Abstract
Previous molecular dynamics simulations have shown that explicit inclusion of electronic polarizability significantly influences correlations in a gramicidin-like channel (ref 1). We now separately consider how water and helix polarization modify structure in the single-file regime of the head-to-head β6.3 helix. Further, we investigate how internal energy barriers are influenced by polarization. We contrast midmonomer properties for small and large cations (Na+ and Cs+, respectively) and for four polarizability scenarios: all polar groups polarizable; only water polarizable; only helix groups polarizable; and no polar groups polarizable. To ensure comparability, the group dipole moments in nonpolarizable cases are adjusted to mimic either mean electrostatic interaction energetics or mean group dipole moments of the fully polarizable water-filled channel. With a polarizable helix, ion−carbonyl correlations strengthen and ion−water correlations weaken. With polarizable water, the opposite holds. The consequences of helix dipole fluctuations are quantitatively more significant. In examining coordination near the local energy extrema, we found that ion-specific differences in the energy barrier correlate with differences in translocation-induced changes in both ion−carbonyl and ion−water correlation. In traversing the local maximum, the number of carbonyl groups tightly solvating Cs+ does not change, but for Na+ the number increases by one. The shortest Na+−water distance increases, while the corresponding Cs+−water distance decreases. Polarizability influences barrier heights in much the same way it influences ion−water and water−water correlations. A polarizable helix tends to raise internal translocation barriers, as ion−carbonyl interactions are strengthened relative to ion−water interactions. Moreover, the water chain is disrupted by intercalating carbonyl groups. Polarizable water tends to lower barriers by enhancing ion−water and water−water interactions, which assist the ion in overcoming the barrier. Consequently, partial incorporation of polarizability may introduce larger errors into the simulation than completely neglecting this property.