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Protein categories & taxonomy
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Map 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. candidate proteins: NIGMS (part of NIH) is supporting research on identifying candidate proteins and their genes, including those that cause variations in human drug metabolism, transport, distribution, and excretion (for both small organic molecules and macromolecular drugs such as peptides and oligonucleotides), that may play a role in determining individual variations in drug responses and candidate proteins and their genes, including those that are direct targets for drug action (e.g., receptors, enzymes, signal transducing molecules, regulatory factors), that may play a role in determining individual variations in drug responses. [National Institute of General Medical Sciences, Recommendations of the NIGMS Working Group -- Understanding Individual Variations in Drug Responses: From Phenotype to Genotype , June 9-10, 1998, Bethesda MD http://www.nigms.nih.gov/news/reports/pharmacogenetics.html Related terms: Pharmacogenomics 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. SWISS- PROT UniProt? 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] Proteins may consist of a single polypeptide chain, as myoglobin does, or of multiple chains linked by disulfide bonds; the two chains of insulin are joined by two disulfide bonds. More complex proteins may consist of multiple chains held together by noncovalent forces. Some protein molecules contain organic structures which are not polypeptide chains. Hemoglobin, for example, includes the additional iron- containing heme group which is essential for its transport of oxygen [JA Plambeck, Dept. of Chemistry, Univ. of Alberta] http://www.chem.ualberta.ca/~plambeck/che/p265/p06232.htm Is there a precise definition of complex proteins? Ones with more than two disulfide bonds? More than one folding domain? The Nature issue with the human genome sequence noted that "Humans have an unusually high number of complex proteins that fit into more than one functional category". Various sources describe categories of "simple proteins" and "conjugated proteins" and "derived proteins" Enzymes are identified as complex proteins. Not the same as protein complexes constitutive proteins: Proteins produced in fixed amounts, regardless of the organism's need for them. Dorland's Illustrated Medical Dictionary, Merck Source http://www.mercksource.com/pp/us/cns/cns_hl_dorlands.jspzQzpgzEzzSzppdocszSzuszSzcommonzSzdorlandszSzdorlandzSzdmd_p_37zPzhtm 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] Horst Ibelgauft's Cytokines Online Pathfinder
Encyclopaedia, 2007 http://www.copewithcytokines.de/ 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 designer proteins: Protein design is currently used for the creation of new proteins with desirable traits. In our lab, we focus on the synthesis of proteins with high essential amino acid content having potential applications in animal nutrition. One of the limitations we face in this endeavour is achieving stable proteins despite a highly biased amino acid content. We report here the synthesis and characterisation of two mutants derived from our MB-1 designer protein. Williams M, Gagnon MC, Doucet A, Beauregard M, "Design of high essential amino acid proteins: two design strategies for improving protease resistance of the nutritious MB-1 protein" Journal of Biotechnology 94(3): 245- 254, Apr. 11, 2002 Designer proteins, Scripps http://mgl.scripps.edu/people/goodsell/pdb/pdb70/pdb70_1.html Designer proteins can also refer to high- protein nutritional supplements. 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. fusion proteins: Wikipedia http://en.wikipedia.org/wiki/Fusion_protein fusion proteins, recombinant: Proteins that are the result of genetic engineering. A regulatory part or promoter of one or more genes is combined with a structural gene. The fusion protein is formed after transcription and translation of the fused gene. This type of fusion protein is used in the study of gene regulation or structure- activity relationships. They might also be used clinically as targeted toxins (immunotoxins). MeSH, 1987 Related term: cell fusion GTP binding proteins: Pharmaceutical biology 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 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 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/about/people/kim-r.htm hydrophobic proteins: Repel water. Related term membrane proteins. Protein structure hypothetical proteins: Many of the gene products of completely sequenced organisms are “hypothetical” – they cannot be related to any previously characterized proteins – and so are of completely unknown function. ..As each [completely sequenced] organism’s genome is analyzed about one third of the observed open reading frames (ORFs), although conserved among several organisms, encode for “hypothetical ‘ proteins that cannot be related to other proteins of known function or structure. Understanding the physiological function of the protein products of these so-called ‘orphan’ genes has emerged as a major challenge. [E Eisenstein et al “Biological function made crystal clear – annotation of hypothetical proteins via structural genomics” Current Opinion in Biotechnology 11(1): 25- 30 Feb. 2000] All predicted protein sequences lacking any significant sequence similarity to characterised proteins are labeled as ‘hypothetical proteins'. The majority of these cases come from the genome sequencing projects. ["SWISS- PROT" in Introduction to Molecular Biology Databases, R. Apweiler, R. Lopez, B. Marx, 