of DHFR, in the presence of its ligands. Our observations ... By contrast, in the presence of micromolar concentrations of the ligands methotrexate, nicotinamide adenine dihydrogen ...
ReceptorsAssayProteinsStudy of ligandMonovalent ligandStrong field ligandsInteractionTypes of bindingAlchemical free energy calculationsStructurallyAffinitiesConformational changesResidues involved in ligandReceptor bindingAntibodiesStructuralSmall ligandsCertain ligandsEquilibriumGPCRSelectively bindNatural ligandsMultivalent ligandsPredictionAssay techniquesAmino acidsCalculationsAssays provideMacromoleculeAgonistsExperimentsEnergiesBiologically activeMolecular DynamicsHydrophobicModulatesCharacterizationMonoclonalDistinctFunctionalMethodsAdenosineEnzymeDomainConstants
- The activity of this protein may be modulated by binding to the decoy receptors TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4, and TNFRSF11B/OPG that cannot induce apoptosis. (mybiosource.com)
- The binding of this protein to its receptors has been shown to trigger the activation of MAPK8/JNK, caspase 8, and caspase 3. (mybiosource.com)
- The foundations for which ligand binding assay have been built are a result of Karl Landsteiner, in 1945, and his work on immunization of animals through the production of antibodies for certain proteins. (wikipedia.org)
- Mutational analysis of the glycine-binding site of the NMDA receptor: structural similarity with bacterial amino acid-binding proteins. (ebi.ac.uk)
- Recognition and biochemical processing of DNA requires that proteins and other ligands are able to distinguish their DNA binding sites from other parts of the molecule. (nih.gov)
- These may include the global conservation of catalytic mechanisms (in the case of enzymes), specific binding to substrates and cofactors, as well as the interaction with other proteins in processes such as cell signaling, the regulation of reactions and the formation of macromolecular complexes. (pnas.org)
- Concerted efforts to determine the atomic structure of GPCRs have proven extremely successful and there are now more than 80 GPCR crystal structure in the PDB database, many of which have been obtained in the presence of receptor ligands and associated G proteins. (springer.com)
- Microbeads can be used as surfaces to allow different ligands to bind to proteins. (aiche.org)
- In this thesis, longstanding problems with regard to ligand binding are treated with computational methods, applied to proteins of key pharmaceutical importance. (dissertations.se)
- General term for proteins that have binding as a major function. (bioontology.org)
- We propose that binding to folding intermediates may dominate the effect of ligands on the stability of multi-domain proteins, and could therefore have a strong impact on protein homeostasis in vivo . (rsc.org)
- The aim of advanced computational techniques is to identify the active sites in specific proteins and moreover to suggest a generalized mechanism by which such protein-ligand (or protein-protein) interactions can be effected. (springer.com)
- This paper describes the use of magnetic levitation (MagLev) to measure the association of proteins and ligands. (harvard.edu)
- Two affibody variants were shown to selectively bind to the extracellular domain of HER2/neu (HER2-ECD), but not to control proteins. (diva-portal.org)
- While we focus on the binding of organic molecules to proteins, the approach is in principle transferable to any pair of molecules. (springer.com)
- Constructing Patch-Based Ligand-Binding Pocket Database for Predicting Function of Proteins. (purdue.edu)
- Often functional clues of unknown proteins can be obtained by predicting small ligand molecules that bind to the proteins. (purdue.edu)
- We tested Patch-Surfer on the extended pocket database to predict binding ligand of 75 non-homologous proteins that bind one of seven different ligands. (purdue.edu)
- Sael, Lee and Kihara, Daisuke, "Constructing Patch-Based Ligand-Binding Pocket Database for Predicting Function of Proteins. (purdue.edu)
- A family of erythrocyte binding proteins of malaria parasites. (ajtmh.org)
- Identification of the erythrocyte binding domains of Plasmodium vivax and Plasmodium knowlesi proteins involved in erythrocyte invasion. (ajtmh.org)
- Ligands (in general small-molecules) bind to proteins within surface cavities. (genomecanada.ca)
- BIND Therapeutics, Inc. (NASDAQ: BIND), a biotechnology company developing targeted and programmable therapeutics called ACCURINS®, today announced a research collaboration with Affilogic, a privately held biotechnology company developing affinity proteins called Nanofitins® that selectively bind and interact with identified targets. (thestreet.com)
