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Map amino acid receptors: Cell surface proteins that bind amino acids and trigger changes which influence the behavior of cells. Glutamate receptors are the most common receptors for fast excitatory synaptic transmission in the vertebrate central nervous system, and GAMMA- AMINOBUTYRIC ACID and glycine receptors are the most common receptors for fast inhibition. MeSH, 1993 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. MeSH, 1966-1999 Related terms: Sequencing sequence homology amino terminus: Narrower term: N-terminus. Compare carboxyl terminus. amino terminus domain: In protein-protein interactions, the N-terminal domain binds to specific DNA sequences. [S. Fields and O. Song “Novel genetic system to detect protein- protein interactions” Nature 340:245-246 July 20 1989] 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. MeSH A building block of proteins. There are 20 different kinds of amino acids; a protein consists of a specific sequence of amino acids. NIGMS amino acids- number of: The great majority of the now classical twenty amino acids have been on the scene for more than a century. Threonine was the last to be discovered in 1936. There was a scoop in 1986 though when it was discovered that the UGA codon could produce a new amino acid altogether: selenocysteine. Selenocysteine, the 21st amino acid, is found in archaea, eubacteria and animals. And why is it new and not simply a modified cysteine? Because it has its own tRNA which is like granting it a passport. Similarly, in May 2002, the existence of a 22nd amino acid was reported: pyrrolysine. Pyrrolysine was found in the sequences of three enzymes which participate in the production of methane in the archaeon Methanosarcina barkeri: mono-, di- and trimethylamine methyltransferases. Like selenocysteine, it is coded from a stop codon, though this time the UAG or amber codon, and sports its own tRNA. [Life's jokers, Vivienne Baillie Gerritsen, Bio.com, 2002] The "classical" amino acids are naturally occurring ones. Others have been synthesized. Related term: proteins - numbers of antibodies: Pharmaceutical biology glossary apoptosis: Cell biology glossary BIOML Biopolymer Markup Language: Biomaterials & bioengineering glossary cell surface receptors: Cell surface proteins that bind signalling molecules external to the cell with high affinity and convert this extracellular event into one or more intracellular signals that alter the behavior of the target cell (From Alberts, Molecular Biology of the Cell, 2nd ed, pp693- 695). Cell surface receptors, unlike enzymes, do not chemically alter their ligands. MeSH, 1994 characterization - protein: Some of the information that can be gathered from a protein chip based characterization includes: post translational modification: phosphorylation, glycosylation, biotinylation, ADP-ribosylation (Cardone et al. 1998) C-terminal sequencing, epitope (binding site) mapping (Hinshelwood et al. 1999) Broader term: characterization Biomolecules glossary C-terminus: The residue that has a free carboxyl group, or at least does not acylate another amino acid residue, (it may, for example, acylate ammonia to give -NH-CHR-CO-NH2), is called C-terminal. [IUPAC Bioinorganic “amino acid residue in a polypeptide”] Also called the carboxyl terminus. carboxyl terminus: See C terminus. Contrast with N-terminus. carboxyl terminus domain: In protein- protein interactions, the C- terminal domain contains acidic regions necessary to activate transcription factors. [S Fields and O Song “Novel genetic system” Nature 340: 245-246 July 20 1989] cell patterning and proteins: Cell biology glossary chemokines: Protein categories co-immunoprecipitation Used to determine protein- protein interactions. An antibody is used to precipitate a protein along with bound proteins. [John Yates, “Mass spectrometry and the Age of the Proteome” Journal Mass Spectrometry 33: 16, 1998] co-localization: With the advent of GFP [green fluorescent protein] and other fluorescent proteins, researchers commonly wish to ask the question: Where is my favorite protein? A typical experiment involves the cloning of my favorite protein and the creation of a fluorescent analog. Fluorescence imaging can then be used to follow the protein through development, over time, or after stimulation of some sort by referencing fluorescent probes for cellular compartments (the nucleus, mitochondria, lysosomes, etc.) or structures (the microtubule network, junctions in the membrane, chromosomes, etc.). [Co- localization, Universal Imaging Inc., 2002] http://www.image1.com/products/apps/colocalization.cfm co-precipitation: Method to identify interacting proteins by using antibodies to bind to the protein if immunoprecipitated under non- denaturing using conditions … (allow any other proteins bound to the protein known to be involved in a process) to precipitate rather than be washed away. cross-annotation: Comparing gels of similar samples and the information attached to them for