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Biophys J, April 1999, p. 1886-1896, Vol. 76, No. 4
*Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England, and #BIOSON Research Institute and Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
Integral membrane proteins containing at least one
transmembrane (TM) 
-helix are believed to account for between 20%
and 30% of most genomes. There are several algorithms that accurately predict the number and position of TM helices within a membrane protein
sequence. However, these methods tend to disagree over the beginning
and end residues of TM helices, posing problems for subsequent modeling
and simulation studies. Molecular dynamics (MD) simulations in an
explicit lipid and water environment are used to help define the TM
helix of the M2 protein from influenza A virus. Based on a comparison
of the results of five different secondary structure prediction
algorithms, three different helix lengths (an 18mer, a 26mer, and a
34mer) were simulated. Each simulation system contained 127 POPC
molecules plus ~3500-4700 waters, giving a total of
~18,000-21,000 atoms. Two simulations, each of 2 ns duration, were
run for the 18mer and 26mer, and five separate simulations were run for
the 34mer, using different starting models generated by restrained in
vacuo MD simulations. The total simulation time amounted to 11 ns.
Analysis of the time-dependent secondary structure of the TM segments
was used to define the regions that adopted a stable -helical
conformation throughout the simulation. This analysis indicates a core
TM region of ~20 residues (from residue 22 to residue 43) that
remained in an -helical conformation. Analysis of atomic density
profiles suggested that the 18mer helix revealed a local perturbation
of the lipid bilayer. Polar side chains on either side of this region
form relatively long-lived H-bonds to lipid headgroups and water molecules.
Biophys J, April 1999, p. 1886-1896, Vol. 76, No. 4
© 1999 by the Biophysical Society 0006-3495/99/04/1886/11 $2.00
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