Structural Homology, Protein: The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.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.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.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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).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.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.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.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.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.Bacterial Proteins: Proteins found in any species of bacterium.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.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.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.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Molecular Weight: The sum of the weight of all the atoms in a molecule.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.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).Cross Reactions: Serological reactions in which an antiserum against one antigen reacts with a non-identical but closely related antigen.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.src Homology Domains: Regions of AMINO ACID SEQUENCE similarity in the SRC-FAMILY TYROSINE KINASES that fold into specific functional tertiary structures. The SH1 domain is a CATALYTIC DOMAIN. SH2 and SH3 domains are protein interaction domains. SH2 usually binds PHOSPHOTYROSINE-containing proteins and SH3 interacts with CYTOSKELETAL PROTEINS.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.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.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Thermotoga maritima: A rod-shaped bacterium surrounded by a sheath-like structure which protrudes balloon-like beyond the ends of the cell. It is thermophilic, with growth occurring at temperatures as high as 90 degrees C. It is isolated from geothermally heated marine sediments or hot springs. (From Bergey's Manual of Determinative Bacteriology, 9th ed)Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Trypsin: A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 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.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Crystallography: The branch of science that deals with the geometric description of crystals and their internal arrangement. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)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.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Kinetics: The rate dynamics in chemical or physical systems.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.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.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.Genes, Bacterial: The functional hereditary units of BACTERIA.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.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.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.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)Crystallization: The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)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.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.Epitopes: Sites on an antigen that interact with specific antibodies.Amino Acids: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.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.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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.Peptide Mapping: Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.Protein Interaction Domains and Motifs: Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.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.Archaeal Proteins: Proteins found in any species of archaeon.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.Serine Endopeptidases: Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.Static Electricity: The accumulation of an electric charge on a objectProtein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.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.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.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).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).)Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Circular Dichroism: A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Antibodies, Monoclonal: Antibodies produced by a single clone of cells.Fungal Proteins: Proteins found in any species of fungus.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Glycoproteins: Conjugated protein-carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins.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.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.Endopeptidases: A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.Disulfides: Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.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.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Chromatography, Gel: Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.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.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.Swine: Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).Viral Proteins: Proteins found in any species of virus.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.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.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.Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.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.Membrane Glycoproteins: Glycoproteins found on the membrane or surface of cells.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.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Brain: The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.PhosphoproteinsBlotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Adaptor Proteins, Signal Transducing: A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymesBlood Proteins: Proteins that are present in blood serum, including SERUM ALBUMIN; BLOOD COAGULATION FACTORS; and many other types of proteins.Genetic Complementation Test: A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.Genes, Viral: The functional hereditary units of VIRUSES.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Genes, Fungal: The functional hereditary units of FUNGI.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.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.Phosphatidylinositol Phosphates: Phosphatidylinositols in which one or more alcohol group of the inositol has been substituted with a phosphate group.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Protein-Tyrosine Kinases: Protein kinases that catalyze the PHOSPHORYLATION of TYROSINE residues in proteins with ATP or other nucleotides as phosphate donors.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.Tyrosine: A non-essential amino acid. In animals it is synthesized from PHENYLALANINE. It is also the precursor of EPINEPHRINE; THYROID HORMONES; and melanin.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Proto-Oncogene Proteins: Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Guanine Nucleotide Exchange Factors: Protein factors that promote the exchange of GTP for GDP bound to GTP-BINDING PROTEINS.Microfilament Proteins: Monomeric subunits of primarily globular ACTIN and found in the cytoplasmic matrix of almost all cells. They are often associated with microtubules and may play a role in cytoskeletal function and/or mediate movement of the cell or the organelles within the cell.Protein Tyrosine Phosphatases: An enzyme group that specifically dephosphorylates phosphotyrosyl residues in selected proteins. Together with PROTEIN-TYROSINE KINASE, it regulates tyrosine phosphorylation and dephosphorylation in cellular signal transduction and may play a role in cell growth control and carcinogenesis.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Protein Tyrosine Phosphatase, Non-Receptor Type 6: A Src-homology domain-containing protein tyrosine phosphatase found in the CYTOSOL of hematopoietic cells. It plays a role in signal transduction by dephosphorylating signaling proteins that are activated or inactivated by PROTEIN-TYROSINE KINASES.Phospholipase C delta: A phosphoinositide phospholipase C subtype that is structurally defined by the presence of an N-terminal pleckstrin-homology and EF-hand domains, a central catalytic domain, and a C-terminal calcium-dependent membrane-binding domain.Protein Tyrosine Phosphatase, Non-Receptor Type 11: A subtype of non-receptor protein tyrosine phosphatases that contain two SRC HOMOLOGY DOMAINS. Mutations in the gene for protein tyrosine phosphatase, non-receptor type 11 are associated with NOONAN SYNDROME.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Two-Hybrid System Techniques: Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Glutathione Transferase: A transferase that catalyzes the addition of aliphatic, aromatic, or heterocyclic FREE RADICALS as well as EPOXIDES and arene oxides to GLUTATHIONE. Addition takes place at the SULFUR. It also catalyzes the reduction of polyol nitrate by glutathione to polyol and nitrite.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Precipitin Tests: Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.3T3 Cells: Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.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.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.Phosphotyrosine: An amino acid that occurs in endogenous proteins. Tyrosine phosphorylation and dephosphorylation plays a role in cellular signal transduction and possibly in cell growth control and carcinogenesis.Isoenzymes: Structurally related forms of an enzyme. Each isoenzyme has the same mechanism and classification, but differs in its chemical, physical, or immunological characteristics.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.Nerve Tissue ProteinsDrosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Phosphoric Monoester Hydrolases: A group of hydrolases which catalyze the hydrolysis of monophosphoric esters with the production of one mole of orthophosphate. EC 3.1.3.Cyanogen Bromide: Cyanogen bromide (CNBr). A compound used in molecular biology to digest some proteins and as a coupling reagent for phosphoroamidate or pyrophosphate internucleotide bonds in DNA duplexes.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.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Immunoblotting: Immunologic method used for detecting or quantifying immunoreactive substances. The substance is identified by first immobilizing it by blotting onto a membrane and then tagging it with labeled antibodies.Actins: Filamentous proteins that are the main constituent of the thin filaments of muscle fibers. The filaments (known also as filamentous or F-actin) can be dissociated into their globular subunits; each subunit is composed of a single polypeptide 375 amino acids long. This is known as globular or G-actin. In conjunction with MYOSINS, actin is responsible for the contraction and relaxation of muscle.Adaptor Proteins, Vesicular Transport: A class of proteins involved in the transport of molecules via TRANSPORT VESICLES. They perform functions such as binding to the cell membrane, capturing cargo molecules and promoting the assembly of CLATHRIN. The majority of adaptor proteins exist as multi-subunit complexes, however monomeric varieties have also been found.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.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.Bacterial Outer Membrane Proteins: Proteins isolated from the outer membrane of Gram-negative bacteria.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.Genes, Plant: The functional hereditary units of PLANTS.GRB2 Adaptor Protein: A signal transducing adaptor protein that links extracellular signals to the MAP KINASE SIGNALING SYSTEM. Grb2 associates with activated EPIDERMAL GROWTH FACTOR RECEPTOR and PLATELET-DERIVED GROWTH FACTOR RECEPTORS via its SH2 DOMAIN. It also binds to and translocates the SON OF SEVENLESS PROTEINS through its SH3 DOMAINS to activate PROTO-ONCOGENE PROTEIN P21(RAS).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.Proline: A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.

