1
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Seifi M, Soltanmanesh A, Shafiee A. Mimicking classical noise in ion channels by quantum decoherence. Sci Rep 2024; 14:16130. [PMID: 38997398 PMCID: PMC11245528 DOI: 10.1038/s41598-024-67106-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024] Open
Abstract
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.
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Affiliation(s)
- Mina Seifi
- Research Group on Foundations of Quantum Theory and Information, Department of Chemistry, Sharif University of Technology, P.O. Box 11365-9516, Tehran, Iran
| | - Ali Soltanmanesh
- Research Group on Foundations of Quantum Theory and Information, Department of Chemistry, Sharif University of Technology, P.O. Box 11365-9516, Tehran, Iran
- Philosophy of Science Group, Sharif University of Technology, Tehran, Iran
| | - Afshin Shafiee
- Research Group on Foundations of Quantum Theory and Information, Department of Chemistry, Sharif University of Technology, P.O. Box 11365-9516, Tehran, Iran.
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2
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Ryan M, Gao L, Valiyaveetil FI, Zanni MT, Kananenka AA. Probing Ion Configurations in the KcsA Selectivity Filter with Single-Isotope Labels and 2D IR Spectroscopy. J Am Chem Soc 2023; 145:18529-18537. [PMID: 37578394 PMCID: PMC10450685 DOI: 10.1021/jacs.3c05339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Indexed: 08/15/2023]
Abstract
The potassium ion (K+) configurations of the selectivity filter of the KcsA ion channel protein are investigated with two-dimensional infrared (2D IR) spectroscopy of amide I vibrations. Single 13C-18O isotope labels are used, for the first time, to selectively probe the S1/S2 or S2/S3 binding sites in the selectivity filter. These binding sites have the largest differences in ion occupancy in two competing K+ transport mechanisms: soft-knock and hard-knock. According to the former, water molecules alternate between K+ ions in the selectivity filter while the latter assumes that K+ ions occupy the adjacent sites. Molecular dynamics simulations and computational spectroscopy are employed to interpret experimental 2D IR spectra. We find that in the closed conductive state of the KcsA channel, K+ ions do not occupy adjacent binding sites. The experimental data is consistent with simulated 2D IR spectra of soft-knock ion configurations. In contrast, the simulated spectra for the hard-knock ion configurations do not reproduce the experimental results. 2D IR spectra of the hard-knock mechanism have lower frequencies, homogeneous 2D lineshapes, and multiple peaks. In contrast, ion configurations of the soft-knock model produce 2D IR spectra with a single peak at a higher frequency and inhomogeneous lineshape. We conclude that under equilibrium conditions, in the absence of transmembrane voltage, both water and K+ ions occupy the selectivity filter of the KcsA channel in the closed conductive state. The ion configuration is central to the mechanism of ion transport through potassium channels.
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Affiliation(s)
- Matthew
J. Ryan
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lujia Gao
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Francis I. Valiyaveetil
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Martin T. Zanni
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Alexei A. Kananenka
- Department
of Physics and Astronomy, University of
Delaware, Newark, Delaware 19716, United States
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3
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Zhu Z, Deng Z, Wang Q, Wang Y, Zhang D, Xu R, Guo L, Wen H. Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design. Front Pharmacol 2022; 13:939555. [PMID: 35837274 PMCID: PMC9275593 DOI: 10.3389/fphar.2022.939555] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Ion channels are expressed in almost all living cells, controlling the in-and-out communications, making them ideal drug targets, especially for central nervous system diseases. However, owing to their dynamic nature and the presence of a membrane environment, ion channels remain difficult targets for the past decades. Recent advancement in cryo-electron microscopy and computational methods has shed light on this issue. An explosion in high-resolution ion channel structures paved way for structure-based rational drug design and the state-of-the-art simulation and machine learning techniques dramatically improved the efficiency and effectiveness of computer-aided drug design. Here we present an overview of how simulation and machine learning-based methods fundamentally changed the ion channel-related drug design at different levels, as well as the emerging trends in the field.
