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Protein categories & taxonomy
<%end if%> Genomic biology map: Guide to terms in these glossaries Site Map This is a sub-category of Proteins, Related glossaries include Protein Technologies Proteomics and Proteomic categories adaptor proteins: A class of proteins involved in the transport of molecules via TRANSPORT VESICLES. They perform functions such as binding to the cell membrane, capturing cargo molecules and promoting the assembly of CLATHRIN. The majority of adaptor proteins exist as multisubunit complexes, however monomeric varieties have also been found. MeSH 2003 antifreeze proteins: Proteins that bind to ice and modify the growth of ice crystals. They perform a cryoprotective role in a variety of organisms. MeSH, 2001 basic proteins: Alkaline proteins, pI approximately above 7.0-7.5 pH. carbohydrate binding proteins CBPs: Our group investigates the roles of carbohydrate binding proteins that mediate cellular processes central to immune regulation and human disease. All projects are inter-related and fall into three main areas: 1) functions of carbohydrate binding proteins expressed on leukocytes, 2) regulation of the synthesis of their carbohydrate ligands during leukocyte activation and differentiation, and 3) development of glycosylation inhibitors that modulate immune function. Our multi-disciplinary approach is complemented by a diverse group of chemists, biochemists, cell biologists, and molecular biologists. Paulson Laboratory Research, Scripps Research Institute http://www.scripps.edu/mb/paulson/research.html carrier proteins: Transport proteins that carry specific substances in the blood or across cell membranes. MeSH, 1973 Narrower term: membrane transport proteins cell cycle proteins, cellular proteins: Cell biology checkpoint control proteins: Proteins that control passage through critical stages of the cell cycle, these might, for example, halt passage through the cell cycle in the case of DNA damage. chemokines: Class of pro-inflammatory cytokines that have the ability to attract and activate leukocytes. They can be divided into at least three structural branches: C; (CHEMOKINES, C); CC; (CHEMOKINES, CC); and CXC; (CHEMOKINES, CXC); according to variations in a shared cysteine motif. MeSH 1996 Related term: Drug targets GPCRs chromosomal proteins: Protein which is associated with chromosomal DNA, including histones, protamines and high mobility group proteins. UNI-PROT KnowledgeBase keywords http://www.expasy.org/cgi-bin/keywlist.pl Swiss Institute of Bioinformatics, Geneva Switzerland, European Bioinformatics Institute, Hinxton, UK, PIR Protein Information Resource, 2011 chromosomal proteins, non-histone: Nucleoproteins which in contrast to histones are acid insoluble. They are involved in chromosomal functions; e.g. they bind selectively to DNA, stimulate transcription resulting in tissue- specific RNA synthesis and undergo specific changes in response to various hormones or phytomitogens. MeSH, 1977 chimera protein: Wikipedia http://en.wikipedia.org/wiki/Chimera_%28protein%29 collagens: Biomaterials & bioengineering complex proteins: Complex proteins usually have more than one folding domain, each involving a sequence of 100 to 300 amino acids. The entire folding architecture of a complex protein must be precisely constructed in order for protein functionality to exist. Science Week 1998 A protein that contains a
simple protein and at least one molecule of another substance, as a
glycoprotein, lipoprotein, nucleoprotein, or hemoglobin. Mosby's Medical Dictionary,
8th edition. © 2009, Elsevier.
http://medical-dictionary.thefreedictionary.com/complex+protein
constitutive proteins: Proteins produced in fixed amounts, regardless of the organism's need for them. Dorland's Illustrated Medical Dictionary Related term? housekeeping proteins cytokines: Non- antibody proteins secreted by inflammatory leukocytes and some non- leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner. MeSH, 1991 Not really different from hormones, but the term tends to be used as
a convenient generic shorthand for interleukins, lymphokines and several
related signalling molecules such as TNF [Tumor Necrosis Factor] and interferons … Rather an imprecise
term, though in very common usage. Lackie 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. MeSH, 1984 disordered proteins: Protein structures factitious protein: A product of genetic engineering; a protein designed for a specific purpose or for its expected properties. [Glick] Factitious implies not natural or contrived. fibrous proteins: Family of proteins which include collagen and keratin. Insoluble. full-length proteins: Compare truncated proteins. gatekeeper protein: A protein that monitors transfer of a protein from the endoplasmic reticulum to the Golgi apparatus and prevents transfer of newly synthesized proteins with inappropriate conformations or with unpaired thiol groups. Glick globular proteins: Water soluble proteins. Narrower term: enzymes glycoproteins: Conjugated protein- carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins. MeSH Glycoproteins are complexes in which carbohydrates are attached covalently to asparagine (N-glycans) or serine/ threonine (O-glycans) residues of peptides. "Glycoproteins: How are glycoprotein sugar chains functioning within us", Glycoforum, Japan 2001 