Intersegment contacts determine geometry of the open and closed states in P-loop channels

Despite impressive progress in experimental studies of ion channels, determinants of their state-dependent geometry are not completely understood. Previous studies of P-loop channels suggested that the gating mechanism involves coupled movement of the S4-S5 cuff and S6 bundle and emphasized importance of specific intersegment contacts in stabilizing different states. However, it is unclear whether or not such contacts are sufficient to computationally reproduce gating rearrangements. Here we analyzed X-ray and cryo-EM structures of several channels in different functional states and selected structures with the wide cuff (open-state Kv1.2) and narrow cuff (closed-state MlotiK1) for detailed analysis. We revealed three categories of inter-residue contacts within the pore domain: (i) state-dependent and state-independent contacts between helices S4-S5 and S5, which provide integrity and state-dependent dimensions of the S4-S5 cuff; (ii) state-independent contacts between helices S4-S5 and S6 that enable their coupled movement during gating and (iii) state-dependent contacts between S6s that stabilize the open and/or closed activation gate. We imposed these contacts to transform the channels from the open to closed state and vice versa using Monte Carlo energy minimizations. In all cases, the target structures were reached with a good precision. Thus, a limited set of inter-residue contacts can be used to predict computationally state-dependent geometry of the pore domain in P-loop channels. Effects of various engineered and naturally occurring mutations (channelopathies) on the channel gating can be rationalized in view of the contacts.Communicated by Ramaswamy H. Sarma.