- DNAM-1/CD226 and TIGIT both bind to CD112/Nectin-2 and CD155/PVR, two proteins that are frequently up-regulated on tumor cells, but they have opposing effects on NK cell activity. (rndsystems.com)
- Because telomestatin causes cellular effects analogous to those due to dysfunctional telomeric proteins, and because POT1 regulates in vitro the G-quadruplex conformation at telomeres ( 13 ), we have investigated the effect of a telomestatin treatment on POT1 binding in vitro and in human cells using a green fluorescent protein (GFP) fusion protein. (aacrjournals.org)
- A monovalent ligand binds to a protein with six in independent, identical binding sites. (physicsforums.com)
- Ligands consist of a geometrically matching rigid polygonal core to which monovalent ligand units are attached via flexible linker polymers, closely mimicking existing experimental designs. (uio.no)
- They investigated the binding interaction for insulin and an insulin-specific antibody, in addition to developing the first radioimmunoassay (RIA) for insulin. (wikipedia.org)
- Moreover, the implication of SDPs in determining the differential binding to substrates and interaction partners has been experimentally followed up in a number of cases ( 14 - 16 ). (pnas.org)
- Similarly, they can take into account the associated conservation at the molecular signatures level (SDPs) in fundamental regions corresponding to ligand-binding sites and protein interaction sites. (pnas.org)
- Due to potential interaction of biological matrix components, for example, rheumatoid factors, heterophilic antibodies and human anti-animal antibodies, with the test analyte or assay reagents, ligand-binding assays are often subjected to various degrees of matrix interferences that lead to an erroneous under- or over-reporting of the analyte concentration. (biomedsearch.com)
- Although a mutation that abolishes JH III binding does not affect a Met-Met complex that forms in the absence of methoprene, it prevents both the ligand-dependent dissociation of the Met-Met dimer and the ligand-dependent interaction of Met with its partner bHLH-PAS protein Taiman. (archives-ouvertes.fr)
- A new phenanthroline-oxazine ligand: synthesis, coordination chemistry and atypical DNA binding interaction. (sigmaaldrich.com)
- The interaction of the T cell glycoprotein CD2 with one ligand, CD58, contributes to T cell function. (sciencemag.org)
- Fig. 1: Assay principle for monitoring protein-ligand interaction using ﬂuorescence polarization. (bmglabtech.com)
- Molecular-genetic and bioinformatic evidence has been presented, however, to suggest that the B-protein subunit of the receptor presents the site for the receptor-ligand interaction ( 6 , 16 , 29 ). (asm.org)
- Only a limited number of CAR ligands have been identified that regulate the receptor through interaction with its ligand binding pocket. (aspetjournals.org)
- Cyanide is much less effective at suppressing 'endogenous' activity in the presence of GEE than with ammonium, which is attributed to impaired binding of cyanide to the catalytic site through steric interaction with GEE bound at the K S site. (biochemj.org)
- The galectin 3 binding protein/galectin-3 interaction appears to play a critical role in venous thrombosis formation in animal models. (guidetopharmacology.org)
- For the first time, a setup is presented for an overall high precision and high accuracy relative protein-ligand alchemical free energy calculations based on open source software. (rsc.org)
- The Ah receptor (AhR) is a ligand-dependent transcription factor that can be activated by structurally diverse synthetic and naturally-occurring chemicals. (nih.gov)
- The mammalian fibroblast growth factors (FGFs) (FGF1-FGF23) constitute a large family of structurally related ligands that are involved in a multitude of biological processes from embryogenesis to adult homeostasis ( 1 ). (pnas.org)
- Low-density lipoprotein receptor-related protein 1 (LRP1) functions in endocytosis and intracellular signaling for a variety of structurally diverse ligands. (sciencemag.org)
- This result supports a hypothesis whereby the four-amino-acid insertion in CAR2 structurally modifies its ligand binding pocket, suggesting that CAR2 is regulated by a set of ligands distinct from those governing the activity of reference CAR. (aspetjournals.org)
- The stability of TPMT was dramatically increased by binding of ANS, which was shown to co-localize with the structurally similar adenine moiety of the cofactor SAM. (dissertations.se)
- In the present study, ligand binding affinities of (−)-arctigenin and its seven metabolites, including DHENL, were investigated for an estrogen receptor alpha, and found that demethylated metabolites had stronger binding affinities than (−)-arctigenin using a ligand binding screen assay method. (mdpi.com)