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Affiliation(s)
- Zhengdan Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Institute of Big Data Research, Beijing, China
| | - Zhenfeng Deng
- DP Technology, Beijing, China
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | | | | | - Duo Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- DP Technology, Beijing, China
| | - Ruihan Xu
- DP Technology, Beijing, China
- National Engineering Research Center of Visual Technology, Peking University, Beijing, China
| | | | - Han Wen
- DP Technology, Beijing, China
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4
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Khalid S, Schroeder C, Bond PJ, Duncan AL. What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes? MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35294337 PMCID: PMC9558347 DOI: 10.1099/mic.0.001165] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial cell envelopes are compositionally complex and crowded and while highly dynamic in some areas, their molecular motion is very limited, to the point of being almost static in others. Therefore, it is no real surprise that studying them at high resolution across a range of temporal and spatial scales requires a number of different techniques. Details at atomistic to molecular scales for up to tens of microseconds are now within range for molecular dynamics simulations. Here we review how such simulations have contributed to our current understanding of the cell envelopes of Gram-negative bacteria.
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Affiliation(s)
- Syma Khalid
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Cyril Schroeder
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), Singapore 138671, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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5
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Tikhonov DB, Zhorov BS. P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models. MEMBRANES 2022; 12:membranes12020229. [PMID: 35207150 PMCID: PMC8876033 DOI: 10.3390/membranes12020229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 01/27/2023]
Abstract
The superfamily of P-loop channels includes potassium, sodium, and calcium channels, as well as TRP channels and ionotropic glutamate receptors. A rapidly increasing number of crystal and cryo-EM structures have revealed conserved and variable elements of the channel structures. Intriguing differences are seen in transmembrane helices of channels, which may include π-helical bulges. The bulges reorient residues in the helices and thus strongly affect their intersegment contacts and patterns of ligand-sensing residues. Comparison of the experimental structures suggests that some π-bulges are dynamic: they may appear and disappear upon channel gating and ligand binding. The AlphaFold2 models represent a recent breakthrough in the computational prediction of protein structures. We compared some crystal and cryo-EM structures of P-loop channels with respective AlphaFold2 models. Folding of the regions, which are resolved experimentally, is generally similar to that predicted in the AlphaFold2 models. The models also reproduce some subtle but significant differences between various P-loop channels. However, patterns of π-bulges do not necessarily coincide in the experimental and AlphaFold2 structures. Given the importance of dynamic π-bulges, further studies involving experimental and theoretical approaches are necessary to understand the cause of the discrepancy.
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6
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Ohmine I, Saito S. Dynamical Behavior of Water; Fluctuation, Reactions and Phase Transitions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Iwao Ohmine
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
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7
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Suzuki Y, Hirata K, Lisy JM, Ishiuchi SI, Fujii M. Double Ion Trap Laser Spectroscopy of Alkali Metal Ion Complexes with a Partial Peptide of the Selectivity Filter in K + Channels─Temperature Effect and Barrier for Conformational Conversions. J Phys Chem A 2021; 125:9609-9618. [PMID: 34637306 DOI: 10.1021/acs.jpca.1c06440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Potassium ion channels selectively permeate K+, as well as Rb+ and Cs+ to some degree, while excluding Na+ and Li+. Conformations of alkali metal complexes of Ac-Tyr-NHMe, a model peptide of the selectivity filter in a K+ channel, were previously found to correlate with the permeability of alkali metal ions to a K+ channel by cold ion trap infrared spectroscopy. With an additional temperature-controlled ion trap, we examined the conformations of the alkali metal complexes, allowing the ions to collide with a He buffer gas at different temperatures, prior to spectroscopic investigation. The conformational distribution of the K+-peptide complex shows the most significant variation with temperature, which suggests that this complex has more flexibility when complexed with K+ and suggests lower barrier heights than other metal-peptide complexes. The variability of the conformational distribution with temperature for the ions follows the same order of ion permeability of a K+ channel. This work demonstrates that the additional temperature-controlled ion trap is a powerful tool to explore the conformational landscape of flexible molecular systems.
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Affiliation(s)
- Yukina Suzuki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - James M Lisy
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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8
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Vallée C, Howlin B, Lewis R. Ion Selectivity in the ENaC/DEG Family: A Systematic Review with Supporting Analysis. Int J Mol Sci 2021; 22:ijms222010998. [PMID: 34681656 PMCID: PMC8536179 DOI: 10.3390/ijms222010998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/16/2022] Open
Abstract
The Epithelial Sodium Channel/Degenerin (ENaC/DEG) family is a superfamily of sodium-selective channels that play diverse and important physiological roles in a wide variety of animal species. Despite their differences, they share a high homology in the pore region in which the ion discrimination takes place. Although ion selectivity has been studied for decades, the mechanisms underlying this selectivity for trimeric channels, and particularly for the ENaC/DEG family, are still poorly understood. This systematic review follows PRISMA guidelines and aims to determine the main components that govern ion selectivity in the ENaC/DEG family. In total, 27 papers from three online databases were included according to specific exclusion and inclusion criteria. It was found that the G/SxS selectivity filter (glycine/serine, non-conserved residue, serine) and other well conserved residues play a crucial role in ion selectivity. Depending on the ion type, residues with different properties are involved in ion permeability. For lithium against sodium, aromatic residues upstream of the selectivity filter seem to be important, whereas for sodium against potassium, negatively charged residues downstream of the selectivity filter seem to be important. This review provides new perspectives for further studies to unravel the mechanisms of ion selectivity.
