Exploring K v 1.2 Channel Inactivation Through MD Simulations and Network Analysis.

Flavio Costa,Carlo Guardiani,Alberto Giacomello

doi:10.3389/fmolb.2021.784276

Flavio Costa, Carlo Guardiani + Show 1 more

Open Access

https://doi.org/10.3389/fmolb.2021.784276

Copy DOI

Abstract

The KCNA2 gene encodes the K v 1.2 channel, a mammalian Shaker-like voltage-gated K+ channel, whose defections are linked to neuronal deficiency and childhood epilepsy. Despite the important role in the kinetic behavior of the channel, the inactivation remained hereby elusive. Here, we studied the K v 1.2 inactivation via a combined simulation/network theoretical approach that revealed two distinct pathways coupling the Voltage Sensor Domain and the Pore Domain to the Selectivity Filter. Additionally, we mutated some residues implicated in these paths and we explained microscopically their function in the inactivation mechanism by computing a contact map. Interestingly, some pathological residues shown to impair the inactivation lay on the paths. In summary, the presented results suggest two pathways as the possible molecular basis of the inactivation mechanism in the K v 1.2 channel. These pathways are consistent with earlier mutational studies and known mutations involved in neuronal channelopathies.

Highlights

The KCNA2 gene encodes the Kv1.2 channel, a mammalian voltage-gated K+ channel featuring up to 80% homology with the Drosophila Shaker channel (Suárez-Delgado et al, 2020)
In addition to Voltage Sensor Domain (VSD)-Selectivity Filter (SF) couplings, we studied in detail the pathways connecting the Pore Domain (PD) to the side-chain re-orientation of Y377 that was chosen to be the key residue of the sink region on the SF for the network analysis
Using the network-theoretical approach, we identified two different families of pathways for the motion propagation (Figure 2) joining the VSD and SF and the PD and the SF, respectively

Summary

Introduction

The KCNA2 gene encodes the Kv1.2 channel, a mammalian voltage-gated K+ channel featuring up to 80% homology with the Drosophila Shaker channel (Suárez-Delgado et al, 2020). Its defections/malfunction are linked to neuronal deficiency inducing encephalopathies, ataxia, cerebellar atrophy (Morrison-Levy et al, 2020), and especially childhood epilepsy (Masnada et al, 2017). This channel was studied using the structure solved by MacKinnon and colleagues of a modified rat Kv1.2 channel where the voltage sensor paddle, encompassing the S3 and S4 helices, was replaced by the voltage sensor paddle from the rat Kv2.1 channel, the so-called “paddle-chimera channel” (Long et al, 2007). There are three functional domains: the T1 domain at the aminoterminus, the Voltage Sensor Domain (VSD) that encompasses helices S1 to helix L45 and is sensitive to the membrane potential variation triggering the channel to open, and the Pore Domain (PD) delimited by the S5 and S6 alpha helices with the P-Loop and the Selectivity Filter (SF) (Figure 1A)

Methods

Results

Conclusion