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Biophys J, June 2002, p. 2934-2942, Vol. 82, No. 6
and
*Theoretical Molecular Biophysics Group, Max-Planck-Institute for
Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany;
Department of Biological Sciences, 2500 University Drive
NW, Calgary, AB T2N 1N4, Canada; and Biophysik,
Forschungsinstitut für Molekulare Pharmakologie, Robert
Rössle Strasse 10, 13125 Berlin, Germany
Multinanosecond molecular dynamics simulations of
gramicidin A embedded in a dimyristoylphosphatidylcholine bilayer show
a remarkable structural stability for both experimentally determined conformations: the head-to-head helical dimer and the double helix. Water permeability was found to be much higher in the double helical conformation, which is explained by lower hydrogen bond-mediated enthalpic barriers at the channel entrance and its larger pore size.
Free-energy perturbation calculations show that the double helical
structure is stabilized by the positive charges at the N termini
introduced by the desformylation, whereas the helical dimer is
destabilized. Together with the recent experimental observation that
desformyl gramicidin conducts water hundredfold better than gramicidin,
this suggests that desformyl gramicidin A predominantly occurs in the
double helical conformation.
Biophys J, June 2002, p. 2934-2942, Vol. 82, No. 6
© 2002 by the Biophysical Society 0006-3495/02/06/2934/09 $2.00
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