*  An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium...

An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium ... An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium ... An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium ... An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium ...

*  Computational Design of a DNA- and Fc-Binding Fusion Protein

However, analogous proteins may have structural homology although this is not a prerequisite. Prominent examples are the ... Protein Z and MyoD. Protein Z is derived from staphylococcal protein A and holds an IgG Fc-binding domain. It consists of a ... MD Simulations of the Protein-DNA Complex. Simulations of the protein-DNA complexes were performed using Amber 10 [25]. Protein ... Protein-DNA reaction sites of the studied complexes were defined based on structural protein-DNA interactions described ...

*  Surface representation of the CDRs.(A) Surface represen | Open-i

Protein Binding/drug effects. *Protein Structure, Secondary. *Sequence Alignment. *Solvents. *Structural Homology, Protein ... Bottom Line: Structural comparison of CDRs from other CD4 binding site antibodies suggests diverse modes of interaction. ... Bottom Line: Structural comparison of CDRs from other CD4 binding site antibodies suggests diverse modes of interaction. ... Thus the structural study identifies the long CDR3 of D7 as the key determinant of interaction and HIV-1 neutralization. ...

*  Structure of Dinosaur Collagen Unravels the Case for a Young Earth

They also argue that the collagen fragments derive from bacterial proteins with structural homology to collagen. ... Collagen's basic structural unit is called a triple helix, consisting of three protein chains intertwining around each other. ... The contact with the surface protects the protein and keeps the pieces of collagen juxtaposed whenever the protein strands ... Once the protein strand breaks, the fragments are held in close proximity by the contact points. This forced closeness allows ...

*  Berkeley Structural Genomics Center: Job Opportunities

A conserved hypothetical protein from Mycoplasma genitalium shows structural homology to nusb proteins. Proteins 55:1082-6. [ ... Protein Sci 15:921-8. [PubMed],[abstract] *Sims GE, Kim SH. 2006. A method for evaluating the structural quality of protein ... Structural characterization of an iron-sulfur cluster assembly protein IscU in a zinc-bound form. Proteins 63:1137. [PubMed] * ... Electrophoresis of proteins and protein-protein complexes in a native agarose gel. Anal Biochem 282:147-9. [PubMed] *Kim SH. ...

*  rHev b 1 Latex - Phadia - Setting the Standard -

stress proteins). LAP: 3/20 (15%). LAP: 11/52 (21%). nt. Hev b 7.01. Low-Medium. Unclear (structural. homology to proteins. ... structural homology. with a Kiwi fruit. protein). HCW: 68-92%. SB: 33-66%. ++. ... Common name: Acidic protein. Biological function: Unknown, a structural protein. Mw: 16 kDa. Allergen description. Hev b 5 (11, ... Rubber particle proteins. The rubber particle proteins comprise the rubber particles and 2 main insoluble proteins, which are ...

*  Cardiac Literature, including Myocardial Infarction, arrthymias, tachycardia, and angina sub-cluster 60

Because prothrombin belongs to the kringle proteins and shares structural homology with a fibrinolytic kringle protein ... Hereditary protein C deficiency is associated with a predisposition to venous thrombosis. It is not clear whether the ... In the present study, we screened for protein C amidolytic activity in patients admitted to the National Cardiovascular Center ... by markedly elevated eosinophil counts and subsequent multiple organ failure due presumably to eosinophil-derived protein ...

*  IJMS | Free Full-Text | Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate...

... the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which ... That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of ... In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural ... In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to ...

*  Patent US8017749 - Compositions and methods to treat cancer with cupredoxins and CpG rich DNA - Google Patents

This method uses the gene for azurin from P. aeruginosa as an expression system for azurin or heterologous proteins in P. ... These methods may be used to express therapeutic or diagnostic proteins near cancer cells in a patient suffering from cancer or ... The present invention further relates to methods to express proteins near cancer cells. ... Examples of studies that determine significant structural homology between cupredoxins and other proteins include Toth et al. ( ...

*  Dale Brown Emeagwali - Wikipedia

Brown, D. D.; Salzman, L. A. (1984-03-01). "Sequence homology between the structural proteins of Kilham rat virus". Journal of ... "Sequence Homology Between the Structural Proteins of Kilham Rat Virus," Journal of Virology 1989 "Modulation of Ras Expression ... Ras proteins play a vital role in the transmission of signals that regulate the growth of cells. When the gene that initiates ... the ras protein becomes mutated, the signals are disrupted in a way that can cause the cells to become cancerous. She also ...

*  Protocols and Video Articles Authored by Beat Keller

Bcg1 encodes a small secreted protein sharing structural homology with ribonucleases and belongs to a family of clustered ... A New Structural Element Containing Glycine-rich Proteins and Rhamnogalacturonan I in the Protoxylem of Seed Plants Journal of ... A new, clearly distinct structural element containing glycine-rich proteins is now visualized for the first time, using ... Of these ESTs, 89% encoded proteins similar to (E value of < or =10(-5)) characterized or annotated proteins from the NCBI non- ...

*  US Patent # 4,839,293. DNA encoding streptavidin, streptavidin produced therefrom, fused polypeptides which include amino...

Both proteins show a clear structural homology with a high preponderance of beta-structure. The alternating hydrophobic, ... The target protein can be any protein of interest. For example, any protein of bacterial or viral origin can be a target ... Several regions of extensive homology were found between both proteins. Of particular interest is the homology around and ... chemically modified proteins in vivo and to isolate proteins when one knows only the sequence of the gene encoding the protein ...

*  Viruses | Free Full-Text | Recombinant Sheep Pox Virus Proteins Elicit Neutralizing Antibodies

SPPV structural proteins were identified by sequence homology with proteins of vaccinia virus (VACV) strain Copenhagen. Four ... structural proteins as candidate subunit vaccines to control sheep pox disease. ... Western blot analysis revealed the antigenic and immunogenic properties of SPPV-060, SPPV-095, SPPV-117 and SPPV-122 proteins ... and SPPV-122 proteins. To our knowledge, this is the first report demonstrating the virus-neutralizing activities of antisera ...

