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.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.Databases, Factual: Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.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.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).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.Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.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.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Databases as Topic: Organized collections of computer records, standardized in format and content, that are stored in any of a variety of computer-readable modes. They are the basic sets of data from which computer-readable files are created. (from ALA Glossary of Library and Information Science, 1983)Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.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.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.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.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.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.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.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.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.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.Databases, Bibliographic: Extensive collections, reputedly complete, of references and citations to books, articles, publications, etc., generally on a single subject or specialized subject area. Databases can operate through automated files, libraries, or computer disks. The concept should be differentiated from DATABASES, FACTUAL which is used for collections of data and facts apart from bibliographic references to them.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.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.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.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.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.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.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.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).Bacterial Proteins: Proteins found in any species of bacterium.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)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.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Kinetics: The rate dynamics in chemical or physical systems.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Information Storage and Retrieval: Organized activities related to the storage, location, search, and retrieval of information.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.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.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.Protein Denaturation: Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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 126.96.36.199.Database Management Systems: Software designed to store, manipulate, manage, and control data for specific uses.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.Loligo: A genus of SQUID in the family Loliginidae, superorder DECAPODIFORMES, with a spindle-shaped body. They are well-studied, common inshore squids of the Atlantic and eastern Pacific Oceans, but their various species are taxonomically unresolved.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.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.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.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.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.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.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.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)Spectrin: A high molecular weight (220-250 kDa) water-soluble protein which can be extracted from erythrocyte ghosts in low ionic strength buffers. The protein contains no lipids or carbohydrates, is the predominant species of peripheral erythrocyte membrane proteins, and exists as a fibrous coating on the inner, cytoplasmic surface of the membrane.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.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.Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).PDZ Domains: Protein interaction domains of about 70-90 amino acid residues, named after a common structure found in PSD-95, Discs Large, and Zona Occludens 1 proteins. PDZ domains are involved in the recruitment and interaction of proteins, and aid the formation of protein scaffolds and signaling networks. This is achieved by sequence-specific binding between a PDZ domain in one protein and a PDZ motif in another protein.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Guanidine: A strong organic base existing primarily as guanidium ions at physiological pH. It is found in the urine as a normal product of protein metabolism. It is also used in laboratory research as a protein denaturant. (From Martindale, the Extra Pharmacopoeia, 30th ed and Merck Index, 12th ed) It is also used in the treatment of myasthenia and as a fluorescent probe in HPLC.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.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).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.Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.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.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.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.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.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.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.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.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.Molecular Weight: The sum of the weight of all the atoms in a molecule.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.Repetitive Sequences, Amino Acid: A sequential pattern of amino acids occurring more than once in the same protein sequence.Chimera: An individual that contains cell populations derived from different zygotes.Spectrometry, Fluorescence: Measurement of the intensity and quality of fluorescence.Chymotrypsin: A serine endopeptidase secreted by the pancreas as its zymogen, CHYMOTRYPSINOGEN and carried in the pancreatic juice to the duodenum where it is activated by TRYPSIN. It selectively cleaves aromatic amino acids on the carboxyl side.Cytoplasm: The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)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.Protein Transport: The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.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)Endopeptidases: A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.Systems Integration: The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.Fungal Proteins: Proteins found in any species of fungus.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.Disulfides: Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Zinc Fingers: Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.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.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.Calorimetry, Differential Scanning: Differential thermal analysis in which the sample compartment of the apparatus is a differential calorimeter, allowing an exact measure of the heat of transition independent of the specific heat, thermal conductivity, and other variables of the sample.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.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Biopolymers: Polymers synthesized by living organisms. They play a role in the formation of macromolecular structures and are synthesized via the covalent linkage of biological molecules, especially AMINO ACIDS; NUCLEOTIDES; and CARBOHYDRATES.CHO Cells: CELL LINE derived from the ovary of the Chinese hamster, Cricetulus griseus (CRICETULUS). The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems for the study of genetic alterations in cultured mammalian cells.Protein Subunits: Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly.Membrane Glycoproteins: Glycoproteins found on the membrane or surface of cells.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.Thermodynamics: A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)Viral Proteins: Proteins found in any species of virus.Antibodies, Monoclonal: Antibodies produced by a single clone of cells.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.Protein Sorting Signals: Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Calorimetry: The measurement of the quantity of heat involved in various processes, such as chemical reactions, changes of state, and formations of solutions, or in the determination of the heat capacities of substances. The fundamental unit of measurement is the joule or the calorie (4.184 joules). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)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.Epitopes: Sites on an antigen that interact with specific antibodies.Models, Structural: A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.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.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Enzyme Stability: The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.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.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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Microscopy, Electron: Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.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.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.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Glycoproteins: Conjugated protein-carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins.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.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.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.Randomized Controlled Trials as Topic: Works about clinical trials that involve at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table.Adenosine Triphosphatases: A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Databases, Chemical: Databases devoted to knowledge about specific chemicals.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Zinc: A metallic element of atomic number 30 and atomic weight 65.38. It is a necessary trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Zinc deficiency is associated with ANEMIA, short stature, HYPOGONADISM, impaired WOUND HEALING, and geophagia. It is known by the symbol Zn.Protein Kinases: A family of enzymes that catalyze the conversion of ATP and a protein to ADP and a phosphoprotein.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.MEDLINE: The premier bibliographic database of the NATIONAL LIBRARY OF MEDICINE. MEDLINE® (MEDLARS Online) is the primary subset of PUBMED and can be searched on NLM's Web site in PubMed or the NLM Gateway. MEDLINE references are indexed with MEDICAL SUBJECT HEADINGS (MeSH).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.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.Genes, Bacterial: The functional hereditary units of BACTERIA.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Serine Endopeptidases: Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.Pattern Recognition, Automated: In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)Calcium: A basic element found in nearly all organized tissues. It is a member of the alkaline earth family of metals with the atomic symbol Ca, atomic number 20, and atomic weight 40. Calcium is the most abundant mineral in the body and combines with phosphorus to form calcium phosphate in the bones and teeth. It is essential for the normal functioning of nerves and muscles and plays a role in blood coagulation (as factor IV) and in many enzymatic processes.Thermolysin: A thermostable extracellular metalloendopeptidase containing four calcium ions. (Enzyme Nomenclature, 1992) 188.8.131.52.Rabbits: The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.Blotting, 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.Data Mining: Use of sophisticated analysis tools to sort through, organize, examine, and combine large sets of information.Guanidines: A family of iminourea derivatives. The parent compound has been isolated from mushrooms, corn germ, rice hulls, mussels, earthworms, and turnip juice. Derivatives may have antiviral and antifungal properties.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.Abstracting and Indexing as Topic: Activities performed to identify concepts and aspects of published information and research reports.Fibronectins: Glycoproteins found on the surfaces of cells, particularly in fibrillar structures. The proteins are lost or reduced when these cells undergo viral or chemical transformation. They are highly susceptible to proteolysis and are substrates for activated blood coagulation factor VIII. The forms present in plasma are called cold-insoluble globulins.Biological Transport: The movement of materials (including biochemical substances and drugs) through a biological system at the cellular level. The transport can be across cell membranes and epithelial layers. It also can occur within intracellular compartments and extracellular compartments.Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.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)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 enzymesChromatography, Gel: Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.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.Bacterial Toxins: Toxic substances formed in or elaborated by bacteria; they are usually proteins with high molecular weight and antigenicity; some are used as antibiotics and some to skin test for the presence of or susceptibility to certain diseases.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Urea: A compound formed in the liver from ammonia produced by the deamination of amino acids. It is the principal end product of protein catabolism and constitutes about one half of the total urinary solids.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.PhosphoproteinsVirulence Factors: Those components of an organism that determine its capacity to cause disease but are not required for its viability per se. Two classes have been characterized: TOXINS, BIOLOGICAL and surface adhesion molecules that effect the ability of the microorganism to invade and colonize a host. (From Davis et al., Microbiology, 4th ed. p486)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.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)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.Oligopeptides: Peptides composed of between two and twelve amino acids.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.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.Information Systems: Integrated set of files, procedures, and equipment for the storage, manipulation, and retrieval of information.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Pancreatic Elastase: A protease of broad specificity, obtained from dried pancreas. Molecular weight is approximately 25,000. The enzyme breaks down elastin, the specific protein of elastic fibers, and digests other proteins such as fibrin, hemoglobin, and albumin. EC 184.108.40.206.
Anion exchanger family
Their N-terminal hydrophilic domains may interact with cytoskeletal proteins and therefore play a cell structural role. Some of ... "2.A.31 The Anion Exchanger (AE) Family". Transporter Classification Database. Saier Lab Bioinformatics Group @ UCSD / SDSC. ... Although the C-terminal domain comprises a small percentage of the size of the protein, this domain in some cases, has (i) ... Nine encode proteins that transport HCO− 3. Functionally, eight of these proteins fall into two major groups: three Cl-HCO− 3 ...
Fiocruz Genome Comparison Project
Additionally, many proteins composed of several structural and/or functional domains are overlooked by automated systems. The ... a protein database, a DNA or a DNA library. The nature of the computation in the project allows it to easily take advantage of ... and possible functions assignment to hypothetical proteins of unknown function. Moreover, proteins with multiple domains and ... All products are in the public domain by contract with WCG. The problem is that a very large information body (structural, ...
Protein domains with structural resemblance to ShK have been described in 688 proteins, most of them from Caenorhabditis ... elegans (InterPro: IPR003582). The SMART database at the EMBL has a list of 688 proteins containing 1315 ShK-like sequences ( ... Other proteins containing domains with similar structures include the cysteine-rich secretory protein snake toxins natrin, ... "The cysteine-rich secretory protein domain of Tpx-1 is related to ion channel toxins and regulates ryanodine receptor Ca2+ ...
