Activation Gating of KcsA: New Insights into Cooperativity and Energy Landscape from Essential Dynamics Simulations

Abstract

Recent crystal structures of the bacterial potassium channel KcsA have shed light on the intermediate and open conformation of the channel (Cuello et al. 2010). Although crystal structures provide excellent insights into different conformations of proteins, they feature only snapshots of dynamical proteins. Therefore, the transition steps and the mechanisms of activation gating are still unknown. In order to elucidate the activation gating dynamics KcsA, we applied essential dynamics (ED) simulations. The successful simulation of activation gating allowed us to calculate the underlying energy landscape by umbrella sampling. The energy profile revealed three energy wells that are separated by two barriers. We identified structural rearrangements of F114 which correspond the first energy barrier. The change in rotameric state of F114 is crucial for initial pore opening. Regarding the second energy barrier, we observed large conformational changes of the TM2 helices which represent the main final activation gate opening. Cooperativity of activation gating was studied by applying our ED protocol to different number of subunits (SUs). Our simulations showed that the movement of a single SU is not sufficient to open the activation gate. But by moving three SUs by ED simulations, the activation gate opened to the same extent as in the four SUs ED simulation protocol. These finding is in line with fluorescence detection studies, which showed that the SUs act cooperatively during gating (Blunck et al. 2008).