*  FKBP6 - Wikipedia

FK506 binding protein 6, also known as FKBP6, is a human gene. The encoded protein shows structural homology to FKBP ... PDB: 3B7X​; "RCSB Protein Data Bank - Structure Summary for 3B7X - Crystal structure of human FK506-Binding Protein 6". ... FKBP6 contains 3 α-helices and 11 β-sheet strands, and as a FK506-family protein, has been shown to be a potent ... Siekierka JJ, Hung SH, Poe M, Lin CS, Sigal NH (October 1989). "A cytosolic binding protein for the immunosuppressant FK506 has ...

*  Specific and conserved sequences in D. melanogaster and C. elegans lamins and histone H2A mediate the attachment of lamins to...

... cDNA sequencing of nuclear lamins A and C reveals primary and secondary structural homology to intermediate filament proteins. ... Purified proteins and peptides were resolved on Tris-glycine SDS-PAGE (12% or 15%). The protein concentration was calculated ... Tris-Tricine SDS-PAGE was used for low molecular mass proteins or small peptides (Schagger and Von Jagow, 1987). The proteins ... C) Wild-type and mutant proteins were expressed, purified to near homogeneity and subjected to 12% SDS-PAGE analysis. Proteins ...

*  Intranuclear membrane structure formations by CaaX-containing nuclear proteins | Journal of Cell Science

... cDNA sequencing of nuclear lamins A and C reveals primary and secondary structural homology to intermediate filament proteins. ... Other proteins that contain a CaaX motif include the Ras proteins and many other small G proteins, fungal mating pheromones and ... stockpiles large amounts of nuclear proteins, including lamin LIII. These maternal proteins serve as a protein pool for the ... They are the major structural components of the nuclear lamina, a protein meshwork associated with the inner nuclear membrane ( ...

*  Cyanase - Wikipedia

The C-terminal domain has an 'open fold' with no structural homology to other proteins. The dimer structure reveals the C- ... The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. ...

*  BMRB Entry 15158

"The solution structure of the adhesion protein Bd37 from Babesia divergens reveals structural homology with eukaryotic proteins ... A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules Member of ... Title: Solution structure of the adhesion protein Bd37 from Babesia divergens PubMed: 18035372. Authors: Auguin, Daniel; Yang, ...

*  Gut-specific homing - Wikipedia

The MadCAM-1 protein has structural homology to the vascular surface receptors VCAM1 and ICAM at 28% and 32% respectively. This ... Structural analysis of the MadCAM-1 protein shows that it is a 41.5 kDa transmembrane protein with a small cytoplasmic tail and ... The ligand for CCR9 proteins is the CCL25 chemokine (which is otherwise known as TECK) protein. CCL25 is a chemokine which, ... The last of which has 33% structural identity to the Ca2 domain of IgA-1. The first two of the domains are predicted to be the ...

*  Serpentine transmembrane antigens expressed in human cancers and uses thereof - HUBERT RENE S.

Two of the proteins in this family are exclusively or predominantly expressed in the prostate, as well as in prostate can ... a high degree of structural conservation among them but show no significant structural homology to any known human proteins. ... a high degree of structural conservation among them but show no significant structural homology to any known human proteins. ... a high degree of structural conservation among them but show no significant structural homology to any known human proteins. ...

*  Plus it

SYT1 protein shows structural and sequence homology to syt7, one of the components of the plasma membrane repair system in ... A homology search of SYT1 against the human protein reference database (Mishra et al., 2006) showed syt7 as the protein with ... The identification of the mutated gene revealed that it encodes a protein with homology to animal synaptotagmins. The ... The truncated SYT1 protein missing the N-terminal part (first 111 bp, 37 amino acids) of the protein was PCR amplified using ...

*  2007 Protein Structural Bioinformatics Course

Homology (Comparative) Modeling *Jmol in Scientific Journals *FirstGlance in Jmol: Nature Structural and Molecular Biology *" ... Introduction to Structural Bioinformatics. Review of Protein Chemistry and Structure. * Central Dogma: DNA mRNA Protein. * 20 ... Is Structural Genomics the answer? Not in the next few years. *Intrinsicially unstructured proteins: About 10% of proteins are ... Sequence specific recognition DNA bases by zinc finger domain of protein *Hydrophobic protein-protein interaction *Nonspecific ...

*  WikiGenes - Respiratory Syncytial Virus, Human

Sequence of the major nucleocapsid protein gene of pneumonia virus of mice: sequence comparisons suggest structural homology ... The NS1 protein (139 amino acids) is one of the two nonstructural proteins of human respiratory syncytial virus (RSV) and is ... The small hydrophobic protein SH of human respiratory syncytial virus (RSV) is a short transmembrane surface protein of unknown ... and F proteins is efficiently mediated by the vesicular stomatitis virus G protein. Oomens, A.G., Megaw, A.G., Wertz, G.W. J. ...

*  Saúde Pública - HIV-2 antibody detection after indeterminate or negative HIV-1 Western blot in Cuba, 2005-2008 HIV-2 antibody...

However, high structural homology between HIV-1 and HIV-2 genomic products, mainly in gag and pol gene derived proteins, causes ... its effect is likely due to high structural homology among proteins derived from the gag, pol and even env genes of HIV-1 and - ... The complete pattern observed in HIV-2-positive WB includes a total of nine structural bands corresponding to proteins (p) and ... to separate viral proteins.[23] These proteins were transferred to 0.2 µm nitrocellulose membrane (Bio-Rad Laboratories, USA) ...

*  ABCC1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 1)

Homology. structural and/or functional homology with other ABC transporter proteins (CFTR, Pgp, MOAT).. ... Multidrug resistance-associated protein: a protein distinct from P-glycoprotein involved in cytotoxic drug expulsion.. ... Protein : pattern, domain, 3D structure. UniProt/SwissProt. P33527 [function] [subcellular_location] [family_and_domains] [ ... Homology/Alignments : Family Browser (UCSC). ABCC1. Gene fusions - Rearrangements Fusion : Mitelman. ABCC1/PRKCB [16p13.11/ ...