The database of three-dimensional interacting domains (3did) is a biological database containing a catalogue of protein-protein ... 3did collects and classifies all structural models of domain-domain interactions in the Protein Data Bank, providing molecular ... 3did uses the Pfam database to define the position of protein domains in the protein structures. 3did was first published in ... Interacting protein domains of known three-dimensional structure". Nucleic Acids Research. 33 (Database issue): D413-7. doi: ...
In addition, the Structural Classification of Proteins database has defined the "ribulose phosphate binding" superfamily for ... The human protein containing this domain is the RPE (gene). Phosphopentose epimerase belongs to two protein families of ... All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure. The systematic name of this ... Other proteins included in this superfamily are 5'-monophosphate decarboxylase (OMPDC), and 3-keto-l-gulonate 6-phosphate ...
SCOP Pfam InterPro Structural domain Gene Ontology Fang, H.; Gough, J. (2012). "DcGO: Database of domain-centric ontologies on ... As a protein domain resource, dcGO includes annotations to both the individual domains and supra-domains (i.e., combinations of ... dcGO is a comprehensive ontology database for protein domains. As an ontology resource, dcGO integrates Open Biomedical ... That is why it is called dcGO, domain-centric Gene Ontology. The second concept is to use ontology-labeled protein domains for ...
subscription required) Folding proteins - from Astbury to Amyloid and Ageing on YouTube Astbury Centre for Structural Molecular ... Sheena Radford's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. ( ... Biology on YouTube Radford, Sheena Elizabeth (1987). Domains and conformational flexibility in the catalytic mechanism of the 2 ... Radford's research investigates protein folding, protein aggregation and amyloid disease. Radford was elected a Fellow of the ...
... shares structural similarities with the class A rhodopsin GPCR subfamily. It has 7 transmembrane domains with short N and ... Upon entering the presynaptic neuron, these compounds activate TAAR1 which, through protein kinase A (PKA) and protein kinase C ... The resulting sequence was not found in any database and coded for TAAR1. ... "TAAR1". The Human Protein Atlas. Retrieved 24 August 2017. Xie Z, Westmoreland SV, Bahn ME, Chen GL, Yang H, Vallender EJ, Yao ...
Family members are identified on a structural basis and contain an amino-terminal domain similar to the T1 domain present in ... Potassium channel tetramerisation domain containing 7 is a protein in humans that is encoded by the KCTD7 gene. Alternative ... EST database analysis showed that KCTD7 is expressed in human and mouse brain. KCTD7 expression hyperpolarizes the cell ... The KCTD7 gene encodes a member of the potassium channel tetramerisation domain-containing protein family. ...
... is a protein database. It consists of entries describing the protein families, domains and functional sites as well as ... detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins". Nucleic Acids ... InterPro - a centralized database, grouping data from databases of protein families, domains and functional sites - part of the ... Uniprot - the universal protein database, a central resource on protein information - PROSITE adds data to it. ...
Hubbard, T.; Murzin, A.; Brenner, S.; Chothia, C. (1997). "SCOP: A structural classification of proteins database". Nucleic ... "Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements". ... Steven Brenner and Tim Hubbard to create the Structural Classification of Proteins (SCOP) database, a periodic table for all ... "Structural genomics and protein structure". Mrc-lmb.cam.ac.uk. Retrieved 24 June 2014. Cyrus Chothia at DBLP Bibliography ...
"Structural basis of Smoothened regulation by its extracellular domains". Nature. 535 (7613): 517-22. doi:10.1038/nature18934. ... Smoothened is a protein that in humans is encoded by the SMO gene. Smoothened is a Class Frizzled (Class F) G protein-coupled ... "Frizzled Receptors: SMO". IUPHAR Database of Receptors and Ion Channels. International Union of Basic and Clinical Pharmacology ... For example, oxysterol 20(S)-OHC is known to activate vertebrate SMO by binding the cysteine rich domain near its extracellular ...
Protein Engineering Design and Selection. 24 (1-2): 33-40. doi:10.1093/protein/gzq081. PMID 21036780. Gómez, FA; Cárdenas, C; ... Toxin-antitoxin database Robson, Jennifer; McKenzie, Joanna L.; Cursons, Ray; Cook, Gregory M.; Arcus, Vickery L. (17 July 2009 ... VapBC operons consist of two genes: VapC encodes a toxic PilT N-terminus (PIN) domain, and VapB encodes a matching antitoxin. ... of VapC-mediated RNase activity is thought to be influenced by both the primary sequence of the target and secondary structural ...
Charles Lawrence (mathematician)
These teams maintain NCBI's macromolecular structure database and Cn3D visualization tool, the Conserved Domain Database and ... His focus is in the area of structural bioinformatics. Dr. Bryant also leads NCBI information resource teams in protein ... the composition of nucleotide sequences and detailed analyses of several protein families. In the past several years, based on ... CDTree analysis tool, and most recently the PubChem cheminformatics database and associated analysis tools. 1971-1975: ...
There is no predicted alternative splicing on the NCBI gene database. The figure below shows the basic primary protein ... while the blue domain is the remainder of the LOC105377021 exon. According to Ali2D (a multiple sequence alignment structural ... A predicted protein modification of LOC105377021 is phosphorylation, with sites throughout the protein, including the serine ... LOC105377021 is a protein which in humans is encoded by the LOC105377021 gene. LOC105377021 exhibits expressional pathology ...
... of protein domain combinations late in evolution, traced evolution of proteins in biological networks (see the MANET database ... and revealed important evolutionary reductive tendencies in the structural make up of proteins. Recently, his group used ... Wang M, Caetano-Anollés G (2006) Global phylogeny determined by the combination of protein domains in proteomes" Molecular ... Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen. Structure 20(1): 67-76. ...
... - Protein family database at EBI UK iPfam - Interactions of Pfam domains in PDB PDBfam - Assignments of Pfam domains to ... Domains are defined as an autonomous structural unit or reusable sequence unit that can be found in multiple protein contexts. ... genes TrEMBL Database performing an automated protein sequence annotation InterPro Integration of protein domain and protein ... a domain database with global coverage of the protein universe" (Free full text). Nucleic Acids Research. 33 (Database issue): ...
... zinc finger DNA-binding protein Krüppel associated box RING finger domain Sequence motif Steroid hormone receptor Structural ... C2H2 family at PlantTFDB: Plant Transcription Factor Database McDowall J. "Protein of the Month: Zinc Fingers". European ... Proteins that contain zinc fingers (zinc finger proteins) are classified into several different structural families. Unlike ... This entry represents the CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains ...
... but in anaerobic fungi they are protein binding domains, referred to as dockerin domains. The dockerin domains are believed to ... CBM28 has a "beta-jelly roll" topology, which is similar in structure to the CBM17 domains. Sequence and structural ... "The Carbohydrate-Active EnZymes database (CAZy): An expert resource for Glycogenomics". Nucleic Acids Research. 37 (Database ... Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. ...
... the integrative protein signature database". Nucleic Acids Research. 37 (Database issue): D211-D215. doi:10.1093/nar/gkn785. ... New developments in the family and domain prediction database". Nucleic Acids Research. 40 (Database issue): D306-D312. doi: ... from a structural perspective". Journal of Molecular Biology. 307 (4): 1113-1143. doi:10.1006/jmbi.2001.4513. ISSN 0022-2836. ... Orengo, Christine Anne; Jones, David T.; Thornton, Janet M. (1994). "Protein superfamilles and domain superfolds". Nature. 372 ...
EF-hands also appear in each structural domain of the signaling protein calmodulin and in the muscle protein troponin-C. The ... Haiech J. "EF-hand protein database (EF-handome)". European Calcium Society and the Université Libre de Bruxelles. Retrieved ... The AQ portion of this protein contains the EF-hand calcium binding domains. Humans proteins containing this domain include: ... The EF hand is a helix-loop-helix structural domain or motif found in a large family of calcium-binding proteins. The EF-hand ...
... is a database of protein families, domains and functional sites in which identifiable features found in known proteins ... SUPERFAMILY has been used to carry out structural assignments to all completely sequenced genomes.. SFLD. TIGRFAMs is a ... Other databases: Protein Data Bank, Ensembl and InterPro. *Specialised genomic databases: BOLD, Saccharomyces Genome Database, ... Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information ...
The Structural Classification of Proteins database and CATH database provide two different structural classifications of ... there are many fewer different domains, structural motifs and folds. A structural domain is an element of the protein's overall ... An example is provided by the protein tyrosine phosphatase domain and C2 domain pair in PTEN, several tensin proteins, auxilin ... domains can be "swapped" by genetic engineering between one protein and another to make chimera proteins. The structural and ...
An update to the database of structure-based sequence alignments of structural domain superfamilies". Nucleic Acids Research. ... Here are a few examples: Pfam - Protein families database of alignments and HMMs PROSITE - Database of protein domains, ... Gene family Protein superfamily Protein subfamily Protein structure Protein domains Sequence alignment Sequence clustering ... Since that time, it was found that many proteins comprise multiple independent structural and functional units or domains. Due ...
Bacterial Structural Genomics Initiative CATH Protein Structure Classification CBS Genome Atlas CDD Conserved Domain Database ... coli interaction database coliBASE (subset of the comparative genomics database xBASE) EcoGene (genome database and website ... and by analyzing the binary interactions among its proteins. Protein complexes. A 2006 study purified 4,339 proteins from ... and found a total of 2,234 protein-protein interactions. This study also integrated genetic interactions and protein structures ...
... to the three-dimensional predicted models and information derived from either Structural Classification of Proteins database ( ... Many proteins contain multiple protein domains. Phyre2 provides a table of template matches color-coded by confidence and ... Applications of Phyre and Phyre2 include protein structure prediction, function prediction, domain prediction, domain boundary ... and these sequences are processed by scanning against a large protein sequence database. The result is a database of profiles ...