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Affiliation(s)
- Cédric Vallée
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK; (C.V.); (B.H.)
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - Brendan Howlin
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK; (C.V.); (B.H.)
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Rebecca Lewis
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK; (C.V.); (B.H.)
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
- Correspondence:
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9
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Abstract
Fast excitatory synaptic transmission in the central nervous system relies on the AMPA-type glutamate receptor (AMPAR). This receptor incorporates a nonselective cation channel, which is opened by the binding of glutamate. Although the open pore structure has recently became available from cryo-electron microscopy (Cryo-EM), the molecular mechanisms governing cation permeability in AMPA receptors are not understood. Here, we combined microsecond molecular dynamic (MD) simulations on a putative open-state structure of GluA2 with electrophysiology on cloned channels to elucidate ion permeation mechanisms. Na+, K+, and Cs+ permeated at physiological rates, consistent with a structure that represents a true open state. A single major ion binding site for Na+ and K+ in the pore represents the simplest selectivity filter (SF) structure for any tetrameric cation channel of known structure. The minimal SF comprised only Q586 and Q587, and other residues on the cytoplasmic side formed a water-filled cavity with a cone shape that lacked major interactions with ions. We observed that Cl- readily enters the upper pore, explaining anion permeation in the RNA-edited (Q586R) form of GluA2. A permissive architecture of the SF accommodated different alkali metals in distinct solvation states to allow rapid, nonselective cation permeation and copermeation by water. Simulations suggested Cs+ uses two equally populated ion binding sites in the filter, and we confirmed with electrophysiology of GluA2 that Cs+ is slightly more permeant than Na+, consistent with serial binding sites preferentially driving selectivity.
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10
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Negoro T, Hirata K, Lisy JM, Ishiuchi SI, Fujii M. Potassium and sodium ion complexes with a partial peptide of the selectivity filter in K + channels studied by cold ion trap infrared spectroscopy: the effect of hydration. Phys Chem Chem Phys 2021; 23:12045-12050. [PMID: 34075971 DOI: 10.1039/d1cp00936b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Potassium channels allow K+ to rapidly diffuse, while the selectivity filter (SF) actively blocks Na+. The presence of water in the SF during ion translocation remains under debate due to the experimental and computational challenges in characterizing the interactions between water, ions, and the SF. Our bottom-up approach has been applied to a system composed of a partial peptide of the SF (Ac-tyrosine-NHMe) with a metal ion and a single water molecule to probe these interactions. The IR photodissociation spectra of M+Ac-tyrosine-NHMe(H2O) (M = Na, K) combined with quantum chemical calculations revealed that the water molecule binding sites are ion-dependent. In addition, the ion-peptide distances are elongated significantly for the K+ complex in comparison to the Na+ complex by the addition of a single water molecule. This striking structural difference with the water molecule is discussed in relation to ion selectivity and translocation within the K+ channel.
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Affiliation(s)
- Takumi Negoro
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan. and School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan. and Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. and Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - James M Lisy
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan. and Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. and Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan. and School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan and Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
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11
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Mironenko A, Zachariae U, de Groot BL, Kopec W. The Persistent Question of Potassium Channel Permeation Mechanisms. J Mol Biol 2021; 433:167002. [PMID: 33891905 DOI: 10.1016/j.jmb.2021.167002] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 02/09/2023]
Abstract
Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K+ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to mammals. The structure of the selectivity filter was determined at atomic resolution by x-ray crystallography, showing a tight coordination of desolvated K+ ions by the channel. However, the molecular mechanism of K+ ions permeation through potassium channels remains unclear, with structural, functional and computational studies often providing conflicting data and interpretations. In this review, we will present the proposed mechanisms, discuss their origins, and will critically assess them against all available data. General properties shared by all potassium channels are introduced first, followed by the introduction of two main mechanisms of ion permeation: soft and direct knock-on. Then, we will discuss critical computational and experimental studies that shaped the field. We will especially focus on molecular dynamics (MD) simulations, that provided mechanistic and energetic aspects of K+ permeation, but at the same time created long-standing controversies. Further challenges and possible solutions are presented as well.