MIPModDB: MIPModDB is a database of comparative protein structure models of MIP (Major intrinsic proteins) family of proteins.Protein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Coles PhillipsReaction coordinateSymmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Database of protein conformational diversity: The Database of protein conformational diversity (PCDB) is a database of diversity of protein tertiary structures within protein domains as determined by X-ray crystallography. Proteins are inherently flexible and this database collects information on this subject for use in molecular research.FERM domain: In molecular biology, the FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane.CS-BLASTLigation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.Phase problem: In physics the phase problem is the name given to the problem of loss of information concerning the phase that can occur when making a physical measurement. The name itself comes from the field of x-ray crystallography, where the phase problem has to be solved for the determination of a structure from diffraction data.DNA binding site: DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.Proximity ligation assay: Proximity ligation assay (in situ PLA) is a technology that extends the capabilities of traditional immunoassays to include direct detection of proteins, protein interactions and modifications with high specificity and sensitivity. Protein targets can be readily detected and localized with single molecule resolution and objectively quantified in unmodified cells and tissues.Transmembrane domain: Transmembrane segment usually denotes a single transmembrane alpha helix of a transmembrane protein, also known as an integral protein.http://www.Ferric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.List of strains of Escherichia coli: Escherichia coli is a well studied bacterium that was first identified by Theodor Escherich, after whom it was later named.Ethyl groupMolar mass distribution: In linear polymers the individual polymer chains rarely have exactly the same degree of polymerization and molar mass, and there is always a distribution around an average value. The molar mass distribution (or molecular weight distribution) in a polymer describes the relationship between the number of moles of each polymer species (Ni) and the molar mass (Mi) of that species.DNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.Specificity constant: In the field of biochemistry, the specificity constant (also called kinetic efficiency or k_{cat}/K_{M}), is a measure of how efficiently an enzyme converts substrates into products. A comparison of specificity constants can also be used as a measure of the preference of an enzyme for different substrates (i.Src homology domain: In biology, a Src homology domain is one of the two small protein binding domains found in the Src oncoprotein. Homologs of both the Src homology 2 and Src homology 3 domains are found in numerous other proteins.Knotted protein: Knotted proteins are proteins whose backbones entangle themselves in a knot. One can imagine pulling a protein chain from both termini, as though pulling a string from both ends.Margaret Jope: Margaret Jope (1913–2004) was a Scottish biochemist, born as Henrietta Margaret Halliday in Peterhead, Scotland.Thermotoga maritima: Thermotoga maritima is a hyperthermophilic organism that is a member of the order Thermotogales.Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Chemically induced dimerization: Chemically Induced Dimerization (CID) is a biological mechanism in which two proteins bind only in the presence of a certain small molecule, enzyme or other dimerizing agent. Genetically engineered CID systems are used in biological research to control protein localization, to manipulate signalling pathways and to induce protein activation.Electron crystallography: Electron crystallography is a method to determine the arrangement of atoms in solids using a transmission electron microscope (TEM).SEA Native Peptide LigationBurst kinetics: Burst kinetics is a form of enzyme kinetics that refers to an initial high velocity of enzymatic turnover when adding enzyme to substrate. This initial period of high velocity product formation is referred to as the "Burst Phase".Lattice protein: Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.Membrane protein: Membrane proteins are proteins that interact with biological membranes. They are one of the common types of protein along with soluble globular proteins, fibrous proteins, and disordered proteins.Mature messenger RNA: Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Unlike the eukaryotic RNA immediately after transcription known as precursor messenger RNA, it consists exclusively of exons, with all introns removed.Zuotin: Z-DNA binding protein 1, also known as Zuotin, is a Saccharomyces cerevisiae yeast gene.Beef cattle: Beef cattle are cattle raised for meat production (as distinguished from dairy cattle, used for milk production). The meat of adult cattle is known as beef.YjdF RNA motifTriparental mating: Triparental mating is a form of Bacterial conjugation where a conjugative plasmid present in one bacterial strain assists the transfer of a mobilizable plasmid present in a second bacterial strain into a third bacterial strain. Plasmids are introduced into bacteria for such purposes as transformation, cloning, or transposon mutagenesis.Nucleic acid structure: Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar.DNA-binding proteinEscherichia coli (molecular biology): Escherichia coli (; commonly abbreviated E. coli) is a gammaproteobacterium commonly found in the lower intestine of warm-blooded organisms (endotherms).Ligand (biochemistry): In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a signal-triggering molecule binding to a site on a target protein.Hexagonal crystal system: In crystallography, the hexagonal crystal system is one of the 7 crystal systems, the hexagonal lattice system is one of the 7 lattice systems, and the hexagonal crystal family is one of the 6 crystal families. They are closely related and often confused with each other, but they are not the same.ParaHox: The ParaHox gene cluster is an array of homeobox genes (involved in morphogenesis, the regulation of patterns of anatomical development) from the Gsx, Xlox (Pdx) and Cdx gene families.SHIFTCORShort linear motifCryptic self epitopes: In immunology, cryptic self epitopes are a source of autoimmunity.Proteinogenic amino acid: Proteinogenic amino acids are amino acids that are precursors to proteins, and are incorporated into proteins cotranslationally — that is, during translation. There are 23 proteinogenic amino acids in prokaryotes (including N-Formylmethionine, mainly used to initiate protein synthesis and often removed afterward), but only 21 are encoded by the nuclear genes of eukaryotes.Restriction fragment: A restriction fragment is a DNA fragment resulting from the cutting of a DNA strand by a restriction enzyme (restriction endonucleases), a process called restriction. Each restriction enzyme is highly specific, recognising a particular short DNA sequence, or restriction site, and cutting both DNA strands at specific points within this site.Eukaryotic transcription: Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells.Acid catalysis: In acid catalysis and base catalysis a chemical reaction is catalyzed by an acid or a base. The acid is the proton donor and the base is the proton acceptor.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Protein subcellular localization prediction: Protein subcellular localization prediction (or just protein localization prediction) involves the computational prediction of where a protein resides in a cell.New Zealand rabbitProlyl endopeptidase: Prolyl endopeptidase (PE) also known as prolyl oligopeptidase or post-proline cleaving enzyme is an enzyme that in humans is encoded by the PREP gene.Spin–lattice relaxation in the rotating frame: Spin–lattice relaxation in the rotating frame is the mechanism by which Mxy, the transverse component of the magnetization vector, exponentially decays towards its equilibrium value of zero, under the influence of a radio frequency (RF) field in nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI). It is characterized by the spin–lattice relaxation time constant in the rotating frame, T1ρ.Cell membraneMolecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.WIN 56,098: WIN 56,098 is a chemical that is considered to be an aminoalkylindole derivative. It is a tricyclic aryl derivative that acts as a competitive antagonist at the CB2 cannabinoid receptor.Translational regulation: Translational regulation refers to the control of the levels of protein synthesized from its mRNA. The corresponding mechanisms are primarily targeted on the control of ribosome recruitment on the initiation codon, but can also involve modulation of the elongation or termination of protein synthesis.X-ray magnetic circular dichroismThermal cyclerMonoclonal antibody therapyLiver sinusoid: A liver sinusoid is a type of sinusoidal blood vessel (with fenestrated, discontinuous endothelium) that serves as a location for the oxygen-rich blood from the hepatic artery and the nutrient-rich blood from the portal vein.SIU SOM Histology GIRNA-binding protein database: The RNA-binding Proteins Database (RBPDB) is a biological database of RNA-binding protein specificities that includes experimental observations of RNA-binding sites. The experimental results included are both in vitro and in vivo from primary literature.

