------------------------------------------------------------------------------ SWISS-PROT Protein Sequence Data Bank. Release 36.0, July 1998 ------------------------------------------------------------------------------ List of nomenclature related references for proteins ------------------------------------------------------------------------------ Amos Bairoch Email: bairoch@medecine.unige.ch Swiss Institute of Bioinformatics and University of Geneva Switzerland ------------------------------------------------------------------------------ Document name: NOMLIST.TXT ------------------------------------------------------------------------------ This document list papers that are important in defining the nomenclature or terminology relative to proteins in general and in particular on specific family or groups of proteins. An important reference which assembles documents of the various international commissions on biochemical nomenclature: Biochemical Nomenclature and Related Documents A Compendium Second edition, 1992 International Union of Biochemistry and Molecular Biology Edited by C. Liebecq Portland Press, London and Chapel Hill ISBN 1 85578 005 4 The full publications list of the nomenclature commissions of IUPAC-IUBMB is available on WWW: http://www.chem.qmw.ac.uk/iupac/jcbn.html Another important reference is the "Genetic nomenclature Guide" published by Trends in Genetics in March 1995. ------------------------------------------------------------------------------ General nomenclature references ------------------------------------------------------------------------------ Nomenclature and symbolism for amino acids and peptides: IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Eur. J. Biochem. 138:9-37(1984). Corrections: Eur. J. Biochem. 152:1-1(1985). Eur. J. Biochem. 213:1-3(1993). http://www.chem.qmw.ac.uk/iupac/AminoAcid/ Nomenclature for multiple forms of enzymes: IUPAC-IUB Commission on Biochemical Nomenclature (CBN). Eur. J. Biochem. 82:1-3(1978). Nomenclature for multienzymes: Nomenclature Committee of the International Union of Biochemistry (NC-IUB). Eur. J. Biochem. 185:485-486(1989). http://www.chem.qmw.ac.uk/iubmb/misc/menz.html Nomenclature of protein splicing elements (inteins and exteins): Perler F.B., Davis E.O., Dean G.E., Gimble F.S., Jack W.E., Neff N., Noren C.J., Thorner J., Belfort M. Nucleic Acids Res. 22:1125-1127(1994). Definition of the terms homology and homologous: Reeck G.R., de Haen C., Teller D.C., Doolittle R.F., Fitch W.M., Dickerson R.E., Chambon P., McLachlan A.D., Margoliash E., Jukes T.H., Zuckerlandl E. Cell 50:667-667(1987). Dover G. Cell 51:515-515(1987). Aboitiz F. Cell 51:515-516(1987). Wegnez M. Cell 51:516-516(1987). Nomenclature for designating mutations: Antonarakis S.E. Hum. Mutat. 11:1-3(1998). Beaudet A.L., Tsui L.-C. Hum. Mutat. 2:245-248(1993). Beutler E. Am. J. Hum. Genet. 53:783-785(1993). Definition of a checking number (CN) for protein sequences: Bairoch A. Biochem. J. 203:527-528(1982). Nomenclature for targeting signals: Varshavsky A. Cell 64:13-15(1991). ------------------------------------------------------------------------------ Species specific nomenclature references ------------------------------------------------------------------------------ Arabidopis thaliana genes: http://mutant.lse.okstate.edu/genepage/namerule.html Bacterial gene naming convention: Demerec M., Adelberg A.E., Clark A.J., Hartmann P.E. Genetics 54:61-76(1966). Caenorhabditis elegans genes: http://eatworm.swmed.edu/Genome/nomen.html Human genes: Shows T.B., McAlpine P.J., Boucheix C., Collins F.S., Conneally P.M., Frezal J., Gershowitz H., Goodfellow P.N., Hall J.G., Issitt P., Jones C.A., Knowles B.B., Lewis M., McKusick V.A., Meisler M., Morton N.E., Rubinstein P., Schanfield M.S., Schmickel R.D., Skolnick M.H., Spence A.M., Sutherland G. Cytogenet. Cell Genet. 