The potassium ion channel: Comparison of linear scaling semiempirical and molecular mechanics representations of the electrostatic potential

The molecular electrostatic potential inside the potassium channel protein from Streptomyces lividans has been investigated using linear scaling semiempirical quantum chemical method, for a variety of geometries, with and without solvating water molecules. The results are compared with those given by a number of popular molecular mechanics force-fields. The difference between the quantum and molecular mechanics electrostatic potentials due to the protein exceeds 30 kcal/mol within the narrow selectivity filter of the channel and is attributed to the neglect of electronic effects, e.g., polarization, in the molecular mechanics force-fields. In particular, mutual electronic interactions between four threonine residues in the selectivity filter are found to have a large effect on the electrostatic potential. Calculations in the presence of water molecules suggest that molecular mechanics methods also overestimate the stabilization of the cation inside the ion channel. The molecular electrostatic potentials computed by molecular mechanics force-fields expressed relative to bulk water, however, reveal a much smaller error.