Computational Analysis of the Crystal and Cryo-EM Structures of P-Loop Channels with Drugs.

Denis B Tikhonov,Boris S Zhorov

doi:10.3390/ijms22158143

Abstract

The superfamily of P-loop channels includes various potassium channels, voltage-gated sodium and calcium channels, transient receptor potential channels, and ionotropic glutamate receptors. Despite huge structural and functional diversity of the channels, their pore-forming domain has a conserved folding. In the past two decades, scores of atomic-scale structures of P-loop channels with medically important drugs in the inner pore have been published. High structural diversity of these complexes complicates the comparative analysis of these structures. Here we 3D-aligned structures of drug-bound P-loop channels, compared their geometric characteristics, and analyzed the energetics of ligand-channel interactions. In the superimposed structures drugs occupy most of the sterically available space in the inner pore and subunit/repeat interfaces. Cationic groups of some drugs occupy vacant binding sites of permeant ions in the inner pore and selectivity-filter region. Various electroneutral drugs, lipids, and detergent molecules are seen in the interfaces between subunits/repeats. In many structures the drugs strongly interact with lipid and detergent molecules, but physiological relevance of such interactions is unclear. Some eukaryotic sodium and calcium channels have state-dependent or drug-induced π-bulges in the inner helices, which would be difficult to predict. The drug-induced π-bulges may represent a novel mechanism of gating modulation.

Highlights

Since the breakthrough structure of the KcsA potassium channel was published in 1998 [1], progress in the X-ray crystallography and development of high-resolution cryo-electron microscopy greatly facilitated structural studies of ion channels in different functional states and in complexes with different ligands
The pore module of P-loop channels has a conserved architecture of the transmembrane region formed by eight transmembrane helices connected by four membrane reentrant P-loops, which harbor the selectivity-filter. The latter divides the ion permeation pathway into the outer pore, which is lined by residues in the C-part of P-loops, and the inner pore, which is lined by the inner helices
The above comparison of published structures of P-loop channels shows greatly diverse patterns of ligand-sensing residues and the pore-targeting drugs, which are scattered in the inner pore from the activation gate to the selectivity-filter and penetrate into fenestrations

Summary

Introduction

Since the breakthrough structure of the KcsA potassium channel was published in 1998 [1], progress in the X-ray crystallography and development of high-resolution cryo-electron microscopy greatly facilitated structural studies of ion channels in different functional states and in complexes with different ligands. This very diverse superfamily includes potassium, sodium, and calcium channels, TRP channels, and ionotropic glutamate receptors [3]. The alpha subunit of eukaryotic sodium and calcium channels folds from a single polypeptide chain of four homologous repeat domains. The pore module of P-loop channels has a conserved architecture of the transmembrane region formed by eight transmembrane helices connected by four membrane reentrant P-loops, which harbor the selectivity-filter. The latter divides the ion permeation pathway into the outer pore, which is lined by residues in the C-part of P-loops, and the inner pore, which is lined by the inner helices. Residues at the C-terminal part of the inner helices contribute to the activation gate, which usually opens up in response to membrane depolarization or hyperpolarization (voltage-gated channels) or binding of various ligands (ligand-gated channels)

Methods

Results

Conclusion