http://www.glycoforum.gr.jp/science/word/glycoprotein/GPA00E.html growth factors: This collective term originally referred to substances that promote cell growth. It is used rather loosely now, comprising molecules that function as growth stimulators (mitogens) but also as growth inhibitors (sometimes referred to as negative growth factors ), factors that stimulate cell migration (see: Motogenic cytokines ) or function as chemotactic agents (see also: Chemotaxis ) or inhibit cell migration or invasion of tumor cells, factors that modulate differentiated functions of cells, factors involved in apoptosis , or factors that promote survival of cells without influencing growth and differentiation. ... In many instances the term is used as a synonym for cytokines. Horst Ibelgauft's Cytokines Online Pathfinder Encyclopaedia http://www.copewithcytokines.de/ Narrower term IGF-1 Insulin like Growth Factor Compare cytokines GTP-binding proteins: Regulatory proteins that act as molecular switches. They control a wide range of biological processes including: receptor signaling, intracellular signal transduction pathways, and protein synthesis. Their activity is regulated by factors that control their ability to bind to and hydrolyze GTP to GDP. EC 3.6.1 MeSH, 1997 Is this different from G- proteins? heat shock proteins: Proteins which are synthesized in eukaryotic organisms and bacteria in response to hyperthermia and other environmental stresses. They increase thermal tolerance and perform functions essential to cell survival under these conditions. MeSH, 1984 Heat shock proteins (HSPs), also called stress proteins, are a group of proteins that are present in all cells in all life forms. They are induced when a cell undergoes various types of environmental stresses like heat, cold and oxygen deprivation. Heat shock proteins are also present in cells under perfectly normal conditions. They act like ‘chaperones,’ making sure that the cell’s proteins are in the right shape and in the right place at the right time. Heat Shock Proteins: Basics, Antigenics, 2004 http://www.antigenics.com/products/tech/hsp/ housekeeping proteins: Highly expressed proteins > 10,000 copies per cell. Blackstock & Weir “Proteomics” Trends in Biotechnology: 121 Mar 1999 Universal proteins. Not the proteins of greatest interest, which are often of low abundance. Compare luxury proteins hub proteins: http://www.bio.com/realm/research.jhtml?realmId=2&cid=900053 Narrower terms: date hubs [interact at different locations or times], party hubs [interact at the same time hyperthermal proteins: Many microorganisms live in extreme environments such as hyperthermal vents, volcanoes, salty lakes, hot springs, and frozen glaciers. The objective of this program is to discover the structural and biochemical basis for understanding the unusual stabilities and biochemical properties of the proteins from these organisms, and to find their application for industrial and medical purposes. Rosalind Kim, Physical Biosciences Division, Lawrence Berkeley National Lab US http://pbd.lbl.gov/PBD_web_site/web_site/html/about/people/kim-r.html hydrophobic proteins: Repel water. Related term membrane proteins. Protein structure immediate-early proteins: Proteins that are coded by immediate- early genes, in the absence of de novo protein synthesis. The term was originally used exclusively for viral regulatory proteins that were synthesized just after viral integration into the host cell. It is also used to describe cellular proteins which are synthesized immediately after the resting cell is stimulated by extracellular signals. MeSH, 1994 immunoglobulin Ig: A protein of the globulin- type found in serum or other body fluids that possesses antibody activity. An individual Ig molecule is built up from two light (L) and two heavy (H) polypeptide chains linked together by disulfide bonds. Igs are divided into five classes based on antigenic and structural differences in the H chains. IUPAC Compendium Glycoproteins present in the blood (ANTIBODIES) and in other tissue. They are classified by structure and activity into five classes (IMMUNOGLOBULIN A; IMMUNOGLOBULIN D; IMMUNOGLOBULIN E; IMMUNOGLOBULIN G; IMMUNOGLOBULIN M). MeSH, 1972 Related term: Gene categories immunoglobulin genes interferons: A class of glycoproteins (with sugar groups attached at specific locations) important in immune function. They are able to inhibit the multiplication of viruses in cells. IUPAC Biotech, IUPAC Compendium Proteins secreted by vertebrate cells in response to a wide variety of inducers. They confer resistance against many different viruses, inhibit proliferation of normal and malignant cells, impede multiplication of intracellular parasites, enhance macrophage and granulocyte phagocytosis, augment natural killer cell activity, and show several other immunomodulatory functions. MeSH, 1983 low-abundance proteins: Often the proteins of greatest interest, but difficult to detect because more abundant proteins predominate. luxury proteins: When specialized differentiated cells are formed, another set of proteins is synthesized, which are commonly known as luxury proteins http://protein.bio.msu.ru/biokhimiya/contents/v70/full/70050612.html Compare housekeeping proteins mitochondrial proteins:
Proteins encoded by the mitochondrial genome or proteins encoded by the nuclear genome that are imported to and resident in the MITOCHONDRIA.
