Ion Channel Factsbook: Voltage-Gated Channels

By William J. Brammar

The Academic Press FactsBooks series has established itself as the best source of easily-accessible and accurate facts about protein groups. Described as 'a growing series of excellent manuals' by Molecular Medicine Today, and 'essential works of reference' by Trends in Biochemical Sciences, the FactsBooks have become the most popular comprehensive data resources available. As they are meticulously researched and use an easy-to-follow format, the FactsBooks will keep you up-to-date with the latest advances in structure, amino acid sequences, physicochemical properties, and biological activity.In a set of four interrelated volumes, The Ion Channel FactsBook provides a comprehensive framework of facts about channel molecules central to electrical signaling phenomena in living cells. The fourth volume is devoted to Voltage-gated Channel Families, including those molecular complexes activated or modulated by calcium, potassium, and chloride.

• Nomenclature
• Expression
• Sequence Analyses
• Structure and function
• Electrophysiology
• Pharmacology
• Information retrieval

• Language: English
• Publisher: Academic Press
• Release date: Oct 16, 1998
• ISBN: 9780080535203

Book preview

THE ION CHANNEL Factsbook IV

Voltage-Gated Channels

First Edition

Edward C. Conley

Molecular Pathology, c/o Ion Channel/Gene Expression University of Leicester/Medical Research Council Centre for Mechanisms of Human Toxicity, U.K.

William J. Brammar

Department of Biochemistry, University of Leicester, UK

Academic Press

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Table of Contents

Cover image

Title page

Copyright page

Cumulative table of contents for volumes I to IV

VOLUME I EXTRACELLULAR LIGAND-GATED CHANNELS

VOLUME II INTRACELLULAR LIGAND-GATED CHANNELS

VOLUME III INWARD RECTIFIER AND INTERCELLULAR CHANNELS

VOLUME IV VOLTAGE-GATED CHANNELS

ION CHANNEL RESOURCES

Acknowledgements

Introduction & layout of entries

HOW TO USE THE ION CHANNEL FACTSBOOK

GUIDE TO THE PLACEMENT CRITERIA FOR EACH FIELD

Abbreviations

Part I: VOLTAGE-GATED CHANNELS

VLG Key facts Voltage-gated channel families – key facts

VLG Ca Voltage-gated calcium channels

NOMENCLATURES

EXPRESSION

SEQUENCE ANALYSES

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

NOTE ADDED IN PROOF

VLG Cl Voltage-gated chloride channels

Nomenclatures

EXPRESSION

SEQUENCE ANALYSIS

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG K A-T [native] Rapidly inactivating, transient outward ‘A-type ‘ K+ currents in native cell types of vertebrates

NOMENCLATURES

EXPRESSION

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG K DR [native] ‘Delayed rectifier’ type K+ currents in native cell types of vertebrates

NOMENCLATURES

EXPRESSION

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG K eag/elk/erg K+ channels encoded by genes related to Drosophila eag (ether-á-go-go) (gene subfamilies eag, elk, erg)

NOMENCLATURES

EXPRESSION

SEQUENCE ANALYSES

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG K KV-beta Cytoplasmic (Kvβ) subunits co-assembling with pore-forming (Kvα) voltage-gated potassium channel subunits

NOMENCLATURES

EXPRESSION

SEQUENCE ANALYSES

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG K Kv1-Shak Vertebrate K+ channels related to Drosophila Shaker (Kvα subunits encoded by gene subfamily Kv1)

NOMENCLATURES

EXPRESSION

SEQUENCE ANALYSES

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG K Kv2-Shab Vertebrate K+ channel subunits related to Drosophila Shab (Kvα subunits encoded by gene subfamily Kv2)

NOMENCLATURES

EXPRESSION

SEQUENCE ANALYSES

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG K Kv3-Shaw Vertebrate K+ channels related to Drosophila Shaw (Kvα subunits encoded by gene subfamily Kv3)

NOMENCLATURES

EXPRESSION

SEQUENCE ANALYSES

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG K Kv4-Shal Vertebrate K+ channel subunits related to Drosophila Shal (Kvα subunits encoded by gene subfamily Kv4)

NOMENCLATURES

EXPRESSION

SEQUENCE ANALYSES

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG K Kvx [unassigned] Listing of cDNA clones encoding Kv channels with unassigned gene I family relationships

NOMENCLATURES

EXPRESSION

SEQUENCE ANALYSES

STRUCTURE AND FUNCTIONS

INFORMATION RETRIEVAL

VLG K M-i [native] ‘Muscarinic-inhibited’ K+channels underlying IM (M-current in native cell types)

Nomenclatures

EXPRESSION

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG (K) minK ‘Minimal’ protein subunits (minK, IsK) eliciting ‘slow-activating’ voltage-gated currents in oocytes

NOMENCLATURES

EXPRESSION

SEQUENCE ANALYSES

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

VLG Na Voltage-gated Sodium Channels

NOMENCLATURES

EXPRESSION

SEQUENCE ANALYSES

STRUCTURE AND FUNCTIONS

ELECTROPHYSIOLOGY

PHARMACOLOGY

INFORMATION RETRIEVAL

Entry Number Rubric

Field Number Rubric

Index

Copyright

This book is printed on acid-free paper

Copyright © 1999 by ACADEMIC PRESS

All rights reserved

No part of this publication may be reproduced or transmitted in any form by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher.

Academic Press

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http://www.hbuk.co.uk/ap/

Academic Press

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ISBN 0-12-184453-6

A catalogue record for this book is available from the British Library

Library of Congress Catalogue Card Number: 98-86472

Typeset in Great Britain by Alden Bookset, Oxford Printed in Great Britain by WBC, Bridgend, Mid Glamorgan

99 00 01 02 03 04 WB 9 8 7 6 5 4 3 2 1

Cumulative table of contents for Volumes I to IV

Contents

Cumulative table of contents for Volumes I to IV (entry 01)

Acknowledgements

Introduction and layout of entries (entry 02)

How to use The Ion Channel FactsBook

Guide to the placement criteria for each field

Abbreviations (entry 03)

VOLUME I EXTRACELLULAR LIGAND-GATED CHANNELS

ELG Key facts (entry 04)

Extracellular ligand-gated receptor-channels – key facts

ELG CAT 5-HT3 (entry 05)

Extracellular 5-hydroxytryptamine-gated integral receptor-channels

ELG CAT ATP (entry 06)

Extracellular ATP-gated receptor-channels (P2xR)

ELG CAT GLU AMPA/KAIN (entry 07)

AMPA / kainate-selective (non-NMDA) glutamate receptor-channels

ELG CAT GLU NMDA (entry 08)

N-Methyl-D-aspartate (NMDA)- selective glutamate receptor-channels

ELG CAT nAChR (entry 09)

Nicotinic acetylcholine-gated integral receptor-channels

ELG Cl GABAA (entry 10)

Inhibitory receptor-channels gated by extracellular gamma-aminobutyric acid

ELG Cl GLY (entry 11)

Inhibitory receptor-channels gated by extracellular glycine

Feedback and access to the Cell- Signalling Network (entry 12)

Rubrics (entry 13)

Entry and field number rubrics

VOLUME II INTRACELLULAR LIGAND-GATED CHANNELS

ILG Key facts (entry 14)

The intracellular ligand-gated channel group – key facts

ILG Ca AA-LTC4 [native] (entry 15)

Native Ca²+ channels gated by the arachidonic acid metabolite leukotriene C4 incorporating general properties of ion channel regulation by arachidonate metabolites