Short linear motif
A database of human protein-protein interactions mediated by phosphoprotein-binding domains". Nucleic Acids Research. 36 ( ... domain databases (such as Pfam and SMART) and experimentally derived structural data (from sources such as PDB) can be used to ... A protein-protein interaction database for PDZ-domains". Bioinformatics. 21 (6): 827-828. doi:10.1093/bioinformatics/bti098. ... are short stretches of protein sequence that mediate protein protein interaction. The first definition was given by Tim Hunt: " ...
Users send a protein sequence and receive a single file with results from database comparisons and prediction methods. PP went ... PP now also identifies putative boundaries for structural domains through the CHOP procedure. Structure prediction methods: ... "Twilight zone of protein sequence alignments". Protein engineering. 12 (2): 85-94. doi:10.1093/protein/12.2.85. PMID 10195279. ... For example, by default PP returns only those proteins found in the database that are very likely to have a similar structure ...
Protein fold class
... the beta-propeller domain, the immunoglobulin fold and B3 DNA binding domain. α+β proteins are a class of structural domains in ... Protein superfamily SCOP database CATH database FSSP database Hubbard, Tim J. P.; Murzin, Alexey G.; Brenner, Steven E.; ... Common examples include the ferredoxin fold, ribonuclease A, and the SH2 domain. α/β proteins is a class of structural domains ... They are one of the common types of protein along with soluble globular proteins, fibrous proteins, and disordered proteins. ...
Protein structure prediction
family (structural context) as used in the FSSP database (Families of structurally similar proteins) and the DALI/FSSP Web site ... The domain may include all of a given protein sequence or only a portion of the sequence. Some domains are complex and made up ... In the SCOP, CATH, and FSSP databases, the known protein structures have been classified into hierarchical levels of structural ... class a term used to classify protein domains according to their secondary structural content and organization. Four classes ...
Non-structural protein 3 - Rotavirus B (isolate RVB/Human/China/ADRV/1982) (RV-B)
Protocols and materials databases. Structural Biology Knowledgebase. Search.... Family and domain databases. Gene3D Structural ... Domaini. Coiled coil. Family and domain databases. Gene3D Structural and Functional Annotation of Protein Families ... 3D structure databases. Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase ... 3D structure databases. Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase ...
RCSB PDB - 3UGD: Structural and functional characterization of an anesthetic binding site in the second cysteine-rich...
Structural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase C ... Structural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase C ... Protein Family Annotation Pfam Database Homepage. Chains. Pfam Accession. Pfam Identifier. Pfam Description. Type. Source. ...
Putative minor structural protein VP5 - Rice ragged stunt virus (isolate Thailand) (RRSV)
Family and domain databases. ProtoNet; Automatic hierarchical classification of proteins. More...ProtoNeti. Search.... ... 3D structure databases. SWISS-MODEL Repository - a database of annotated 3D protein structure models ... p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.,p>,a ... Protein predictedi ,p>This indicates the type of evidence that supports the existence of the protein. Note that the protein ...
CiteSeerX - Citation Query The ProDom database of protein domain families: more emphasis on 3D.
The ProDom database of protein domain families: more emphasis on 3D. ... superfamilies of predicted protein structural domains ...". Abstract - Cited by 12 (9 self) - Add to MetaCart superfamilies of ... The ProDom database of protein domain families: more emphasis on 3D. (2005) by C Bru, E Courcelle, S Carrere, Y Beausse, S ... GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains by David A. Lee, Robert ...
IUCr) Acta Crystallographica Section D Volume 54, Part 6, Number 1 November 1998
Databases of protein structural domains (DDBASE), aligned homologous protein structures (HOMSTRAD) and structurally aligned ... Protein Three-Dimensional Structural Databases: Domains, Structurally Aligned Homologues and Superfamilies. R. Sowdhamini, D. F ... Classifying a Protein in the CATH Database of Domain Structures. C. A. Orengo, A. M. Martin, G. Hutchinson, S. Jones, D. J. ... The CATH database of protein domain structures classifies structures according to their (C)lass, (A)rchitecture, (T)opology or ...
Structural maintenance of chromosomes protein 1A (Q14683) | InterPro | EMBL-EBI
We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their ... InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites ... individual strengths to produce a powerful integrated database and diagnostic tool. ... Protein family membership. *Structural maintenance of chromosomes protein (IPR024704)*Structural maintenance of chromosomes ...
BSc Medical Science, Bangor University
Scientific Databases a. Ensembl Genome Browser 2. Protein & Gene Analysis a. Alignments b. Domain structures c. Post- ... Protein & Gene Analysis a. Alignments b. Domain structures c. Post-translational Modification 3. Structural Analysis a. ... The module will cover the key molecules involved in metabolism, cell division and protein expression within the human body, ... The module will cover the key molecules involved in metabolism, cell division and protein expression within the human body, ...
RCSB PDB - 4L6E: Crystal Structure of the RanBD1 fourth domain of E3 SUMO-protein ligase RanBP2. Northeast Structural Genomics...
Crystal Structure of the RanBD1 fourth domain of E3 SUMO-protein ligase RanBP2. Northeast Structural Genomics Consortium (NESG ... Crystal Structure of the RanBD1 fourth domain of E3 SUMO-protein ligase RanBP2. Northeast Structural Genomics Consortium (NESG ... Crystal Structure of the RanBD1 fourth domain of E3 SUMO-protein ligase RanBP2.. Vorobiev, S., Su, M., Seetharaman, J., Mao, L. ... Protein Workshop , Ligand Explorer. Global Symmetry: Asymmetric - C1 Global Stoichiometry: Monomer - A Biological assembly 1& ...
Protein Structural Bioinformatics Course
1pgb a small protein domain, one chain. *2hhd four protein chains with ligands. *1d66 protein and DNA. *104d DNA/RNA hybrid. * ... Primary and Derived 3D Structure Databases IV. FirstGlance in Jmol for exploring any macromolecule. ... Structural Bioinformatics and Genomics. Homology (Comparative) Modeling *Structural Genomics: Worldwide Protein 3D Structure ... Review of Protein Chemistry and Structure. Introduction to Structural Bioinformatics. * Central Dogma: DNA mRNA Protein. DNA ...
Rv1592c - Probable inactive lipase Rv1592c - Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) - Rv1592c gene & protein
Family and domain databases. Gene3D Structural and Functional Annotation of Protein Families ... Protein-protein interaction databases. STRINGi. 83332.Rv1592c. Protein family/group databases. ESTHERi. myctu-MT1628 Fungal- ... Proteomic databases. PaxDb, a database of protein abundance averages across all three domains of life ... Protein family/group databases. ESTHER database of the Alpha/Beta-hydrolase fold superfamily of proteins ...
stard13a - StAR-related lipid transfer (START) domain-containing 13a - Danio rerio (Zebrafish) - stard13a gene & protein
Family and domain databases. Gene3D Structural and Functional Annotation of Protein Families ... Pfam protein domain database. More...Pfami. View protein in Pfam. PF00620 RhoGAP, 1 hit. PF07647 SAM_2, 1 hit. PF01852 START ... PROSITE; a protein domain and family database. More...PROSITEi. View protein in PROSITE. PS50238 RHOGAP, 1 hit. PS50848 START ... Simple Modular Architecture Research Tool; a protein domain database. More...SMARTi. View protein in SMART. SM00324 RhoGAP, 1 ...
WAPL domain-containing protein - Oryza meridionalis
Family and domain databases. Gene3D Structural and Functional Annotation of Protein Families ... Protein-protein interaction databases. STRINGi. 40149.OMERI10G11170.1. Genome annotation databases. EnsemblPlantsi. ... Family and domain databases. Gene3Di. 220.127.116.11, 1 hit. InterProi. View protein in InterPro. IPR011989 ARM-like. IPR039874 ... present in a protein.,p>,a href=/help/family_and_domains_section target=_top>More...,/a>,/p>Family & Domainsi. Domains and ...
Protein Structural Bioinformatics Course
1pgb a small protein domain, one chain. *2hhd four protein chains with ligands. *1d66 protein and DNA. *104d DNA/RNA hybrid. * ... Protein Data Bank & PDB Codes Crystallographic Resolution * Primary vs. Derived 3D Macromolecular Structure Databases: * The ... Review of Protein Chemistry and Structure. Introduction to Structural Bioinformatics. * Central Dogma: DNA mRNA Protein. DNA ... About Protein Structure * Introduction to Structural Bioinformatics and Genomics * Erics Favorite Protein Structure Literature ...
IJMS | Free Full-Text | Novel Strategies for Drug Discovery Based on Intrinsically Disordered Proteins (IDPs) | HTML
It is found out that IDPs have unique structural features such as high flexibility and random coil-like conformations which ... For example, the tumor suppressor protein p53 is an intrinsically disordered protein and also a hub protein in the p53 ... These disease-associated IDPs commonly play principal roles in the disease-associated protein-protein interaction networks. ... The disease-associated IDPs may provide potential targets for drugs modulating protein-protein interaction networks. Therefore ...
Domains number statistic
Hello some protein domain (like Ig domain or TK domain) are highly ,represented in the different data base other not. Do you ... Population statistics of protein structures: lessons from structural classifications. Current Opinion in Structural Biology 7: ... find a web site or a paper that review al the protein domains and the ,number of times they are represented in the different ... Domains number statistic. Ram Samudrala ram.samudrala at nojunkemail.stanford.edu Wed Oct 22 10:03:47 EST 1997 *Previous ...
Computational-biology] First African Structural Biology Conference (FASB 2006)
Protein Classification Methods for NCBIs Conserved Domain Database. 10:00 am Dr Frank Von Delft (/Structural Genomics ... 3:30 pm Prof Mamannamana Vijayan /(Indian Institute of Science, India). Structural biology of Mycobacterial Proteins the Indian ... Solution structure of the RING finger domain from the human RBBP6 splicing-associated protein. 4:40 pm Contributed Papers 5:00 ... Structural studies on biosynthetic enzymes 9:00 am Prof Andreas Hoenger /(University of Colorado at Boulder, USA). Structural ...
