The permeation mechanism of organic cations through a CNG mimic channel

Luisa M R Napolitano (1, 2) , Arin Marchesi (3) , Alex Rodriguez (1) , Matteo de March (2) , Silvia Onesti (2) , Alessandro Laio (4, 1) , Vincent Torre (1, 5, 6)

1 SISSA / ISAS - Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies
2 Structural Biology Laboratory [Trieste, Italy]
3 Microscopie à Force Atomique de Protéines Membranaires en Membranes Natives
4 ICTP - Abdus Salam International Centre for Theoretical Physics [Trieste]
5 CNITECH - Cixi Institute of Biomedical Engineering [Zhejiang, P.R. China]
6 CAMS - Chinese Academy of Medical Sciences [Chengdu, China]

Several channels, ranging from TRP receptors to Gap junctions, allow the exchange of small organic solute across cell membrane. However, very little is known about the molecular mechanism of their permeation. Cyclic Nucleotide Gated (CNG) channels, despite their homology with K + channels and in contrast with them, allow the passage of larger methyl-ated and ethylated ammonium ions like dimethylammonium (DMA) and ethylammonium (EA). We combined electrophysiology and molecular dynamics simulations to examine how DMA interacts with the pore and permeates through it. Due to the presence of hydrophobic groups, DMA enters easily in the channel and, unlike the alkali cations, does not need to cross any barrier. We also show that while the crystal structure is consistent with the presence of a single DMA ion at full occupancy, the channel is able to conduct a sizable current of DMA ions only when two ions are present inside the channel. Moreover, the second DMA ion dramatically changes the free energy landscape, destabilizing the crystallographic binding site and lowering by almost 25 kJ/mol the binding affinity between DMA and the channel. Based on the results of the simulation the experimental electron density maps can be re-interpreted with the presence of a second ion at lower occupancy. In this mechanism the flexibility of the channel plays a key role, extending the classical multi-ion permeation paradigm in which conductance is enhanced by the plain interaction between the ions.

Domaines: Biophysique; Biologie structurale [q-bio.BM]

Luisa M R Napolitano, Arin Marchesi, Alex Rodriguez, Matteo de March, Silvia Onesti, et al.. The permeation mechanism of organic cations through a CNG mimic channel. PLoS Computational Biology, 2018, 14 (8), pp.e1006295. ⟨10.1371/journal.pcbi.1006295⟩. ⟨hal-01871260⟩