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

Tobias Linder,Bert L De Groot,Anna Stary-Weinzinger,Emad Tajkhorshid

doi:10.1371/journal.pcbi.1003058

Tobias Linder, Bert L De Groot + Show 2 more

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https://doi.org/10.1371/journal.pcbi.1003058

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Abstract

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.

Highlights

K+ channels play a crucial role in a wide variety of physiological and pathophysiological processes including action potential modeling [1], cancer cell proliferation [2], and metabolic pathways mediation [3]
Local structural rearrangements correspond to energy barrier 1 By analyzing the dihedral angles of all side chains, a single residue in the helix bundle crossing region was identified (F114) whose conformational changes correspond to the first energy barrier (Figure 4B)
The results presented here show that the essential dynamics (ED) simulation approach successfully sampled transition pathways between closed and open states of an ion channel on the nanosecond time scale and allowed investigations on activation gating

Summary

Introduction

K+ channels play a crucial role in a wide variety of physiological and pathophysiological processes including action potential modeling [1], cancer cell proliferation [2], and metabolic pathways mediation [3]. While the extracellular facing SF tunes the selection of different ions and modulates inactivation, the main conformational changes regulating ion flow, are found at the TM2 helices These motions, referred to as activation gating, are thought to involve an iris-like motion of the TM2 helices that constrict the permeation pathway at the helix bundle crossing region [7,8,9,10]. Starting in 1998, several different pore domain structures of KcsA in its closed state [6,11] and more recently in intermediate and open states have been solved [12] These crystal structures provide excellent insights into different conformations of proteins; they feature only snapshots of dynamical proteins [13]. The KcsA crystal structures (pdb identifier: 1k4c, closed; 3fb, intermediate; 3f7v, open) were adjusted at the N- and Ctermini so that all states started from residue 29 and ended at

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