Exploring ion permeation energetics in gramicidin A using polarizable charge equilibration force fields.

All-atom molecular dynamics simulations have been applied in the recent past to explore the free energetics underlying ion transport processes in biological ion channels. Roux and co-workers, Kuyucak and co-workers, Busath and co-workers, and others have performed rather elegant and extended time scale molecular dynamics simulations using current state-of-the-art fixed-charge (nonpolarizable) force fields to calculate the potential of mean force defining the equilibrium flux of ions through prototypical channels such as gramicidin A. An inescapable conclusion of such studies has been the gross overestimation of the equilibrium free energy barrier, generally predicted to be from 10 to 20 kcal/mol depending on the force field and simulation protocol used in the calculation; this translates to an underestimation of experimentally measurable single channel conductances by several orders of magnitude. Next-generation polarizable force fields have been suggested as possible alternatives for more quantitative predictions of the underlying free energy surface in such systems. (1) Presently, we consider ion permeation energetics in the gramicidin A channel using a novel polarizable force field. Our results predict a peak barrier height of 6 kcal/mol relative to the channel entrance; this is significantly lower than the uncorrected value of 12 kcal/mol for nonpolarizable force fields such as GROMOS and CHARMM27 which do not account for electronic polarization. These results provide promising initial indications substantiating the long-conjectured importance of polarization effects in describing ion-protein interactions in narrow biological channels.