ILG Ca Ca InsP4S [native] (entry 16)

Native Ca²+ channels sensitive to inositol 1,3,4,5-tetrakisphosphate (InsP4)

ILG Ca Ca RyR-Caf (entry 17)

Caffeine-sensitive Ca²+-release channels (ryanodine receptors, RyR)

ILG Ca CSRC [native] (entry 18)

Candidate native intracellular-ligand-gated Ca²+-store repletion channels

ILG Ca InsP3 (entry 19)

Inositol 1,4,5-trisphosphate-sensitive Ca²+-release channels (InsP3R)

ILG CAT Ca [native] (entry 20)

Native calcium-activated non-selective cation channels (NSCa)

ILG (CAT) cAMP (entry 21)

Cation channels activated in situ by intracellular cAMP

ILG CAT cGMP (entry 22)

Cation channels activated in situ by intracellular cGMP

ILG Cl ABC-CF (entry 23)

ATP-binding and phosphorylation-dependent Cl− channels (CFTR)

ILG Cl ABC-MDR/PG (entry 24)

Volume-regulated Cl− channels (multidrug-resistance P-glycoprotein)

ILG Cl Ca [native] (entry 25)

Native calcium-activated chloride channels (ClCa)

ILG K AA [native] (entry 26)

Native potassium channels activated by arachidonic acid (KAA) incorporating general properties of ion channel regulation by free fatty acids

ILG K Ca (entry 27)

Intracellular calcium-activated K+ channels (KCa)

ILG K Na [native] (entry 28)

Native intracellular sodium-activated K+ channels (KNa)

VOLUME III INWARD RECTIFIER AND INTERCELLULAR CHANNELS

INR K Key facts (entry 29)

Inwardly-rectifying K+ channels – key facts

INR K ATP-i [native] (entry 30)

Properties of intracellular ATP-inhibited K+ channels in native cells

INR K G/ACh [native] (entry 31)

Properties of muscarinic-activated K+ channels underlying IKACh in native cells

INR K [native] (entry 32)

Properties of ‘classical’ inward rectifier K+ channels in native cells (excluding types covered in entries 30 & 31)

INR K [subunits] (entry 33)

Comparative properties of protein subunits forming inwardly- rectifying K+ channels (heterologously-expressed cDNAs of the KIR family)

INR (K/Na) IfhQ (entry 34)

Hyperpolarization-activated cation channels underlying the inward currents if, ih, iQ

JUN [connexins] (entry 35)

Intercellular gap junction channels formed by connexin proteins

MEC [mechanosensitive] (entry 36)

Survey of ion channel types activated by mechanical stimuli

MIT [mitochondrial] (entry 37)

Survey of ion channel types expressed in mitochondrial membranes

NUC [nuclear] (entry 38)

Survey of ion channel types expressed in nuclear membranes

OSM [aquaporins] (entry 39)

The vertebrate aquaporin (water channel) family

SYN [vesicular] (entry 40)

Channel-forming proteins expressed in synaptic vesicle membranes (synaptophysin)

VOLUME IV VOLTAGE-GATED CHANNELS

VLG Key facts (entry 41)

Voltage-gated channels – key facts

VLG Ca (entry 42)

Voltage-gated calcium channels

VLG Cl (entry 43)

Voltage-gated chloride channels

VLG K A-T (entry 44)

Properties of native ‘A-type’ (transient outward) potassium channels in native cells

VLG K DR (entry 45)

Properties of native delayed rectifier potassium channels in native cells

VLG K eag/elk/erg (entry 46)

K+ channels related to Drosophila gene subfamilies eag,elk,erg

VLG K Kv-beta (entry 47)

Beta subunits associated with Kv (alpha subunit) channel complexes

VLG K Kv1-Shak (entry 48)

Vertebrate K+ channel subunits related to Drosophila Shaker (Kv subfamily 1) incorporating general features of Kv channel expression in heterologous cells

VLG K Kv2-Shab (entry 49)

Vertebrate K+ channel subunits related to Drosophila Shab (Kv subfamily 2)

VLG K Kv3-Shaw (entry 50)

Vertebrate K+ channel subunits related to Drosophila Shaw (Kv subfamily 3)

VLG K Kv4-Shal (entry 51)

Vertebrate K+ channel subunits related to Drosophila Shal (Kv subfamily 4)

VLG K Kvx (Kv5.1/Kv6.1) (entry 52)

Features of the ‘non-expressible’ cDNAs IK8 and K13

VLG K M-i [native] (entry 53)

Properties of native ‘muscarinic-inhibited’ K+ channels underlying IM

VLG (K) minK (entry 54)

‘Minimal’ protein subunits inducing ‘slow-activating’ voltage-gated K+ currents

VLG Na (entry 55)

Voltage-gated sodium channels

ION CHANNEL RESOURCES

Resource documents and/or links supporting their scope will appear on the Ion Channel Network web site (www.le.ac.uk/csn/) from January 1999.

Resource A

G protein-linked receptors regulating ion channel activities (alphabetical listing)

Resource B

‘Generalized’ electrical effects of endogeneous receptor agonists

Resource C

Compounds and proteins used in ion channel research

Resource D

‘Diagnostic’ tests

Resource E

Ion channel book references (sorted by year of publication)

Resource F

Supplementary ion channel reviews (listed by subject)

Resource G

Reported ‘consensus sites’ and ‘motifs’ in primary sequences of ion channels

Resource H

Listings of cell types

Resource I

Framework of cell-signalling molecule types (preliminary listing)

Resource J

Search criteria & CSN development

Resource K

Framework for a multidisciplinary glossary

Feedback: Comments and suggestions regarding the scope, arrangement and other matters relating to the coverage/contents can be sent to the e-mail feedback file [e-mail]. (see field 57 of most entries for further details)

Acknowledgements

Thanks are due to the following people for their time and help during compilation of the manuscripts: Professors Peter Stanfield, Nick Standen and Gordon Roberts (Leicester), and Ole Petersen (Liverpool) for advice; to Chris Hankins and Richard Mobbs of the Leicester University Computer Centre, and to Dr Tessa Picknett and Chris Gibson of Academic Press for their enthusiasm and patience.

Gratitude is also expressed to all of the anonymous manuscript readers who supplied much constructive feedback, as well as the following who provided advice, information and encouragement: Ihab Awad (Center for Neuroscientific Databases, Minnesota), Jonathan Bard (Edinburgh), Mark Boyett (Leeds), David Brown (London), Cecilia Canessa (Yale), Marty Chalfie (Columbia), K. George Chandy (UC Irvine), David Clapham (Mayo Foundation), Noel Davies (Leicester), Dario DiFrancesco (Milano), Ian Forsythe (Leicester), Harry Fozzard (Chicago), Klaus Groschner (Graz), George Gutman (UC Irvine), Mike Huerta (NIMH, HBP), Rolf Joho (Texas SMC), Benjamin Kaupp (Jülich), Steve Kozlow (NIMH, HBP), Jeremy Lambert (Dundee), Neil Marrion (OHSU), Shigetada Nakanishi (Kyoto), Jitendra Patel (Zeneca USA), Martin Ringwald (Jackson Labs), Gordon Shepherd (Yale), David Spray (Yeshiva), Zhong-ping Sun (Columbia), Steve Watson (Oxford) and George Wilcox (Center for Neuroscientific Databases, Minnesota).