46:11-2(1987). White J.A., McAlpine P.J., Antonarakis S., Cann H., Eppig J.T., Frazer K., Frezal J., Lancet D., Nahmias J., Pearson P., Pters J., Scott H., Spurr N., Talbot C. Jr., Povery S. Genomics 45:468-471(1997). http://www.gene.ucl.ac.uk/nomenclature/ Mouse genes: Maltais L.J., Blake J.A., Eppig J.T., Davisson M.T. Genomics 45:471-476(1997). http://www.informatics.jax.org/nomen/ Chicken genes: http://www.ri.bbsrc.ac.uk/chickmap/Nomenclature.html Zebrafish (Zebra danio): http://zfish.uoregon.edu/zf_info/zfbook/chapt7/7.1.html Plant genes: Nomenclature of sequenced plant genes. Commission on Plant Gene Nomenclature (CPGN) Plant Mol. Biol. Rep. Vol. 12, Number 2, Supplement, June 1994. http://jiio6.bbsrc.ac.uk/ Rat genes: Levan G., Hedrich H.J., Remmers E.F., Serikawa T., Yoshida M.C. Mamm. Genome 6:447-448(1995). http://ratmap.gen.gu.se/ratmap/WWWNomen/Nomen.html Yeast genes: http://genome-www.stanford.edu/Saccharomyces/gene_guidelines.html ------------------------------------------------------------------------------ Protein families specific nomenclature references ------------------------------------------------------------------------------ Alcohol dehydrogenases: http://www.gene.ucl.ac.uk/nomenclature/ADH.shtml Allergens: IUIS/WHO Allergen Nomenclature Subcommittee. Bull. World Health Organ. 64:767-770(1986). Marsh D.G., Goodfriend L., King T.P., Loewenstein H., Platts-Mills T.A.E. Clin. Allergy 18:201-209(1988). WHO/IUS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. ACI News 6/2:38-44(1994). IUIS/WHO Allergen Nomenclature Subcommittee. Bull. World Health Organ. 72:797-806(1994). Amyloid fibril proteins: WHO/IUIS Nomenclature Sub-Committee. Bull. World Health Organ. 71:105-108(1993). Annexins: Crumpton M.J., Dedman J.R. Nature 345:212-212(1990). Calcium channels: Spedding M., Paoletti R. Pharm. Rev. 44:363-376(1992). Lory P., Ophoff R.A., Nahmias J. Hum. Genet. 100:149-150(1997). Caspases: Alnemri E.S., Livingston D.J., Nicholson D.W., Salvesen G., Thornberry N.A., Wong W.W., Yuan J.Y. Cell 87:171-171(1996). CD antigens: Schlossman S.F., Boumsell L., Gilks W., Harlan J.M., Kishimoto T., Morimoto C., Shaw S., Silverstein R.L., Springer T.A., Tedder T.F., Todd R.F. J. Immunol. 152:1-2(1994). Also in: Bull. World Health Organ. 72:807-808(1994). IUIS/WHO Subcommittee on CD Nomenclature Bull. World Health Organ. 75:385-387(1997). Complement component C2 variants: WHO-IUS Nomenclature Sub-Committee. Bull. WHO 70:527-528(1992). Complement component C4 allotypes: Mauff G., Alper C.A., Dawkins R., Doxiadias G., Giles C.M., Hauptmann G., Rittner C., Schneider P.M. Complement Inflamm. 7:261-268(1990). WHO-IUS Nomenclature Sub-Committee. Bull. World Health Organ. 70:531-535(1992). Complement factor B allotypes: Geserick G., Abbal M., Mauff G., Siemens I. Complement Inflamm. 7:255-260(1990). WHO-IUS Nomenclature Sub-Committee. Bull. World Health Organ. 70:541-543(1992). Connexins: Kumar N.M., Giluda N.B. Semin. Cell Biol. 3:3-16(1992). Coronaviruses structural proteins: Cavanagh D., Brian D., Enjuanes L., Holmes K., Lai M., Laude H., Siddell S., Spaan W., Taguchi F., Talbot P. Adv. Exp. Med. Biol. 276:1-2(1990). Electron-transfer proteins: Nomenclature Committee of the International Union of Biochemistry (NC-IUB). Eur. J. Biochem. 200:599-611(1991). Corrections: Eur. J. Biochem. 213:1-3(1993). Ephrins and their receptors: Eph Nomenclature Committee. Cell 90:403-404(1997). Eukaryotic DNA polymerases: Burgers P.M.J., Bambara R.A., Campbell J.L., Chang L.M.S., Downey K.M., Huebscher U., Lee M.Y.W.T., Linn S.M., So A.G., Spadari S. Eur. J. Biochem. 