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Affiliation(s)
- Andrei Mironenko
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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12
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Cholasseri R, De S. Dual-Site Binding of Quaternary Ammonium Ions as Internal K +-Ion Channel Blockers: Nonclassical (C-H···O) H Bonding vs Dispersive (C-H···H-C) Interaction. J Phys Chem B 2021; 125:86-100. [PMID: 33371683 DOI: 10.1021/acs.jpcb.0c09604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular-level study of the influence of the alkyl chain length of quaternary ammonium ions (QAs) on the blocking action and the mode of binding with the bacterial KcsA K+-ion channel is carried out by molecular dynamics (MD) simulations as well as quantum mechanics/molecular mechanics (QM/MM) methods. The present work unveils distinct modes of binding for different QAs, due to differences in size and hydrophobicity. The QAs bind near the channel gate as well as at the central cavity, leading to a possible dual-site blocking action. Small-sized tetraethylammonium (TEA) and tetrabutylammonium (TBA) ions enter inside the channel cavity in the open state of KcsA but bind strongly in the closed state. TEA binds to the polar hydroxyl group of threonine residues situated at the channel gate via nonclassical H-bonding interaction (C-H···O), while TBA binds to a second binding site, the central cavity, with hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues via alkyl-π and hydrophobic interactions (C-H···H-C). On the contrary, large tetrahexylammonium (THA) and tetraoctylammonium (TOA) ions bind the hydrophobic side-chain methyl and isopropyl of alanine and valine at the channel gate both in the open and closed states, thereby restricting the free movement of large QAs toward the center of the cavity. However, the binding to the hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues in the closed state is thermodynamically preferable. Also, the binding energy is found to increase with an increase in the alkyl chain length from ethyl (-16.4 kcal/mol) to octyl (-65.5 kcal/mol), due to an almost linear increase in dispersive interaction.
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Affiliation(s)
- Rinsha Cholasseri
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673 601, India
| | - Susmita De
- Department of Applied Chemistry, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India.,Inter University Centre for Nanomaterials and Devices, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India
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13
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Cosseddu SM, Choe EJ, Khovanov IA. Unraveling of a Strongly Correlated Dynamical Network of Residues Controlling the Permeation of Potassium in KcsA Ion Channel. ENTROPY (BASEL, SWITZERLAND) 2021; 23:E72. [PMID: 33418985 PMCID: PMC7825352 DOI: 10.3390/e23010072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/23/2020] [Accepted: 01/02/2021] [Indexed: 12/26/2022]
Abstract
The complicated patterns of the single-channel currents in potassium ion channel KcsA are governed by the structural variability of the selectivity filter. A comparative analysis of the dynamics of the wild type KcsA channel and several of its mutants showing different conducting patterns was performed. A strongly correlated dynamical network of interacting residues is found to play a key role in regulating the state of the wild type channel. The network is centered on the aspartate D80 which plays the role of a hub by strong interacting via hydrogen bonds with residues E71, R64, R89, and W67. Residue D80 also affects the selectivity filter via its backbones. This network further compromises ions and water molecules located inside the channel that results in the mutual influence: the permeation depends on the configuration of residues in the network, and the dynamics of network's residues depends on locations of ions and water molecules inside the selectivity filter. Some features of the network provide a further understanding of experimental results describing the KcsA activity. In particular, the necessity of anionic lipids to be present for functioning the channel is explained by the interaction between the lipids and the arginine residues R64 and R89 that prevents destabilizing the structure of the selectivity filter.
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Affiliation(s)
| | | | - Igor A. Khovanov
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK; (S.M.C.); (E.J.C.)
