Nomenclatural subunits

HT3 receptors are an exception to the general nomenclature of numbering subunits and denoting stoichiometry by subscripts. The 5-HT3 receptor subtype is denoted by the subscript 3 and the two known subunits are referred to as A and B . When expressed alone, 5-HT3-A subunits form functional homomeric receptors but these have a much smaller single channel conductance (less than 1.0 pS) and altered pharmacology compared to native 5-HT3 receptors. Native 5-HT3 receptors are likely to be pentameric heteromers of 5-HT3-A and 5-HT3-B subunits. 5-HT3-B subunits, unlike 5-HT3-A subunits, do not form functional receptors when expressed alone but when co-expressed with 5-HT3-A subunits, the receptors formed have functional properties similar to native 5-HT3 receptors. Synaptic transmission mediated by 5-HT3 receptors has been... 

Lukas, RJ, Changeux, JP, Le Novere, N, Albuquerque, EX, Balfour, DJ, Berg, DK, Bertrand, D, Chiappinelli, VA, Clarke, PB, Collins, AC, Dani, JA, Grady, SR, Kellar, KJ, Lindstrom, JM, Marks, MJ, Quik, M, Taylor, PW and Wonnacott, S (1999) International Union of Pharmacology. XX. Current status of the nomenclature for nicotinic acetylcholine receptors and their subunits. Pharmacol. Rev. 51(2) 397 01. 

FIGURE 3.5 Alignment of the TM2 amino acid sequences. The nomenclature of the rings is based on the a7 sequence. Selectivity indicates the charge of the permeant ions. Mutl and Mut2 are site-directed mutants (indicated by the asterisks) of the a7 subunit (see text). 

Ten specific mammalian calcium channel subtypes have been identified based on the sequence of their membrane pore-forming oq subunit. As illustrated in Table 1, calcium channels may be individually identified by their oq subunit, or more commonly using a systematic nomenclature based on a gene subfamily (Cavl-Cav3) and the order of discovery of the oq subunit (e.g., Cavl.l-Cav 1.4) [7]. 

Khakh, B. S., Burnstock, G., Kennedy, C. et al. International union of pharmacology. XXIV. Current status of the nomenclature and properties of P2X receptors and their subunits. Pharmacol. Rev. 53 107-118, 2001. 

PSI] nomenclature SUP35 Wild-type gene encoding a subunit of the translation termination factor... 

All of these experimental approaches have been adopted in neutrophil studies to show that activation of several receptor-mediated functions occurs via the participation of heterotrimeric G-proteins. In many cases, the conventional Gai/Gas nomenclature is used to describe these G-proteins, even though the subunits may not be linked to either inhibition or activation of adenylate cyclase. The nomenclature used is based on structural and functional similarities to other Ga-subunits in other cell types, and also on their sensitivities to cholera and pertussis toxins. Several of these G-proteins... 

The currently used stereochemical nomenclature systems for configurations with four or more ligands are chirality oriented, refering to rigid configurations, or their monocentric subunits. The preceding discussion demonstrates, however, that in many cases it is preferable to use a polycentric representation. 

PA700/19S RP has been studied in many different species, and many individual subunits were identified prior to realization that they were components of PA700. These factors have resulted in a diverse and confusing subunit nomenclature (Table 11.1). The rational and increasingly accepted Rpt/Rpn and S nomenclatures (see below) will be used in the current presentation. An introductory description of PA700/19S PR subunits follows immediately below. Additional details of subunit functions and regulatory features in proteolysis by the 26S proteasome are presented in later sections. 

The component subunits of PA700 range in size from 112 to 28 kDa. The S nomenclature identifies subunits on the basis of their relative mobility during SDS polyacrylamide-gel electrophoresis, whereas the Rpt/Rpn nomenclature distinguishes between the AAA ATPase subunits (Regulatory particle triple-A protein) and the non-AAA ATPase subunits (Regulatory particle non-ATPase) (see below). 

Fig. 13.1. S ubunit-subunit interactions of the CSN and interactions of CSN subunits with other proteins. Subunits are numbered according to the unified nomenclature [1], CSN subunit-subunit interactions have been published before [19]. Darker shading indicates...