SCOPe 2.07: Structural Classification of Proteins - extended
... extended database, and ASTRAL compendium for protein structure and sequence analysis ... 3Dee Protein Domain Definitions * Protein Data Bank (PDB) * Macromolecular Structure Database (EBI) * Nucleic Acid Database ( ... Pfam database of protein families and HMMs * Integrated resource for protein families (InterPro) * CATH/Gene3D structural and ... ECOD evolutionary classification of protein domains * Dali structural comparison and FSSP structural classification * ...
SDAP : Structural Database of Allergenic Proteins
Pfam is a database of multiple sequence alignments and hidden Markov models covering protein domains and families. Inspect ... Protein Databases. PDB. MMDB - Entrez. SWISS-PROT. NCBI - Entrez. PIR. Protein Classification. CATH. CE. FSSP. iProClass. ... [email protected]: PROSITE search performed at PIR - Protein Information Resources. Cha o 1 - Protein Sequence Properties. Protein ... Cha o 1 - Pfam domains. Sequence. Pfam sequence. Pfam family. Allergens from. this Pfam family. Pfam database. Pfam region. ...
Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative | PNAS
Rapid Evolution of Protein Sequence Databases.. We analyzed the taxonomic composition of the NR protein sequence database and ... 1A). A breakdown of structural coverage on a residue basis for different domains of life reveals some interesting insights. ... To assess the structural coverage of the protein universe, we compared all of the sequences in the NR database against all of ... Despite many years of continuous effort, 60% of known protein families in the Pfam database (17) still lack structural ...
Serres, M.H., and Riley, M. (2004). "Structural domains, protein modules, and sequence similarities enrich our understanding of ... an updated and improved analysis of functions of Escherichia coli K-12 proteins." Nucleic Acids Res, 32(Database issue), D300- ... Alliegro, M.C. (2000). "A C-terminal carbohydrate-binding domain in the endothelial cell regulatory protein, pigpen: new ... Gribble, K.E., Snell, T.W., and Mark Welch, D.B. (2011). "Gene and protein structure of the mate recognition protein gene ...
An ambiguity principle for assigning protein structural domains | Science Advances
... when he introduced the concept of protein domains. For these proteins, neither the CATH nor the SCOP databases contain domain ... Structural domains in proteins and their role in the dynamics of protein function. Prog. Biophys. Mol. Biol. 42, 21-78 (1983). ... These domain decompositions agree with the manual annotations from the MultiDom database (19), in which structural domains are ... Identification of structural domains in proteins by a graph heuristic. Proteins 35, 338-352 (1999).. ...
Mitochondrial outer membrane translocase complex, Tom20 domain superfamily (IPR023392) | InterPro | EMBL-EBI
We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their ... InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites ... individual strengths to produce a powerful integrated database and diagnostic tool. ... This superfamily represents the structural domain of Tom20 that binds to mitochondrial precursor proteins. It consists of five ...
A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary. - Semantic Scholar
This averaged view requires that the structural similarities between proteins having the same metafold be recognized by ... Pairwise comparisons of domains on the basis of their fold classifications show that much of the disagreement between the ... These classifications make use of different methods of defining and categorizing protein folds that lead to different views of ... By comparing these folds for a nonredundant set of proteins, the consensus method breaks up broad fold classifications and ...
Chimera-Related Databases and Software
Databases ASTRAL. Experimentally determined protein structures, divided into domains as defined by SCOP (Structural ... RCSB Protein Data Bank (PDB), Protein Data Bank in Europe (PDBe), Protein Data Bank Japan (PDBj) Experimentally determined ... the aim is to go beyond static structural snapshots of proteins by uncovering structural ensembles. The program depends on ... Chimera-Related Databases and Software *Databases *Software *Mailing Lists See also: Web services used by UCSF Chimera, sites ...
SCOPe 2.07: Structural Classification of Proteins - extended
... extended database, and ASTRAL compendium for protein structure and sequence analysis ... Database cross-references and differences (RAF-indexed): *Uniprot P08515 (0-213) *engineered (49) Domains in SCOPe 2.07: ... Description: Structural characterization of an engineered allosteric protein. Class: transferase. Keywords: protein design, ... SCOPe: Structural Classification of Proteins - extended. Release 2.07 (updated 2019-04-11, stable release March 2018) Copyright ...
Orientations of Proteins in Membranes database - Wikipedia
Kutateladze, Tatiana; Overduin, Michael (2001). "Structural Mechanism of Endosome Docking by the FYVE Domain". Science. 291 ( ... Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane protein structures with respect to ... The database provides spatial arrangement of proteins in the lipid bilayer. Data types. captured. Protein structures from the ... Proteins structures are taken from the Protein Data Bank. OPM also provides structural classification of membrane-associated ...
The Negatome database: a reference set of non-interacting protein pairs
The database currently contains experimentally supported non-interacting protein pairs derived from two distinct sources: by ... The Negatome is a collection of protein and domain pairs that are unlikely to be engaged in direct physical interactions. ... Additionally, non-interacting protein domains have been derived from the stringent manual and structural data, respectively. ... The Negatome database: a reference set of non-interacting protein pairs Nucleic Acids Res. 2010 Jan;38(Database issue):D540-4. ...
A single domain antibody fragment that recognizes the adaptor ASC defines the role of ASC domains in inflammasome assembly | JEM
Research Collaboratory for Structural Bioinformatics Protein Data Base code [RCSB PDB]: 2KN6; de Alba, 2009), neither VHHASC ... Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor. Science. ... maltose-binding protein. PA. protective antigen. PMA. phorbol-12-myristate-13-acetate. PYD. Pyrin domain. WR. Western Reserve. ... No structural information on the filamentous structure of ASCCARD exists, but CARD domains exhibit a sufficient degree of ...
A Novel Methodology for Structural, Functional and Toxicological Analysis of Mutant Angiogenin Protein in Human
Angiogenin is a protein of 14.1 kDa encoded by ANG gene and belongs to a superfamily of pancreatic ribonuclease A. Angiogenin ... 2007) CDD: A conserved domain database for interactive domain family analysis. Nucleic Acids Res 35: D237-D240. ... Analysis of Conserved Domain of Angiogenin Protein CDD confirmed a domain of Pancreatic Ribonuclease A from amino acid to 26 to ... Protein 3d modeling and detection of hydrogen bonding and clashes. MODELLER was used to predict the 3D protein structure by ...
Prediction of Protein Domains from Sequence Information Using Support Vector Machines | SpringerLink
Guessing the boundaries of structural domains has been an important and challenging problem in experimental and computational ... structural biology. Predictions were based on intuition, biochemical... ... Murzin, G., Brenner, S.E., Hubbard, T., Chothia, C.: SCOP: a Structural Classification of Proteins Database for the ... Galzitskaya, O.V., Melnik, B.S.: Prediction of Protein Domain Boundaries from Sequence alone. Protein Science 12, 696-701 (2003 ...