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14
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Strong SE, Hestand NJ, Kananenka AA, Zanni MT, Skinner JL. IR Spectroscopy Can Reveal the Mechanism of K + Transport in Ion Channels. Biophys J 2019; 118:254-261. [PMID: 31812356 DOI: 10.1016/j.bpj.2019.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/28/2019] [Accepted: 11/12/2019] [Indexed: 01/18/2023] Open
Abstract
Ion channels like KcsA enable ions to move across cell membranes at near diffusion-limited rates and with very high selectivity. Various mechanisms have been proposed to explain this phenomenon. Broadly, there is disagreement among the proposed mechanisms about whether ions occupy adjacent sites in the channel during the transport process. Here, using a mixed quantum-classical approach to calculate theoretical infrared spectra, we propose a set of infrared spectroscopy experiments that can discriminate between mechanisms with and without adjacent ions. These experiments differ from previous ones in that they independently probe specific ion binding sites within the selectivity filter. When ions occupy adjacent sites in the selectivity filter, the predicted spectra are significantly redshifted relative to when ions do not occupy adjacent sites. Comparisons between theoretical and experimental peak frequencies will therefore discriminate the mechanisms.
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Affiliation(s)
- Steven E Strong
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Nicholas J Hestand
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Department of Natural and Applied Sciences, Evangel University, Springfield, Missouri
| | - Alexei A Kananenka
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Department of Physics and Astronomy, University of Delaware, Newark, Delaware
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - J L Skinner
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois.
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15
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Wen H, Zheng W. Decrypting the Heat Activation Mechanism of TRPV1 Channel by Molecular Dynamics Simulation. Biophys J 2019; 114:40-52. [PMID: 29320695 DOI: 10.1016/j.bpj.2017.10.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/11/2017] [Accepted: 10/23/2017] [Indexed: 11/29/2022] Open
Abstract
As a prototype cellular sensor, the TRPV1 cation channel undergoes a closed-to-open gating transition in response to various physical and chemical stimuli including noxious heat. Despite recent progress, the molecular mechanism of heat activation of TRPV1 gating remains enigmatic. Toward decrypting the structural basis of TRPV1 heat activation, we performed extensive molecular dynamics simulations (with cumulative simulation time of ∼11 μs) for the wild-type channel and a constitutively active double mutant at different temperatures (30, 60, and 72°C), starting from a high-resolution closed-channel structure of TRPV1 solved by cryo-electron microscopy. In the wild-type simulations, we observed heat-activated conformational changes (e.g., expansion or contraction) in various key domains of TRPV1 (e.g., the S2-S3 and S4-S5 linkers) to prime the channel for gating. These conformational changes involve a number of dynamic hydrogen-bond interactions that were validated with previous mutational studies. Next, our mutant simulations observed channel opening after a series of conformational changes that propagate from the channel periphery to the channel pore via key intermediate domains (including the S2-S3 and S4-S5 linkers). The gating transition is accompanied by a large increase in the protein-water electrostatic interaction energy, which supports the contribution of desolvation of polar/charged residues to the temperature-sensitive TRPV1 gating. Taken together, our molecular dynamics simulations and analyses offered, to our knowledge, new structural, dynamic, and energetic information to guide future mutagenesis and functional studies of the TRPV1 channels and development of TRPV1-targeting drugs.
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Affiliation(s)
- Han Wen
- Department of Physics, State University of New York at Buffalo, Buffalo, New York
| | - Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, New York.
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16
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Calabrò E, Magazù S. Resonant interaction between electromagnetic fields and proteins: A possible starting point for the treatment of cancer. Electromagn Biol Med 2018; 37:155-168. [DOI: 10.1080/15368378.2018.1499031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Emanuele Calabrò
- Department of Mathematical and Informatics Sciences, Physical Sciences and Earth Sciences of Messina University, Messina, Italy
- CISFA - Interuniversity Consortium of Applied Physical Sciences (Consorzio Interuniversitario di Scienze Fisiche Applicate), Messina, Italy
| | - Salvatore Magazù
- Department of Mathematical and Informatics Sciences, Physical Sciences and Earth Sciences of Messina University, Messina, Italy
- Le Studium, Loire Valley Institute for Advanced Studies, Orléans & Tours, Orléans, France
- Centre de Biophysique Moleculaire (CBM), rue Charles Sadron, Laboratoire Interfaces, Confinement, Matériaux et Nanostructures (ICMN) – UMR 7374 CNRS, Université d’Orléans, Orleans, France