verification based solely upon mobility cytokines: Protein categories denaturation: The process of partial or total alteration of the native structure of a macromolecule resulting from the loss of tertiary or tertiary and secondary structure that is a consequence of the disruption of stabilizing weak bonds. Denaturation can occur when proteins and nucleic acids are subjected to elevated temperature or to extremes of pH, or to non- physiological concentrations of salt, organic solvents, urea or other chemical agents. [IUPAC Biotech] depletion: Method of sample preparation which removes high abundance proteins (not of interest) from the sample. Related term: low- abundance proteins. difficult to express proteins: Expression glossary directed protein evolution: Proteomics glossary Related term: phage display Genetic manipulation & disruption glossary enzymes: Pharmaceutical biology glossary exteins: Sequences, DNA & beyond glycosylation: Glycoscience glossary hormone: Pharmaceutical biology glossary hypothetical proteins: Protein categories inclusion bodies: Insoluble aggregates of misfolded proteins which must be solubilized and refolded into an active form to be functional. inteins: Sequences, DNA & beyond kinases: See Protein categories protein kinases Laser Capture Microdissection LCM: Cell biology glossary Can be used to help isolate low- abundance proteins. localization: SEE protein localization low-abundance proteins: Protein categories Related terms: depletion; Laser Capture Microdissection Cell biology ; sample prep Technologies overview and Assays, labels, signaling & detection glossary. membrane proteins: Protein structure glossary methylation: Attachment of methyl groups (-CH3) to DNA most commonly at cytosine residues. May be involved in regulation of gene expression. Also may prevent some restriction endonucleases from cutting DNA at their recognition sites. [Schlwindlein] DNA Methylation Database, Institut de Génétique Humaine (CNRS) Montpellier, France http://www.methdb.de/ Related terms: Functional genomics Post Translational Gene Silencing; Gene definitions epigenetics; Omes & omics epigenomics, epigenotype molecular motors: Nanoscience & Miniaturization glossary multiprotein complexes: Most proteins do not act alone but instead are organized into multiprotein complexes that carry out activities needed for metabolic activity, communication, growth, and structure. The first goal of Genomes to Life is to systematically identify, characterize, and begin to understand these "machines of life." This will provide the essential knowledge base and set the stage for linking proteome dynamics and architecture to cellular and organismic function. Identifying and characterizing multiprotein complexes on a genome- wide scale will require new tools and research strategies designed to increase throughput, reliability, and sensitivity. Molecular Machines of Life, DOE Genomes to Life, US http://www.doegenomestolife.org/program/goal1.html naked proteins: We call these proteins "naked" because genomic information does not allow the efficient prediction of all the post- translational modifications (PTM) of which the majority of proteins are the target. Human Proteomics Initiative, Amos Bairoch, ExPaSy, Swiss Institute of Bioinformatics, 2003 http://au.expasy.org/sprot/hpi/hpi_desc.html Google = about 156 Jan. 11, 2006 Related? term: DNA glossary naked DNA N-terminus: The residue in a peptide that has an amino group that is free, or at least not acylated by another amino acid residue (it may, for example, be acylated or formylated), is called N-terminal; it is the N-terminus. [IUPAC Bioinorganic] Also called the amino terminus. PEGS: The Protein Engineering Summit April 27-May 2, 2008 • Boston, MA peptide aptamers: Functional genomics glossary Peptide Mass Fingerprinting PMF: A means of protein identification, using mass spectrometry peptide sequencing: How is this different from protein sequencing (except that peptides are shorter than proteins)? peptides: Amides derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from a- amino acids, but it includes any amino carboxylic acid. [IUPAC Compendium] Related term: polypeptides peptidome, peptidomics: -Omes & -omics glossary phosphorylation: A process involving the transfer of a phosphate group (catalyzed by enzymes) from a donor to a suitable acceptor;. [IUPAC Bioinorganic] Broader term: post- translational modifications poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties. MeSH, 1976 polyadenylation: The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLTRANSFERASE) adds 60- 200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here. MeSH, 2002 During the maturation of messenger RNA, about 200 adenosine nucleotides are added in a polyadenylation reaction at the 3' end. These are not coded by the corresponding gene. In certain cases there are multiple alternative polyadenylation sites in the primary transcript. This was first observed in adenoviruses [127 - 131]. In cellular genes many alternative