The permeation mechanism of organic cations through a CNG mimic channel

• Published in: PLoS computational biology 2018-08, Vol.14 (8), p.e1006295-e1006295
• Main Authors: Napolitano, Luisa M R, Marchesi, Arin, Rodriguez, Alex, De March, Matteo, Onesti, Silvia, Laio, Alessandro, Torre, Vincent
• Format: Article
• Language: English
• Subjects: Ammonium; Animals; Bias; Binding sites; Biochemistry, Molecular Biology; Biology; Biology and Life Sciences; Biophysical Phenomena; Biophysics; Cations; Cations - metabolism; Cell membranes; Channels; Collaboration; Computer Simulation; Conductance; Crystal structure; Crystallography; Cyclic Nucleotide-Gated Cation Channels - metabolism; Cyclic Nucleotide-Gated Cation Channels - physiology; Dimethylamines - metabolism; Electron density; Electrophysiology; Free energy; Gap junctions; Gap Junctions - metabolism; Homology; Hydrophobicity; Ion channels; Ions; Laboratories; Life Sciences; Medicine and Health Sciences; Membrane Potentials - physiology; Methods; Molecular dynamics; Molecular Dynamics Simulation; Nucleotides; Occupancy; Oocytes - physiology; Organic Cation Transport Proteins - physiology; Penetration; Photoreceptors; Physical Sciences; Physiological aspects; Physiological research; Quaternary Ammonium Compounds - metabolism; Receptors; Resistance; Signal transduction; Sodium - metabolism; Structural Biology; Xenopus laevis
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1006295

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 methylated 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.