(1/1667) Hidden Markov models-based system (HMMSPECTR) for detecting structural homologies on the basis of sequential information.

HMMSPECTR is a tool for finding putative structural homologs for proteins with known primary sequences. HMMSPECTR contains four major components: a data warehouse with the hidden Markov models (HMM) and alignment libraries; a search program which compares the initial protein sequences with the libraries of HMMs; a secondary structure prediction and comparison program; and a dominant protein selection program that prepares the set of 10-15 "best" proteins from the chosen HMMs. The data warehouse contains four libraries of HMMs. The first two libraries were constructed using different HHM preparation options of the HAMMER program. The third library contains parts ("partial HMM") of initial alignments. The fourth library contains trained HMMs. We tested our program against all of the protein targets proposed in the CASP4 competition. The data warehouse included libraries of structural alignments and HMMs constructed on the basis of proteins publicly available in the Protein Data Bank before the CASP4 meeting. The newest fully automated versions of HMMSPECTR 1.02 and 1.02ss produced better results than the best result reported at CASP4 either by r.m.s.d. or by length (or both) in 64% (HMMSPECTR 1.02) and 79% (HMMSPECTR 1.02ss) of the cases. The improvement is most notable for the targets with complexity 4 (difficult fold recognition cases).  (+info)

(2/1667) Modelling the structure of the fusion protein from human respiratory syncytial virus.

The fusion protein of respiratory syncytial virus (RSV-F) is responsible for fusion of virion with host cells and infection of neighbouring cells through the formation of syncytia. A three-dimensional model structure of RSV-F was derived by homology modelling from the structure of the equivalent protein in Newcastle disease virus (NDV). Despite very low sequence homology between the two structures, most features of the model appear to have high credibility, although a few small regions in RSV-F whose secondary structure is predicted to be different to that in NDV are likely to be poorly modelled. The organization of individual residues identified in escape mutants against monoclonal antibodies correlates well with known antigenic sites. The location of residues involved in point mutations in several drug-resistant variants is also examined.  (+info)

(3/1667) Novel carbohydrate specificity of the 16-kDa galectin from Caenorhabditis elegans: binding to blood group precursor oligosaccharides (type 1, type 2, Talpha, and Tbeta) and gangliosides.

Galectins, a family of soluble beta-galactosyl-binding lectins, are believed to mediate cell-cell and cell-extracellular matrix interactions during development, inflammation, apoptosis, and tumor metastasis. However, neither the detailed mechanisms of their function(s) nor the identities of their natural ligands have been unequivocally elucidated. Of the several galectins present in the nematode Caenorhabditis elegans, the 16-kDa "proto" type and the 32-kDa "tandem-repeat" type are the best characterized so far, but their carbohydrate specificities have not been examined in detail. Here, we report the carbohydrate-binding specificity of the recombinant C. elegans 16-kDa galectin and the structural analysis of its binding site by homology modeling. Our results indicate that unlike the galectins characterized so far, the C. elegans 16-kDa galectin interacts with most blood group precursor oligosaccharides (type 1, Galbeta1,3GlcNAc, and type 2, Galbeta1,4GlcNAc; Talpha, Galbeta1,3GalNAcalpha; Tbeta, Galbeta1,3GalNAcbeta) and gangliosides containing the Tbeta structure. Homology modeling of the C. elegans 16-kDa galectin CRD revealed that a shorter loop containing residues 66-69, which enables interactions of Glu(67) with both axial and equatorial -OH at C-3 of GlcNAc (in Galbeta1,4GlcNAc) or at C-4 of GalNAc (in Galbeta1,3GalNAc), provides the structural basis for this novel carbohydrate specificity.  (+info)

(4/1667) A comprehensive analysis of 40 blind protein structure predictions.

BACKGROUND: We thoroughly analyse the results of 40 blind predictions for which an experimental answer was made available at the fourth meeting on the critical assessment of protein structure methods (CASP4). Using our comparative modelling and fold recognition methodologies, we made 29 predictions for targets that had sequence identities ranging from 50% to 10% to the nearest related protein with known structure. Using our ab initio methodologies, we made eleven predictions for targets that had no detectable sequence relationships. RESULTS: For 23 of these proteins, we produced models ranging from 1.0 to 6.0 A root mean square deviation (RMSD) for the Calpha atoms between the model and the corresponding experimental structure for all or large parts of the protein, with model accuracies scaling fairly linearly with respect to sequence identity (i.e., the higher the sequence identity, the better the prediction). We produced nine models with accuracies ranging from 4.0 to 6.0 A Calpha RMSD for 60-100 residue proteins (or large fragments of a protein), with a prediction accuracy of 4.0 A Calpha RMSD for residues 1-80 for T110/rbfa. CONCLUSIONS: The areas of protein structure prediction that work well, and areas that need improvement, are discernable by examining how our methods have performed over the past four CASP experiments. These results have implications for modelling the structure of all tractable proteins encoded by the genome of an organism.  (+info)

(5/1667) The SBP2 and 15.5 kD/Snu13p proteins share the same RNA binding domain: identification of SBP2 amino acids important to SECIS RNA binding.

Selenoprotein synthesis in eukaryotes requires the selenocysteine insertion sequence (SECIS) RNA, a hairpin in the 3' untranslated region of selenoprotein mRNAs. The SECIS RNA is recognized by the SECIS-binding protein 2 (SBP2), which is a key player in this specialized translation machinery. The objective of this work was to obtain structural insight into the SBP2-SECIS RNA complex. Multiple sequence alignment revealed that SBP2 and the U4 snRNA-binding protein 15.5 kD/Snu13p share the same RNA binding domain of the L7A/L30 family, also found in the box H/ACA snoRNP protein Nhp2p and several ribosomal proteins. In corollary, we have detected a similar secondary structure motif in the SECIS and U4 RNAs. Combining the data of the crystal structure of the 15.5 kD-U4 snRNA complex, and the SBP2/15.5 kD sequence similarities, we designed a structure-guided strategy predicting 12 SBP2 amino acids that should be critical for SECIS RNA binding. Alanine substitution of these amino acids followed by gel shift assays of the SBP2 mutant proteins identified four residues whose mutation severely diminished or abolished SECIS RNA binding, the other eight provoking intermediate down effects. In addition to identifying key amino acids for SECIS recognition by SBP2, our findings led to the proposal that some of the recognition principles governing the 15.5 kD-U4 snRNA interaction must be similar in the SBP2-SECIS RNA complex.  (+info)

(6/1667) Group D prothrombin activators from snake venom are structural homologues of mammalian blood coagulation factor Xa.

