Abstract
We simulate the transmission of K+ ions through the KcsA potassium ion channel filter region at physiological temperatures, employing classical molecular dynamics (MD) at the atomic scale together with a quantum mechanical version of MD simulation (QMD), treating single ions as quantum wave packets. We provide a direct comparison between both concepts, embedding the simulations into identical force fields and thermal fluctuations. The quantum simulations permit the estimation of coherence times and wave packet dispersions of a K+ ion over a range of 0.5 nm (a range that covers almost 50% of the filter domains longitudinal extension). We find that this observed extension of particle delocalization changes the mean orientation of the coordinating carbonyl oxygen atoms significantly, transiently suppressing their ‘caging action’ responsible for selective ion coordination. Compared to classical MD simulations, this particular quantum effect allows the K+ ions to ‘escape’ more easily from temporary binding sites provided by the surrounding filter atoms. To further elucidate the role of this observation for ion conduction rates, we compare the temporal pattern of single conduction events between classical MD and quantum QMD simulations at a femto-sec time scale. A finding from both approaches is that ion permeation follows a very irregular time pattern, involving flushes of permeation interrupted by non-conductive time intervals. However, as compared with classical behavior, the QMD simulation shortens non-conductive time by more than a half. As a consequence, and given the same force-fields, the QMD-simulated ion current appears to be considerably stronger as compared with the classical current. To bring this result in line with experimentally observed ion currents and the predictions based on Nernst–Planck theories, the conclusion is that a transient short time quantum behavior of permeating ions can successfully compromise high conduction rates with ion selectivity in the filter of channel proteins.
Highlights
Electrical signals generated in nerve cells are generated by membrane proteins that catalyze a selective electro-diffusion of ions across plasma membranes
Due to the slow dispersion of the initially well-localized wave packet, the enclosing present to compare classical a quantum mechanical interpretation of ion motion, the carbonylintention oxygen atoms tend toa be pushedwith some distance aside, and this leads to a higher probability for classical environment hadthis to site be designed in a way thatInsubsequently allowed the extension to to a the particle to escape from within a given time [7]
The reason can be found within extended halting scale, conduction appeared to follow a quite different temporal characteristic than one would times that are largely suppressed in the macroscopic approximation of a continuous ion flow
Summary
Electrical signals generated in nerve cells are generated by membrane proteins that catalyze a selective electro-diffusion of ions across plasma membranes. The proteins are embedded in the lipid bilayer of membranes and provide currents at the pico-ampere level, combining fast conduction with a high selectivity for particular ions. In voltage-gated potassium channels, this selective control of ion conduction is organized by a specific arrangement of amino-acids within a narrow ‘selectivity filter’. Domain of the protein [1,2]. The most frequently studied filter model is based on the bacterial-derived. KcsA channel motif (KcsA, potassium crystallographically sited activation channel) where the filter. Sci. 2019, 9, x FOR PEER REVIEW for their carbonyl groups oriented towards the pore axis to change their vibrational motion.
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