Thanks are also due to the Department of Pathology at the University of Leicester, Harcourt Brace, the Medical Research Council, the British Heart Foundation and Zeneca Pharmaceuticals, for providing generous sponsorship, equipment and facilities.

We would like to acknowledge the authors of all those papers and reviews which in the interest of completeness we have quoted, but have not had space to cite directly.

ECC would like to thank Professors Denis Noble in Oxford, Anthony Campbell in Cardiff and Richard Gregory in Bristol for help and inspiration, and would like to dedicate his contributions to Paula, Rebecca and Katherine for all their love and support.

Left: Edward Conley, Right: William Brammar

Introduction & layout of entries

Edward C. Conley

Entry 02 resumé

The Ion Channel FactsBook is intended to provide a ‘summary of molecular properties’ for all known types of ion channel protein in a cross-referenced and ‘computer-updatable’ format. Today, the subject of ion channel biology is an extraordinarily complex one, linking several disciplines and technologies, each adding its own contribution to the knowledge base. This diversity of approaches has left a need for accessible information sources, especially for those reading outside their own field. By presenting ‘facts’ within a systematic framework, the FactsBook aims to provide a ‘logical place to look’ for specific information when the need arises. For students and researchers entering the field, the weight of the existing literature, and the rate of new discoveries, makes it difficult to gain an overview. For these readers, The Ion Channel FactsBook is written as a directory, designed to identify similarities and differences between ion channel types, while being able to accommodate new types of data within the framework. The main advantages of a systematic format is that it can speed up identification of functional links between any ‘facts’ already in the database and maybe provide a raison d’être for specific experiments where information is not known. Although such ‘facts’ may not go out-of-date, interpretations based on them may change considerably in the light of additional, more direct evidence. This is particularly true for the explosion of new information that is occurring as a direct consequence of the molecular cloning of ion channel genes. It can be anticipated that many more ion channel genes will be cloned in the near future, and it is also likely that their functional diversity will continue to exceed expectations based on pharmacological or physiological criteria alone.

An emphasis on properties emergent from ion channel molecular functions

Understanding how the interplay of currents through many specific ion channel molecules determines complex electrophysiological behaviour of cells remains a significant scientific challenge. The approach of the FactsBook is to associate and relate this complex cell phenotypic behaviour (e.g. its physiology and pharmacology) to ion channel gene expression-control wherever possible even where the specific gene has not yet been cloned. Thus the ion channel molecule becomes the central organizer, and accordingly arbitrates whether information or topics are included, emphasized, sketched-over or excluded. In keeping with this, ion channel characteristics are described in relation to known structural or genetic features wherever possible (or where they are ultimately molecular characteristics). Invariably, this relies on the availability of sequence data for a given channel or group of channels. However, a number of channel types exist which have not yet been sequenced, or display characteristics in the native form which are not precisely matched by existing clones expressed in heterologous cells (or are otherwise ambiguously classified). To accommodate these channel types, summaries of characteristics are included in the standard entry field format, with inappropriate fieldnames omitted. Thus the present ‘working arrangement’ of entries and fields is broad enough to include both the ‘cloned’ and ‘uncloned’ channel types, but in due course will be gradually supplanted by a comprehensive classification based on gene locus, structure, and relatedness of primary sequences. In all cases, the scope of the FactsBook entries is limited to those proteins forming (or predicted to form) membrane-bound, integral ionic channels by folding and association of their primary protein sequences. Activation or suppression of the channel current by a specified ligand or voltage step is generally included as part of the channel description or name (see below). Thus an emphasis is made throughout the book on intrinsic features of channel molecule itself and not on those of separately encoded, co-expressed proteins. In the present edition, there is a bias towards descriptions of vertebrate ion channels as they express the full range of channel types which resemble characteristics found in most eukaryotes.

Anticipated development of the dataset – Integration of functional information around molecular types

Further understanding of complex cellular electrical and pharmacological behaviour will not come from a mere catalogue of protein properties alone. This book therefore begins a process of specific cross-referencing of molecular properties within a functional framework. This process can be extended to the interrelationships of ion channels and other classes of cell-signalling molecules and their functional properties. Retaining protein molecules (i.e. gene products) as ‘fundamental units of classification’ should also provide a framework for understanding complex physiological behaviour resulting from co-expressed sets of proteins. Significantly, many pathophysiological phenotypes can also be linked to selective molecular ‘dysfunction’ within this type of framework. Finally, the anticipated growth of raw sequence information from the human genome project may reveal hitherto unexpected classes and subtypes of cell-signalling components – in this case the task then will be to integrate these into what is already known (see also description of Field number 06: Subtype classifications and Field number 05: Gene family).

The Cell-Signalling Network (CSN)

From the foregoing discussion, it can be seen that establishment and consolidation of an integrated ‘consensus database’ for the many diverse classes of cell signalling molecules (including, for example, receptors, G proteins, ion channels, ion pumps, etc.) remains a worthwhile goal. Such a resource would provide a focus for identifying unresolved issues and may avoid unnecessary duplication of research effort. Work has begun on a prototype cell-signalling molecule database cooperatively maintained and supported by contributions from specialist groups: The Cell-Signalling Network (CSN) in mid-1996 has been designed to disseminate consensus properties of a wide range of molecules involved in cell signal transduction. While it will take some time (and much good-will) to establish a comprehensive network, the many advantages of such a co-operative structure are already apparent. Immediately, these include an ‘open’ mechanism for consolidation and verification of the dataset, so that it holds a ‘consensus’ or ‘validated’ set of information about what is known about each molecule and practical considerations such as nomenclature recommendations (see, for example, the IUPHAR nomenclature sections under the CSN ‘home page’).

The CSN also allows unlimited cross-referencing by pointing to related information sets, even where these are held in multiple centres. On-line descriptions of technical terms (glossary items, indicated by dagger symbols (†) throughout the text) and reference to explanatory references (e.g. on associated signalling components such as G protein†-linked receptors†) are being written for use with this book. Eventually, applications could include (for instance) direct ‘look-up’ of graphical resources for protein structure, in situ and developmental gene expression atlases†, interactive molecular models for structure/function analysis, DNA/protein sequences linked to feature tables, gene mapping resources and other pictorial data. These developments (not presently supported) will use interactive electronic media for efficient browsing and maintenance. For a brief account of the Cell-Signalling Network, see Feedback & CSN access, entry 12. For a full specification, see Resource J – Search criteria & CSN development.

HOW TO USE THE ION CHANNEL FACTSBOOK

Common formats within the entries

A proposed organizational hierarchy for information about ion channel molecules

Information on named channel types is grouped in entries under common headings which repeat in a fixed order – e.g. for ion channel molecules which have been sequenced, there are broad sections entitled NOMENCLATURES, EXPRESSION, SEQUENCE ANALYSES, STRUCTURE & FUNCTIONS, ELECTROPHYSIOLOGY, PHARMACOLOGY, INFORMATION RETRIEVAL and REFERENCES, in that order. Within each section, related fieldnames are listed, always in alphabetical order and indexed by a field number (see below), which makes electronic cross-referencing and ‘manual’ comparisons easier.

While the sections and fields are not rigid categories, an attempt has been made to remain consistent, so that corresponding information for two different channels can be looked up and compared directly. If a field does not appear, either the information was not known or was not found during the compilation period. Pertinent information which has been published but is absent from entries would be gratefully received and will be added to the ‘entry updates’ sections within the CSN (see Feedback & CSN access, entry 12). Establishment of this ‘field’ format has been designed so that most ‘facts’ should have their logical ‘place’. In the future, this arrangement may help to establish ‘consensus’ properties of any given ion channel or other cell-signalling molecule. This validation process critically depends on user feedback to contributing authors. The CSN (above) establishes an efficient electronic mechanism to do this, for continual refinement of entry contents.