Procoagulant venoms of several Australian elapids contain proteinases that specifically activate prothrombin; among these, Group D activators are functionally similar to coagulation factor Xa (FXa). Structural information on this class of prothrombin activators will contribute significantly towards understanding the mechanism of FXa-mediated prothrombin activation. Here we present the purification of Group D prothrombin activators from three Australian snake venoms (Hoplocephalus stephensi, Notechis scutatus scutatus and Notechis ater niger) using a single-step method, and their N-terminal sequences. The N-terminal sequence of the heavy chain of hopsarin D (H. stephensi) revealed that a fully conserved Cys-7 was substituted with a Ser residue. We therefore determined the complete amino acid sequence of hopsarin D. Hopsarin D shows approximately 70% similarity with FXa and approximately 98% similarity with trocarin D, a Group D prothrombin activator from Tropidechis carinatus. It possesses the characteristic Gla domain, two epidermal growth factor-like domains and a serine proteinase domain. All residues important for catalysis are conserved, as are most regions involved in interactions with factor Va and prothrombin. However, there are some structural differences. Unlike FXa, hopsarin D is glycosylated in both its chains: in light-chain residue 52 and heavy-chain residue 45. The glycosylation on the heavy chain is a large carbohydrate moiety adjacent to the active-site pocket. Overall, hopsarin D is structurally and functionally similar to mammalian coagulation FXa.  (+info)

(7/1667) Structural aspects of oligomerization taking place between the transmembrane alpha-helices of bitopic membrane proteins.

Recent advances in biophysical methods have been able to shed more light on the structures of helical bundles formed by the transmembrane segments of bitopic membrane proteins. In this manuscript, I attempt to review the biological importance and diversity of these interactions, the energetics of bundle formation, motifs capable of inducing oligomerization and methods capable of detecting, solving and predicting the structures of these oligomeric bundles. Finally, the structures of the best characterized instances of transmembrane alpha-helical bundles formed by bitopic membrane proteins are described in detail.  (+info)

(8/1667) Interaction of three Caenorhabditis elegans isoforms of translation initiation factor eIF4E with mono- and trimethylated mRNA 5' cap analogues.

Translation initiation factor eIF4E binds the m(7)G cap of eukaryotic mRNAs and mediates recruitment of mRNA to the ribosome during cap-dependent translation initiation. This event is the rate-limiting step of translation and a major target for translational control. In the nematode Caenorhabditis elegans, about 70% of genes express mRNAs with an unusual cap structure containing m(3)(2,2,7)G, which is poorly recognized by mammalian eIF4E. C. elegans expresses five isoforms of eIF4E (IFE-1, IFE-2, etc.). Three of these (IFE-3, IFE-4 and IFE-5) were investigated by means of spectroscopy and structural modelling based on mouse eIF4E bound to m(7)GDP. Intrinsic fluorescence quenching of Trp residues in the IFEs by iodide ions indicated structural differences between the apo and m(7)G cap bound proteins. Fluorescence quenching by selected cap analogues showed that only IFE-5 forms specific complexes with both m(7)G- and m(3)(2,2,7)G-containing caps (K(as) 2 x 10(6) M(-1) to 7 x 10(6) M(-1)) whereas IFE-3 and IFE-4 discriminated strongly in favor of m(7)G-containing caps. These spectroscopic results quantitatively confirm earlier qualitative data derived from affinity chromatography. The dependence of K(as) on pH indicated optimal cap binding of IFE-3, IFE-4 and IFE-5 at pH 7.2, lower by 0.4 pH units than that of eIF4E from human erythrocytes. These results provide insight into the molecular mechanism of recognition of structurally different caps by the highly homologous IFEs.  (+info)

haploid germ cells

  • This gene which is abundantly expressed in testicular haploid germ cells encodes a protein that is recognized by sperm-agglutinating antibodies and implicated in infertility. (


  • In this day of exploding bioinformatics information from genomics and proteomics, it is ever more important to be conversant with macromolecular three-dimensional structure, and how it relates to protein and nucleic acid function and drug design. (
  • Adopted by Nature Structural and Molecular Biology and other bioinformatics resources . (
  • Introduction to Structural Bioinformatics. (
  • She is best known for her work aimed at providing mechanistic insight into the structure, dynamics, and function of G protein-coupled receptors using methods such as molecular modeling, bioinformatics, cheminformatics, enhanced molecular dynamics simulations, and rational drug design approaches. (
  • To obtain rigorous mechanistic insight into the structure, dynamics, and function of GPCRs and beta3 integrins, the Filizola lab uses several computational structural biology tools, ranging from molecular modeling, bioinformatics, cheminformatics, molecular dynamics simulations, a variety of enhanced sampling algorithms, and rational drug design approaches. (
  • SWISS-MODEL is a structural bioinformatics web-server dedicated to homology modeling of protein 3D structures. (


  • The deduced amino acid sequence of orf240 showed significant homology to Escherichia coli Fnr and R. meliloti FixK. (
  • Protein expression in Escherichia coli. (


  • The solution structure of the adhesion protein Bd37 from Babesia divergens reveals structural homology with eukaryotic proteins involved in membrane trafficking" J. Mol. (
  • Eukaryotic translation initiation factor 3 subunit A (eIF3a) is a protein that in humans is encoded by the EIF3A gene. (
  • ATG8 proteins are present in all known eukaryotic organisms. (

membrane proteins

  • Moreover, in transfected HeLa cells, chimeric GFP containing a nuclear localization signal and a C-terminal CaaX motif of N-Ras induces intranuclear membrane stacks that resemble those induced by lamins and ER-like cisternae that are induced in the cytoplasm upon increased synthesis of integral ER membrane proteins. (
  • Filizola is a computational biophysicist who studies membrane proteins and with extensive experience in the application of methods of computational chemistry and theoretical chemistry to biochemical and biomedical problems, as well as to drug discovery. (

protein's structure

  • Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (
  • Since the loop is the least conserved portion of a protein's structure, the homology-based method cannot always find a known template that aligns with the target sequence. (


  • At the molecular level, such responses include changes in the transcription or translation of genes, and post-translational and conformational changes in proteins, as well as changes in their location. (

recombinant protein

  • Effect of osmotic stress and heat shock in recombinant protein overexpression and crystallization. (

disulfide bonds

  • SLPI is a highly cationic single-chain protein with eight intramolecular disulfide bonds. (


  • Genetic analysis reveals links between lipid A structure and expression of the outer membrane protein gene, ropB, in Rhizobium leguminosarum. (
  • In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. (
  • This method uses the gene for azurin from P. aeruginosa as an expression system for azurin or heterologous proteins in P. aeruginosa or heterologous cells. (
  • Methods are provided for using the fused gene to produce labeled, chemically modified proteins in vivo and to isolate a protein knowing only the nucleotide sequence of the gene encoding the protein. (
  • FK506 binding protein 6, also known as FKBP6, is a human gene. (
  • Survivin, also called baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5, is a protein that, in humans, is encoded by the BIRC5 gene. (
  • A-kinase anchor protein 4 is a scaffold protein that in humans is encoded by the AKAP4 gene. (
  • An X-linked gene encodes a major human sperm fibrous sheath protein, hAKAP82. (
  • Microtubule-associated proteins 1A/1B light chain 3B (hereafter referred to as LC3) is a protein that in humans is encoded by the MAP1LC3B gene. (
  • C-jun-amino-terminal kinase-interacting protein 4 is a scaffold protein that in humans is encoded by the SPAG9 gene. (
  • The protein encoded by this gene is a scaffolding protein that brings together mitogen-activated protein kinases and their transcription factor targets for the activation of specific signaling pathways. (