StructuresFunctionalHomologySuperfamiliesResiduesAlignmentsCharacterizationBIOLOGYPutativeMulti-domain proteinsPfamAbstractInterProComplexesUniProtComputationalSignal TransductionAminoLigandAlpha-helicesGenesGenomes2018PhylogeneticNCBISaccharomyces2002FunctionSuperfamily of proteinsMembrane proteinMoleculeEukaryoticMonotopic proteinsPathwaysMembranesExperimentallyTransmembrane proteinsReceptorsNucleic Acid DatabaseClassification of proteinBinds
- The Protein Data Bank (PDB) at Brookhaven National Laboratory, a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules, with approximately 8000 entries, is described. (iucr.org)
- Domain structures c. (bangor.ac.uk)
- Students will learn what percentage of proteins have known 3D structures, and the importance of crystallographic models compared to homology models, or theoretical models. (umass.edu)
- Use the sequence of your protein to search for 3D structures. (umass.edu)
- Intrinsically disordered proteins (IDPs) are proteins that usually do not adopt well-defined native structures when isolated in solution under physiological conditions. (mdpi.com)
- According to the traditional sequence-to-structure-to-function paradigm, active proteins have well-defined three-dimensional structures under physiological conditions. (mdpi.com)
- However, as early as in the 1990s, it was reported that there is another class of proteins, which have no well-defined structures under physiological conditions, but still have biological functions [ 1 , 2 ]. (mdpi.com)
- 1997. Population statistics of protein structures: lessons from structural classifications. (bio.net)
- 10:00 am Contributed papers 10:30 am Tea 11:00 am EMBO Lecture: Prof Helen Saibil, FRS /(University of London, UK) One Sequence, Two Structures: protein conformational changes that cause disease. (bio.net)
- Meanwhile, the number of known protein structures is approximately 200 times smaller, and the pace of discovery of new folds is slowing. (pnas.org)
- Structural genomics efforts contributed ∼50% of this new structural coverage, despite determining only ∼10% of all new structures. (pnas.org)
- At the same time, the number of experimentally determined protein structures has lagged increasingly behind, owing to the inherently slower, more resource-intensive, and less-predictable nature of these experiments ( 2 ). (pnas.org)
- To validate the use of these protein units for decomposing protein structures into domains, we set up an extensive benchmark made of expert annotations of structural domains and including state-of-the-art domain parsing algorithms. (sciencemag.org)
- Experimentally determined protein structures, divided into domains as defined by SCOP (Structural Classification of Proteins). (ucsf.edu)
- Crystallographic electron density maps for Protein Data Bank x-ray structures. (ucsf.edu)
- A database of human nonsynonymous single-nucleotide polymorphisms (nsSNPs) mapped onto protein structures. (ucsf.edu)
- Experimentally determined protein and nucleic acid structures. (ucsf.edu)
- it integrates structural biology and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. (ucsf.edu)
- Orientations of Proteins in Membranes ( OPM ) database provides spatial positions of membrane protein structures with respect to the lipid bilayer . (wikipedia.org)
- Proteins structures are taken from the Protein Data Bank . (wikipedia.org)
- The site allows visualization of protein structures with membrane boundary planes through Jmol . (wikipedia.org)
- This is the case when all membrane-anchoring parts of the proteins ( amphiphilic alpha helices , exposed nonpolar residues, or lipidated amino acid residues ) are missing in the experimental structures. (wikipedia.org)
- The database also does not include lower resolution structures with only main chain atoms provided by the Protein Data Bank . (wikipedia.org)
- The calculated spatial arrangements of the lower resolution protein structures in the lipid bilayer can be found in other resources, such as PDBTM. (wikipedia.org)
- These structures have thus far been shown only in vitro, or in cells that overexpress single domains of ASC fused to fluorescent proteins. (rupress.org)
- Structural alignments were computed by the VAST algorithm [ 16 ] and only those structures which had more than 80% mutual overlap between the VAST alignment footprint and CDD footprint were considered in the analysis. (biomedcentral.com)
- CATH--a hierarchic classification of protein domain structures. (semanticscholar.org)
- It has been shown from known structures that about a quarter of structural domains are discontinuous. (wikipedia.org)
- a structural classification of proteins database for the investigation of sequences and structures. (cam.ac.uk)
- Two of the main sources for generating the new families added to release 27.0 were Protein Data Bank (PDB) structures =-=(8)-=- and human sequences. (psu.edu)
- We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. (psu.edu)
- The simulated annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small b sheet containing proteins. (psu.edu)
- Further, sequence domain families were mapped to structures in the protein databank (PDB) and the protein domain structure classification database (SCOP). (ncbs.res.in)
- Ferdous, S. and Martin, A.C.R. (2018) AbDb: antibody structure database - a database of PDB derived antibody structures . (bioinf.org.uk)
- Domain insertions in protein structures. (sanger.ac.uk)
- The example below is the investigation of protein variability and evolution by combining protein structures with sequences. (labo.de)
- Together with the 100,000+ structures in the Protein Data Base (PDB), this remarkable data for comprehending the important structural and sequence relationships. (labo.de)
- We pioneered such approaches with protein structures in 1985 by extracting potentials for interacting amino acids when we were able to use only 42 protein structures, which were sufficient for extracting the counts of the 190 types of amino acid pairs . (labo.de)
- Amino acid substitutions in proteins can be significantly better understood by considering the closely interacting groups of amino acids within structures, which have been combined naturally for favorable collective multibody interactions tight packing. (labo.de)
- The CATH database is a classification of protein structures from Protein Data Bank. (labo.de)
- Protein structures that have same topology level share particular structural features. (labo.de)
- The information on proteins is organised in databases that store their sequences, domain organisation, three‐dimensional structures, posttranslational modifications, interactions, molecular functions and other protein features. (els.net)
- CExonic and CORSAIR determine patterns of conservation of exonic structures using different type of alignment strategies, similar to the one provided by databases on orthologs and interspecies alignments (see http://questfororthologs.org/orthology_databases ). (els.net)
- Through quantitative analysis on a unique dataset of 154 core-domain-only and cap- domain-only structures, basic principles of their evolution have been uncovered. (slideshare.net)
- HAD superfamily The universe of protein structures is vast and diverse, yet these innumerable structures can be categorized into a ﬁnite num- ber of folds (1). (slideshare.net)
- A related problem of considerable importance is domain docking where the aim is to predict the structure of a multi-domain protein from the structures of its component domains. (biomedcentral.com)
- Structural genomics projects are in fact determining a large number of structures, but focusing primarily at the level of individual domains. (biomedcentral.com)
- The performance of the tested statistical potentials is not likely to improve significantly with an increase in the number of known protein structures used in their derivation. (nih.gov)
- The parameters of fold assessment whose optimal values vary significantly with model size include the size of the known protein structures used to derive the potential and the distance range of the accessible surface potential. (nih.gov)
- The team found that other proteins that had similar structural features were associated with telomeres, the cap-like structures at the end of chromosomes. (innovations-report.com)
- We have crystallized SOUL alone and the complex of its BH3 domain peptide with Bcl-xL and solved their three-dimensional structures. (proteopedia.org)
- Real-SPINE is trained with a large data set of 2640 protein chains, sequence profiles generated from multiple seq-uence alignment, representative amino-acid prop-erties, a slow learning rate, overfitting protection, and predicted secondary structures. (psu.edu)
- It contains the large-scale interface data for proteins whose 3D-structures are known. (biomedcentral.com)
- Such prediction relies on the well-established paradigms that similar protein sequences imply similar three-dimensional structures. (stanford.edu)
- Three-dimensional structures of ~160 different integral membrane proteins have been determined at atomic resolution by X-ray crystallography or nuclear magnetic resonance spectroscopy . (wikipedia.org)
- In addition, structures of many water - soluble protein domains of IMPs are available in the Protein Data Bank . (wikipedia.org)
- The Protein Structure Initiative (PSI), funded by the U.S. National Institute of General Medical Sciences (NIGMS), part of the National Institutes of Health (NIH), has among its aim to determine three-dimensional protein structures and to develop techniques for use in structural biology , including for membrane proteins. (wikipedia.org)
- The Structure database provides three-dimensional structures of macromolecules for a variety of research purposes and allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. (re3data.org)
- Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. (re3data.org)
- Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships. (re3data.org)
- These tools will be used to study some class of specific structures, (such as membrane, nucleic acid binding, regulatory, structural, or metabolic proteins). (amherst.edu)
- And finally, there are papers that continue to address the fundamental unresolved problem of how protein sequences encode for the three-dimensional structures of proteins. (mdpi.com)
- The number of protein-ligand complex structures from both in silico and experimental methods have highly increased during the past decade. (igi-global.com)
- Three-dimensional structures of only ~160 different integral membrane proteins are currently determined at atomic resolution by X-ray crystallography or Nuclear magnetic resonance spectroscopy due to the difficulties with extraction and crystallization. (thefullwiki.org)
- The PDB is the main primary database for 3D structures of biological macromolecules determined by X-ray crystallography and NMR. (avatar.se)
- Structural biologists usually deposit their structures in the PDB on publication, and some scientific journals require this before accepting a paper. (avatar.se)
- The PDB entries contain the atomic coordinates , and some structural parameters connected with the atoms (B-factors, occupancies), or computed from the structures (secondary structure). (avatar.se)
- Its purpose is to classify protein 3D structures in a hierarchical scheme of structural classes . (avatar.se)
- It is maintained by experts ("by hand"), and all protein structures in the PDB are classified, and it is updated as new structures are deposited in the PDB. (avatar.se)
- it is based on data in a primary database (in this case the PDB), but adds information through analysis and/or organisation, in this case the classification of protein 3d structures into a hierarchical scheme of folds, superfamilies and families. (avatar.se)
- The CATH database (Class, architecure, topology, homologous superfamily) is a hierarchical classification of protein domain structures, which clusters proteins at four major structural levels . (avatar.se)
- In order to derive unbiased statistics from the structural alignments, we introduce a multidimensional QR factorization which produces a nonredundant set of structures. (asm.org)
- 1995). "scop: a structural classification of proteins database for the investigation of sequences and structures" Journal of Molecular Biology 247:536-540. (yale.edu)
