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

2020 ◽  
Vol 10 (12) ◽  
pp. 4250
Author(s):  
Johann Summhammer ◽  
Georg Sulyok ◽  
Gustav Bernroider
Keyword(s):  
Ion Channel ◽  
Force Fields ◽  
Quantum Effect ◽  
Ion Selectivity ◽  
Wave Packets ◽  
Thermal Fluctuations ◽  
Carbonyl Oxygen ◽  
Atomic Scale ◽  
Quantum Mechanical ◽  
Time Pattern

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.

scholarly journals Quantum Calculations on Ion Channels: Why Are They More Useful Than Classical Calculations, and for Which Processes Are They Essential?

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 655
Author(s):  
Alisher M. Kariev ◽  
Michael E. Green
Keyword(s):  
Charge Transfer ◽  
Ion Channels ◽  
Correlation Energy ◽  
Force Fields ◽  
Critical Role ◽  
Atomic Scale ◽  
Quantum Calculations ◽  
Interatomic Distances ◽  
Classical Analogue ◽  
Exchange And Correlation

There are reasons to consider quantum calculations to be necessary for ion channels, for two types of reasons. The calculations must account for charge transfer, and the possible switching of hydrogen bonds, which are very difficult with classical force fields. Without understanding charge transfer and hydrogen bonding in detail, the channel cannot be understood. Thus, although classical approximations to the correct force fields are possible, they are unable to reproduce at least some details of the behavior of a system that has atomic scale. However, there is a second class of effects that is essentially quantum mechanical. There are two types of such phenomena: exchange and correlation energies, which have no classical analogues, and tunneling. Tunneling, an intrinsically quantum phenomenon, may well play a critical role in initiating a proton cascade critical to gating. As there is no classical analogue of tunneling, this cannot be approximated classically. Finally, there are energy terms, exchange and correlation energy, whose values can be approximated classically, but these approximations must be subsumed within classical terms, and as a result, will not have the correct dependence on interatomic distances. Charge transfer, and tunneling, require quantum calculations for ion channels. Some results of quantum calculations are shown.

scholarly journals A transferable active-learning strategy for reactive molecular force fields

2021 ◽  
Author(s):  
Tom Young ◽  
Tristan Johnston-Wood ◽  
Volker L. Deringer ◽  
Fernanda Duarte
Keyword(s):  
Machine Learning ◽  
Active Learning ◽  
Learning Strategy ◽  
Force Fields ◽  
Molecular Simulations ◽  
Quantum Mechanical ◽  
Interatomic Potentials ◽  
Molecular Force ◽  
High Level ◽  
Active Learning Strategy

Predictive molecular simulations require fast, accurate and reactive interatomic potentials. Machine learning offers a promising approach to construct such potentials by fitting energies and forces to high-level quantum-mechanical data, but...

scholarly journals On the Importance of Atomic Fluctuations, Protein Flexibility, and Solvent in Ion Permeation

2004 ◽  
Vol 124 (6) ◽  
pp. 679-690 ◽  
Author(s):  
Toby W. Allen ◽  
O.S. Andersen ◽  
Benoit Roux
Keyword(s):  
Ion Channel ◽  
Protein Function ◽  
Channel Model ◽  
Protein Structures ◽  
Thermal Fluctuations ◽  
Model Parameters ◽  
Ion Permeation ◽  
Model Calculations ◽  
Channel Interactions ◽  
Solvent Molecules

