Ligand-Gated Ion Channels are transmembrane proteins that can exist under different conformations, at least one forming a pore through the membrane connecting the two neighbour compartments. The equilibrium between the various conformations is affected by the binding of ligands on the channels. Phenomenologically, the ligands "open" or "close" the channel.
There are three different superfamilies of extracellularly activated ligand-gated ion channel subunits:
Due to the lack of evolutionary relationship, these three superfamilies are treated separately.
In the LGIC Database you will find the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available. The LGIC Database redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. See the LGIC Database FAQ for more details about the database construction.
The Ligand Gated Ion Channel Database currently contains 554 entries of ligand-activated ion channel subunits.
Construction of the LGIC DatabaseThe LGIC database has been initially developed by Nicolas Le Novère within the team of Jean-Pierre Changeux at the Pasteur Institute, with the help of Catherine Letondal. It was further developed at the EMBL-EBI by Marie-Ange Djite and Antonia Mayer. It is now maintained by the Le Novere Lab group at the Babraham Institute.
SubmittersThe following people submitted sequences, structures or database accession numbers: Howard Baylis, Igor Baskin, Alain Bessis, Thon De Boer, Thomas Boyd, David C. Chiara, Raphael Courjanet, Steve Ennion, Michael Hollmann, Michaela Jansen, Benoît Lacombe, Pierre Paoletti, David Reeves, Wladimir Saudek, Ralf Schoepfer, Pim van Nierop.
Other helpersThe following people helped with advice, corrections, general comments, etc.: Mikael Andersson, Jim Boulter, Robert Choy, Alban de Kerchove D'Exaerde, Anne Devillers-Thiéry, Marco Donizelli, Aymeric Duclert, Sebastien Dutertre, Ronald Lukas, Daniel McGreal, Alexandre Mourot, Richard Olsen, Yoav Paas, Nicolas Rodriguez, Mike White, Hongjie Yang.
Free (in the sense of freedom) programs used to develop the LGIC DatabaseThe static web pages were written with GNU emacs and Kwrite.
The alignments were performed with the program ClustalW.
The phylogenetic studies were performed with Phylip.
The structures are displayed with JmolApplet.
The different file formats of the database are written with Perl scripts, using bioperl.