- EmrR was found to bind putative ligands of the EmrAB pump-2,4-dinitrophenol, carbonyl cyanide m -chlorophenylhydrazone, and carbonyl cyanide p -(trifluoro-methoxy)phenylhydrazone-with affinities in the micromolar range. (asm.org)
- This accounts for the broad but selective binding by ORs as well as their relatively low ligand-binding affinities. (jneurosci.org)
- The calculated binding affinities quantitatively agree with experimental studies for cholera toxin (n = 5) and anthrax receptor (n = 7) and allow to predict optimal core size and optimal linker length. (uio.no)
- Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. (springer.com)
- Our analysis pinpoints ligand-induced conformational changes that are difficult to detect from the global perspective used in other studies of DNA structure. (nih.gov)
- DNA may undergo conformational changes to B-form, A-form, Z-form, quadruplexes, triplexes and other structures as a result of the binding process to different compounds. (mdpi.com)
- These studies show that CD spectroscopy is a powerful technique to monitor DNA conformational changes resulting from drug binding and also shows its potential to be a drug-screening platform in the future. (mdpi.com)
- As an example, LLPC demonstrated that isoforms of lactate dehydrogenase as well as of hexokinase existed in a ligand-dependent equilibrium between two forms and that conformational changes occurred when monoclonal antibodies bound haptens. (lu.se)
- Kim J, Wess J, van Rhee AM et al (1995) Site-directed mutagenesis identifies residues involved in ligand recognition in the human A2a adenosine receptor. (springer.com)
- The large body of structural data available for several members of the QS LuxR family complexed with different classes of ligands (AHLs and other compounds), has been exploited to dissect the cartography of their regulatory domains through structure-based multiple sequence alignments, structural superimposition and a comparative analysis of the contact residues involved in ligand binding. (mdpi.com)
- Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd3+. (ebi.ac.uk)
- The past twenty years has seen the development of an increasing armoury of biophysical methods that not only detect such binding, but also provide varying degrees of information about the kinetics, thermodynamics and structural aspects of the process. (worldcat.org)
- It is a powerful technique to detect ligand induced changes in biomolecules as it has distinct signals and provides different levels of structural information. (dissertations.se)
- This structural feature was taken advantage of to establish its use as reporter for ligand contact measuring polarized fluorescence emission. (uni-muenchen.de)
- The structural models of biotin, keto-biotin, and testosterone were placed in the ligand-binding pocket of the protein structures by molecular docking. (uta.fi)
- This method of binding has already demonstrated effectiveness in removal of families of viruses, such as parvoviruses, and preliminary data indicates that certain ligands may remove more than one class of viruses," stated Dr. David Hammond, PRDT's chief scientific officer. (infectioncontroltoday.com)
- Metal ions preferentially bind certain ligands. (wikipedia.org)
- Equilibrium dialysis experiments suggested one bound ligand per monomer of the dimeric EmrR. (asm.org)
- This parameter change enabled calculating the equilibrium binding constant and kinetic rate constants. (uni-muenchen.de)
- The first equilibrium describes the reversible binding reaction, in which the agonist associates with and dissociates from the ligand-binding site. (aspetjournals.org)
- The equilibrium dissociation constant ( K A ) is the ratio of the dissociation ( k -1 ) and association ( k +1 ) rate constants for ligand binding to the receptor. (aspetjournals.org)
- There is a substantial amount of historical ligand binding data available from site-directed mutagenesis (SDM) studies of many different GPCR subtypes. (springer.com)
- This information was generated prior to the wave of GPCR crystal structure, in an effort to understand ligand binding with a view to drug discovery. (springer.com)
- Analysis of more than 200 ligand-bound G protein-coupled receptor (GPCR) structures revealed that most ligands bind the traditional sites, but one receptor that binds leukotriene and sends immune cells to infection sites appears to bind a 'double' ligand. (acm.org)
- The current study reveals the molecular environment of the odorant-binding site, and it further advances the understanding of GPCR pharmacology. (jneurosci.org)