Independent presentation of ‘facts’ and conventions for cross-referencing

The FactsBook departs from a traditional review format by presenting its information in related groups, each under a broader heading. Entries are not designed or intended to be read ‘from beginning to end’, but each ‘fact’ is presented independently under the most pertinent fieldname. Independent citation of ‘facts’ may sometimes result in some repetition (redundancy) of general principles between fields, but if this is the case some effort has been made to ‘rephrase’ these for clarity (suggested improvements for presentation of any ‘fact’ are welcome – see Field number 57: Feedback).

For readers unfamiliar with the more general aspects of ion channel biology, some introductory information applicable to whole groups of ion channel molecules is needed, and this is incorporated into the ‘key facts’ sections preceding the relevant set of entries. These sections, coupled with the glossary items (available on-line, and indicated by the dagger† symbol, see below) provide a basic overview of principles associated with detailed information in the main entries of the book.

Extensive cross-referencing is a feature of the book. For example, cross-references between fields of the same entry are of the format (see Fieldname, xx-yy). Cross-references between fields of different channel type entries are generally of the format see fieldname under SORTCODE, xx-yy; for example – see mRNA distribution, under ELG Cl GABAA, 10-13. This alphabetical ‘sortcode’ and numerical ‘entry numbers’ (printed in the header to each page) are simply devices to make cross- referencing more compact and to arrange the entries in an approximate running order based on physiological features such as mode of gating†, ionic selectivity†, and agonist† specificity. A ‘sort order’ based on physiological features was judged to be more intuitive for a wider readership than one based on gene structure alone, and enables ‘cloned’ and ‘uncloned’ ion channel types to be listed together. The use and criteria for sortcode designations are described under the subheading Derivation of the sortcode (see Field number 02: Category (sortcode)). Entry ‘running order’ is mainly of importance in book-form publications. New entries (or mergers/subdivisions between existing entries) will probably use different serial entry numbers as ‘electronic pointers’ to appropriate files.

Cross-references are frequently made to an on-line index of glossary items by dagger symbols† wherever they might assist someone with technical terms and concepts when reading outside their own field. The glossary is designed to be used side-by- side with the FactsBook entries and will be accessible in updated form over the Internet with suitable software (for details, see Feedback & CSN access, entry 12).

Contextual markers and styles employed within the entries

Throughout the books, a six-figure index number (xx-yy-zz, e.g. 19-44-01:) separates groups of facts about different aspects of the channel molecule, and carries information about channel type/entry number (e.g. 19- ~ InsP3 receptor–channels), information type/field number (e.g. -44-, Channel modulation) and running paragraph number (datatype) (e.g. -01). This simple ‘punctate’ style has been adopted for maximum flexibility of updating (both error-correction and consolidation with new information), cross-referencing and multi-authoring. The CSN specification includes longer term plans to further structure field-based information into convenient data-types which will be indexed by a zz numerical designation.

Italicized subheadings are employed to organize the facts into related topics where a field has a lot of information associated with it. Specific illustrated points or features within a field are referenced to adjacent figures. Usage of abbreviations and common symbols are defined in context and/or within the main abbreviations index at the front of each book. Abbreviated chemical names and those of proprietary pharmaceutical compounds are listed within Resource C – Compounds & proteins.

Generally, highlighting of related subtopics emergent from the molecular properties (‘facts’) associated with the ion channel under description are indicated within a field by lettering in bold. Throughout the main text, italics draw attention to special cases, caveats, hypotheses and exceptions. The ‘Note: ’ prefix has been used to indicate supplemental or comparative information of significance to the quoted data in context.

Special considerations for integrating properties derived from ‘cloned’ and ‘native’ channels

While a certain amount of introductory material is given to set the context, the emphasis on molecular properties means the treatment of many important biological processes or phenomena is reduced to a bare outline. References given in the Related sources and reviews field and Resource F – Supplementary ion channel reviews are intended to address this imbalance.

For summaries of key molecular features, a central channel ‘protein domain topography model’ is presented. Individual features that are illustrated on the protein domain topography model are identified within the text by the symbol [PDTM].

Wherever molecular subtype-specific data are quoted (such as the particular behaviour of a ion channel gene family† member or isoform†) a convention of using the underlined trivial or systematic name as a prefix has been adopted – e.g. mIRKI:; RCK1:; Kv3.1: etc.

GUIDE TO THE PLACEMENT CRITERIA FOR EACH FIELD

Criteria for NOMENCLATURES sections

This section should bring together for comparison present and previous names of ion channels or currents, with brief distinctions between similar terms. Where systematic names have already been suggested or adopted by published convention, they should be included and used in parallel to trivial names.

Field number 01: Abstract/general description: This field should provide a summary of the most important functional characteristics associated with the channel type.

Field number 02: Category (sortcode): The alphabetical ‘sortcode’ should be used for providing a logical running order for the individual entries which make up the book. It is not intended to be a rigorous channel classification, which is under discussion, but rather a practical index for finding and cross-referencing information, in conjunction with the six-figure index number (see above). The Category (sortcode) field also lists a designated electronic retrieval code (unique embedded identifier or UEI) for ‘tagging’ of new articles of relevance to the contents of the entry. For further details on the use and implementation of UEIs, see the description for Resource J (in this entry) and for a full description, see Resource J – Search criteria & CSN development.

Derivation of the sortcode: Although we do not yet have a complete knowledge of all ion channel primary† structures, knowledge of ion channel gene family† and superfamily† structure allows a working sort order to be established. To take an example, the extracellular ligand-gated (ELG) receptor–channels share many structural features, which reflects the likely duplication and divergent evolution of an ancestral gene. The present-day forms of such channels reflect the changes that have occurred through adaptive radiation† of the ancestral type, particularly for gating† mechanism and ionic selectivity† determinants. Thus, the entry running order (alphabetical, via the sortcode) of the FactsBook entries should depend primarily on these two features. The sortcode therefore consists of several groups of letters, each denoting a characteristic of the channel molecule: Entries are sorted first on the principal means for channel gating† (first three letters), whether this is by an extracellular ligand† (ELG), small intracellular ligand† (ILG) or transmembrane voltage (VLG). For convenience, the ILG entries also include certain channels which are obligately dependent on both ligand binding and hydrolysis for their activation – e.g. channels of the ATP-binding cassette (ABC) superfamily. Other channel types may be subject to direct mechanical gating (MEC) or sensitive to changes in osmolarity (OSM) – see the Cumulative tables of contents and the first page of each entry for descriptions and scope. Due to their unusual gating characteristics, a separate category (INR) has been created for inward rectifier-type channels.

The second sort (the next three letters of the sortcode) should be on the basis of the principal permeant ions, and may therefore indicate high selectivity for single ions (e.g. Ca, Cl, K, Na) or multiple ions of a specified charge (e.g. cations – CAT). Indefinite sortcode extensions can be assigned to the sortcode if it is necessary to distinguish similar but separately encoded groups of channels (e.g. compare ELG Cl GABAA, entry 10 and ELG Cl GLY, entry 11).

