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Biophys J, January 2001, p. 331-346, Vol. 80, No. 1
and
*Laboratory of Molecular Biophysics, Department of Biochemistry,
University of Oxford, The Rex Richards Building, South Parks
Road, Oxford OX1 3QU, United Kingdom; Dept. of
Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
Understanding the binding and insertion of peptides in
lipid bilayers is a prerequisite for understanding phenomena such as antimicrobial activity and membrane-protein folding. We describe molecular dynamics simulations of the antimicrobial peptide alamethicin in lipid/water and octane/water environments, taking into account an
external electric field to mimic the membrane potential. At cis-positive potentials, alamethicin does not insert into a
phospholipid bilayer in 10 ns of simulation, due to the slow dynamics
of the peptide and lipids. However, in octane N-terminal insertion
occurs at field strengths from 0.33 V/nm and higher, in simulations of up to 100 ns duration. Insertion of alamethicin occurs in two steps,
corresponding to desolvation of the Gln7 side chain, and the backbone
of Aib10 and Gly11. The proline induced helix kink angle does not
change significantly during insertion. Polyalanine and alamethicin form
stable helices both when inserted in octane and at the water/octane
interface, where they partition in the same location. In water, both
polyalanine and alamethicin partially unfold in multiple simulations.
We present a detailed analysis of the insertion of alamethicin into the
octane slab and the influence of the external field on the peptide
structure. Our findings give new insight into the mechanism of channel
formation by alamethicin and the structure and dynamics of
membrane-associated helices.
Biophys J, January 2001, p. 331-346, Vol. 80, No. 1
© 2001 by the Biophysical Society 0006-3495/01/01/331/16 $2.00
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