Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA

The bacterial potassium channel KcsA, which has been crystallized in several conformations, offers an ideal model to investigate activation gating of ion channels. In this study, essential dynamics simulations are applied to obtain insights into the transition pathways and the energy profile of KcsA pore gating. In agreement with previous hypotheses, our simulations reveal a two phasic activation gating process. In the first phase, local structural rearrangements in TM2 are observed leading to an intermediate channel conformation, followed by large structural rearrangements leading to full opening of KcsA. Conformational changes of a highly conserved phenylalanine, F114, at the bundle crossing region are crucial for the transition from a closed to an intermediate state. 3.9 µs umbrella sampling calculations reveal that there are two well-defined energy barriers dividing closed, intermediate, and open channel states. In agreement with mutational studies, the closed state was found to be energetically more favorable compared to the open state. Further, the simulations provide new insights into the dynamical coupling effects of F103 between the activation gate and the selectivity filter. Investigations on individual subunits support cooperativity of subunits during activation gating. Author Summary: Voltage gated ion channels are membrane embedded proteins that initiate electrical signaling upon changes in membrane potential. These channels are involved in biological key processes such as generation and propagation of nerve impulses. Mutations may lead to serious diseases such as cardiac arrhythmia, diabetes or migraines, rendering them important drug targets. The activity of ion channels is controlled by dynamic conformational changes that regulate ion flow through a central pore. This process, which involves opening and closing of the channels, is known as gating. To fully understand or to control ion channel gating, we need to unravel the underlying principles. Crystal structures, especially of K+ channels, have provided excellent insights into the conformation of different channel states. However, the transition states and structural rearrangements are still unknown. Here we use molecular dynamics simulations to simulate the full transition pathway and energy landscape of gating. Our results suggest that channel gating involves local structural changes followed by global conformational changes. The importance of many of the residues identified in our simulations is supported by experimental studies. The ability to accurately simulate the gating transitions of ion channels may be beneficial for a better understanding of ion channel related diseases and drug development.