Field number 03: Channel designation: This field should contain a shorthand designation for the ion channel molecule – mostly of the form XY or X(Y) where X denotes the major ionic permeabilities† (e.g. K, Ca, cation) and Y denotes the principal mechanism of gating† where this acts directly on the channel molecule itself (e.g. cGMP, voltage, calcium, etc.). Otherwise, this field contains a shorthand designation for the channel which is used in the entry itself.

Field number 04: Current designation: This field should contain a shorthand designation for ionic currents conducted by the channel molecule, which is mostly of the form IX(Y), IX,Y or IX-Y where X and Y are defined as above.

Field number 05: Gene family: This field should indicate the known molecular relationships to other ion channels or groups of ion channels at the level of amino acid primary sequence homology†, within gene families† or gene superfamilies†. Where multiple channel subunits are encoded by separate genes, a summary of their principal features should be tabulated for comparison. Where the gene family is particularly large, or cannot be easily described by functional variation, a gene family tree† derived by a primary sequence alignment algorithm† (see Resource D – ‘Diagnostic’ tests) may be included as a figure in this field.

Field number 06: Subtype classifications: This field should include supplementary information about any schemes of classification that have been suggested in the literature. Generally, the most robust schemes are those based on complete knowledge of gene family† relationships (see above) and this method can identify similarities that are not easily discernible by pharmacological or electrophysiological criteria alone – see, for example, the entries JUN (connexins), entry 35, and INR K (subunits), entry 33. Note, however, that some native† channel types are more conveniently ‘classified’ by functional or cell-type expression parameters which take into account interactions of channels with other co-expressed proteins (see, for example, discussion pertaining to the cyclic nucleotide-gated (CNG-) channel family in the entries ILG Key facts, entry 14,1LG CAT cAMP, entry 21, and ILG CAT cGMP, entry 22. Debate on the ‘best’ or ‘most appropriate’ channel classification schemes is likely to continue for some time, and it is reasonable to suppose that alternative subtype classifications may be applied and used by different workers for different purposes.

Since the ‘running order’ of the FactsBook categories depends on inherent molecular properties of channel cDNAs†, genes† or the expressed proteins, future editions will gradually move to classification on the basis of separable gene loci†. Thus multiple channel protein variants resulting from processes of alternative RNA splicing† but encoded by a single gene locus† will only ever warrant one ‘channel-type’ entry (e.g. see BKCa variants under ILG K Ca, entry 27). Distinct proteins resulting from transcription† of separable gene loci, for example in the case of different gene family members, will (ultimately) warrant separate entries. For the time being, there is insufficient knowledge about the precise phenotypic† roles of many ‘separable’ gene family members to justify separate entries (as in the case of the VLG K Kv series entries).

Classification by gene locus designation (see Field number 18: Chromosomal location) can encompass all structural and functional variation, while being ‘compatible’ with efforts directed to identifying phenotypic and pathophysiological† roles of individual gene products (e.g. by gene-knockout†, locus replacement† or disease-linked gene mapping† procedures – see Resource D – ‘Diagnostic’ tests). Subtype classifications based on gene locus control can also incorporate the marked developmental changes which pertain to many ion channel genes (see Field number 11: Developmental regulation) and can be implemented when the ‘logic’ underlying gene expression-control† for each family member is fully appreciated. A ‘genome-based’ classification of FactsBook entries may also help comprehend and integrate equivalent information based for other (‘non-channel’) cell-signalling molecules (see Resources G, H and I).

Field number 07: Trivial names: This field should list commonly used names for the ion channel (or its conductance†). Often a channel will be (unsystematically) named by its tissue location or unusual pharmacological/physiological properties, and these are also listed in this field. While unsystematic names do not indicate molecular relatedness, they are often more useful for comparative/descriptive purposes. For these and historical reasons, trivial names (e.g. clone/isolate names for K+ channel isoforms) are used side-by-side with systematic names, where these exist. A standardized nomenclature for ion channels is under discussion, e.g. see the series of articles by Pongs, Edwards, Weston, Chandy, Gutman, Spedding and Vanhoutte in Trends Pharmacol Sci (1993) 14: 433–6. Future recommendations on standardized nomenclature will appear in files accessible under the IUPHAR entry of the Cell-Signalling Network (see Feedback & CSN access, entry 12).

Criteria for EXPRESSION sections

This section should bring together information on expression patterns of the ion channel gene, indicating functional roles of specific channels in the cell type or organism. The complex and profound roles of ionic currents in vertebrate development (linking plasma membrane signalling and genome activation) are also emphasized within the fields of this section.

Field number 08: Cell-type expression index: Comprehensive systems relating the expression of specified molecular components to specified anatomical and developmental loci (‘expression atlases’) are being developed in a number of centres and in due course will form a superior organizational framework for this type information (see discussion below). In the meantime, the range of cell-type expression should be indicated in this field in the form of alphabetized listings. Notably, there is a substantial literature concerned with the electrophysiology of ion channels where the tissue or cell type forms the main focus of the work. In some cases, this has resulted in detailed ‘expression surveys’, revealing properties of interacting sets of ion channels, pumps, transporters and associated receptors. Such review-type information is of importance when discussing the contribution of individual ion channel molecules to a complex electrophysiological phenotype† and/or overall function of the cell. For further references to ‘cell-type-selective’ reviews, see Resource H – Listings of cell types.

Problems and opportunities in listing ion channel molecules by cell type: Understanding the roles which individual ionic channels play in the complex electro-physiological phenotypes of native† cells remains a significant challenge. The overwhelming range of studies covering aspects of ion channel expression in vertebrate cells offers unique problems when compiling a representative overview. Certainly the linking of specific ion channel gene expression to cell type is a first step towards a more comprehensive indexing, and towards this goal, cell-type- selective studies are useful for a number of reasons. First, they can help visualize the whole range of channel expression by providing an inventory of conductances† observed. Secondly, these studies generally define the experimental conditions required to observe a given conductance. Thirdly, they include much information directly relating specified ionic conductances to the functions of the cell type concerned. Collated information such as this should be of increasing utility in showing the relationship of electrophysiological phenotype to mechanistic information on their gene structure and expression-control (which largely correlates with cell-type lineage). At this time it is difficult to build a definitive catalogue of ion channel gene expression patterns mapped to cell type, not only because the determinants of gene expression are scarcely explored, but also because there remain many unavoidable ambiguities in phenotype definition. Some of these problems are discussed below.

Problems of uneven coverage/omissions: Certain cell preparations have been intensely studied for ion channel expression while others have received very little attention for technical, anatomical or other reasons. Furthermore, a large number of native† ionic currents can be induced or inhibited by agonists† that bind to co-expressed G protein†-coupled receptors†. Thus a difficulty arises in deciding whether channel currents can be unambiguously defined in terms of action at a separately encoded receptor protein. While it is valid to report that an agonist-sensitive current is expressed in a defined cell type, the factors of crosstalk† and receptor-transducert subtype specificities in signalling systems are complex and may produce an ambiguous classification. Receptor-coupled agonist-sensitivities are an important factor contributing to cell-pharmacological and -electrical phenotype†, but the treatment here has been limited to a number of tabular summaries of ion channel regulation through coupling to G protein-linked effector† molecules (see Resource A – G protein-linked receptors). As stated earlier, the entries are not sorted on agonist specificity except where the underlying ion channel protein sequence would be expected to form an integral ionic channel whose gating† mechanism is also part of the assembled protein complex.

