Zip gating of the KcsA channel studied by targeted molecular dynamics

The gating process of the KcsA protein is simulated using targeted molecular dynamics. Calculations show that the residues at the innermost part of the M2 helices act as precursors of a zipper aperture. A sudden disruption of the narrow part of the gate is observed for a position restraint force constant equal to 0.5 kcal mol−1 Å−2. The gate diameter reaches its maximum of about 5.0 Å by doubling the restraint value. The opening energy corresponds to about 14 kT per Cα atom at 300 K.