  • genus Capripoxvirus , family Poxviridae ) structural proteins as candidate subunit vaccines to control sheep pox disease. (
  • Most commonly, ILRs resembles the β1 subunit found in integrin proteins. (
  • Some ILRs mimic the α-subunit of integrin proteins containing the ligand binding region known as the I-domain. (
  • The A-kinase anchor proteins (AKAPs) are a group of structurally diverse proteins, which have the common function of binding to the regulatory subunit of protein kinase A (PKA) and confining the holoenzyme to discrete locations within the cell. (

shows structural

  • An Fnr-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium meliloti FixK. (
  • The encoded protein shows structural homology to FKBP immunophilins, which bind to the immunosuppressants FK506 and rapamycin. (
  • The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. (


  • 2007. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. (
  • Structurally, STEAP-1 is a 339 amino acid protein characterized by a molecular topology of six transmembrane domains and intracellular N- and C-termini, suggesting that it folds in a "serpentine" manner into three extracellular and two intracellular loops. (
  • Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalysed by protein kinases, which ultimately results in a cellular response. (
  • However, the molecular architecture and folding conformation of these proteins are all very similar. (
  • Following three years as Co-Director of the Structural/Chemical Biology and Molecular Design (SMD) Graduate Program, and one year as Co-Director of the Biophysics and Systems Pharmacology (BSP) Graduate Program, she was appointed Dean of the Graduate School of Biomedical Sciences at Mount Sinai in May 2016. (
  • The molecular mechanisms of survivin regulation are still not well understood, but regulation of survivin seems to be linked to the p53 protein. (


  • The problem arises often in homology modeling, where the tertiary structure of an amino acid sequence is predicted based on a sequence alignment to a template, or a second sequence whose structure is known. (


  • Integrin-like receptors and integrin-linked kinases together have been implicated in surface adhesion, immune response, and ion accumulation in plant cells in a manner akin to the family of integrin proteins. (
  • Extracellular signals are transduced into cells through mitogen-activated protein kinases. (
  • The structural organization of these kinases into specific signaling domains is facilitated by scaffolding proteins involved in closely tethering different kinases so that successive phosphorylation events can occur. (


  • 2005. Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization. (
  • The Ribose repressor (RbsR) is a bacterial DNA-binding transcription repressor protein and a member of the LacI/GalR protein family. (


  • The nuclear lamina is composed of lamins and lamin-associated proteins. (
  • Lamins bind chromatin both directly and indirectly via lamin-associated proteins ( Mattout-Drubezki and Gruenbaum, 2003 ). (


  • They also argue that the collagen fragments derive from bacterial proteins with structural homology to collagen. (


  • We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein. (
  • Other proteins that contain a CaaX motif include the Ras proteins and many other small G proteins, fungal mating pheromones and large G protein subunits. (
  • A structural feature common to all IAP family proteins is that they all contain at least one baculoviral IAP repeat (BIR) domain characterized by a conserved zinc-coordinating Cys/His motif at the N-terminal half of the protein. (
  • LC3 is also enriched in nucleoli via its triple arginine motif, and associates with a number of different nuclear and nucleolar constituents including: MAP1B, tubulin, and several ribosomal proteins. (


  • Lymphocytes migrate from the blood stream via a distinctive 'rolling interaction' mediated by interactions between cellular surface proteins. (
  • Further interactions between proteins or activation via chemokines cause more stable forces to be formed between the cell and the vessel. (
  • Participants will be enabled to incorporate computer visualization and qualitative analysis of 3D structure of protein, DNA, RNA, and protein-ligand interactions into their teaching and research. (
  • This loss of activity appears to result from the absence of key amino acid residues that produce structural differences that hinder the key interactions necessary for the protease activity seen in BPTI. (


  • Because protein function is determined by its shape and the physiochemical properties of its exposed surface, it is important to create an accurate model for protein/ligand interaction studies. (


  • Mammalian integrins are heterodimer transmembrane proteins that play a large role bidirectional signal transduction. (
  • As transmembrane proteins, integrins connect the extracellular matrix (ECM) to the plasma membrane of the animal cell. (
  • This structural similarity between ILRs and integrins was determined through various imaging techniques, SDS-PAGE, western blotting, and kinetic studies. (
  • These proteins are around 55 to 110 kDa and some studies have found them to react with animal anti-β1 antibodies suggesting the structural similarity between animal integrins and these plant integrin-like receptors. (
  • A plant protein with structural similarity to integrins contains the amino acid sequence Asn-Gly-Asp (NGD). (
  • This protein shares functional homology with mammalian integrins in that it connects the ECM to the intracellular matrix to both stabilize the cell structure and allow for signal exchange. (


  • Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (
  • It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB files (3D-Coffee). (
  • In its latest version, T-Coffee can be used to combine protein sequences and structures, RNA sequences and structures. (

amino acid

  • 1. A STEAP-2 protein having an amino acid sequence shown in FIG. 9 A-D (SEQ ID NO: 8). (
  • Most of the positively charged amino acid residues of dendrotoxins are located in the lower part of the structure, creating a cationic domain on one side of the protein. (

transmembrane region

  • Synaptotagmins constitute a family of membrane-trafficking proteins that are characterized by an N-terminal transmembrane region, a linker of variable size, and two C-terminal C2 domains in tandem ( Craxton, 2004 ). (


  • One of the methods that have been proposed is a multiobjective optimization, in which protein stability and catalytic activity are simultaneously optimized [ 4 , 5 ]. (
  • Several methods have been proposed to design novel stable proteins, such as multi-objective optimization, in which protein stability and catalytic activity are simultaneously optimized. (
  • Finally, collagen's association with the bone matrix provides added stability to the collagen proteins. (
  • A good body of research has found ILR proteins that model the glycoproteins vitronectin and fibronectin, two important molecules in membrane stability and homeostasis. (
  • His work is reported to have assisted in the understanding of the behaviour of several seed proteins from a stability perspective and revealed more about their structural biology. (
  • All dendrotoxins are cross-linked by three disulfide bridges, which add stability to the protein and greatly contribute to its structural conformation. (

hypothetical protein

  • 2007. Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus. (
  • 2005. Crystal structure of the conserved hypothetical protein MPN330 (GI: 1674200) from Mycoplasma pneumoniae. (