191:617-618(1990). Extracellular protein modules: Bork P., Bairoch A. Extracellular protein modules: a proposed nomenclature. Trends Biochem. Sci. 20:Special poster supplement TIBSC02(1995). Fc receptors (FcR): IUIS Subcommittee on Nomenclature. Bull. World Health Organ. 67:449-449(1989). IUIS/WHO Subcommittee on Nomenclature of Fc receptors. Bull. World Health Organ. 72:809-809(1994). Fibrinogen gamma chains: Francis C.W., Mosesson M.W. Thromb. Haemost. 62:813-814(1989). Fibroblast growth factors: Ann. N Y Acad. Sci. 638:XIII-XVI(1991). Flavin-containing monooxygenases: Lawton M.P., Cashman J.R., Cresteil T., Dolphin C.T., Elfarra A.A., Hines R.N., Hodgson E., Kimura T., Ozols J., Phillips I.R., Philpot R.M., Poulsen L.L., Rettie A.E., Shephard E.A., Williams D.E., Ziegler D.M. Arch. Biochem. Biophys. 308:254-257(1994). Galectins (beta-galactoside-binding lectins): Barondes S.H., Castronovo V., Cooper D.N.W., Cummings R.D., Drickamer K., Feizi T., Gitt M.A., Hirabayashi J., Hughes C., Kasai K.-I., Leffler H., Liu F.-T., Lotan R., Mercurio A.M., Monsigny M., Pillai S., Poirer F., Raz A., Rigby P.W.J., Rini J.M., Wang J.L. Cell 76:597-598(1994). Human glutathione transferases: Mannervik B., Awasthi Y.C., Board P.G., Hayes J.D., Di Ilio C., Ketterer B., Listowsky I., Morgenstern R., Muramatsu M., Pearson W.R., Pickett C.P., Sato K., Widerstein M., Wolf C.R. Biochem. J. 282:305-306(1992). Glycosyl hydrolases: Henrissat B. Biochem. J. 280:309-316(1991). Henrissat B., Bairoch A. Biochem. J. 293:781-788(1993). Henrissat B., Bairoch A. Biochem. J. 316:695-696(1996). HLA system: Bodmer J.G., Marsh S.G., Albert E.D., Bodmer W.F., Dupont B., Erlich H.A., Mach B., Mayr W.R., Parham P., Sasazuki T., Schreuder G.M.T., Strominger J.L., Svejgaard A., Terasaki P. Immunobiology 187:51-69(1993). HOX genes: Scott M.P. Cell 71:551-553(1992). Scott M.P. Nucleic Acids res. 21:1687-1688(1993). IGF binding proteins: Endocrinology 130:1736-1737(1992). Immunoglobulins: Rowe D.S. Nature 228:509-511(1970). Immunochemistry 7:497-500(1970). Initiation, elongation and termination factors for translation in eukaryotes: Nomenclature Committee of the International Union of Biochemistry (NC-IUB). Eur. J. Biochem. 186:1-3(1989). Human interferon genes: J. Interferon Res. 13:443-444(1993). Interleukins: WHO/IUIS Nomenclature Subcommittee on Interleukin Designation. Bull. World Health Organ. 69:483-484(1991). IUIS/WHO Standing Committee on Interleukin Designation. Bull. World Health Organ. 72:811-811(1994). IUIS/WHO Standing Committee on Interleukin Designation. Bull. World Health Organ. 74:451-452(1996). IUIS/WHO Standing Committee on Interleukin Designation. Bull. World Health Organ. 75:175-175(1997). Kallikrein-kinin genes: Carretero O.A., Carbini L.A., Scicli A.G. J. Hypertens. 11:693-697(1993). Scicli A.G.,Carbini L.A., Carretero O.A. J. Hypertens. 11:775-780(1993). Carbini L.A., Scicli A.G., Carretero O.A. J. Hypertens. 11:893-898(1993). Laminins: Burgeson R.E., Chiquet M., Deutzmann R., Ekblom P., Engel J., Kleinman H., Martin G.F., Meneguzzi G., Paulsson M., Sanes J., Timpl R., Tryggvason K., Yamada Y., Yurchenco P.D. Matrix Biol. 14:209-211(1994). Lantibiotics: de Vos W.M., Jung G., Sahl H.-G. (In) Nisin and novel antibiotics; Jung G., Sahl H.-G., Eds, pp.457-463, ESCOM Science Publishers, Leiden, (1991). ISBN: 90-72199-1-1 Metallothioneins: Kojima Y. Meth. Enzymol. 205:8-10(1991). Mitochondrial peptidases: Kalousek F., Neupert W., Omura T., Schatz G., Schmitz U.K. Trends Biochem. Sci. 18:249-249(1994). Mucins: Taylor-Papadimitriou J. Int. J. Cancer 49:1-5(1991). NF-kappa B/I kappa B family: Nabel G.J., Verma I.M. Genes Dev. 7:2063-2063(1993). Orosomucoid variants: Yuasa I., Weidinger S., Umetsu K., Suenaga K., Ishimoto G., Eap B.C., Duche J.