Paper Citing NAMD - Abstract
Bastug, Turgut; Kuyucak, Serdar
Free energy simulations of single and double ion occupancy in gramicidin A
JOURNAL OF CHEMICAL PHYSICS, 126 Art. No. 105103, MAR 14 2007
Simultaneous occupancy of the two binding sites in gramicidin A by monovalent cations is a well known property of this channel, but the energetic feasibility of this process in molecular dynamics simulations has not been established so far. Here the authors study the energetics of single and double ion occupancy in gramicidin A by constructing the potential of mean force for single and pair of cations. As representatives of small and large ions, they consider both Na+ and K+ ions in the calculations. Binding constants of ions are estimated from the free energy profiles. Comparisons with the experimental results indicate 3-4 kT discrepancy in the binding energies. They also study the coordination of the ions in their respective binding sites and the dynamic behavior of the channel water during the double ion binding process. (c) 2007 American Institute of Physics.
