Do selectivity filter carbonyls in K+ channels flip away from the pore? Two-dimensional infrared spectroscopy study

Abstract

Highlights • This work makes a critical contribution towards understanding the structure of K+ channels. • We use computational two-dimensional infrared (2D IR) spectroscopy to design an experiment that would test the existence of a selectivity filter configuration in which one of the Val carbonyls flips away from the pore. • This configuration was hypothesized to be relevant for C-type inactivation of K+ channels. • Existing structural biology tools could not provide a decisive evidence for Val flipped configuration. • Our paper shows that 2D IR spectroscopy is capable of detecting such a configuration.

Abstract Molecular dynamics simulations revealed that the carbonyls of the Val residue in the conserved selectivity filter sequence TVGTG of potassium ion channels can flip away from the pore to form hydrogen bonds with the network of water molecules residing behind the selectivity filter. Such a configuration has been proposed to be relevant for C-type inactivation. Experimentally, X-ray crystallography of the KcsA channel admits the possibility that the Val carbonyls can flip, but it cannot decisively confirm the existence of such a configuration. In this study, we combined molecular dynamics simulations and line shape theory to design two-dimensional infrared spectroscopy experiments that can corroborate the existence of the selectivity filter configuration with flipped Val carbonyls. This ability to distinguish between flipped and unflipped carbonyls is based on the varying strength of the electric field inside and outside the pore, which is directly linked to carbonyl stretching frequencies that can be resolved using infrared spectroscopy.

Graphical abstract available at: https://doi.org/10.1016/j.yjsbx.2024.100108