Proteins, including ion channels, often are described in terms of some average structure and pictured as rigid entities immersed in a featureless solvent continuum. This simplified view, which provides for a convenient representation of the protein's overall structure, incurs the risk of deemphasizing important features underlying protein function, such as thermal fluctuations in the atom positions and the discreteness of the solvent molecules. These factors become particularly important in the case of ion movement through narrow pores, where the magnitude of the thermal fluctuations may be comparable to the ion pore atom separations, such that the strength of the ion channel interactions may vary dramatically as a function of the instantaneous configuration of the ion and the surrounding protein and pore water. Descriptions of ion permeation through narrow pores, which employ static protein structures and a macroscopic continuum dielectric solvent, thus face fundamental difficulties. We illustrate this using simple model calculations based on the gramicidin A and KcsA potassium channels, which show that thermal atomic fluctuations lead to energy profiles that vary by tens of kcal/mol. Consequently, within the framework of a rigid pore model, ion-channel energetics is extremely sensitive to the choice of experimental structure and how the space-dependent dielectric constant is assigned. Given these observations, the significance of any description based on a rigid structure appears limited. Creating a conducting channel model from one single structure requires substantial and arbitrary engineering of the model parameters, making it difficult for such approaches to contribute to our understanding of ion permeation at a microscopic level.

Predictive abilities of scaled quantum-mechanical molecular force fields: application to 2-methylbuta-1,3-diene (isoprene)

2008 ◽  
Vol 19 (3) ◽  
pp. 421-428 ◽  
Author(s):  
Yurii N. Panchenko ◽  
Charles W. Bock ◽  
Joseph D. Larkin ◽  
Alexander V. Abramenkov ◽  
Frank Kühnemann
Keyword(s):  
Force Fields ◽  
Quantum Mechanical ◽  
Molecular Force

scholarly journals Quantum mechanical rotation of a photon polarization by Earth’s gravitational field

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Hansol Noh ◽  
Paul M. Alsing ◽  
Doyeol Ahn ◽  
Warner A. Miller ◽  
Namkyoo Park
Keyword(s):  
Gravitational Field ◽  
Quantum Effect ◽  
Quantum Phase ◽  
Quantum Mechanical ◽  
Photon Polarization ◽  
Wigner Rotation ◽  
Photon State ◽  
Earth’S Gravitational Field ◽  
Classical Effect ◽  
Mechanical Rotation

AbstractWe describe the quantum mechanical rotation of a photon state, the Wigner rotation—a quantum effect that couples a transformation of a reference frame to a particle’s spin, to investigate geometric phases induced by Earth’s gravitational field for observers in various orbits. We find a potentially measurable quantum phase of the Wigner rotation angle in addition to the rotation of standard fame, the latter of which is computed and agrees well with the geodetic rotation. When an observer is in either a circular or a spiraling orbit containing non-zero angular momentum, the additional quantum phase contributes 10−6 degree to 10−4 degree respectively, depending on the altitude of the Earth orbit. In the former case, the additional quantum phase is dominant over the near-zero classical geodetic rotation. Our results show that the Wigner rotation represents a non-trivial semi-classical effect of quantum field theory on a background classical gravitational field.

The Future

1992 ◽  
Author(s):  
John A. Tossell ◽  
David J. Vaughan
Keyword(s):  
Ab Initio ◽  
Quantum Chemical ◽  
Force Fields ◽  
Structural Characteristics ◽  
Future Research ◽  
Quantum Mechanical ◽  
Bond Lengths ◽  
Hartree Fock ◽  
Qualitative Level ◽  
Dynamics Simulations