- Istituto Nazionale di Alta Matematica “F. Severi” – INDAM – Gruppo Nazionale per la Fisica Matematica – GNFM, Rome, Italy
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17
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Zhang B, Hao GJ, Cao HJ, Tang H, Zhang YY, Deng SG. The cryoprotectant effect of xylooligosaccharides on denaturation of peeled shrimp (Litopenaeus vannamei) protein during frozen storage. Food Hydrocoll 2018. [DOI: 10.1016/j.foodhyd.2017.09.038] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Single-channel recordings of RyR1 at microsecond resolution in CMOS-suspended membranes. Proc Natl Acad Sci U S A 2018; 115:E1789-E1798. [PMID: 29432144 DOI: 10.1073/pnas.1712313115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Single-channel recordings are widely used to explore functional properties of ion channels. Typically, such recordings are performed at bandwidths of less than 10 kHz because of signal-to-noise considerations, limiting the temporal resolution available for studying fast gating dynamics to greater than 100 µs. Here we present experimental methods that directly integrate suspended lipid bilayers with high-bandwidth, low-noise transimpedance amplifiers based on complementary metal-oxide-semiconductor (CMOS) integrated circuits (IC) technology to achieve bandwidths in excess of 500 kHz and microsecond temporal resolution. We use this CMOS-integrated bilayer system to study the type 1 ryanodine receptor (RyR1), a Ca2+-activated intracellular Ca2+-release channel located on the sarcoplasmic reticulum. We are able to distinguish multiple closed states not evident with lower bandwidth recordings, suggesting the presence of an additional Ca2+ binding site, distinct from the site responsible for activation. An extended beta distribution analysis of our high-bandwidth data can be used to infer closed state flicker events as fast as 35 ns. These events are in the range of single-file ion translocations.
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19
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Yao Y, Kanai Y. Free Energy Profile of NaCl in Water: First-Principles Molecular Dynamics with SCAN and ωB97X-V Exchange–Correlation Functionals. J Chem Theory Comput 2018; 14:884-893. [DOI: 10.1021/acs.jctc.7b00846] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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20
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De S, C. H. R, Thamleena A. H, Joseph A, Ben A, V. U. K. Roles of different amino-acid residues towards binding and selective transport of K+ through KcsA K+-ion channel. Phys Chem Chem Phys 2018; 20:17517-17529. [DOI: 10.1039/c8cp01282b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Each amino acid in the selectivity filter plays a distinct role towards binding and transport of K+ ion through KcsA.
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Affiliation(s)
- Susmita De
- Department of Applied Chemistry
- Cochin University of Science and Technology
- Trikakkara
- Kochi
- India – 682 022
| | - Rinsha C. H.
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Hanna Thamleena A.
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Annu Joseph
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Anju Ben
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
| | - Krishnapriya V. U.
- Theoretical and Computational Chemistry Laboratory
- Department of Chemistry
- National Institute of Technology Calicut
- Kozhikode
- India – 673 601
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21
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Lee M, Kolev V, Warshel A. Validating a Coarse-Grained Voltage Activation Model by Comparing Its Performance to the Results of Monte Carlo Simulations. J Phys Chem B 2017; 121:11284-11291. [PMID: 29156125 DOI: 10.1021/acs.jpcb.7b09530] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Simulating the nature of voltage-activated systems is a problem of major current interest, ranging from the action of voltage-gated ion channels to energy storage batteries. However, fully microscopic converging molecular simulations of external voltage effects present a major challenge, and macroscopic models are associated with major uncertainties about the dielectric treatment and the underlying physical basis. Recently we developed a coarse-grained (CG) model that represents explicitly the electrodes, the electrolytes, and the membrane/protein system. The CG model provides a semimacroscopic way of capturing the microscopic physics of voltage-activated systems. Our method was originally validated by reproducing macroscopic and analytical results for key test cases and then used in modeling voltage-activated ion channels and related problems. In this work, we further establish the reliability of the CG voltage model by comparing it to the results of Monte Carlo (MC) simulations with a microscopic electrolyte model. The comparison explores different aspects of membrane, electrolyte, and electrode systems ranging from the Gouy-Chapman model to the determination of the electrolyte charge distribution in the solution between two electrodes (without and with a separating membrane), as well as the evaluation of gating charges. Overall the agreement is very impressive. This provides confidence in the CG model and also shows that the MC model can be used in realistic simulation of voltage activation of membrane proteins with sufficient computer time.