Cell preparation methods are variable: A further problem inherent in classifying ion channels by their patterns of expression is that the choice of tissue or cell preparation method may influence phenotype†. The behaviour of channel-mediated ionic currents can be measured in native† cells, e.g. in the tissue slice, which has the advantages of extracellular ionic control, mechanical stability, preserved anatomical location, lack of requirement for anaesthetics and largely undisturbed intercellular communication. Cell-culture techniques show similar advantages, with the important exceptions that normal developmental context, anatomical organization and synaptic arrangements are lost and (possibly as a consequence) the ‘expression profile’ of receptor and channel types might change. Cultured cell preparations may also be affected by ‘de-differentiation†’ processes and (by definition) cell lines† are uncoupled from normal processes of cell proliferation†, differentiation† and apoptosis†. Acutely dissociated cells from native† tissue may provide cell-type- specific expression data without anomalies introduced by intercellular (gap junctional) conductances, but the enzymatic or dispersive treatments used may also affect responses in an unknown way.

Verbal descriptions of cell-type expression divisions are arbitrary and are not rigorous: Definitive mapping of specific ion channel subtype expression patterns has many variables. Localization of specific gene products are most informative when in situ localizations are linked to the regulatory factors controlling their expression (see glossary entry on Gene expression-control†). The complexity of this task can extend to processes controlling, for example, developmental regulation, co-expressed protein subunit stoichiometries and subcellular localizations.

Complete integration of all structural, anatomical, co-expression and modulatory data for ion channels could eventually be accommodated within interactive graphical databases which are capable of providing ‘overlays’ of separately collected in situ expression data linked to functional properties of the molecules. By these methods, new data can be mathematically transformed to superimpose on fixed tissue or cell co-ordinates for comparison with existing database information.

Software development efforts focused on the acquisition, analysis and exchange of complex datasets in neuroscience and mouse development have been described, and the next few years should hopefully see their implementation. For further information, see

Baldock, R., Bard, J., Kaufman, M. and Davidson, D. (1992) A real mouse for your computer, Bioessays 14: 501–2

Bloom, F. (1992) Brain Browser, v 2.0. Academic Press (Software).

Kaufman, M. (1992) The Atlas of Mouse Development, Academic Press

Wertheim, S. and Sidman, R. (1991) Databases for Neuroscience, Nature 354: 88–9

To help rationalize the choices available for selection of these ‘prototype’ classifications, see Resource H – Listings of cell types. These listings may also have some practical use for sorting the subject matter of journal articles into functionally related groups. A proposed integration of information resources relating different aspects of cell-signalling molecule gene expression is illustrated in Fig. 4 of the section headed Feedback & CSN access, entry 12.

Field number 09: Channel density: This field should contain information about estimated numbers of channel molecules per unit area of membrane in a specified preparation. This field lists information derived from local patch-clamp ‘sampling’ or autoradiographic detection in membranes using anti-channel antibodies. The field should also describe unusually high densities of ion channels (‘clustering’) in specified membranes where these are of functional interest.

Field number 10: Cloning resource: This field should refer to cell preparations relatively ‘rich’ in channel-specific mRNA (although it should be noted that many ion channel mRNAs are of low abundance†). Otherwise, this field defines a ‘positive control’ preparation likely to contain messenger† RNA† encoding the channel. Preparations may express only specific subtypes of the channel and therefore related probes (especially PCR† probes) may not work. Alternatively, a genomic† cloning resource may be cited.

Field number 11: Developmental regulation: This field should contain descriptions of ion channel genes demonstrated (or expected to be) subject to developmental gene regulation – e.g. where hormonal, chemical, second messenger† or other environmental stimuli appear to induce (or repress) ion channel mRNA or protein expression in native† tissues (or by other experimental interventions). Protein factors in trans† or DNA structural motifs† in cis† which influence transcriptional activation†, transcriptional enhancement† or transcriptional silencing† should also be listed under this fieldname. Information about the timing of onset for expression should also be included if available, together with evidence for ion channel activity influencing gene activation† or patterning† during vertebrate development.

Field number 12: Isolation probe: This field should include information on probes used to relate distinct gene products by isolation of novel clones following low-stringency cross-hybridization screens†. The development of oligonucleotide† sets which have been used to unambiguously detect subtype-specific sequences by PCR†, RT-PCR† or in situ hybridization† should be identified with source publication. Both types of sequence may be able to serve as unique gene isolation probes, dependent upon the library† size, target abundance†, screening stringency† and other factors.

Field number 13: mRNA distribution: This field should report either quantitative/semi-quantitative or presence/absence (±) descriptions of specific channel mRNAs in defined tissues or cell types. This type of information is generally derived from Northern hybridization†, RNAase protection† analysis, RT-PCR† or in situ expression assays. See also notes on expression atlases under Field number 08: Cell-type expression index.

Field number 14: Phenotypic expression: This field should include information on the proposed phenotype† or biological roles of specified ion channels where these are discernible from expression studies of native† (wild-type) genes. Phenotypict consequences of naturally occurring (spontaneous) mutationst in ion channel genes are included where these have been defined, predicted or interpreted (see also Fields 26–32 of the STRUCTURE & FUNCTIONS section for interpretation of site-directed mutagenesis† procedures as well as Resource D – ‘Diagnostic’ tests). Associations of ion channels with pathological states, or where molecular ‘defects’ could be ‘causatory’ or contribute to the progression of disease should be listed in this field (for links with established cellular and molecular pathology databases, see Fig. 4 of Feedback & CSN access, entry 12).

The Phenotypic expression field may include references to mutations in other (‘non-channel’) genes which affect channel function when the proteins are co-expressed. It is also used to link descriptions of specific (cloned) molecular components to native cell-electrophysiological phenotypes. In due course, this field will be used to hold information on phenotypic† effects of transgenic† manipulations of ion channel genes including those based on gene knockout† or gene locus† replacement† protocols.

Field number 15: Protein distribution: This field should report results of expression patterns determined with probes such as antibodies raised to channel primary† sequences or radiolabelled affinity ligands†.

Field number 16: Subcellular locations: This field should describe any notable arrangements or intracellular locations related to the functional role of the channel molecule, e.g. when the channel is inserted into a specified subcellular membrane system or is expressed on one pole of the cell only (e.g. the basolateral† or apical† face).

Field number 17: Transcript size: This field should list the main RNA transcript† sizes estimated (in numbers of ribonucleotides) by Northern† hybridization analysis. Multiple transcript sizes may indicate (i) alternative processing (‘splicing†’) of a primary transcript†, (ii) the use of alternative transcriptional start sites†, or (iii) the presence of ‘pre-spliced’ or ‘incompletely spliced’ transcripts identified with homologous nucleotide probes† in total cell mRNA† populations. Note that probes can be chosen selectively to identify each of these categories; ‘full-length’ coding sequence† (exonic†) probes are the most likely to identify all variants, while probes based on intronic† sequences (where appropriate) will identify ‘pre-splice’ variants.

Criteria for SEQUENCE ANALYSES sections

This section should bring together data and interpretations derived from the nucleic acid or protein sequence of the channel molecule. The symbol [PDTM] denotes an illustrated feature on the channel monomer protein domain topography model, which is presented as a central figure in some entries for sequenced ion channels. These models are only intended to visualize the relative lengths and positions of features on the whole molecule (see the description for field number 30, Predicted protein topography). The PDTMs as presented are highly diagrammatic – the actual protein structure will depend on patterns of folding, compact packing and multi-subunit associations. In particular, the relative positions of motifs, domain shapes and sizes are subject to re-interpretation in the light of better structural data. Links to information resources for protein and nucleic acid sequence data are described in the Database listings field towards the end of each entry.