polyadenylation sites have also been found [see 132 for review]. Alternative polyadenylation sites usually involve the untranslated trailer sequence in the messenger RNA, but they can also involve translated sequences, and in this case they can affect the structure of the encoded protein. Thus multiple polyadenylation sites are one mechanism whereby a single gene can control the synthesis of more than one polypeptide. Petter Portin in "The Origin, Development and Present Status of the Concept of the Gene: A Short Historical Account of the Discoveries" Univ. of Turku, Finland, Current Genomics, 2000 http://www.bentham.org/cg/sample/cg1-1/Portin.pdf polypeptides: Biomolecules glossary Protein categories post-translational modifications: Proteins once synthesized on the ribosomes, are subject to a multitude of modification steps. They are cleaved (thus eliminating signal sequences, transit or pro- peptides and initiator methionines); many simple chemical groups can be attached to them … as well as some more complex molecules, such as sugars and lipes. Finally they can be internally or externally cross- linked. More than a hundred different types of post- translational modifications are currently known (Aug. 1999) and many more are yet to be discovered. The complexity due to all these modifications is compounded by the high level of diversity that alternative splicing can produce at the level of sequence. Thus the number of different protein molecules expressed by the human genome is probably closer to a million than to the hundred thousand generally considered by genome scientists. Human Proteomics Initiative, A Bairoch http://au.expasy.org/sprot/hpi/hpi_desc.html Post-translational modification is a point of concern in the development of strategies for proteomics. Because these modifications cannot be inferred directly from gene sequence, they generally can only be characterized directly. This raises issues about sequence coverage and stoichiometry of modifications that are not presented by proteomics problems focused on protein identification. In particular, the complexity and diversity of glycosylation events significantly complicates the linkage between genetic sequence and mature, active proteins. Because glycosylation is mediated by a wide range of factors, discovery- based analytical tools that can survey the complexities of glycosylation on a system-wide basis may have significant biological impact. NCRR National Center for Research Resources, NIH, Integrated Biomedical Technology Research Resources for Proteomics and Glycomics, RELEASE DATE: July 22, 2002 PA NUMBER: PA-02-132 http://grants.nih.gov/grants/guide/pa-files/PA-02-132.html Narrower terms: biotinylation, glycosylation, pegylation, phosphorylation, polyadenylation, prenylation, protein isoprenylation; Related terms: post- translational protein processing, proteolytic processing, ubiquitination; In silico & molecular modeling: post- translational modification prediction post-translational protein processing: Any of various enzymically catalyzed post- translational modifications of peptides or proteins in the cell of origin. These modifications include carboxylation, hydroxylation, acetylation, glycosylation, methylation, phosphorylation, oxidation- reduction, degradation and lysis, peptide bond formation, and changes in molecular weight and electrophoretic motility. MeSH, 1983 Related terms: post- translational modifications; prefractionation: Sample preparation method, capable of being automated. prenylation: Attachment of an isoprenoid to the C-terminal cysteine residue. [SWISS-PROT keywords] http://www.expasy.ch/cgi-bin/get-entries?KW=Prenylation primary structure: In the context of macromolecules such as proteins, the constitutional formula, usually abbreviated to a statement of the sequence and if appropriate cross- linking of chains. [IUPAC Compendium] See also amino acid sequence. probable protein (similarity): When a protein exhibits extensive sequence similarity to a characterised protein and/ or has the same conserved regions then the label ‘probable' is used in the DE line. "SWISS- PROT" in Introduction to Molecular Biology Databases, R. Apweiler, R. Lopez, B. Marx, 1999 http://www.ebi.ac.uk/swissprot/Publications/mbd1.html Related term: Protein categories putative protein proteasome: Breaking down unneeded proteins — a task equal in importance to synthesizing new proteins — is accomplished by the orderly action of several multiprotein complexes. At the heart of this process is a multiprotein complex called the proteasome. This is a fundamental kind of machine that has been highly conserved during evolution. Proteasomes: The Machines of Life, DOE Genomes to Life, US http://www.doegenomestolife.org/science/proteinmachines.html protein: See proteins protein analysis: Proteomics glossary protein arrays; protein chips: Microarrays glossary protein complexes: Proteomics glossary protein databases: Proteomics glossary See also Databases & software directory protein delivery: Drug discovery & development protein detection: New fluorescent stains (such as Sypro) have improved both the dynamic range of protein detection and protein quantification in 2D gels. "Current State of Proteomic Technology" CHI's Genome Link 3.1, 2001 http://www.healthtech.com/newsarticles/issue3_1.ASP protein engineering: A technique used to produce proteins with altered or novel amino acid sequences. The methods used are: 1. Transcription and translation systems from synthesized lengths of DNA or RNA with novel sequences. 