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Affiliation(s)
- Myungjin Lee
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-1062, United States
| | - Vesselin Kolev
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-1062, United States
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22
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Zhang B, Fang CD, Xu JH, Cao HJ. Depuration of Cadmium from Blue Mussel (Mytilus edulis) by Protein Hydrolysate-Fe 2+ Complex: The Role of Metallothionein. J Food Sci 2017; 82:2767-2773. [PMID: 29030874 DOI: 10.1111/1750-3841.13939] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/30/2017] [Accepted: 09/06/2017] [Indexed: 11/29/2022]
Abstract
Metallothionein (MT) plays a major role in the detoxification of toxic metal ions in mussel. This study served to investigate the effects of prepared protein hydrolysate-Fe2+ (PH-Fe2+ ) on depuration of cadmium salt (Cd2+ ) from blue mussel (Mytilus edulis). The results indicated that Cd2+ concentrations in control ranged from 46.1 to 47.1 μg/g during 15 d of depuration. While, 40 mg/L PH-Fe2+ feed mussels exhibited obvious changes in Cd2+ concentration variables, which decreased by 22.8 μg/g after 15 d of depuration, making them significantly lower than the values of the control. Our assumption was that Cd2+ could be dissociated effectively from the complex of MT-Cd2+ in mussels affected by the incorporation of PH-Fe2+ during the feeding period. Further results of homology modeling and molecular dynamics (MD) confirmed that the combined power between MT and Cd2+ weakened significantly by PH-Fe2+ . This condition affected the charge density and/or the loop flexibility of MT and decreased the interaction energy within MT-Cd2+ complex and resulted in the release of Cd2+ from the complex, thereby exhibiting excretion detoxification. Finally, by comparing the experimental results to MD results, significant positive correlations were observed between PH-Fe2+ and the depuration of Cd2+ from MT-Cd2+ complex. Overall, the findings of this study may help better understand the depuration mechanisms of Cd2+ combined with MT, and the PH-Fe2+ can be recommended as a depuration agent to decrease Cd2+ concentrations in mussels. PRACTICAL APPLICATION Metallothionein (MT) is a low-molecular-weight protein with high metal-ion affinity. If the intracellular concentrations of metals are too high or if toxic metals are present within the cell, then the synthesis of MTs is induced and generated. In our previous work, it was found that the prepared hydrolysate-metal element complex showed obvious depuration activity of heavy metals (Cd2+ ) from blue mussel (Mytilus edulis). This study provided further the depuration mechanisms of Cd2+ from mussel (M. edulis), in particular to the role of MT and its chelate during the depuration process.
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Affiliation(s)
- Bin Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhejiang Ocean Univ., Zhoushan, Zhejiang, China.,School of Medicine, Ocean Univ. of China, No.1 Searoad, Marine building 214-1, Changzhi Island, Lincheng, Zhoushan, Zhejiang, China
| | - Chuan-Dong Fang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhejiang Ocean Univ., Zhoushan, Zhejiang, China
| | - Jun-Hui Xu
- Zhoushan Entry-Exit Inspection and Quarantine Bureau, Zhoushan, China
| | - Hui-Juan Cao
- Zhoushan Entry-Exit Inspection and Quarantine Bureau, Zhoushan, China
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23
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Zhang B, Wu HX, Yang HC, Xiang XW, Li HB, Deng SG. Cryoprotective roles of trehalose and alginate oligosaccharides during frozen storage of peeled shrimp ( Litopenaeus vannamei ). Food Chem 2017; 228:257-264. [DOI: 10.1016/j.foodchem.2017.01.124] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 01/14/2017] [Accepted: 01/25/2017] [Indexed: 11/29/2022]
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24
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Tikhonov DB, Zhorov BS. Mechanism of sodium channel block by local anesthetics, antiarrhythmics, and anticonvulsants. J Gen Physiol 2017; 149:465-481. [PMID: 28258204 PMCID: PMC5379917 DOI: 10.1085/jgp.201611668] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/08/2016] [Accepted: 02/03/2017] [Indexed: 11/20/2022] Open
Abstract
Local anesthetics, antiarrhythmics, and anticonvulsants include both charged and electroneutral compounds that block voltage-gated sodium channels. Prior studies have revealed a common drug-binding region within the pore, but details about the binding sites and mechanism of block remain unclear. Here, we use the x-ray structure of a prokaryotic sodium channel, NavMs, to model a eukaryotic channel and dock representative ligands. These include lidocaine, QX-314, cocaine, quinidine, lamotrigine, carbamazepine (CMZ), phenytoin, lacosamide, sipatrigine, and bisphenol A. Preliminary calculations demonstrated that a sodium ion near the selectivity filter attracts electroneutral CMZ but repels cationic lidocaine. Therefore, we further docked electroneutral and cationic drugs with and without a sodium ion, respectively. In our models, all the drugs interact with a phenylalanine in helix IVS6. Electroneutral drugs trap a sodium ion in the proximity of the selectivity filter, and this same site attracts the charged group of cationic ligands. At this position, even small drugs can block the permeation pathway by an electrostatic or steric mechanism. Our study proposes a common pharmacophore for these diverse drugs. It includes a cationic moiety and an aromatic moiety, which are usually linked by four bonds.