  • Here, we show that loss of function of the homologous Arabidopsis thaliana Synaptotagmin 1 protein (SYT1) reduces the viability of cells as a consequence of a decrease in the integrity of the plasma membrane. (
  • PSI-Coffee aligns distantly related proteins using homology extension (slow and accurate) TM-Coffee aligns transmembrane proteins using homology extension Pro-Coffee aligns homologous promoter regions Accurate automatically combine the most accurate modes for DNA, RNA and Proteins (experimental! (


  • Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. (
  • 2007. StrBioLib: a Java library for development of custom computational structural biology applications. (
  • She returned to Mount Sinai as an Assistant Professor in the Department of Structural and Chemical Biology where she was later promoted Associate Professor (with Tenure since January 2013), and then Full Professor in 2014. (


  • Despite the structural homology between these two proteins, dendrotoxins do not appear to exhibit any measurable inhibitory protease activity like BPTI. (


  • 2007. Crystal structure of a novel single-stranded DNA binding protein from Mycoplasma pneumoniae. (


  • 2007. Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans. (
  • 2006. Structural characterization of an iron-sulfur cluster assembly protein IscU in a zinc-bound form. (
  • 2005. Structural and functional characterization of a 5,10-methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087). (


  • Implications for the synthesis of CaaX-containing proteins are discussed and the difference from intranuclear fibrous lamina annulate lamellae formations is emphasized. (


  • Structural comparison of CDRs from other CD4 binding site antibodies suggests diverse modes of interaction.Mutational analysis identified CDR3 as a key component of gp120 interaction as determined by surface plasmon resonance.Furthermore, our data confirm that the structural plasticity of gp120 can accommodate multiple modes of antibody binding within the CD4 binding site. (
  • Structural comparison of CDRs from other CD4 binding site antibodies suggests diverse modes of interaction. (
  • Thus the structural study identifies the long CDR3 of D7 as the key determinant of interaction and HIV-1 neutralization. (
  • It is thus possible that C8 employs different structural principles for gp120 interaction and neutralization . (
  • Even with these differences, research indicates that similar proteins involved in the interaction between the ECM and animals cells are also involved in the interaction of the cell wall and plant cells. (
  • ILRs play a role in protein-protein interaction and are found in the plasma membrane of plant cells in the leaf, root and vasculature of plants. (


  • In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information. (
  • Because of their high potency and selectivity for potassium channels, dendrotoxins have proven to be extremely useful as pharmacological tools for studying the structure and function of these ion channel proteins. (
  • It is shown to be conserved in function across evolution as homologues of the protein are found both in vertebrates and invertebrates. (


  • Integrin-like receptors (ILRs) are found in plants and carry unique functional properties similar to true integrin proteins. (
  • Proteins responsible for detecting stimuli are generally termed receptors, although in some cases the term sensor is used. (
  • Dr. Filizola's research program is mainly focused on G Protein-Coupled Receptors (GPCRs), which are the targets for about half of all currently used drugs. (


  • At certain points along the triple helix, the individual protein strands are chemically bound to each other to form cross-links. (


  • 2005. Update on the Pfam5000 Strategy for Selection of Structural Genomics Targets. (


  • 2006. Structural proteomics of minimal organisms: Conservation of protein fold usage and evolutionary implications. (
  • Structural genomics of minimal organisms and protein fold space. (
  • The C-terminal domain has an 'open fold' with no structural homology to other proteins. (


  • That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. (


  • Structural analysis of the MadCAM-1 protein shows that it is a 41.5 kDa transmembrane protein with a small cytoplasmic tail and a large extracellular region. (


  • However, Imredy and MacKinnon have proposed that delta-dendrotoxin may have an off-center binding site on their target proteins, and may inhibit the channel by altering the structure of the channel, rather than physically blocking the pore. (
  • The survivin protein functions to inhibit caspase activation, thereby leading to negative regulation of apoptosis or programmed cell death. (


  • In this work, we generated and optimized a new synthetic fusion protein using an evolutionary approach. (


  • Western blot analysis revealed the antigenic and immunogenic properties of SPPV-060, SPPV-095, SPPV-117 and SPPV-122 proteins when injected with adjuvant into experimental rabbits. (


  • The nuclear lamina is a protein meshwork lining the nucleoplasmic face of the nuclear envelope. (
  • Nuclear lamins belong to the class of intermediate filament proteins. (
  • Lamins are the only nuclear isoprenylated proteins known to date. (
  • The importance of the nuclear functions of autophagy proteins should not be underestimated. (

structure prediction

  • Currently, the SWISS-MODEL server pipeline is participating in the CAMEO3D (Continuous Automated Model EvaluatiOn) project which continuously evaluates the accuracy and reliability of protein structure prediction services in a fully automated manner. (
  • Loop modeling is a problem in protein structure prediction requiring the prediction of the conformations of loop regions in proteins with or without the use of a structural template. (


  • The human STEAPs exhibit a high degree of structural conservation among them but show no significant structural homology to any known human proteins. (
  • Prakash is known to have done extensive research in structural homology of seed proteins and the association-dissociation and denaturation profiles of these proteins. (
  • As mentioned above homology-based methods use a database to align the target protein gap with a known template protein. (


  • 2005. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. (


  • More recently, scientists recovered fragments of the protein collagen from this specimen as well. (
  • New research from an interdisciplinary team of scientists provides further response to this question by demonstrating how collagen's structural features allow fragments to survive for eons . (
  • Once the protein strand breaks, the fragments are held in close proximity by the contact points. (


  • LC3 has a LDS (LIR docking site)/hydrophobic binding interface in the N terminus which interacts with LIR (LC3 Interacting Region) containing proteins. (


  • More constrained versions of loop modeling are also used in the data fitting stages of solving a protein structure by X-ray crystallography, because loops can correspond to regions of low electron density and are therefore difficult to resolve. (
  • The accuracy of such short loops may be almost as accurate as that of the homology model upon which it is based. (


  • This domain is rich in hydrophobic amino acids, the mutation of which impairs the ability of LC3 binding with LIR containing proteins, many of which are autophagy cargo adapter proteins. (

plant protein

  • True Latex allergy develops from plant protein in the Latex sap itself, whereas concomitant allergies may also develop from the chemicals added during processing. (


  • Vitamin A-derived retinoic acid regulates the expression of these cell surface proteins. (
  • STEAP-1 protein expression is maintained at high levels across various stages of prostate cancer. (


  • In this case only the sequence or UniProt accession code of the protein is required as input. (


  • VH is derived from a single protein domain of 35 residues [ 9 ]. (
  • Positive charge results from lysine (Lys) and arginine (Arg) residues that are concentrated in three primary regions of the protein: near the N-terminus (Arg3, Arg4, Lys5), near the C-terminus (Arg54, Arg55) and at the narrow β-turn region (Lys28, Lys29, Lys30). (