Quantum Interference and Selectivity through Biological Ion Channels

Mimicking classical noise in ion channels by quantum decoherence

The mechanism of selectivity in ion channels is still an open question in biology. Recent studies suggest that the selectivity filter may exhibit quantum coherence, which could help explain how ions are selected and conducted. However, environmental noise causes decoherence and loss of quantum effects. It is hoped that the effect of classical noise on ion channels can be modeled using the framework provided by quantum decoherence theory. In this paper, the behavior of the ion channel system was simulated using two models: the Spin-Boson model and the stochastic Hamiltonian model under classical noise. Additionally, using a different approach, the system's evolution was modeled as a two-level Spin-Boson model with tunneling, interacting with a bath of harmonic oscillators, based on decoherence theory. We investigated under what conditions the decoherence model approaches and deviates from the noise model. Specifically, we examined Gaussian noise and Ornstein-Uhlenbeck noise in our model. Gaussian noise shows a very good agreement with the decoherence model. By examining the results, it was found that the Spin-Boson model at a high hopping rate of potassium ions can simulate the behavior of the system in the classical noise approach for Gaussian noise.

The significance of bioelectricity on all levels of organization of an organism. Part 1: From the subcellular level to cells

Bioelectricity plays an essential role in the structural and functional organization of biological organisms. In this first article of our three-part series, we summarize the importance of bioelectricity for the basic structural level of biological organization, i.e. from the subcellular level (charges, ion channels, molecules and cell organelles) to cells.

Quantum coherence on selectivity and transport of ion channels

Recently, it has been suggested that ion channel selectivity filter may exhibit quantum coherence, which may be appropriate to explain ion selection and conduction processes. Potassium channels play a vital role in many physiological processes. One of their main physiological functions is the efficient and highly selective transfer of K⁺ ions through the membranes into the cells. To do this, ion channels must be highly selective, allowing only certain ions to pass through the membrane, while preventing the others. The present research is an attempt to investigate the relationship between hopping rate and maintaining coherence in ion channels. Using the Lindblad equation to describe a three-level system, the results in different quantum regimes are examined. We studied the distillable coherence and the second order coherence function of the system. The oscillation of distillable coherence from zero, after the decoherence time, and also the behavior of the coherence function clearly show the point that the system is coherent in ion channels with high throughput rates.

Microtubule Disruption Without Learning Impairment in the Unicellular Organism, Paramecium: Implications for Information Processing in Microtubules

Introduction

Information processing in microtubules is an open question that has not been adequately addressed. It was suggested that microtubules could store and process information in the nervous system or even support consciousness. The unicellular organism, Paramecium caudatum, has a microtubular structure but lacks a neuron or neural network. However, it shows intelligent behaviors such as associative learning. This property may suggest that the microtubules are involved in intelligent behavior, information storage, or information processing in this organism.

Methods

To test this hypothesis and study the role of microtubules in P. caudatum learning, we utilized a learning task in which the organism associates brightness in its swimming medium with attractive cathodal shocks. To see if microtubules are an integral part of information storage and processing in P. caudatum, we disrupted the microtubular dynamics in the organism using an antimicrotubular agent (parbendazole).

Results

We observed that while a partial allosteric modulator of GABA (midazolam) could disrupt the learning process in P. caudatum, the antimicrotubular agent could not interfere with the learning.

Conclusion

Microtubules are probably not vital for the learning behavior in P. caudatum. Consequently, our results call for further investigation of the microtubular information processing hypothesis.

Highlights

Importance of Information processing in microtubules;Microtubules could store and process information in the nervous system;Unicellular organism, Paramecium caudatum, has a microtubular structure but lacks a neuron or neural network.

Plain Language Summary

Information processing in microtubules is an open question that has not been adequately addressed. It was suggested that microtubules could store and process information in the nervous system or even support consciousness. The unicellular organism, Paramecium caudatum, has a microtubular structure but lacks a neuron or neural network. However, it shows intelligent behaviors such as associative learning. This property may suggest that the microtubules are involved in intelligent behavior, information storage, or information processing in this organism. To test this hypothesis and study the role of microtubules in P. caudatum learning, we utilized a learning task in which the organism associates brightness in its swimming medium with attractive cathodal shocks. To see if microtubules are an integral part of information storage and processing in P. caudatum, we disrupted the microtubular dynamics in the organism using an antimicrotubular agent (parbendazole). We observed that while a partial allosteric modulator of GABA (midazolam) could disrupt the learning process in P. caudatum, the antimicrotubular agent could not interfere with the learning. Microtubules are probably not vital for the learning behavior in P. caudatum. Consequently, our results call for further investigation of the microtubular information processing hypothesis.