- Intrinsically disordered proteins (IDPs) make up a large class of proteins that lack stable structures in solution, existing instead as dynamic conformational ensembles. (sdbonline.org)
- The National Institutes of Health-supported Protein Structure Initiative and related worldwide structural genomics efforts facilitate functional annotation of proteins through structural characterization. (pnas.org)
- Based on current trends, it is expected that ∼55% structural coverage (the level required for significant functional insight) will be achieved within 15 y, whereas without structural genomics efforts, realizing this goal will take approximately twice as long. (pnas.org)
- Functional cooperation of mitochondrial protein import receptors in yeast. (ebi.ac.uk)
- VHH ASC leaves the Pyrin domain of ASC functional and stabilizes a filamentous intermediate of inflammasome activation. (rupress.org)
- The result demonstrates that the utility of the method can help not only in predicting the complete 3D structure of a protein but also in the study of proteins' building blocks and for functional analysis. (springer.com)
- Architectures and functional coverage of protein-protein interfaces. (semanticscholar.org)
- Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. (wikipedia.org)
- DNA- and RNA-binding studies confirmed that PUR domains are indeed functional nucleic-acid binding domains. (pnas.org)
- Importantly, the in silico modeling approach assessed here provides an exciting prospect of being able to identify and classify currently unknown (orphan) kinases, as a foundation for their subsequent structural and functional investigation. (g3journal.org)
- Domains are the structural, functional or evolutionary units of proteins. (sanger.ac.uk)
- Even in the absence of functional information, grouping proteins into families can indicate those amino acids within the proteins that are conserved and hence are potentially functionally important. (iucr.org)
- Combining annotations from different publications and database to produce a representative description of protein characteristics and functional properties is known as information integration. (els.net)
- The APPRIS database contains information on human splice isoforms annotating them with protein structural and functional and evolutionary features. (els.net)
- Accordingly, a thorough analysis of protein superfamilies at the sequence level is necessary in order to maximize the chances of gleaning non-trivial structural and functional inferences, as opposed to a single search, initiated, for example, with the sequence of a protein whose structure is available. (embl-heidelberg.de)
- 2008) Large-scale production of functional membrane proteins. (creative-biostructure.com)
- Therefore, it becomes significant to study the structural and functional features of this enzyme for a better understanding of its molecular mechanisms. (springer.com)
- The detailed computational investigation of the canine lysyl oxidase protein was analyzed in silico with respect to its physicochemical properties, secondary and tertiary structure predictions and functional analysis using standard bioinformatic tools. (springer.com)
- Understanding the structural and functional properties of the protein will facilitate a better understanding of its mechanism of enzyme action. (springer.com)
- Such organization has possible applications in phylogeny, modeling of functional evolution and structural determination. (harvard.edu)
- The inclusion of network context information in the comparison of protein interaction networks increased the number of similar subgraphs found consisting of proteins involved in the same functional process. (imperial.ac.uk)
- Realization of such remote homologues with vivid length variations could contribute to better understanding of functional variety within protein domain superfamilies. (igi-global.com)
- We also discuss the effect of functional specificity on protein shape over the complex evolutionary course of the tRNA synthetases. (asm.org)
- As protein synthesis evolved and the resulting proteins themselves became more complex, they invaded functional niches, previously occupied by ribozymes, to enhance enzymatic activities. (asm.org)
- In this paper, the structural and functional features of these proteins in Eucalyptus are summarized. (ufrgs.br)
- Superfamily and family analyses provide an effective tool for the functional classification of proteins, but must be automated for use on large datasets. (biomedcentral.com)
- With large volumes of sequence and structural data now available, functional characterization of proteins has become the rate-limiting step in putting biological information to practical use. (biomedcentral.com)
- Even when direct transfer of the full functional annotation is not possible, evolutionarily related proteins usually share some functional relationship. (biomedcentral.com)
- Predictions were based on intuition, biochemical properties, statistics, sequence homology and other aspects of predicted protein structure. (springer.com)
- Sonnhammer, E.L., Kahn, D.: Modular Arrangement of Proteins as Inferred From Analysis of Homology. (springer.com)
- This molecular view of diseases has contributed to the importance of combining primary sequence data with three-dimensional structure and has increased the awareness of computational homology modeling and its potential to elucidate protein function. (asm.org)
- PUR proteins lack sequence homology to proteins with known structure. (pnas.org)
- The domain has a novel, all-helical fold which we name the AP180like NH 2 -terminal homology (ANTH) domain. (bl.uk)
- The epsin NH 2 -terminal homology (ENTH) domain of epsin is structurally similar to the ANTH domain - the first 7 helices superpose well - though it lacks the lysine-rich motif. (bl.uk)
- In the current study, we used sequence alignment and homology modeling to identify features common to nonturreted Reoviridae capping enzymes and to predict the domain organization, structure, and active sites of rotavirus VP3. (asm.org)
- Sequence conservation and homology modeling suggested that the insertion in the guanine-N7-methyltransferase domain is a ribose-2′- O -methyltransferase domain for most rotavirus species. (asm.org)
- The structure of most domains will soon be known either directly from experiments or through accurate homology modeling. (biomedcentral.com)
- strain PCC 7002, a photosystem I protein that shows structural homology with SH3 domains. (xfam.org)
- The SOUL protein is known to induce apoptosis by provoking the mitochondrial permeability transition and a sequence homologous to the Bcl-2 homology 3 (BH3) domains has been recently identified in it thus making it a potential new member of the BH3-only protein family. (proteopedia.org)
- curate, hybrid domain prediction server (DOMAC) that integrates homology modeling, domain parsing and ab initio methods together. (psu.edu)
- We have focused on the hardest problem in homology modeling: the refinement of a near-native structure to make it more precisely like the actual native structure of protein. (stanford.edu)
- Homology modeling can be used to construct an atomic-resolution model of the "target" integral protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein. (wikipedia.org)
- These proteins will provide the framework for discussion of such concepts as domains, motifs, molecular motion, structural homology, etc., as well as for addressing how specific biological problems are solved at the atomic level. (amherst.edu)
- Homology modelling of the protein 3D structure was performed using Modeller followed by the validation using PROCHECK. (ssrn.com)
- By using structural alignments of all of the aminoacyl-tRNA synthetases of known structure in combination with a new measure of structural homology, we have reconstructed the evolutionary history of these proteins. (asm.org)
- OPM also provides structural classification of membrane-associated proteins into families and superfamilies, membrane topology , quaternary structure of proteins in membrane-bound state, and the type of a destination membrane for each protein. (wikipedia.org)
- Pritha Ghosh, Teerna Bhattacharya, Oommen K. Mathew and R. Sowdhamini (2019) PASS2 version 6 a database of structure based sequence alignments of protein domain superfamilies in accordance with SCOPe. (ncbs.res.in)
- Iyer MS, Joshi AG, Sowdhamini R. Genome-wide survey of remote homologues for protein domain superfamilies of known structure reveals unequal distribution across structural classes. (ncbs.res.in)
- The DNA-binding families, with no structural information, were clustered together into potential superfamilies based on sequence associations. (ncbs.res.in)
- Collectively, these results hint at intramolecular coevolution where the fold diverges differentially in the context of an accessory domain, a feature that might also apply to other multidomain superfamilies. (slideshare.net)
- Certain protein folds have given rise to several large superfamilies of ligand-binding domains. (biomedcentral.com)
- Resultant ~6000 proteins (spread across 635 superfamilies) of different superfamilies and groups were scaled up to work automatically for the protocol standardized (Figure 1). (igi-global.com)
- Each of these mechanistically diverse superfamilies may contain hundreds or even thousands of proteins, representing many different overall functions and utilizing a wide range of substrates. (biomedcentral.com)
- Protein tyrosine kinases phosphorylate cellular substrates on tyrosine residues, and much progress has been made over the last 20 years in elucidating their significance in signal transduction (for reviews, see references 26 , 30 , 31 , 33 , 71 , and 72 ). (asm.org)
- Generally proteins have a core of hydrophobic residues surrounded by a shell of hydrophilic residues. (wikipedia.org)
- Although RAG1 has recently been shown to contain the catalytic residues of the recombinase and can alone bind the RSS in part through a helix-turn-helix motif homologous to the DNA binding domain of the Hin recombinase ( 11 , 12 , 13 , 14 , 15 ), such a complex cannot mediate DNA nicking ( 16 , 17 , 18 ). (jimmunol.org)
- The minimal regions of both proteins that are sufficient for mediating recombination in vivo are referred to as the active cores and span residues 384-1008 in RAG1 ( 28 ) and residues 1-383 in RAG2 ( 24 , 29 ). (jimmunol.org)
- In multiple-sequence alignments of a given protein from different biological sources these co-evolving residues can be identified. (labo.de)
- The GTases of DNA viruses contain two domains and often conserve active-site residues, including a catalytic lysine within a KxDG(I/L) motif (where x is any residue) ( 3 , 4 ). (asm.org)
- We show that it correctly predicts some contacts and that predicted residues tend to be significantly closer to each other than other pairs of residues in the same domains. (biomedcentral.com)
- These mutations affect critical residues in the cytoplasmic BTK protein and are highly variable and uniformly dispersed throughout the molecule. (medscape.com)
- G,H ) Template domain coverage (the fraction of the template domain residues that were aligned to the target chain). (nih.gov)
- Here we present NMR, SPR and crystallographic evidence that a peptide spanning SOUL residues 147 - 172 interacts with the anti-apoptotic protein Bcl-xL. (proteopedia.org)
- The BH3 domain extends across 15 residues at the end of the second helix and 8 amino acids in the chain following it. (proteopedia.org)
- Protein phosphatases were originally identified as enzymes responsible for dephosphorylating Ser and Thr residues on enzymes involved in mammalian glycogen metabolism. (plantphysiol.org)
- In this case, experiments can focus on detailed molecular mechanisms, at the level of individual residues, that may be similar or different between the two proteins. (rupress.org)
- We present a novel method that combines protein structure information with protein interaction data to identify residues that form part of an interaction interface. (biomedcentral.com)
- We describe a method that combines protein structure with experimental protein interaction data in order to computationally identify residues that form part of a binding interface. (biomedcentral.com)