MeSH, 2002
molecular chaperones: Protein structure moonlighting proteins: A protein that has more than one independent function. Petsko, Gregory A. 2001. Size doesn't matter. Genome Biology 2:1003.1-1003.2 mosaic proteins: Proteins with many (often repeated) domains
are termed mosaic proteins. These domains or modules may be considered
to be connected units which are independent in terms of their structure,
function and folding behaviour. Principles of protein structure
using the Internet, Dept. of Crystallography, Birkbeck College, Univ. of
London, UK 1997-98 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. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 Amos Bairoch* Rolf Apweiler Nucleic Acids Research 28 (1): 45-48 http://nar.oxfordjournals.org/content/28/1/45.full?ref=klasshop.com Related? term: naked DNA Google = about 156 Jan. 11, 2006 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. MeSH, 1988 Any other way of characterizing? nucleoproteins: Proteins conjugated with nucleic acids. MeSH oncogene proteins: Proteins coded by oncogenes. They include proteins resulting from the fusion of an oncogene and another gene (ONCOGENE PROTEINS, FUSION). MeSH, 1993 orphan proteins:
proteins
that do not have significant sequence identity(>10%) with other known
proteins. Bio Bulletin Board 2005 http://www.bioinformatics.org/pipermail/bbb/2005-July/002624.html
Proteins without sequence (and/or structural?) similarity to previously characterized proteins. overexpressed proteins, overexpression: Expression gene & protein polypeptides: Peptides containing ten or more amino acids. IUPAC Compendium polyproteins: Proteins which are synthesized as a single polymer and then cleaved into several distinct proteins. MeSH, 2000 proteases: Enzymes that catalyse the hydrolysis of proteins. Usually several proteolytic enzymes are necessary for the complete breakdown of polypeptides to their amino acids. IUPAC Biotech, IUPAC Compendium repressor proteins: Proteins which are normally bound to the operator locus of an operon, thereby preventing transcription of the structural genes. In enzyme induction, the substrate of the inducible enzyme binds to the repressor protein, causing its release from the operator and freeing the structural genes for transcription. In enzyme repression, the end product of the enzyme sequence binds to the free repressor protein, the resulting complex then binds to the operator and prevents transcription of the structural genes. MeSH, 1991 RING finger proteins: Display a series of histidine and cysteine residues with a characteristic spacing that allows the coordination of two zinc ions. RING finger domains are found in many proteins and have been implicated in various cellular functions. RINGs presumably do not function as chemical catalysts but as molecular scaffolds that bring together other proteins such as E3 ubiquitin ligases with E2 ubiquitin conjugating enzymes and the corresponding substrate. Apoptopedia, Cell Death Encyclopedia, 2001 http://www.celldeath.de/encyclo/index/r.htm K.L. Lorick, J.P. Jensen, S.Y. Fang, A.M. Ong, S. Hatakeyama, A.M. Weissman, "RING fingers mediate ubiquitin- conjugating enzyme (E2)-dependent ubiquitination," PNAS Proceedings from the National Academy of Sciences, 96(20): 11364- 11369, Sept. 28, 1999 C.A.P. Joazeiro, S.S. Wing, H.K. Huang, J.D. Leverson, T. Hunter, Y.C. Liu, "The tyrosine kinase negative regulator c-Cbl as a RING- type, E2-dependent ubiquitin- protein ligase," Science, 286: 309- 312, Oct. 8, 1999
RING stands for really interesting new gene http://en.wikipedia.org/wiki/RING_finger_domain
structural proteins: Wikipedia http://en.wikipedia.org/wiki/Category:Structural_proteins Contrast with nonstructural proteins. transport proteins: See membrane transport proteins. Are there any transport proteins which are not membrane proteins? transcription factors: Sequences, DNA & beyond ubiquitins: A family of proteins that are structurally-related to Ubiquitin. Ubiquitins and ubiquitin- like proteins participate in diverse cellular functions, such as protein degradation and HEAT- SHOCK RESPONSE, by conjugation to other proteins. MeSH, 2002 wild-type proteins: Native proteins, as found in the wild. This seems analagous to wild- type [genes] Genetic variations. Are there any other implications? Zinc Finger Proteins ZFP: A domain, found in certain DNA- binding proteins, comprising a helix- loop structure in which a zinc ion is coordinated to 2- 4 cysteine sulfurs, the remaining ligands being histidines. In many proteins of this type the domain is repeated several times. IUPAC Bioinorganic ZFPs are naturally occurring, zinc- containing DNA- binding proteins that serve as transcription factors. Researchers have discovered the rules by which ZFPs recognize specific DNA sequences. This knowledge allows them to rapidly generate proteins that selectively regulate target genes of interest. Genetic constructs that code for these ZFPs can be transfected into cells in culture or into animals, resulting in the downregulation or upregulation of target genes. Bibliography How to look for other unfamiliar terms IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry. |