Field number 18: Chromosomal location: This field should provide a chromosomal locus† designation (chromosome number, arm, position) for channel gene(s) in specified organisms, where this is known. Notes on interactive linking to gene mapping database resources appear under an option of the Cell-Signalling Network ‘home page’ (see Feedback & CSN access, entry 12).

Field number 19: Encoding: This field should report open reading frame† lengths as numbers of nucleotides or amino acid residues encoding monomeric channel proteins (i.e. spanning the first A of the ATG translational start codon† to the last base of the translational termination codon†). The field should report and compare any channel protein length variants in different tissues or organisms. If considered especially relevant or informative, selected primary† sequence alignments of different gene family members may appear under this field.

Field number 20: Gene organization: This field should describe known intron† and exon† junctions within or outside the protein coding sequence, together with positional information on gene expression-control† elements and polyadenylationt sites where known. Note: Functional changes as a result of gene expression- control should be listed under the Developmental regulation field.

Field number 21: Homologous isoforms: This field should indicate independently isolated and sequenced forms of entire channels which either show virtual identity or of such high homology† that they can be considered equivalent should also appear in this field (but see note on percentage conservation values under Field number 28: Domain conservation). Isoforms†* of a channel protein can exist between closely related species or between different tissues of the same species (i.e. the same gene may be expressed in two or more different tissues, sequenced by two groups but named independently). Some tissue-specific variation may also result from alternative splicing†, yielding subtly distinct forms of channel protein. Since small numbers of amino acid changes may exist from individual-to-individual (as a result of normal sequence polymorphism† in populations) separate isolates may yield sequence isoforms which can be shown to be ‘equivalent’ by Southern hybridizationt procedures (see Field number 25: Southerns).

molecular constitutions and functional roles in specified cell types of closely related species. Comparative information on different gene family† members or multiple variants affecting particular protein domains† may also be included under the Gene family and Domain conservation fields respectively.

Field number 22: Protein molecular weight (purified): This field should state reported molecular weights estimated from relative protein mobilities using SDS–PAGE† methods (e.g. following affinity† purification from native† or heterologous† cell membranes). Data derived from native† preparations generally includes the weight contribution from oligosaccharide† chains added during post-translational protein glycosylation†. In general, extracellular saccharide† components of glycoproteins† may contribute 1–85% by weight, ranging from a few to several hundred oligosaccharide chains per glycoprotein molecule.

Field number 23: Protein molecular weight (calc.): This field should list the molecular weight of monomeric channel proteins equivalent to the summated (calculated) molecular weights of constituent amino acids in the reported sequence (e.g. derived from open reading frames† of cDNA† sequences). If ‘calculated’ molecular weights are less than ‘purified’ molecular weights (previous field) this may indicate the existence of post-translational glycosylation† on native† expressed protein subunits in vivo.

Field number 24: Sequence motifs: This field should report the position of putative regulatory sites as deduced from the protein or nucleic acid primary† sequence (with the exception of potential phosphorylation sites for protein kinases†, which are listed under Field number 32: Protein phosphorylation). Positions of sequence motifs† illustrated on the monomer protein domain topography model are denoted by the symbol [PDTM]. Typical consensus† sites include those for enzymes such as glycosyl transferases†, ligand†-binding sites, transcription factor†-binding sites† etc. N-glycosylation† motifs are sometimes indicated using the shorthand designation N- gly:. Signal peptide cleavage sites (sometimes designated by Sig:) can be derived by comparing sizes of the signal peptide† and the mature chain†.

Field number 25: Southerns: This field should include information which reports the existence of closely related DNA sequences in the genome† or reports the copy number† of individual genes via Southern hybridization† procedures. Note that native† diploid somatic† cells will generally maintain two copies of a given ion channel gene locus†, but stable† heterologous† expression procedures may result in multiple locus insertion†. Multiple locus insertion can be quantitated in Southern† hybridization procedures using two probes of similar length and hybridization affinity†, one specific for a native locus (which will identify two copies) and one for the heterologous gene (which will yield a hybridization signal proportional to the copy number). Note also that the copy number parameter can not be equated to the physiological expression level of the recombinant† protein unless locus control regions are incorporated as part of the channel expression construct (for details, see the section entitled Gene copy number under Resource D – ‘Diagnostic’ tests, and the section describing heterologous ion channel gene expression under Resource H – Listings of cell types).

Criteria for STRUCTURE & FUNCTIONS sections

This section should bring together information based on functional analysis or interpretation of ion channel structural elements. This section includes data derived from functional studies following site-directed mutagenesis† of ion channel genes and molecular modelling studies at atomic scale. Future developments linking on-line information resources for protein structure to ‘functional datasets’ are illustrated in Fig. 5 of Feedback & CSN access, entry 12, and in Resource J – Search criteria & CSN development.

Field number 26: Amino acid composition: This field should include information on channel protein hydrophilicity† or hydrophobicity† where this is of structural or functional significance. Similarities to other related proteins should be emphasized.

Field number 27: Domain arrangement: This field should describe the predicted number and arrangement of protein domains† when folded in the membrane as determined by hydropathicity analysis† of the primary† sequence. Note that structural predictions of transmembrane domains† on the basis of hydrophobicity† plots may be misleading and prematurely conclusive. For example, high resolution (~9 Å) structural studies of the nicotinic acetylcholine receptor (nAChR, see ELG CAT nAChR, entry 09) predict that only one membrane-spanning α-helix† (likely to be M2, a pore-lining domain) is present per subunit, with the other hydrophobic regions being present as β-sheets† (see Unwin, J Mol Biol (1993) 229: 1101–24). By contrast, extracellular ligand-gated (ELG) channels such as the nAChR display four predicted membrane-spanning regions (M1–M4) on the basis of hydrophobicity plots. From the foregoing it must be emphasized that all assignments given for the number or arrangement of ‘predicted’ domains in this field are tentative.

Field number 28: Domain conservation: This field should point out known structural and/or functional motif† sequences which have been conserved as protein subregions of ion channel primary† sequences during their evolution (such as those encoding a particular type of protein domain†). Cross-references should be made to functionally related domains conserved in different proteins including ‘non ion channel’ proteins. Note that ‘percentage conservation’ values are not absolute as they depend on which particular subregions of channel sequences are aligned, the numbers and availability of samples, and/or which sequence alignment algorithms† are used.

Field number 29: Domain functions (predicted): This field should indicate predicted functions of channel molecular subregions based on structural or functional data – e.g. regions affecting properties such as voltage-sensitivity, ionic selectivity†, channel gating† or agonist† binding.

Field number 30: Predicted protein topography: This field should include information on the stoichiometric† assembly† patterns of protein subunits derived from the same or different genes. This field indicates whether channel monomers are likely to form homomultimers†, heteromultimers† or both, and lists estimated physical dimensions of the protein if these have been published. Note: ‘topography’ is a convenient term borrowed from cartography which when applied to proteins, implies a ‘map’ at a level of detail or scale intermediate between that of an amino acid sequence and a larger-scale representation such as a protein multimeric complex. Topographic maps (or ‘models’) are therefore particularly useful for displaying selected sets of (inter-related) datatypes within a single ‘visual framework’. The protein domain topography models (symbolized by [PDTM] throughout the entries) provide prototypes for this form of data representation. The considerable scope for further development of ‘shared’ topographical models which interactively report and illustrate many different features in the text are described in Search Criteria & CSN Development (Resource J). The terms ‘protein topography’ and ‘protein topology’ are often used interchangeably (sic), but the latter should be reserved for those physical or abstract properties of a molecule which are retained when it is subjected to ‘deformation’.

