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Biophysical Journal 74: 3-10 (1998)
© 1998 the Biophysical Society
Biophys J, January 1998, p. 3-10, Vol. 74, No. 1
*Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, and #Thomas J. Watson Research Center, International Business Machines Corporation, Yorktown Heights, New York 10598 USA
A molecular dynamics simulation has been performed on a
synthetic membrane-spanning ion channel, consisting of four 
-helical peptides, each of which is composed of the amino acids leucine (L) and
serine (S), with the sequence
Ac-(LSLLLSL)3-CONH2. This four-helix bundle has
been shown experimentally to act as a proton-conducting channel in a
membrane environment. In the present simulation, the channel was
initially assembled as a parallel bundle in the octane portion of a
phase-separated water/octane system, which provided a membrane-mimetic
environment. An explicit reversible multiple-time-step integrator was
used to generate a dynamical trajectory, a few nanoseconds in duration
for this composite system on a parallel computer, under ambient
conditions. After more than 1 ns, the four helices were found to adopt
an associated dimer state with twofold symmetry, which evolved into a
coiled-coil tetrameric structure with a left-handed twist. In the
coiled-coil state, the polar serine side chains interact to form a
layered structure with the core of the bundle filled with
H2O. The dipoles of these H2O molecules tended
to align opposite the net dipole of the peptide bundle. The calculated
dipole relaxation function of the pore H2O molecules
exhibits two reorientation times. One is ~3.2 ps, and the other is
~100 times longer. The diffusion coefficient of the pore
H2O is about one-third of the bulk H2O value.
The total dipole moment and the inertia tensor of the peptide bundle
have been calculated and reveal slow (300 ps) collective oscillatory
motions. Our results, which are based on a simple united atom
force-field model, suggest that the function of this synthetic ion
channel is likely inextricably coupled to its dynamical behavior.
Biophys J, January 1998, p. 3-10, Vol. 74, No. 1
© 1998 by the Biophysical Society 0006-3495/98/01/03/08 $2.00
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