Mo. Ortells, PREDICTION OF THE SECONDARY STRUCTURE OF THE NICOTINIC ACETYLCHOLINE-RECEPTOR NONTRANSMEMBRANE REGIONS, Proteins, 29(3), 1997, pp. 391-398
A consensus prediction for the secondary structure of the muscle nicot
inic acetylcholine receptor (alpha, beta, gamma, and delta subunits) e
xtracellular regions is presented, This protein is a member of the lig
and-gated ion channel superfamily, which also encompasses the 5HT(3),
GABA(A), and glycine receptors, The strategy used here is based on the
application of six different prediction methods to an alignment of 11
8 sequences of this superfamily, A consensus prediction was finally pr
oduced for each of the four different subunits of the muscle nicotinic
receptor nonmembrane regions, The predicted percentages, with respect
to the total receptor length, and averaged for the four subunits are
as follows: alpha-helix 29.7%, beta-sheet 24.9%, and turn+coil 21.7%,
When adding to these values the estimations of the secondary structure
reported for the transmembrane region only, the results are in agreem
ent with those obtained experimentally by Yager et al.(1) and Methot e
t al.(2) The deviations with respect to these experimental estimations
are a-helix +2.8%, beta-sheet -4/-5% and turn+coil +3/+2%, respective
ly. Considering the predictions made for individual subunits, the best
approximation was obtained for the a subunit, with deviations of -0.2
% for alpha-helix, -2.5/-1.5% for beta-sheet, and +0.9/+1.9% for turncoil. The prediction was used to infer the residues involved in formin
g three helices that presumably flank the ligand-binding pocket and to
propose mechanism for transferring-the information of the ligand bind
ing to the ion channel. (C) 1997 Wiley-Liss, Inc.