Naming proteins

The Newsletter 1992 of our committees [39] had already devoted one of its sections to protein nomenclature, "an outstanding example of a problem that is in need of solution but which has seen little or no progress ... during the many years of existence of the successive nomenclature committees of IUBMB".

Two editorials have been devoted to this problem by Tim Hunt [40] and by Ralph A. Bradshaw (together with Daniel Birnbaum) [41], both former editors of Trends in Biochemical Sciences. Both point out how important it is for scientists discovering new proteins to name them unambiguously.

Bradshaw and Birnbaum insist that journals and their overseers - editors, associate editors, and members of their boards - should have a vested and active interest in nomenclature and the process by which things are named. Journals can help enormously by generally supporting efforts to systematize names.

The problems of protein nomenclature are multifaceted and can probably be rationalised only by a series of small projects, some of which are summarized here:

The Swiss-Prot Data Bank

Terminology in immunology

Allergen nomenclature

Receptor nomenclature

The Swiss-Prot Data Bank

The Swiss-Prot data bank (for a description, see [42]) is a curated protein sequence database maintained collaboratively by the University of Geneva and the European Institute of Bioinformatics (EBI). It strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy, a high level of integration with other databases, and is distributed with a variety of documents. One of them, called NOMLIST.TXT, lists nomenclature references for proteins. It may be accessed on the World Wide Web at

General nomenclature references include many of the documents published by our committees and reprinted in the Compendium [17], such as amino acids and peptides, multiple forms of enzymes and multienzymes, but also documents dealing with homology, designation of mutations, plant genes, checking number (CN) for protein sequences, targeting signals, and the list of HUGO/genomic database editors (nomenclature of human genes).

Specific nomenclature references, listed in alphabetical order, are: allergens; annexins; bacterial gene-naming conventions; calcium channels; CD antigens; complement components C4 allotypes; connexins; coronaviruses structural proteins; electron-transfer proteins; eukaryotic DNA polymerases; extracellular protein modules; factor B allotypes; fibrinogen -chains; fibroblast growth factors; flavin-containing monooxygenases; galectins (-galactoside-binding lectins); glycosylhydrolases; the HLA system; HOX genes; human glutathione transferases; IGF-binding proteins; immunoglobulins (*); initiation, elongation and termination factors for translation in eukaryotes (**); (human) interferon genes; kallikrein-kinin genes; laminins; lantibiotics; mitochondrial peptidases, mouse genes; mucins; the NF-B/IB family; orosomucoid variants; P-450; peptide hormones (**); pharmacological receptors; phytochromes; protein-transport machinery of the mitochondrial membranes; PTS-system proteins and domains; purinoreceptors; the RAS superfamily of GTP-binding proteins; rat genes; restriction enzymes; RTX-toxins; S100 calcium-binding proteins; serine/threonine protein phosphatases; UDP-glucuronosyltransferases.

One asterisk (*) indicates that the document may be found in the 1978 edition of the Compendium [44] whereas two asterisks (**) indicate that it may be found in the 1992 edition [17].

Terminology in immunology

Several biochemical journals published in 1973, 1974 and 1975, a document entitled Recommendations for the nomenclature of human immunoglobulins [43]. The document was reproduced in the 1978 edition of Biochemical nomenclature and related documents [44]. It was not reproduced in the 1992 edition as it was felt that they had become textbook knowledge.

A concise description of the terminology in immunology may be found in the section on Immunologic systems in the book written by the Style Manual Committee of the Council of Biology Editors (pages 462-466 in [45]): the HLA system, immunoglobulins, complement, lymphocytes and surface antigens of immune cells, interleukins and interferons, and allergens.

A list of nomenclature documents approved by the International Union of Immunological Societies (IUIS) and published in the Bulletin of the World Health Organization (WHO), was kindly provided by Malcolm W. Turner, chairman of the WHO/IUIS Nomenclature Committee. Some of them have been reprinted in other journals.