The fundamental principles and the basic rules of the structure-based nomenclature are given first, accompanied by detailed extensions and applications. An Appendix contains names of common subunits as well as a list of acceptable source-based names, along with the corresponding structure-based names, of common polymers. There is no strong preference for the use of structure-based names over source-based names for polymers where the latter are clear and unambiguous, but for certain purposes one system of naming may be preferred to the other. 

This nomenclature method rests upon the selection of a preferred constitutional repeating unit (CRU) of which the polymer molecule is a multiple. Wherever possible, the CRU and subunits are named according to the lUPAC-recommended nomenclature of organic chemistry [4, 5]. 

The subunits and substituted subunits, which are parenthesized or bracketed, are named by organic nomenclature rules [4,5] with the following exceptions ... 

The fact that several representations are possible automatically necessitates the development of rules which would allow a researcher to decide upon a preferred representation. To this end, lUPAC has developed an elaborate rules-based system using the seniority of subunits , the direction of citation, etc. [65]. However, rules-based systems are subject to the same limitations as nomenclature systems in that they, too, suffer from (potential) historical discontinuities and require acceptance by a broad community. 

In the IUPAC system locants are placed immediately before the part of the name to which they apply for instance subunits such as pyridine-2,4-diyl and l-methylpropane-l,3-diyl. One of the few exceptions is the phenylene subunit, for example, 1,4-phenylene in XV. The IUPAC nomenclature system is always evolving and some of the details (e.g., the names of some subunits) have changed in recent years. One should use caution when using less recent nomenclature references than those listed in this text. 

Before proceeding one needs to mention Chemical Abstracts (CA), a journal published by the American Chemical Society, that abstracts the world s chemical hterature and has developed its own nomenclature rules. The CA rules are generally very close to the IUPAC rules, but there are some differences. Most of the differences are not important at the level of the discussions in this book. One difference that needs to be mentioned is the placement of locants. CA does not place locants immediately before the part of the name to which they apply. Thus, the CA name for the first subunit in XV is 2,4-pyridinediyl instead of pyridine-... 

The constituent subunit of highest seniority must contain one or more central atoms bridging groups between central atoms in the backbone of the polymer cannot be senior subunits. This is consistent with the principle of coordination nomenclature, in which the emphasis is laid on the coordination centre. 

Fig. 5.23. Diversity of regulation of adenylyl cyclase. The figure summarizes schematically the regulation of adenylyl cyclases of type I, II, V and VI (after Taussig and Gilman, 1995). The individual subtypes are negatively (-) or positively (+) regulated by heterotrimeric G-proteins by various pathways. Regulation takes place both via G -subunits and via Py-complexes. For nomenclature of the G-proteins, see 5.5.1 PKC protein kinase C Ca VCaM Ca Vcalmodulin (see Chapters 6 and 7).

Fig. 16.4. Subunit structure of voltage-con-trolled ion channels. The subunit structure of various voltage-controlled ion channels is shown in schematic form with nomenclature of the different subunits. Phosphorylation sites (P) in the cytoplasmic part are also shown, as well as glycosylation sites (Y) in the extracellular part of the ion channels.

Milk protein system. The nomenclature and physico-chemical properties of the major milk proteins and their subunits have been provided by Whitney et al. (13) and Brunner (1 ). The conformation and related properties of the individual proteins and their subunits and aggregates have been reviewed by Morr (15) with special reference to their functional properties in food systems, and drawing heavily upon previous considerations by Bloomfield and Mead (16) and Slatterly (17). 

It should be mentioned here that the data have been extracted from the literature and critically evaluated by qualified scientists. On the other hand, the original authors nomenclature for enzyme forms and subunits is retained. In order to keep the tables concise, redundant information is avoided as far as possible (e.g. if Km values are measured in the presence of an obvious cosubstrate, only the name of the cosubstrate is given in parentheses as a commentary without reference to its specific role). 

All information except the nomenclature of the enzymes (which is based on the recommendations of the Nomenclature Committee of lUBMB (International Union of Biochemistry and Molecular Biology) and lUPAC (International Union of Pure and Applied Chemistry) is extracted from original literature (or reviews for very well characterized enzymes). The quality and reliability of the data depends on the method of determination, and for older literature on the techniques available at that time. This is especially true for the fields Molecular Weight and Subunits. 

Table 2 Subtypes of voltage-gated sodium channel a-subunits nomenclature and distribution (Goldin et al., 2000)...

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