-C., Baumann P. Vox Sang. 64:47-55(1993). P450: Nelson D.R., Kamataki T., Waxman D.J., Guengerich F.P., Estrabrook R.W., Feyereisen R., Gonzalez F.J., Coon M.J., Gunsalus I.C., Gotoh O., Okuda K., Nebert D.W. DNA Cell Biol. 12:1-51(1993). Peptides hormones: IUPAC-IUB Commission on Biochemical Nomenclature (CBN). Eur. J. Biochem. 55:485-486(1975). Peroxisome biogenesis factors: Distel B., Erdmann R., Gould S.J., Blobel G., Crane D.I., Cregg J.M., Dodt G., Fujiki Y., Goodman J.M., Just W.W., Kiel J.A.K.W., Kunau W.-H., Lazarow P.B., Mannaerts G.P., Moser H.W., Osumi T., Rachubinski R.A., Roscher A., Subramani S., Tabak H.F., Tsukamoto T., Valle D., van der Klei I., van Veldhoven P.P., Veenhuis M. J. Cell Biol. 135:1-3(1996). Pharmalogical receptors: Kenakin T.P., Bond R.A., Bonner T.I. Pharm. Rev. 44:351-362(1992). Phosphodiesterases: http://weber.u.washington.edu/~pde/Nomenclature.html Phytochromes: Quail P.H., Briggs W.R., Chory J., Hangarter R.P., Harberd N.P., Kendrick R.E., Koornneef M., Parks B., Sharrock R.A., Schaefer E., Thompson W.F., Whitelam G.C. Plant Cell 6:468-471(1994). Potassium channels: Pongs O. Trends Pharmacol. Sci. 14:435-435(1993). Protein transport machinery of the mitochondrial membranes: Pfanner N., Douglas M.G., Endo T., Hoogenraad N.J., Jensen R.E., Meijer M., Neupert M., Schatz G., Schmitz U.K., Shore G.C. Trends Biochem. Sci. 21:51-52(1996). PTS system proteins and domains: Saier M.H. Jr., Reizer J. J. Bacteriol. 174:1433-1438(1992). Purinoceptors: Fredholm B.B., Abbracchio M.P., Burnstock G., Daly J.W., Harden T.K., Jacobson K.A., Leff P., Williams M. Pharmacol. Rev. 46:143-156(1994). RAS superfamily of GTP-binding proteins: Kahn R.A., Der C.J., Bokoch G.M. FASEB J. 6:2512-2513(1992). Receptor and ion channels: 1998 Receptors and Ion Channel Nomenclature Supplement Ninth Edition IUPHAR, Alexander S.P.H., Peters J.A. Trends in Pharmacological Sciences ISSN 1357 485X Restriction enzymes: Roberts R.J., Macelis D. Nucleic Acids Res. 25:248-262(1997). RNA adenosine deaminases: Bass B.L., Nishikura K., Keller W., Seeburg P.H., Emeson R.B., O'Connell M.A., Samuel C.E., Herbert A. RNA 3:947-949(1997) RTX-toxins: Frey J., Bosse J.T., Chang Y.-F., Cullen J.M., Fenwich B., Gerlach G.F., Gygi D., Haesebrouck F., Inzana T.J., Jansen R., Kamp E.M., McDonald J., McInnes J.I., Mittal K.R., Nicolet J., Rycroft A.N., Segers R.P.A.M., Smits M.A., Stenbaek E., Struck D.K., van den Bosch J.F., Willson P.J., Young R. J. Gen. Microbiol. 139:1723-1728(1993). S100 calcium-binding proteins: Schaefer B.W., Wicki R., Engelkamp D., Mattei M.-G., Heizmann C.W. Genomics 25:638-643(1995). Serine/threonine protein phosphatases: Cohen P.T.W. Adv. Potein Phosphat. 8:371-376(1994). Serotonin receptors: Branchek T. Curr. Biol. 3:315-317(1993). T-cell receptor (TCR) gene segments: WHO-IUS Nomenclature Sub-Committee on TCR Designation. Bull. World Health Organ. 71:113-115(1993). UDP-glucuronosyltransferases: Burchell B., Nebert D.W., Nelson D.R., Bock K.W., Iyanagi T., Jansen P.L., Lancet D., Mulder G.J., Chowdhury J.R., Siest G., Tephly T.R., Mackenzie P.I. DNA Cell Biol. 10:487-494(1991). Mackenzie P.I., Owens I.S., Burchell B., Bock K.W., Bairoch A., Belanger A., Fournel-Gigleux S., Green M., Hum D.W., Iyanagi T., Lancet D., Louisot P., Magdalou J., Chowdhury J.R., Ritter J.K., Schachter H., Tephly T.R., Tipton K.F., Nebert D.W. Pharmacogenetics 7:255-269(1997). http://www.unisa.edu.au/hlt/prm/Gluc_trans/Gt_ttl.htm ------------------------------------------------------------------------------