Transport threshold in a quantum model for the KscA ion channel

The mechanism behind the high throughput rate in K⁺channels is still an open problem. However, recent simulations have shown that the passage of potassium through the K⁺channel core, the so-called selectivity filter (SF), is water-free against models where the strength of Coulomb repulsion freezes ions conduction. Thus, it has been suggested that coherent quantum hopping might be relevant in mediating ion conduction. Within the quantum approach and the hypothesis of desolvated ions along the pathway, we start with several particles in a source to see how they go across a SF, modeled by a linear chain of sites, to be collected in a drain. We show that the average SF occupancy is three ions, and the ion transfer rate is ∼10⁸ions s^-1, results which agree with the recent findings in the literature.

Mathematical Modeling of Ion Quantum Tunneling Reveals Novel Properties of Voltage-Gated Channels and Quantum Aspects of Their Pathophysiology in Excitability-Related Disorders

Voltage-gated channels are crucial in action potential initiation and propagation and there are many diseases and disorders related to them. Additionally, the classical mechanics are the main mechanics used to describe the function of the voltage-gated channels and their related abnormalities. However, the quantum mechanics should be considered to unravel new aspects in the voltage-gated channels and resolve the problems and challenges that classical mechanics cannot solve. In the present study, the aim is to mathematically show that quantum mechanics can exhibit a powerful tendency to unveil novel electrical features in voltage-gated channels and be used as a promising tool to solve the problems and challenges in the pathophysiology of excitability-related diseases. The model of quantum tunneling of ions through the intracellular hydrophobic gate is used to evaluate the influence of membrane potential and gating free energy on the tunneling probability, single channel conductance, and quantum membrane conductance. This evaluation is mainly based on graphing the mathematical relationships between these variables. The obtained mathematical graphs showed that ions can achieve significant quantum membrane conductance, which can affect the resting membrane potential and the excitability of cells. In the present work, quantum mechanics reveals original electrical properties associated with voltage-gated channels and introduces new insights and implications into the pathophysiology of excitability- related disorders. In addition, the present work sets a mathematical and theoretical framework that can be utilized to conduct experimental studies in order to explore the quantum aspects of voltage-gated channels and the quantum bioelectrical property of biological membranes.

Quantum Mechanical Coherence of K+ Ion Wave Packets Increases Conduction in the KcsA Ion Channel

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.

Excitation energy transport with noise and disorder in a model of the selectivity filter of an ion channel

A selectivity filter is a gate in ion channels that is responsible for the selection and fast conduction of particular ions across the membrane (with high throughput rates of 10⁸ ions s^-1 and a high 1:10⁴ discrimination rate between ions). It is made of four strands as the backbone, and each strand is composed of sequences of five amino acids connected by peptide units H-N-C=O in which the main molecules in the backbone that interact with ions in the filter are carbonyl (C=O) groups that mimic the transient interactions of ion with binding sites during ion conduction. It has been suggested that quantum coherence and possible emergence of resonances in the backbone carbonyl groups may play a role in mediating ion conduction and selectivity in the filter. Here, we investigate the influence of noise and disorder on the efficiency of excitation energy transfer (EET) in a linear harmonic chain of N  =  5 sites with dipole-dipole couplings as a simple model for one P-loop strand of the selectivity filter backbone in biological ion channels. We include noise and disorder inherent in real biological systems by including spatial disorder in the chain, and random noise within a weak coupling quantum master equation approach. Our results show that disorder in the backbone considerably reduces EET, but the addition of noise helps to recover high EET for a wide range of system parameters. Our analysis may help for better understanding of the coordination of ions in the filter as well as the fast and efficient functioning of the selectivity filters in ion channels.

Coulomb interaction rules timescales in potassium ion channel tunneling

Assuming the selectivity filter of KcsA potassium ion channel may exhibit quantum coherence, we extend a previous model by Vaziri and Plenio (2010 New J. Phys. 12 085001) to take into account Coulomb repulsion between potassium ions. We show that typical ion transit timescales are determined by this interaction, which imposes optimal input/output parameter ranges. Also, as observed in other examples of quantum tunneling in biological systems, the addition of moderate noise helps coherent ion transport.

Information transmission in microbial and fungal communication: from classical to quantum

Microbes have their own communication systems. Secretion and reception of chemical signaling molecules and ion-channels mediated electrical signaling mechanism are yet observed two special ways of information transmission in microbial community. In this article, we address the aspects of various crucial machineries which set the backbone of microbial cell-to-cell communication process such as quorum sensing mechanism (bacterial and fungal), quorum sensing regulated biofilm formation, gene expression, virulence, swarming, quorum quenching, role of noise in quorum sensing, mathematical models (therapy model, evolutionary model, molecular mechanism model and many more), synthetic bacterial communication, bacterial ion-channels, bacterial nanowires and electrical communication. In particular, we highlight bacterial collective behavior with classical and quantum mechanical approaches (including quantum information). Moreover, we shed a new light to introduce the concept of quantum synthetic biology and possible cellular quantum Turing test.