抄録
Crystal structure of channel proteins opened a new era that channel function can be related to structure in atomic resolution. To build up a dynamic (functioning) picture of ion channels from atomic (static) coordinates, several methods have been applied: Conformational changes upon gating were detected by spectroscopic methods; ion distributions in the selectivity filter were resolved by crystallography. Among them availability of atomic coordinates for the pore gave a chance to simulate permeation process using molecular dynamics method. These calculations reached to a time range of nanosecond, which is far from the average time of ion permeation through the pore (microsecond). To fill the gap, several methods have been proposed. We reviewed these methods and presented our approaches on gating and permeation processes. For ion permeation, coupling between permeation and gating was made used to isolate elementary steps of ion permeation. In HERG potassium channel the fast inactivation was sensitive to permeating ion-species and concentrations. Thus, occupancy probability of ions in the selectivity filter was estimated from the inactivation kinetics. Similar method was applied to KcsA potassium channel, in which fast gating is also sensitive to concentration of ion species. Based on these observations, a permeation model was constructed. [Jpn J Physiol 54 Suppl:S10 (2004)]
