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bioRxiv · 10.1101/2024.04.19.590249

Effect Of Two Activators On The Gating Of A K2P Channel

Mendez-Otalvaro, E.·Kopec, W.·de Groot, B. L.
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Abstract

TREK1, a two-pore-domain (2P) mammalian potassium (K+) channel, regulates the resting potential across cell membranes, presenting a promising therapeutic target for neuropathy treatment. The gating of this channel converges in the conformation of the narrowest part of the pore: the selectivity filter (SF). Various hypotheses explain TREK1 gating modulation, including the dynamics of loops connecting the SF with transmembrane helices and the stability of hydrogen bond (HB) networks adjacent to the SF. Recently, two small molecules (Q6F and Q5F) were reported as activators to affect TREK1 by increasing its open probability in single-channel current measurements. Here, using molecular dynamics (MD) simulations, we investigate the effect of these ligands on the previously proposed modulation mechanisms of TREK1 gating compared to the apo channel. Our findings reveal that loop dynamics at the upper region of the SF exhibit only a weak correlation with permeation/ non-permeation events, whereas the HB network behind the SF appears more correlated. These non-permeation events arise from both distinct mechanisms: A C-type inactivation (resulting from dilation at the top of the SF), which has been described previously; and a carbonyl flipping in a SF binding site. We find that, besides the prevention of C-type inactivation in the channel, the ligands increase the probability of permeation by modulating the dynamics of the carbonyl flipping, influenced by a threonine residue at the bottom of the SF. These results offer insights for rational ligand design to optimize the gating modulation of TREK1 and related K+ channels.

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Mendez-Otalvaro, E., Kopec, W., de Groot, B. L.. 2024-04-24. Effect Of Two Activators On The Gating Of A K2P Channel. https://doi.org/10.1101/2024.04.19.590249

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