Non-bonded interactions NTP experiences revealed by MD.

The plots compare the energetic contribution of non-bonded interactions (electrostatic + vdW) along the main channel and secondary channel for: (a) NTP and its environment (the Pol II complex and solvent); (b) NTP and the Pol II complex; and (c) NTP and solvent. In these calculations, the Pol II complex includes the protein and nucleotides. The solvent contains water molecules together with the counter-ions. The results shown in (a) are the total contributions from the Pol II complex (shown in (b)) and the solvent (shown in (c)) (see Methods).