Field number 31: Protein interactions: This field should report well-documented examples of the channel protein working directly in consort with separate proteins in its normal cellular role(s). The ‘protein interactions’ described need not involve physical contact between the proteins (generally referred to as ‘protein–protein’ interactions), but may involve a messenger† molecule. The scope of this field therefore includes notable examples of protein co-localization or functional interaction. For instance, reproduction of native† channel properties in heterologous† cell expression systems may require accessory subunit expression (e.g. see VLG K Kv-beta, entry 47). Common channel–receptor or G protein–channel interactions are described in principle under Resource A – G protein-linked receptors, and Field number 49: Receptor/transducer interactions.

Field number 32: Protein phosphorylation: This field should describe examples of experimentally determined ‘phosphomodulation’ of ion channel proteins, and if possible list sites and positions of phosphorylation motifs† within the channel sequence. Only those consensus sites† explicitly reported in the literature are shown, and these may not be a complete description and may not be based on functional studies. Examples of primary† sequence motifs† for in vitro phosphorylation by several kinases† are listed in Resource C – Compounds & proteins and Resource G – Reported ‘Consensus sites’ and ‘motifs’. Abbreviations used within this field for various enzyme motifs† (e.g. Phos/PKA) are listed in Abbreviations, entry 03. Electrophysiological or pharmacological effects of channel protein phosphorylation in vitro by use of purified protein kinases† should also be described or cross-referenced in this field.

Criteria for ELECTROPHYSIOLOGY sections

This section should bring together information concerning the electrical characteristics of ion channel molecules – how currents are turned on and off, which ions carry them, their sensitivity to applied membrane voltage or agonists, and how individual molecules contribute to total membrane conductance in specified cell types.

Field number 33: Activation: This field should contain information on experimental conditions or factors which activate (open) the channel, such as the binding of ligands†, membrane potential changes or mechanical stimulation. Descriptions of characteristic gating† behaviour such as flickering†, bursting†, activation latency† or threshold† of opening are also included. Applicable models of activation and the time course of current flow are briefly described here or referred to Field number 38: Kinetic model.

Field number 34: Current type: Where clarification is required, this field should contain general descriptive information on the type, shape, size and direction of ionic current.

Field number 35: Current–voltage relation: This field should report the behaviour of the channel current passed in response to a series of specified membrane potential shifts from a holding potential† under a specified recording configuration† For ligand†-gated channels (i.e. those with sortcodes beginning ELG and ILG) entries should report the current evoked by specific concentrations of agonist† applied at various holding potentials. This field should attempt to illustrate channel behaviour by listing a range of parameters such as slope conductance†, reversal potentials† and steepness† of rectifying† (non-ohmic†) behaviour. The conventions used for labelling the axes of I–V relations for different charge carriers† are outlined in the on-line glossary.

Field number 36: Dose-response: This field should contain information relating activator ‘dose’ (e.g. concentration) to channel ‘response’ parameters (e.g. open time†, open probability†) and whether there are maxima or minima in the response. Agonist† dose–response experiments are used to derive parameters such as the Hill coefficient† and Equilibrium dissociation constant†.

Field number 37: Inactivation: This field should describe any inactivation† behaviour of the channel in the continued presence of activating stimulus. The field includes information on voltage- and agonist†-dependence, with indications of time course and treatments which extend or remove the inactivation response. Where known, this field will distinguish channel inactivation from receptor desensitization† processes, which are of particular significance for the extracellular ligand†-gated (ELG) channel types (see ELG Key facts, entry 04).

Field number 38: Kinetic model: This field should contain references to major theoretical and functional studies on the kinetic behaviour of selected ion channels. The field contents is limited to a simple description of parameters, terms and fundamental equations.

Field number 39: Rundown: This field should collate information on channel ‘rundown†’ (‘washout’) phenomena observed during whole-cell† voltage clamp†/cytoplasm dialysis† or patch-clamp† experiments. Conditions known to accelerate or retard the development of rundown should also be listed.

Field number 40: Selectivity: This field should report data on relative ionic permeabilities† under stated conditions by means of permeability ratio† and/or selectivity ratio† parameters. The field may also compare measured reversal potentials† in response to ionic equilibrium potentials† with specified charge carriers under physiological conditions. This field also lists estimated physical dimensions of ionic selectivity filters† where derived from ion permeation† or electron micrographic studies.

Field number 41: Single-channel data: This field should report examples of singlechannel current amplitudes and single-channel conductances† measured under stated conditions. In the absence of authentic single-channel data, estimates of channel conductances† derived from whole-cell recording† and fluctuation analysis† may be listed.

Field number 42: Voltage sensitivity: This field should describe the behaviour of the channel in terms of parameters (e.g. Popen†) which are directly dependent upon applied membrane voltage. A distinction should be made between ‘voltage sensitivity’ resulting from intrinsic voltage-gating† phenomena (i.e. applicable to channels possessing integral voltage sensors†) and indirect effects of applied membrane voltage influencing general physical parameters such as electrochemical driving force†.

Criteria for PHARMACOLOGY sections

This section should bring together information concerning pharmacological or endogenous modulators of ion channel molecule activity. Regulatory cascades in cells may simultaneously activate or inhibit many different effector proteins, including ion channels. Analysis of patterns of sensitivity to messengers† and exogenous compounds can help elucidate the molecular signalling pathway in the context of defined cell types.

Field number 43: Blockers: This field should list compounds which reduce or eliminate an ionic current by physical blockade of the conductance† pathway. The field should include notes on specificity, sidedness and/or voltage sensitivity of block, together with effective concentrations and resistance to classes of blockers where appropriate. Where sites of block have been determined by site-directed mutagenesist, these should be cross-referenced to Domain functions, field 29.

Field number 44: Channel modulation: This field should summarize information on effects of important pharmacological or endogenous modulators, including descriptions of extracellular or intracellular processes known to modify channel behaviour. Loci of modulatory sites on the channel protein primary† sequence (as determined by site-directed mutagenesis† procedures) should be cross-referenced to Domain functions, field 29.

Field number 45: Equilibrium dissociation constant: This field should list published values of Kd for agents whose concentration affects the rate of a specified process. See also on-line glossary entry for equilibrium dissociation constant†.

Field number 46: Hill coefficient: This field records calculated Hill coefficients† of ligand†-activated processes. The Hill coefficient (n) generally estimates the minimum number of binding/activating ligands although the actual number could be larger. For example, a Hill coefficient reported as n 3 suggests that complete channel activation requires co-operative binding of at least four ligand molecules (e.g. see ILG CAT cGMP, entry 22). See also Field number 36: Dose–response.

Field number 47: Ligands: This field should include principal high-affinity radio-ligands† which have been used to investigate receptor–channel function and that are commercially available. Note that numbers of ligand†-binding sites cannot be equated to functional receptors because they only indicate the presence of a ligand-binding entity that may not necessarily be linked to an effector† moiety†.

Field number 48: Openers: This field should list compounds (or other factors) which increase the open probability† (Popen) or open time† of the channel in native† tissues.

Field number 49: Receptor/transducer interactions: This field should briefly discuss known links to discrete (i.e. separately encoded) receptor and G protein molecules (see also Resource A – G protein-linked receptors, accessible via the CSN). Types of ‘receptor/transducer/channel’ interactions account for many of the physiological responses of