- MONTREAL -- ProMetic Life Sciences Inc. has announced that its joint venture with the American Red Cross, Pathogen Removal and Diagnostic Technology Inc. (PRDT), has demonstrated that its proprietary Ligand technology can selectively bind and remove families of viruses from blood and blood products. (infectioncontroltoday.com)
- Scientists at the Swiss Federal Institute of Technology in Lausanne used a computer simulation to discover a novel binding site for natural ligands and drugs. (acm.org)
- Using a computer model of the muscarinic acetylcholine receptor, researchers at the Swiss Federal Institute of Technology in Lausanne (EPFL) in Switzerland have found a unique binding site for natural ligands and drugs. (acm.org)
- Natural Ligands of the B Cell Adhesion Molecule CD22.beta. (freepatentsonline.com)
- Fluorescence resonance energy transfer (FRET), fluorescent ligands, and radioactivity are some of the existing assay techniques used in the analysis of ligands binding to GPCRs. (news-medical.net)
- A number of assay techniques are used to study ligand binding to GPCRs in living cells. (bmglabtech.com)
- Substitution of individual amino acids, predicted to form a ligand-binding pocket, with residues possessing bulkier side chains reduces JH III binding likely because of steric hindrance. (archives-ouvertes.fr)
- Our results indicate that several amino acids in the transmembrane domains formed a ligand-binding pocket. (jneurosci.org)
- One form of CAR, termed CAR2, contains an additional four amino acids (SPTV) that are predicted to reshape the ligand-binding pocket. (aspetjournals.org)
- Specifically, we studied the codons of amino acids that bind or do not bind small molecular ligands. (uzh.ch)
- We found that the codons of ligand-binding amino acids are on average more robust than those of non-binding amino acids. (uzh.ch)
- In section 3, we describe pKa calculations for a series of ligands binding to the serine proteases trypsin and thrombin. (uni-marburg.de)
- Aldeghi M, Bodkin MJ, Knapp S, Biggin PC (2017) A statistical analysis on the performance of MMPBSA versus absolute binding free energy calculations: bromodomains as a case study. (springer.com)
- Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC (2017) Predictions of ligand selectivity from absolute binding free energy calculations. (springer.com)
- Here, we present a user-friendly web interface, CHARMM-GUI Ligand Binder (http://www.charmm-gui.org/input/gbinding), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. (ku.edu)
- The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three non-polar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. (ku.edu)
- Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). (ku.edu)
- CHARMM-GUI Ligand Binder provides a convenient and reliable way to setup the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems. (ku.edu)
- Such problems arise in the spectral analysis of ligand binding to macromolecule. (hindawi.com)
- Without the exact knowledge of the spectra of bound and free ligands, the strong dependence of the model with ligand distribution, experimental data obtained near the detection limit, or high noise or scattering (for a long path length) may impair the ability to determine binding parameters with reproductivity and confidence, particularly when the ligand/macromolecule ratio ( ) is low. (hindawi.com)
- Among these quantities is the free energy of binding of a small molecule to a macromolecule, such as a protein. (springer.com)
- The saturation binding experiments with alprenolol-TAMRA were then performed by adding serially diluted alprenolol-TAMRA to the wells, with or without 10μM alprenolol, and incubating the plate at room temperature for 120 minutes. (news-medical.net)
- The saturation binding experiments with alprenolol- TAMRA were performed by operating the CLARIOstar plate reader in endpoint mode. (news-medical.net)
- B , Mφ were preincubated with HBSA, rHSP60, or rH-Ag for 30 min at 37°C, followed by incubation with viable Hc yeasts, HK yeasts, or the F/T Hc yeasts for 30 min at 37°C. The data are the mean attachment index (the number of yeasts bound/100 cells) of two experiments performed in duplicate. (jimmunol.org)
- Here, we present an introductory overview of a protocol that allows for the estimation of ligand binding free energies via molecular dynamics simulations. (springer.com)
- We'll discuss advanced implementations of molecular dynamics for studying the motions of biochemical systems and dissecting free energies in drug binding and molecular recognition. (nvidia.com)
- Here, we demonstrate that Met specifically binds JH III and its biologically active mimics, methoprene and pyriproxyfen, through its C-terminal PAS domain. (archives-ouvertes.fr)
