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

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.

Modulation of Pore Opening of Eukaryotic Sodium Channels by π-Helices in S6

“…In our recent studies of bacterial Nav channels NavMs and NavAb, we found that introducing a short π-helical stretch in S6 of the channel resulted in the rotation of the S6 C-terminus and in increased pore hydration, allowing sodium ion permeation. This mechanism is consistent with that described in some TRP channels. , The presence of π-helices in the pore lining helices of different channels with similar architecture is considered to be conserved and to play an important role in drug binding. , Inspired by these observations, we hypothesized that eukaryotic Nav channel opening might involve a transition to the π-helix in one or more of the DI/DII/DIV S6 helices. Additionally, given the heterogeneity of eukaryotic Nav channels and the stabilization of different secondary structures in their S6 helices, we hypothesized that an α-/π-helix conformation in different S6 helices might give rise to different subconductance levels, resulting in different open states.…”

Mechanisms of dihydropyridine agonists and antagonists in view of cryo-EM structures of calcium and sodium channels

“…3-D alignment of available structures of P-loop channels suggests that calcium and sodium channels have similar folding of the pore domain, which differs from that in potassium, TRP, and glutamate-gated channels ( Tikhonov and Zhorov, 2021 , 2022 ). Therefore, crystal and cryo-EM structures of sodium and calcium channels can be used as templates to model channel Cav1.1 in different functional states.…”

“…Recent structural studies revealed an interesting peculiarity of S6 segments in sodium, calcium, and TRP channels. In some structures, these segments are not entirely α-helical but contain a π-helical turn at a position where the glycine gating hinge is located in potassium channels ( Tikhonov and Zhorov, 2017 , 2021 , 2022 ). Since a π-helix has an extra residue per turn as compared with an α-helix, the π-helical turn is seen as a bulge in the helix.…”

“…Although the exact role of π-helical turns is still unclear, available data suggest that transitions between the α and π forms of S6 may be important for gating ( Zubcevic and Lee, 2019 ). Another interesting observation is that such transitions can be induced by ligand binding in the pore (for review, see Tikhonov and Zhorov, 2021 ). Importantly, the π-helical bulges appear exactly at the DHP binding region.…”

Modulation of Pore Opening of Eukaryotic Sodium Channels by π-helices in S6

“…This mechanism is consistent with that described in some TRP channels (26,27). The presence of π-helices in the pore lining helices of different channels with similar architecture (28) is considered to be conserved and to play an important role in drug binding (20,29). Inspired by these observations, we hypothesized that eukaryotic Nav channel opening might involve a transition to π-helix in one or more of the DI/DII/DIV S6 helices.…”