Role of ions on structure and stability of a synthetic gramicidin ion channel in solution. A molecular dynamics study

被引:1
作者
Morra, G
Koert, U
Knapp, EW
机构
[1] Free Univ Berlin, Inst Chem, Dept Biol Chem & Pharm, D-14195 Berlin, Germany
[2] Univ Marburg, Dept Chem, Marburg, Germany
关键词
D O I
10.1021/jp044191u
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
We performed a molecular dynamics (MD) simulation to the investigate structure and stability of a synthetic gramicidin-like peptide in solution with and without ions. The starting structures of the MD simulations were taken from two recently solved NMR structures of this peptide in isotropic solution, which forms stable monomers or dimers in the presence or absence of ions, respectively. The monomeric structure is channel like and is assumed to be stabilized by the presence of two Cs+ ions bound in the channel, each one close to one channel entrance. In our MD simulations, we observed how the Cs+ ions bind in the channel formed by the monomeric gramicidin-like peptide using implicit solvent and explicit ions with a concentration of 2 M. MD simulations were performed with and without explicit ions but with an implicit solvent model defined by the generalized Born approximation, which was used to mimic the dielectric properties of the solvent and to speed up the computations.
引用
收藏
页码:10441 / 10448
页数:8
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