Ion channels are of vital importance in many biological processes, particularly in the nervous system. However, there is much that is unknown about both their structure and their mechanism of operation. In this group we use computer simulation to try to tackle these questions. The figure above is a semi-schematic representation of the Nicotinic Acetylcholine Receptor (nAChR), a cation-selective ion channel found in the nerve-muscle synapse and in neurons. This channel, which is the present focus of my work, is the best-understood member of its family, the ligand-gated ion channels. The nAChR proper consists of 5 similar protein molecules, labelled alpha (2 copies), beta, gamma and delta in the figure. It is shown as it is believed to exist in vivo: inserted into the cell membrane, glycosylated on the extracellular side and associated with a 43 kd peripheral membrane protein that anchors it to the cell's cytoskeleton.
I still haven't got round to this.
mostly text
A VRML version of our model of the M2 helix bundle of the nAChR.
The water molecules are grey v-shapes, and the protein is space-filling,
colour-coded red for negatively charged residues,
blue for positively charged, yellow for
polar and green otherwise. There is a (purple) Sodium ion in the pore.
I find it best to press ^K so you get the 'walk viewer' thing, then
you can fly round the model or go plunging into the pore, etc.
It seems to take a long time to load (though the file is only 76k;
gzipped wrl).
The state of my work in late 1996, as reported in a conference poster. Deals with the physical properties of water and the energetics of sodium ions in a model of the M2 helix bundle.
A more up-to-date report on recent work I have been doing
to use simulation to measure the diffusion coefficients of
ions in models of the nicotinic receptor and other channels, including
the fungal peptide alamethicin and an artificial Leucine-Serine peptide
(They turn out to be quite substantially reduced). Also contains
a bit about the effective dielectric constant
of pore water (also reduced).
possible future developments in our studies of the nAChR and related channels.
you may well ask...