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Biophys J, January 1999, p. 40-49, Vol. 76, No. 1
*BIOSON Research Institute and Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands, and #Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England
Alamethicin is an 
-helical channel-forming peptide,
which inserts into lipid bilayers in a voltage-dependent, asymmetrical fashion. Nanosecond molecular dynamics simulations have been used to
compare alamethicin conformation and dynamics in three different environments: 1) in water; 2) in methanol; and 3) inserted into a lipid
(palmitoyl-oleoyl-phosphatidylcholine) bilayer to form a transmembrane
helix. In the bilayer and in methanol, there was little change (C
RMSD 
0.2 nm over 2 ns and 1 ns) from the initial helical
conformation of the peptide. In water there were substantial changes
(C RMSD 0.4 nm over 1 ns), especially in the C-terminal segment of the peptide, which lost its -helical conformation. In the
bilayer and in methanol, the alamethicin molecule underwent hinge-bending motion about its central Gly-X-X-Pro sequence motif. Analysis of H-bonding interactions revealed that the polar C-terminal side chains of alamethicin provided an "anchor" to the
bilayer/water interface via formation of multiple H-bonds that
persisted throughout the simulation. This explains why the preferred
mode of helix insertion into the bilayer is N-terminal, which is
believed to underlie the asymmetry of voltage activation of alamethicin channels.
Biophys J, January 1999, p. 40-49, Vol. 76, No. 1
© 1999 by the Biophysical Society 0006-3495/99/01/40/10 $2.00
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