2. Chemical modification of 'normal' proteins. 3. Solid- state polypeptide synthesis to form proteins. [IUPAC Compendium] Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes. MeSH 2003 Protein Engineering Summit April 27-May 2, 2008 • Boston, MA Procedures by which nonrandom single- site changes are introduced into structural genes (site- specific mutagenesis) in order to produce mutant genes which can be coupled to promoters that direct the synthesis of a specifically altered protein, which is then analyzed for structural and functional properties and then compared with the predicted and sought- after properties. The design of the protein may be assisted by computer graphic technology and other advanced molecular modeling techniques. [MeSH, 1989] protein expression, protein expression profiling: Expression glossary protein family: Protein structure glossary protein folding disorders: Molecular medicine glossary protein function, protein identification, protein informatics: Proteomics glossary protein inhibition: An alternative approach to [gene expression] downregulation, but in this case, the protein, not the gene, is the target. As with downregulation of gene expression, protein inhibition is a powerful target validation tool. The major approach to protein inhibition is based on phage libraries, which are used to select antibodies against targets of interest. protein interactions: Proteomics glossary protein isoprenylation: A post- translational modification of proteins by the attachment of an isoprenoid to the C-terminal cysteine residue. The isoprenoids used, farnesyl diphosphate or geranylgeranyl diphosphate, are derived from the same biochemical pathway that produces cholesterol. MeSH, 1993 Broader term: post- translational modification protein knockouts: Proteomics glossary protein localization: There is an ever- increasing number of genes that have been sequenced but are of completely unknown function. The ability to determine the location of such gene products within the cell, either by the use of antibodies or by the production of chimeras with green fluorescent protein, is a vital step towards understanding what they do. This is one major reason why fluorescence microscopy is enjoying a revival. [Protein Localization by Fluorescence Microscopy: A Practical Approach Edited by VICTORIA J. ALLAN, Oxford University Press, 2000] http://www.oup-usa.org/isbn/0199637415.html Protein expression analysis can indicate what proteins are expressed, but it is also important to know where proteins are expressed, and where they go over time (as with secreted proteins). Accordingly, there is an increasing shift away from general protein expression analysis and toward mapping proteins’ distribution, relative abundance, tissue specificity, and movement. By tracking these parameters (in healthy versus diseased tissue and in control versus treated tissue), researchers can gain a greater understanding of these proteins’ functions and determine which are likely to be the best drug targets. Protein localization studies can be classified as being done at a tissue or subcellular level. "Protein Localization Studies provide key insights into protein function" CHI's GenomeLink 15.2 http://www.healthtech.com/newsarticles/issue15_2.asp Narrower terms: subcellular localization, tissue specific localization; Related terms Cell biology: subcellular fractionation; Gene definitions: gene localization; Omes & omics localizome protein networks: Proteomics glossary protein nomenclature: Nomenclature protein protein interactions: Proteomics glossary protein purification: John Wagner's Logic of Molecular Approaches to Biological Problems (Cornell Univ. Graduate School of Medical Science, US ) has a section on the value of protein purification. http://www-users.med.cornell.edu/~jawagne/proteins_%26_purification.html protein regulation: Related term: Gene definitions: gene regulation protein sequence: A process that includes the determination of an amino acid sequence of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence. MeSH, 2002 See also amino acid sequence. protein sorting signals: Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments. MeSH, 2001 Protein Spotlight, Swiss-Prot http://au.expasy.org/spotlight/ One month, one protein protein superfamily: Protein structure glossary protein synthesis: See transcription, translation. Sequences, DNA & beyond glossary protein therapeutics: Drug discovery & development glossary 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. MeSH, 2001 