In this final chapter, an attempt is made to provide an overview of the capabilities of quantum-mechanical methods at the present time, and to highlight the needs for future development and possible future applications of these methods, particularly in areas related to mineral structures, energetics, and spectroscopy. There is also a brief account of some new areas of application, specific directions for future research, and possible developments in the perception and use of quantum-mechanical approaches. The book ends with an epilog on the overall role of “theoretical geochemistry” in the earth and environmental sciences. The local structural characteristics of minerals such as Mg2SiO4, which contain only main-group elements, are reasonably well reproduced by ab initio Hartree-Fock-Roothaan (SCF) cluster calculations at the mediumbasis- set level. Calculations incorporating configuration interaction will inevitably follow and probably lead to somewhat better agreement with experiment. The most pressing needs in this area of study are for the development of systematic procedures for cluster selection and embedding, for a greater understanding of the results at a qualitative level, and for more widespread efficient application of the quantum-chemical results currently available. In the last area, substantial progress has already been made by Lasaga and Gibbs (1987), Sanders et al. (1984), Tsuneyuki et al. (1988), and others, who have used ab initio calculations to generate theoretical force fields which can then be used in molecular-dynamics simulations. If the characteristics of the resultant force fields can be understood at a first-principles level, then it may be possible to understand details of the simulated structures at the same level. Unfortunately, as regards a greater qualitative understanding of the quantum-mechanical calculations, little progress has been made. Rather old qualitative theories describe some aspects of bond-angle variation (Tossell, 1986), but no general model to interpret variations in bond lengths has been developed within either chemistry or geochemistry beyond the model of additive atomic (Slater) or ionic (Shannon and Prewitt) radii. Indeed, global theories of bond-length variations within an ab initio framework seem to be nonexistent. Nonetheless, quantum-chemical studies have shown the presence of intriguing systematics in bond lengths (Gibbs et al., 1987), which had been already noted empirically.

scholarly journals Molecular Dynamics Simulation of Transmembrane Transport of Chloride Ions in Mutants of Channelrhodopsin

Biomolecules ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 852
Author(s):  
Wenying Zhang ◽  
Ting Yang ◽  
Shuangyan Zhou ◽  
Jie Cheng ◽  
Shuai Yuan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ion Channel ◽  
Ion Selectivity ◽  
Potential Of Mean Force ◽  
Chloride Ions ◽  
Dynamics Simulation ◽  
Mutant Proteins ◽  
Transmembrane Channel ◽  
Anion Conduction

Channelrhodopsins (ChRs) are light-gated transmembrane cation channels which are widely used for optogenetic technology. Replacing glutamate located at the central gate of the ion channel with positively charged amino acid residues will reverse ion selectivity and allow anion conduction. The structures and properties of the ion channel, the transport of chloride, and potential of mean force (PMF) of the chimera protein (C1C2) and its mutants, EK-TC, ER-TC and iChloC, were investigated by molecular dynamics simulation. The results show that the five-fold mutation in E122Q-E129R-E140S-D195N-T198C (iChloC) increases the flexibility of the transmembrane channel protein better than the double mutations in EK-TC and ER-TC, and results in an expanded ion channel pore size and decreased steric resistance. The iChloC mutant was also found to have a higher affinity for chloride ions and, based on surface electrostatic potential analysis, provides a favorable electrostatic environment for anion conduction. The PMF free energy curves revealed that high affinity Cl− binding sites are generated near the central gate of the three mutant proteins. The energy barriers for the EK-TC and ER-TC were found to be much higher than that of iChloC. The results suggest that the transmembrane ion channel of iChloC protein is better at facilitating the capture and transport of chloride ions.

Ion Channel Permeation and Selectivity

2019 ◽  
Author(s):  
Juan J. Nogueira ◽  
Ben Corry
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Ion Selectivity ◽  
Ionic Currents ◽  
Biological Processes ◽  
Ion Permeation ◽  
Voltage Gated ◽  
Physical Mechanisms ◽  
Theoretical Approaches ◽  
Mechanistic Insight

Many biological processes essential for life rely on the transport of specific ions at specific times across cell membranes. Such exquisite control of ionic currents, which is regulated by protein ion channels, is fundamental for the proper functioning of the cells. It is not surprising, therefore, that the mechanism of ion permeation and selectivity in ion channels has been extensively investigated by means of experimental and theoretical approaches. These studies have provided great mechanistic insight but have also raised new questions that are still unresolved. This chapter first summarizes the main techniques that have provided significant knowledge about ion permeation and selectivity. It then discusses the physical mechanisms leading to ion permeation and the explanations that have been proposed for ion selectivity in voltage-gated potassium, sodium, and calcium channels.

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