A Conquest study of the gramicidinA ion channel has been published in J. Roy. Soc.:Interface . The study uses exact diagonalisation to assess the effect of side-chains on the potential in the channel, and tests the range required for accurate linear scaling calculations.
We find that the side chains do not change the channel potential, as shown in the figure below, which compares the electrostatic potential for the complete ion channel (1MAG structure from PDB) and an artificial channel where all side chain amino acids have been replaced with alanine.
A preprint is available on arXiv.
DFT electrostatic potential [eV]: (a)-(c) are cross sections perpendicular to the channel axis (z) at 9.6 A from the centre of the channel. (a) 1MAG geometry; (b) alanine channel;(c) 1MAG and alanine channel potential difference. Note the different scale in (c). (d) and (e) are also potential difference between 1MAG and alanine channel, but cross sections along the channel axis, xz and yz planes, respectively.
 J. Roy. Soc.:Interface 10, 20130547 (2013) DOI:10.1098/rsif.2013.0547
This entry was posted on 2013/9/4.