All new proteins in the cell have a tag on them, telling whether the protein is to be sent out of the cell or to a special part in the cell. By comparing tags from known proteins the scientist can find out where an unknown protein will be located. PhD programme in Medical Bioinformatics, Karolinska Institutet http://www.cbb.ki.se/fmb/leaflet.pdf proteins: Naturally occurring and synthetic polypeptides having molecular weights greater than about 10,000 (the limit is not precise). [IUPAC Compendium] Polymers of amino acids linked by peptide bonds. The specific sequence of amino acids determines the shape and function of the protein. MeSH Proteins provide the critical link between genes and disease, and as such are the key to understanding of basic biological processes including disease pathology, diagnosis, and treatment. The pervasiveness of protein function and their potential for therapeutic intervention are attracting increasing attention from the pharmaceutical and biotechnology industries. Proteins are the main catalysts, structural elements, signaling messengers and molecular machines of biological tissues. David Eisenberg et al. “Protein function in the post-genomic era” Nature 405: 823-826, 15 June 2000 Narrower terms: Cell biology cell cycle proteins, cellular protein complexes; Protein categories antifreeze proteins, basic proteins, , checkpoint control proteins, factitious proteins, fusion proteins, gatekeeper proteins, heat shock proteins, housekeeping proteins, hydrophobic proteins, hypothetical proteins, immediate- early proteins, low- abundance proteins, luxury proteins, membrane proteins, mitochondrial proteins, oncogene proteins, orphan proteins, polypeptides, probable proteins, protein kinases, putative proteins, secreted proteins, therapeutic proteins, trans- acting proteins, tumor- suppressor proteins, wild- type proteins, zinc finger proteins; Protein structures disordered proteins, membrane proteins, molecular chaperones, mosaic proteins, multi- domain proteins, oligomeric proteins, protein families, protein superfamily Protein databases see Databases & software directory. proteins - numbers of: Nobody is sure how many naturally occurring proteins will eventually be identified. The precise number of genes will take some years to identify. The extent of alternative splicing is now known to be more than originally expected, before the draft version of the Human Genome Project was published. Post- translational modifications further increase the number of proteins. proteolysis: The breaking down of proteins by enzymes called proteases. [Life Sciences] proteolytic processing: Related terms proteolysis Broader term post- translational modification receptor: Pharmaceutical biology glossary Narrower terms: amino acid receptors, cell surface receptors residue: When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino acid residue. [IUPAC Bioinorganic] Related terms C-terminus, N-terminus secreted proteins: Protein categories sequence homology: Sequencing glossary subcellular localization: A variety of approaches—including tagging and fluorescence technologies, cellular isolation methods, gels, and mass spectrometry—are being used in these studies, which aim to track the location and/or movement of proteins or protein complexes in subcellular compartments. "Protein Localization Studies provide key insights into protein function" CHI's GenomeLink 15.2 http://www.healthtech.com/newsarticles/issue15_2.asp A key functional characteristic of proteins. To co-operate for a common physiological function (metabolic pathway, signal transduction cascade, structural associate etc.), proteins must be localized in the same cellular compartment. [Frank Eisenhaber and Peer Bork, "Subcellular Localization: Automatic analysis of SWISS-PROT annotations with Meta _ A(nnotator)", 2000] http://mendel.imp.univie.ac.at/CELL_LOC/ subcellular issue-specific localization: A major methodology is an immunohistochemistry approach that uses antibodies (typically visualized via an enzyme- linked antibody assay) that specifically bind to proteins of interest. This method allows one not only to assess levels of a protein but also to localize the protein within cells in a tissue sample. "Protein Localization Studies provide key insights into protein function" CHI's GenomeLink 15.2 http://www.healthtech.com/newsarticles/issue15_2.asp therapeutic proteins: Protein categories transcription Sequences, DNA & beyond glossary. transcription factors: Sequences, DNA & beyond glossary. translation: Sequences, DNA & beyond glossary Another approach to downregulating gene expression See also Genetic Manipulation & Disruption RNAi; Pharmaceutical biology antisense; RNA glossary ribozymes. ubiquitin: Wikipedia
http://en.wikipedia.org/wiki/Ubiquitin Broader term: post- translational modification wild-type proteins: Protein categories Bibliography How to look for other unfamiliar terms IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry. |
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