Density-functional theory study of gramicidin A ion channel geometry and electronic properties.
Understanding the mechanisms underlying ion channel function from the atomic-scale requires accurate ab initio modelling as well as careful experiments. Here, we present a density functional theory (DFT) study of the ion channel gramicidin A (gA), whose inner pore conducts only monovalent cations and whose conductance has been shown to depend on the side chains of the amino acids in the channel. We investigate the ground state geometry and electronic properties of the channel in vacuum, focusing on their dependence on the side chains of the amino acids. We find that the side chains affect the ground state geometry, while the electrostatic potential of the pore is independent of the side chains. This study is also in preparation for a full, linear scaling DFT study of gA in a lipid bilayer with surrounding water. We demonstrate that linear scaling DFT methods can accurately model the system with reasonable computational cost. Linear scaling DFT allows ab initio calculations with 10,000-100,000 atoms and beyond, and will be an important new tool for biomolecular simulations.
National Institute for Materials Science, , 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan.
Milica
M
Todorović
David R
DR
Bowler
Michael J
MJ
Gillan
Tsuyoshi
T
Miyazaki
D055724:Electrophysiological Phenomena; D006096:Gramicidin / Q000737:chemistry*; D007473:Ion Channels / Q000737:chemistry*; D016014:Linear Models; D008956:Models, Chemical; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D055672:Static Electricity
D007473:Ion Channels; D006096:Gramicidin
DFT; electronic structure calculation; gramicidin; ion channel; linear scaling