1999] http://www.ebi.ac.uk/swissprot/Publications/mbd1.html 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: Pharmaceutical biology 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 ion channels: Gated, ion- selective glycoproteins that traverse membranes. The stimulus for channel gating can be a membrane potential, drug, transmitter, cytoplasmic messenger, or a mechanical deformation. Ion channels which are integral parts of ionotropic neurotransmitter receptors are not included. MeSH, 1979 kinases: See protein kinases low-abundance proteins: Often the proteins of greatest interest, but difficult to detect because more abundant proteins predominate. luxury proteins: http://protein.bio.msu.ru/biokhimiya/contents/v70/full/70050612.html membrane proteins: Bioprocessing 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 See also under Proteomic categories mitochondrial proteome 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 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: We define orphans as those proteins that we can identify in a protein mass spectrometric analysis of rice tissues, so we are sure they exist in plant cells, but which have no known function or homology to known proteins. This will require an exhaustive proteomic analysis of rice tissues as a first stage, that will produce a table of orphan proteins that are candidates for further study. Paul A Haynes, Director of Proteomics, Univ. of Arizona, 2007 http://lifescience.arizona.edu/faculty.php?faculty_id=2848 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 predicted proteins: ORFs with no similarity to other sequence were named predicted proteins. MIT, Broad Institute, Methanosarcina project information, 2004 http://www.broad.mit.edu/annotation/microbes/methanosarcina/background.html probable protein: See under putative proteins 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] protein expression: Expression gene and protein protein kinases: putative proteins: Some similarity to one or more existing entries It is in this category that the adjective "putative" comes into play. For these cases, again there is no experimental proof that the protein exists and there is only limited evidence to point the protein to a particular family. Again, we have no fixed rules on what is "limited" and what isn't. It is a judgment that we make based on which family it is and which, if any, areas are conserved. A primer on UniProtKB/Swiss-Prot annotation Name: ANNBIOCH.TXT Release: 54.0 of 24-Jul-2007 http://www.expasy.ch/cgi-bin/lists?annbioch.txt The label ‘putative' is used in the DE [descriptor] line of proteins that exhibit limited sequence similarity to characterised proteins. These proteins often have a conserved site e.g. ATP-binding site but no other significant similarity to a characterised protein. It is most frequently used for sequences from genome projects. The assignment of the labels ‘probable' and ‘putative' is dependent primarily on the results of sequence similarity searches against SWISS- PROT. It is important to point out here that no specific cut- off point is used to assign a protein as ‘putative' or ‘probable'. "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 probable protein (similarity) receptors: Pharmaceutical biology regulatory proteins: A detailed understanding of the interplay between regulating proteins and DNA targets is required to interpret transcriptomic data and to model the dynamics of genetic networks. Two key problems in this respect are the control of protein traffic on DNA and the combined effects of several regulating proteins operating on the same target gene. [International Workshop on Regulatory Proteins Interplay and Traffic on DNA, July 12-13, 2002, Evry, France http://www.lami.univ-evry.fr/~epigenese/Ecoles/Autrans/workshop.html 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 Current algorithms, while being very powerful, are not capable of detecting with certainty all exons, are not well equipped to distinguish different splice variants and are unable to detect small proteins, which are numerous and crucial to many biological processes. When all potential coding regions have been predicted, the user community will have at its disposition the sequence of 80'000 to 100'000 predicted proteins lacking any information on post- translational modifications (PTM) of which the majority of proteins are the target. The Human Proteomics Initiative of SIB and EBI, Rolf Apweiler, Amos Bairoch, Bioinformer 5, 1999] http://bioinformer.ebi.ac.uk/newsletter/archives/5/hpi.html interesting new gene. secreted proteins: Encoded (usually) by genes with signal sequences, and such proteins include potential therapeutic proteins such as hormones, cytokines, and growth factors. Related terms: Biomarkers structural proteins: Wikipedia http://en.wikipedia.org/wiki/Category:Structural_proteins Contrast with nonstructural proteins. therapeutic proteins: Although small molecules (which allow oral delivery) are preferred for drugs, a number of therapeutic proteins are available, and the number has increased with progress in biotechnology and genetic engineering. Important commercial products include insulin, monoclonal antibodies, growth factors, and various blood and plasma proteins. Related terms: Pharmaceutical biology transport proteins: See membrane transport proteins. Are there any transport proteins which are not membrane proteins? transcription factors: Sequences, DNA & beyond tumor suppressor proteins: Proteins that are normally involved in holding cellular growth in check. Deficiencies or abnormalities in these proteins may lead to unregulated cell growth and tumor development. MeSH, 2002 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. |