- Additionally, the surface of ACCURINS® can be functionalized with a variety of biologically active ligands, potentially with multiple types of ligands on the same particle. (thestreet.com)
- In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding. (dissertations.se)
- The team utilized 'molecular dynamics simulations' to model the atomic and molecular movements of the receptor's M3 and M4 subtypes and identify the binding site. (acm.org)
- In Bacillus subtilis , BmrR, a MerR family transcriptional activator, binds chemically unrelated hydrophobic cations, such as tetraphenylphosphonium and rhodamine, and activates transcription of the BMR pump ( 1 ). (asm.org)
- The design of the binding site agrees well with its ability to accommodate a broad range of hydrophobic cations. (asm.org)
- In Staphylococcus aureus , QacR, belonging to the TetR family of repressors, also binds various hydrophobic cations and controls the expression of the QacA MDR pump ( 5 ). (asm.org)
- PRDT's Ligand technology targets hydrophobic pockets or 'canyons' in viruses. (infectioncontroltoday.com)
- Investigators use a large range of experimental methods based on physical differences between bound and free ligands to determine binding constants. (hindawi.com)
- K. B. Hall and J. K. Kranz, 'Nitrocellulose Filter Binding for Determination of Dissociation Constants,' Methods in Molecular Biology , 118 , 1999 pp. 105-114. (wolfram.com)
- Hydrogen bonding patterns, ligand motion, and protein residue motion were found as applicable analysis methods. (uta.fi)
- Crystal structure of hormone-bound atrial natriuretic peptide receptor extracellular domain: rotation mechanism for transmembrane signal transduction. (ebi.ac.uk)
- ESR1 ligand-binding domain mutations in hormone-resistant breast cancer. (nih.gov)
- We conducted a comprehensive genetic analysis of two independent cohorts of metastatic ER-positive breast tumors and identified mutations in ESR1 affecting the ligand-binding domain (LBD) in 14 of 80 cases. (nih.gov)
- In addition, the lack of information regarding the actual three-dimensional structure of the AhR ligand binding domain (LBD) has hindered detailed analysis of the molecular mechanisms by which these ligands bind to and active AhR signal transduction. (nih.gov)
- Here we report the 1.8 A crystal structure of a progesterone-bound ligand-binding domain of the human progesterone receptor. (rcsb.org)
- A hormone-induced stabilization of the carboxy-terminal secondary structure of the ligand-binding domain of the progesterone receptor accounts for the stereochemistry of this distinctive dimer, explains the receptor's characteristic pattern of ligand-dependent protease resistance and its loss of repression, and indicates how the anti-progestin RU486 might work in birth control. (rcsb.org)
- The structure of the C-terminal ligand binding domain ( 13 ) of BmrR was recently resolved ( 20 ). (asm.org)
- In the current work we studied the effect of ligand binding on the stability of the multi-domain protein adenylate kinase from E. coli (AKE). (rsc.org)
- In addition, injection of the ligand-binding domain of LRP1 into dorsal root ganglia in rats increased Trk receptor phosphorylation. (sciencemag.org)
- Injection of the LRP1-binding domain of α 2 M into rat dorsal root ganglia induced Trk receptor phosphorylation, which was blocked by receptor-associated protein, an antagonist of ligand binding to LRP1. (sciencemag.org)
- Affibody® (affibody) ligands that are specific for the extracellular domain of human epidermal growth factor receptor 2 (HER2/neu) have been selected by phage display technology from a combinatorial protein library based on the 58 amino acid residue staphylococcal protein A-derived Z domain. (diva-portal.org)
- In a second series of studies, Affibody® (affibody) ligands directed to the extracellular domain of human epidermal growth factor receptor 2 (HER2/neu), which is known to be overexpressed in ∼ 20-30% of breast cancers, were isolated by phage display in vitro selection from a combinatorial protein library based on the 58 amino acid residue staphylococcal protein A-derived Z domain. (diva-portal.org)
- Ligand binding to monocyte alpha 5 beta 1 integrin activates the alpha 2 beta 1 receptor via the alpha 5 subunit cytoplasmic domain and protein kinase C. (jimmunol.org)
- Overexpression of the RXRα ligand binding domain was critical for achieving these effects. (aspetjournals.org)
- This structure allows for the structure-based rationalization of the largest number of disease-associated mutations described for the AR ligand binding domain (LBD), which have been involved in prostate cancer and androgen insensitivity syndromes. (endocrine-abstracts.org)