Cooperative nature of gating transitions in K ⁺ channels as seen from dynamic importance sampling calcualations

The growing dataset of K ⁺ channel x-ray structures provides an excellent opportunity to begin a detailed molecu-lar understanding of voltage-dependent gating. These structures, while differing in sequence, represent either a stable open or closed state. However, an understanding of the molecular details of gating will require models for the transitions and experimentally testable predictions for the gating transition. To explore these ideas, we apply dynamic importance sampling to a set of homol-ogy models for the molecular confor-mations of K ⁺ channels for four differ-ent sets of sequences and eight different states. In our results, we highlight the importance of particular residues upstream from the Pro-Val-Pro (PVP) region to the gating transition. This supports growing evidence that the PVP region is important for influencing the flexibility of the S6 helix and thus the opening of the gating domain. The results further suggest how gating on the molecular level depends on intra-subunit motions to influence the coop-erative behavior of all four subunits of the K ⁺ channel. We hypothesize that the gating process occurs in steps: first sidechain movement, then inter-S5-S6 subunit motions, and lastly the large-scale domain rearrangements.