1. Proposed rules for the designation of immunoglobulins of animal origin. Bull. W.H.O. 56, 815-817 (1978).

2. A proposal for the definition of terms related to locomotion of leukocytes and other cells. Bull. W.H.O. 58, 505-509 (1980).

3. Nomenclature for factors of the HLA system. Bull. W.H.O. 58, 945-948 (1980).

4. Nomenclature of the alternative activating pathway of complement. Bull. W.H.O. 59, 489-491 (1981).

5. Nomenclature for synthetic peptides representative of immunoglobulin chain sequences. Bull. W.H.O. 68, 109-114 (1990).

6. Nomenclature for human complement component C2. Bull. W.H.O. 70, 527-530 (1992).

7. Revised nomenclature of human complement component C4. Bull. W.H.O. 70, 531-540 (1992).

8. Nomenclature for human complement factor B. Bull. W.H.O. 70, 541-546 (1992).

9. Nomenclature of amyloid and amyloidosis. Bull. W.H.O. 71, 105-112 (1993).

10. Nomenclature for T cell receptor (TCR) gene segments of the immune system. Bull. W.H.O. 71, 113-115 (1993).

11. Allergen nomenclature. Bull. W.H.O. 72, 797-806 (1994). A revised nomenclature (see below).

12. CD antigens 1993. An updated nomenclature for clusters of differentiation on human cells. Bull. W.H.O. 72, 807-808 (1994).

13. Nomenclature of the Fc receptors. Bull. W.H.O. 72, 809-810 (1994).

14. Nomenclature for secreted regulatory proteins of the immune system (interleukins). Update. Bull. W.H.O. 72, 811 only (1994).

15. Interleukin-16 (IL-16). Bull. W.H.O. 74, 451-452 (1996).

Allergen nomenclature

The World Health Organization/International Union of Immunological Societies (WHO/IUIS) published a revised nomenclature for protein allergens in 1994 (see above, document No. 11 of the WHO/IUIS list). These recommendations extend the original taxonomic source-based nomenclature to permit the designation of allergen genes; the proposals have been fully implemented in the Swiss-Prot database (http://www.expasy.ch/cgi-bin/lists?allergen.txt). Readers are encouraged to submit information on new protein allergens to the IUIS Allergen Nomenclature Subcommittee for the assignment of an approved name. A submission form is available upon request from Henning Løwenstein, ALK Laboraratories, Bøge Allé 10-12, DK-2970 Hørsholm, Denmark. This document - newallergen.txt - is also available via the Internet by anonymous FTP on the server biobase.dk in the directory /pub/who-iuis

Receptor nomenclature

The following is reprinted from Chem. Int. 16, 228 (1994) by permission of the Executive Secretary of IUPAC.

The International Union of Pharmacology Committee on Receptor Nomenclature and Drug Classification (NC-IUPHAR) has published, in a special issue of Pharmacological Reviews (June 1994), seven official documents relating to receptors. The special issue contains three distinct categories of reports.

First, the NC-IUPHAR recognizes that the fields of adrenoreceptors, 5-hydroxytryptamine receptors and protanoid receptors have reached maturity and that enough information is available to propose an official nomenclature to be recommended for usage as such in all journals and books dealing with pharmacology of cell membrane receptors.

Secondly, in new areas of science, such as the report on endothelin receptors, the NC-IUPHAR has made every possible effort to interact early with the major contributors in the field, to prevent ill-considered attempts at unsuitable classifications and to implement its general principles of nomenclature. These also represent the official IUPHAR nomenclature, which may be elaborated and extended as more knowledge is accumulated but should not change in terms of general design.

The third category concerns classifications that have been accepted by the NC-IUPHAR only until more information allows the development of a more logical framework and system of classification. The article in the special issue of Pharmacological Reviews on purinoreceptors falls into this category.

NC-IUPHAR says that although such documents cannot be considered definitive, they, nevertheless, provide an important forum accessible to the whole pharmacological fraternity for a debate that should lead to improvements based on scientific grounds only.

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