- In order to identify residues in a protein that are involved in a protein interaction, we devised a method that combines structural and experimental information. (biomedcentral.com)
- We then select positions that form residue-to-residue contacts between distinct polypeptide chains in these structural templates and record the corresponding positions in the target proteins as potentially interacting residues. (biomedcentral.com)
- The utilities of SAVES and the data about active site residues were obtained from the literatures on the α-D-phosphohexomutase superfamily proteins whose active sites are conserved. (ssrn.com)
- Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. (psu.edu)
- Protein structure will be related to function, evolutionary conservation and multiple-sequence alignments, and drug design. (umass.edu)
- The method is based on analyzing multiple sequence alignments that are derived from a database search. (springer.com)
- Pfam is a database of curated protein families, each of which is defined by two alignments and a profile hidden Markov model (HMM). (labo.de)
- Sequence alignments revealed conserved motifs and suggested that rotavirus and orbivirus capping enzymes contain a variable N-terminal domain, a central guanine-N7-methyltransferase domain that contains an additional inserted domain, and a C-terminal guanylyltransferase and RNA 5′-triphosphatase domain. (asm.org)
- In this study, we used sequence- and structure-based alignments with related proteins to predict the structure of VP3 and identify enzymatic domains and active sites therein. (asm.org)
- We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. (xfam.org)
- In order to understand the molecular mechanisms underlying the consequences of protein ubiquitination, scientists have to face the challenging task of producing ubiquitinated proteins for structural characterization with X-ray crystallography and/or nuclear magnetic resonance (NMR) spectroscopy. (mdpi.com)
- Explanations of structural biology terms and concepts , e.g. asymmetric unit, Protein Data Bank, hydrogen bonds, temperature value, etc. all at About Macromolecular Structure . (umass.edu)
- Using laptop computers, students will learn how to find 3D protein molecular models for proteins in their research, and how to use Proteopedia.Org and FirstGlance in Jmol (adopted by Nature Structure & Molecular Biology ) to investigate key structural features. (umass.edu)
- Current Opinion in Structural Biology 7:369-376. (bio.net)
- The First African Structural Biology Conference* *Macromolecular Structure, Health and Biotechnology in Developing Countries* The Wilderness, Western Cape, South Africa 24-27 October 2006 The First African Structural Biology (FASB) conference will be held in The Wilderness, South Africa. (bio.net)
- Structural Biology is fundamental to rational drug design and central to the drug discovery process. (bio.net)
- The conference will focus on the contributions and potential contributions of Structural Biology to science in Africa with some emphasis on biotechnology and health. (bio.net)
- To promote structural biology in Africa, particularly in South Africa 2. (bio.net)
- To discuss strategic and funding policies for structural biology and benchmark South Africa against other developing countries, notably Brazil and India 6. (bio.net)
- Structural Biology and Modern Drug Discovery. (bio.net)
- The role of NMR in structural biology and drug discovery. (bio.net)
- Structural Biology and an Effective HIV-1 Vaccine 10:00 am Dr Alan Roseman /(MRC LMB, Cambridge, UK). (bio.net)
- From drugs to herbicides: the impact of structural biology on rational design. (bio.net)
- Guessing the boundaries of structural domains has been an important and challenging problem in experimental and computational structural biology. (springer.com)
- Unprecedented advances in molecular and cellular biology, in bio- chemistry, in genetics, and in structural biology-occurring at an accelerating rate over the past decade define this as a unique and opportune moment in our history: For the first time we can envision obtaining easy access to the complete sequence of the 3 billion nucleotides in human DNA and deciphering much of the information contained therein. (nap.edu)
- Martin, A.C.R. (2014) Structural biology of moonlighting - lessons from antibodies . (bioinf.org.uk)
- Henderson, B. and Martin, A.C.R. (2014) Protein moonlighting: a new factor in biology and medicine . (bioinf.org.uk)
- In molecular biology, the ACT domain is a protein domain that is found in a variety of proteins involved in metabolism. (wikipedia.org)
- Together, these findings provide insight into a poorly understood area of rotavirus biology and are a springboard for future biochemical and structural studies of VP3. (asm.org)
- The information on protein function, as essential component of biological systems, is essential for the development of biology and biomedicine. (els.net)
- Fernández‐Suárez XM, Rigden DJ and Galperin MY (2014) The 2014 nucleic acids research database issue and an updated NAR online molecular biology database collection. (els.net)
- The study appears in Nature Structural & Molecular Biology on Nov. 13. (innovations-report.com)
- The Chp1-Tas3 core is a multifunctional platform critical for gene silencing by RITS," appears in Nature Structural & Molecular Biology on Nov. 13. (innovations-report.com)
- It incorporates elements of molecular biology, database computing and internet. (eventbrite.com)
- The largest open reading frame encodes a large putative protein, p130. (academicjournals.org)
- The putative structural implications of all of the missense mutations are provided in the database. (medscape.com)
- Localization studies of 13 putative importin (imp) alpha- and 11 imp beta-like proteins revealed that imp alpha-like proteins are nucleus specific--nine localized to the germ line micronucleus--but that most imp beta-like proteins localized to both types of nuclei. (nih.gov)
- Expression analysis of Arabidopsis phosphatase genes differentially amplified in plants (specifically the C-terminal domain phosphatase-like phosphatases) shows patterns of tissue-specific expression with a statistically significant number of correlated genes encoding putative signal transduction proteins. (plantphysiol.org)
- In multi-domain proteins, the domains almost always occur end-to-end, i.e., one domain follows the C-terminal end of another domain. (sanger.ac.uk)
- However, there are exceptions to this common pattern, where multi-domain proteins are formed by insertion of one domain (insert) into another domain (parent). (sanger.ac.uk)
- The AARSs are, in all known cases, multi-domain proteins. (asm.org)
- The current release of Pfam (22.0) contains 9318 protein families. (psu.edu)
- Pfam-B entries are automatically generated from the ProDom database =-=(3)-=-, and are represented by a single alignment. (psu.edu)
- INTRODUCTION InterPro (1) is an integrative database which was founded 10 years ago when the PROSITE (2), PRINTS (3), Pfam (4) and ProDom =-=(5)-=- databases formed a consortium to amalgamate the predictive signatures they individually produced into a single resource. (psu.edu)
- In ProtCID, protein chains in the protein data bank (PDB) are grouped based on their PFAM domain architectures. (semanticscholar.org)
- Pfam is a large collection of protein families and domains. (psu.edu)
- We have made a concerted effort to build families from CATH domains (http://www.cathdb.info/) (9) that did not match a Pfam family in Pfam 26.0. (psu.edu)
- Domains of unknown function (DUFs) are a large set of uncharacterized protein families that are found in the Pfam database. (iucr.org)
- For example, if one or more members of a Pfam family have an experimentally determined function then this function can be tentatively assigned to the other proteins in that family. (iucr.org)
- Domains of unknown function, or DUFs, are a large set of families within the Pfam database that do not include any protein of known function. (iucr.org)
- Although no further DUFs appeared in SMART, DUF1 and DUF2 were added to Pfam in 1997 and little did Chris Ponting realise that he was starting a trend that would see thousands of uncharacterized and largely anonymous families being added to the protein-family databases. (iucr.org)
- Cytosolic sensors and adaptors in myeloid cells integrate information to initiate a strong inflammatory response through the assembly of macromolecular protein complexes called inflammasomes. (rupress.org)
- With respect to more standard docking algorithms it might be more suitable to handle protein conformational changes and to predict complexes starting from protein models. (biomedcentral.com)
- Experimental studies, though, are faced with remarkable technical difficulties and the number of solved complexes deposited in the Protein Data Bank (PDB) [ 4 ] is still relatively small. (biomedcentral.com)
- InterPare uses three methods to detect interfaces: 1) the geometric distance method for checking the distance between atoms that belong to different domains, 2) Accessible Surface Area (ASA), a method for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, and 3) the Voronoi diagram, a computational geometry method that uses a mathematical definition of interface regions. (biomedcentral.com)
- This procedure has been extensively used for ligand - G protein-coupled receptors (GPCR) and their complexes. (wikipedia.org)
- In the public domain, availability of over 5000 small molecule complexes within databases is the result of many effective studies performed in this field (Deng, Chuaqui, & Singh, 2004). (igi-global.com)
- Responses to TGF-β/BMP signals are mediated by Smad proteins, which form complexes and accumulate in the nucleus to directly bind and regulate enhancers of BMP-targets upon signaling. (sdbonline.org)
- p>When browsing through different UniProt proteins, you can use the 'basket' to save them, so that you can back to find or analyse them later. (uniprot.org)
- As a result of that, databases such as the Online Mendelian Inheritance in Man (OMIM) [ 6 ] and UniProt [ 7 ] together contain almost 30,000 experimentally verified mutations. (biomedcentral.com)
- 2013). An appropriate mapping between known properties of candidate proteins and their likelihood of interaction is key to the success of computational approaches. (deepdyve.com)
- Several groups have introduced computational geometric and topology methods for the study of protein interfaces. (biomedcentral.com)
- In addition to the computational research the center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. (re3data.org)
- PTPs are a key group of signal transduction enzymes which, together with protein tyrosine kinases, control the levels of cellular protein tyrosine phosphorylation. (asm.org)
- Typically, these small molecule-binding domains (SMBDs) are combined, within the same polypeptide, to a number of conserved domains that are directly involved in signal transduction. (biomedcentral.com)
- Get the amino acid sequence of your protein. (umass.edu)
- Whereas noncatalytic domains may target the PTPs to specific intracellular compartments in which the effective local concentration of substrate is high ( 3 , 19 , 51 ), the PTP catalytic domains themselves confer site-selective protein dephosphorylation by recognizing both the phosphotyrosine residue to be dephosphorylated and its flanking amino acids in the substrate. (asm.org)
- Protein ubiquitination consists of the covalent attachment of the ε-amino group of a target protein lysine to the carboxylic group of the ubiquitin (Ub) C-terminal glycine via an isopeptide bond. (mdpi.com)
- Domains vary in length from between about 25 amino acids up to 500 amino acids in length. (wikipedia.org)
- ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. (wikipedia.org)
- Because they are close, if one of them is replaced with a smaller amino acid, one of its neighbors may be replaced by a larger one, to maintain protein stability. (labo.de)
- In a protein, amino acids co-evolve with other amino acids in ways to compensate for changes that are introduced. (labo.de)
- It also provides statistics such as the amino acid propensities of queried protein according to its interior, surface, and interface region. (biomedcentral.com)
