Paper Citing NAMD - Abstract
Tayefeh, Sascha; Kloss, Thomas; Kreim, Michael; Gebhardt, Manuela; Baumeister, Dirk; Hertel, Brigitte; Richter, Christian; Schwalbe, Harald; Moroni, Anna; Thiel, Gerhard; Kast, Stefan M.
Model Development for the Viral Kcv Potassium Channel
BIOPHYSICAL JOURNAL, 96:485-498, JAN 21 2009
A computational model for the open state of the short viral Kcv potassium channel was created and tested based on homology modeling and extensive molecular-dynamics simulation in a membrane environment. Particular attention was paid to the structure of the highly flexible N-terminal region and to the protonation state of membrane-exposed lysine residues. Data from various experimental sources, NMR spectroscopy, and electrophysiology, as well as results from three-dimensional reference interaction site model integral equation theory were taken into account to select the most reasonable model among possible variants. The final model exhibits spontaneous ion transitions across the complete pore, with and without application of an external field. The nonequilibrium transport events could be induced reproducibly without abnormally large driving potential and without the need to place ions artificially at certain key positions along the transition path. The transport mechanism through the filter region corresponds to the classic view of single-file motion, which in our case is coupled to frequent exchange of ions between the innermost filter position and the cavity.
