End-point targeted molecular dynamics: large-scale conformational changes in potassium channels.

Large-scale conformational changes in proteins that happen often on biological time scales may be relatively rare events on the molecular dynamics time scale. We have implemented an approach to targeted molecular dynamics called end-point targeted molecular dynamics that transforms proteins between two specified conformational states through the use of nonharmonic "soft" restraints. A key feature of the method is that the protein is free to discover its own conformational pathway through the plethora of possible intermediate states. The method is applied to the Shaker K(v)1.2 potassium channel in implicit solvent. The rate of cycling between the open and closed states was varied to explore how slow the cycling rate needed to be to ensure that microscopic reversibility along the transition pathways was well approximated. Results specific to the K(+) channel include: 1), a variation in backbone torsion angles of residues near the Pro-Val-Pro motif in the inner helix during both opening and closing; 2), the identification of possible occlusion sites in the closed channel located among Pro-Val-Pro residues and downstream; 3), a difference in the opening and closing pathways of the channel; and 4), evidence of a transient intermediate structural substate. The results also show that likely intermediate conformations during the opening-closing process can be generated in computationally tractable simulation times.