- Questions we are trying to answer include: How can a protein be stabilized by a single amino acid change? (stanford.edu)
- Single pass TM proteins can be categorized as Type I, which are positioned such that their carboxyl-terminus is towards the cytosol , or Type II, which have their amino-terminus towards the cytosol. (wikipedia.org)
- NOD) domain, and an effector domain (amino-terminal), which can be a pyrin domain (PYD), a caspase recruitment domain (CARD), or a baculovirus inhibitor of apoptosis protein repeat (BIR) domain [ 1 ]. (hindawi.com)
- ASC encodes a 22-kDa protein that contains a carboxy-terminal CARD and an amino-terminal PYD, suiting as an adaptor molecule between PYD- and CARD-containing proteins. (hindawi.com)
- TM proteins can be categorized as Type I, which are positioned such that their amino-terminus is outside of the membrane, or Type II, which have their carboxy-terminus outside of the membrane. (thefullwiki.org)
- These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the correct amino acid. (asm.org)
- First, amino acids are covalently linked to their cognate tRNAs via an aminoacylation reaction catalyzed by a diverse group of proteins, the aminoacyl-tRNA synthetases (AARSs). (asm.org)
- The HNOBA domain functionally interacts with the HNOB domain, and possibly binds a ligand, either in cooperation, or independently of the latter domain. (biomedcentral.com)
- Protein Ligand Interaction Fingerprints. (igi-global.com)
- Different classifications approaches for the protein-ligand interaction fingerprints were also discussed in this chapter. (igi-global.com)
- However, these mobile elements facilitate large rearrangements that alter the order and orientation of essential protein-encoding genes, which otherwise exhibit little nucleotide sequence diversity. (pubmedcentralcanada.ca)
- By 1990s, five different LOX genes (LOX, LOXL1, LOXL2, LOXL3, and LOXL4) encoding proteins were identified which shared a highly conserved C terminal domain and a diverse N-terminal. (springer.com)
- We have searched the protein data sets encoded by the well-finished nuclear genomes of the higher plants Arabidopsis ( Arabidopsis thaliana ) and Oryza sativa , and the latest draft data sets from the tree Populus trichocarpa and the green algae Chlamydomonas reinhardtii and Ostreococcus tauri , for homologs to several classes of novel protein phosphatases. (plantphysiol.org)
- The evolution of these proteins is of particular interest for understanding the evolution of translation and the transition from the RNA world to the modern form of life dominated by protein-enzymes and DNA genomes. (asm.org)
- Rajan Kumar Pandey, Surbhi Dahiya, Jarjapu Mahita, Ramanathan Sowdhamini, Vijay K umar Prajapati (2018) Vaccination and immunization strategies to design Aedes aegypti salivary protein based subunit vaccine tackling Flavivirus infection. (ncbs.res.in)
- Proteins , (2018), https://doi.org/10.1002/prot.25471 . (ncbs.res.in)
- The phylogenetic relationship of canine lysyl oxidase with a vast range of mammalian species indicates that the protein was very well conserved throughout the course of evolution. (springer.com)
- Phyletic profiles and phylogenetic analysis suggest that the HNOB and HNOBA domains were acquired by the animal lineage via lateral transfer from a bacterial source. (biomedcentral.com)
- Phylogenetic analysis of these proteins reveals a pattern of evolution where a diverse set of protein phosphatases was present early in the history of eukaryotes, and the division of plant and animal evolution resulted in two distinct sets of protein phosphatases. (plantphysiol.org)
- Based on the phylogenetic history of NACHT domain (which is only present in NLR), and on the particular type of effector domain, the 22 NLR family members can be classified in two large subfamilies: the NODs (NLR family, CARD domain containing) also called NLRCs, and the NALPs (NLR family, pyrin domain containing) also called NLRPs. (hindawi.com)
- These ancient proteins are found in all extant organisms, and their inception likely predates the root of the universal phylogenetic tree ( 57 , 62 ). (asm.org)
- One of the few organisms where direct protein concentrations are available on a nearly proteome wide level is the yeast Saccharomyces cerevisiae . (biomedcentral.com)
- The similar pairs of subgraphs found in the protein-protein interaction networks of Drosophila melanogaster and Saccharomyces cerevisiae also include central processes such as cell division but, interestly, also include protein sub-networks involved in pre-mRNA processing. (imperial.ac.uk)
- Insights into Function from Structural Studies on Complement Components and VCP 1:00 pm Lunch 2:30 pm Canoeing on the Wilderness Lagoon sponsored by Rigaku MSC 6:30 pm Gala Dinner 7:30 pm Posters *Friday 27 October 2006( 8:00 am Dr Jonathan Spencer /(University of Cambridge, UK). (bio.net)
- After this geometrical definition, many manual and automated methods for assigning structural domains have been based on additional criteria, such as folding autonomy, function, thermodynamic stability, or domain motions ( 2 ). (sciencemag.org)
- Tom20, Tom37, Tom70, and Tom72 function as redundant receptor proteins, while Tom40 constitutes a protein conducting channel with the aid of Tom22 [ PMID: 9774109 , PMID: 10519552 ]. (ebi.ac.uk)
- Loops apparently do not contribute much to protein stability but may be quite important for protein specific function and for the interaction with other components of the cell. (biomedcentral.com)
- In a multidomain protein, each domain may fulfill its own function independently, or in a concerted manner with its neighbours. (wikipedia.org)
- In addition, this protein has been shown to have an antimicrobial function, inhibiting the replication of herpes simplex virus. (genecards.org)
- Proteins involved in energy metabolism as well as those with binding function were also found in high copy number while proteins annotated with the terms metabolism, transcription, transport, and cellular organization were rare. (biomedcentral.com)
- Over the next 10 years, I believe probably 90 percent of the proteins will have an assigned function. (scripps.edu)
- Even for the most intensively experimentally studied organisms there are many proteins for which we have no clue as to their function. (iucr.org)
- We use a scoring function that combines structural, physicochemical and evolutionary information, where each potential residue contact is assigned a value according to the scoring function and the hypothesis is that the real configuration of contacts is the one that maximizes the score. (biomedcentral.com)
- The different imp alpha proteins exhibit substantial sequence divergence and do not appear to be simply redundant in function. (nih.gov)
- Thus, nucleus-specific protein import and nuclear function in Tetrahymena are regulated by diverse, specialized karyopherins. (nih.gov)
- RITS might be exerting its effect at centromeres through Ago1 and the RNAi machinery, but might enforcing its function at the telomeres through Chp1 and its PIN domain. (innovations-report.com)
- The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals. (biomedcentral.com)
- He not only investigated the physicochemical properties of protein interfaces, but also tried to understand the geometric features of protein interfaces using a spline function [ 13 , 14 ]. (biomedcentral.com)
- A membrane that contains this particular protein is able to function in photosynthesis. (wikipedia.org)
- Additionally, the structural analysis of the protein provided insights on the domain movements which seems to be important for the protein function where the fourth domain of the protein consisting of antiparallel β-sheets connected to the other three domains via a loop showed less flexibility when bound to substrate and more flexibility in the apo form which were analyzed from the MD simulation trajectories. (ssrn.com)
Superfamily of proteins1
- Phosphoglucosamine mutase (GlmM) belonging to the superfamily of proteins called α-D-phosphohexomutases is involved in the UDP-N-acetylglucosamine (UDP-GlcNAc) biosynthetic pathway by converting glucosamine-6-phosphate (G6P) to glucosamine-1-phosphate (G1P) leading to the synthesis of UDP-GlcNAc which is an essential precursor in peptidoglycan layer synthesis in Mycobacterium sp. (ssrn.com)
- Cell lines derived from COS, CHO, BHK-21, HEK293, HeLa and GH3 can be generally used for membrane protein expression. (creative-biostructure.com)
- We provide other various Mempro™ membrane protein production services . (creative-biostructure.com)
- Mammalian membrane protein expression in baculovirus-infected insect cells. (creative-biostructure.com)
- Proteins that cross the membrane are surrounded by annular lipids , which are defined as lipids that are in direct contact with a membrane protein. (wikipedia.org)
- In this case the integral membrane protein spans the phospholipid bilayer seven times. (wikipedia.org)
- In vitro studies of membrane protein folding. (thefullwiki.org)
- Solving the membrane protein folding problem. (thefullwiki.org)
- Helical membrane protein folding, stability, and evolution. (thefullwiki.org)
- Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-Î² (TRIF) provides insights into its auto-inhibited state. (ncbs.res.in)
- There are important structural differences in the BH3 domain in the intact SOUL molecule and the same sequence bound to Bcl-xL. (proteopedia.org)
- Protein ubiquitination is an important post-translational modification involved in several essential signalling pathways. (mdpi.com)
- The molecular mechanisms responsible for the effects of non-proteolytic protein ubiquitination are in most cases elusive, but seem to be important in several completely different pathways. (mdpi.com)
- Ras-association domain family protein 6 induces apoptosis via both caspase-dependent and caspase-independent pathways. (springer.com)
- Pathways are authored and peer-reviewed by domain experts. (iscb.org)
- We report similar subgraphs in metabolic pathways and in protein-protein interaction networks. (imperial.ac.uk)
- The protein follows numerous pathways en route to its bound and folded conformation, occasionally becoming stuck in kinetic traps. (sdbonline.org)
- Here we show that the WD repeat‐containing C‐terminal domain ( WD 40 CTD ) of ATG 16L1 is essential for LC 3 recruitment to endolysosomal membranes during non‐canonical autophagy, but dispensable for canonical autophagy. (embopress.org)
- Ligase complex component ATG 16L1 is required for LC 3 lipidation of double‐membrane autophagsomes and of single membranes during phagocytosis and influenza infection, but only single membrane lipidation depends on ATG 16L1's C‐terminal WD 40 domain. (embopress.org)
- Together these observations suggest that ANTH domains may be responsible for recruiting host proteins to membranes containing PtdIns(4,5)P 2 . (bl.uk)
- However, the ENTH domain also binds to inositol polyphosphates and to membranes containing PtdIns(4,5)P 2 . (bl.uk)
- Such proteins can only be separated from the membranes by using detergents , nonpolar solvents , or sometimes denaturing agents. (wikipedia.org)
- The sensor involved determines the specificity of the inflammasome and is typically a member of two conserved protein families: NLRs (nucleotide-binding domain [NBD]- and leucine-rich repeat [LRR]-containing proteins), and ALRs (AIM2-like receptors). (rupress.org)
- These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. (embl-heidelberg.de)
- We detected HNOB domains in several bacterial lineages, where they occur fused to methyl accepting domains of chemotaxis receptors or as standalone proteins. (biomedcentral.com)
- G protein coupled receptors (e.g. (wikipedia.org)
- The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. (osti.gov)
Nucleic Acid Database1
Classification of protein1
- This superfamily represents the structural domain of Tom20 that binds to mitochondrial precursor proteins. (ebi.ac.uk)
- Structural analysis combined with mutational studies suggest that a PUR domain binds nucleic acids through two independent surface regions involving concave β-sheets. (pnas.org)
- Chromatin reader protein that recognizes and binds acetylated histones and plays a key role in transmission of epigenetic memory across cell divisions and transcription regulation. (genecards.org)