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Affiliation(s)
- Denis B Tikhonov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 194223 St. Petersburg, Russia
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S4L8, Canada
| | - Boris S Zhorov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 194223 St. Petersburg, Russia
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S4L8, Canada
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25
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Fluctuation-Driven Transport in Biological Nanopores. A 3D Poisson–Nernst–Planck Study. ENTROPY 2017. [DOI: 10.3390/e19030116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Zhang B, Yang HC, Tang H, Hao GJ, Zhang YY, Deng SG. Insights into Cryoprotective Roles of Carrageenan Oligosaccharides in Peeled Whiteleg Shrimp (Litopenaeus vannamei) during Frozen Storage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1792-1801. [PMID: 28190351 DOI: 10.1021/acs.jafc.6b05651] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The cryoprotective effects of carrageenan oligosaccharides on peeled whiteleg shrimp were investigated and compared with sodium pyrophosphate treatment during frozen storage, primarily the interaction mechanisms between oligosaccharides and shrimp myosin. Data revealed significant profitable effects on water-holding capacity and textural variables in oligosaccharide-treated shrimp compared to the control. Chemical analyses showed that these saccharides maintained a higher myofibrillar protein content and Ca2+-ATPase activity in frozen shrimp. Additionally, the hematoxylin and eosin staining results indicated that the saccharides significantly slowed the damage to muscle tissue structures. The assumption was that water replacement hypothesis played a leading role in cryoprotection of frozen shrimp. Furthermore, the homology modeling and molecular dynamics simulations confirmed that the saccharides substituted water molecules around the shrimp myosin surface by forming hydrogen bonds with polar residues of amino acids, thereby stabilizing the structures in the absence of water, leading to an increase in protein stability during frozen storage.
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Affiliation(s)
- Bin Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University , Zhoushan, 316022 Zhejiang, P. R. China
| | - Hui-Cheng Yang
- Zhejiang Marine Development Research Institute , Zhoushan, 316021 Zhejiang, P. R. China
| | - He Tang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University , Zhoushan, 316022 Zhejiang, P. R. China
| | - Gui-Juan Hao
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University , Zhoushan, 316022 Zhejiang, P. R. China
| | - Yang-Yang Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University , Zhoushan, 316022 Zhejiang, P. R. China
| | - Shang-Gui Deng
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University , Zhoushan, 316022 Zhejiang, P. R. China
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27
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Xiang Z, Liu G, Tang C, Yan L. A model of ion transport processes along and across the neuronal membrane. J Integr Neurosci 2017; 16:33-55. [DOI: 10.3233/jin-160002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Z.X. Xiang
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - G.Z. Liu
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - C.X. Tang
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - L.X. Yan
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
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28
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Wen H, Qin F, Zheng W. Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation. Proteins 2016; 84:1938-1949. [PMID: 27699868 DOI: 10.1002/prot.25177] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/03/2016] [Accepted: 09/24/2016] [Indexed: 01/01/2023]
Abstract
As a key cellular sensor, the TRPV1 cation channel undergoes a gating transition from a closed state to an open state in response to various physical and chemical stimuli including noxious heat. Despite years of study, the heat activation mechanism of TRPV1 gating remains enigmatic at the molecular level. Toward elucidating the structural and energetic basis of TRPV1 gating, we have performed molecular dynamics (MD) simulations (with cumulative simulation time of 3 μs), starting from the high-resolution closed and open structures of TRPV1 solved by cryo-electron microscopy. In the closed-state simulations at 30°C, we observed a stably closed channel constricted at the lower gate (near residue I679), while the upper gate (near residues G643 and M644) is dynamic and undergoes flickery opening/closing. In the open-state simulations at 60°C, we found higher conformational variation consistent with a large entropy increase required for the heat activation, and both the lower and upper gates are dynamic with transient opening/closing. Through ensemble-based structural analyses of the closed state versus the open state, we revealed pronounced closed-to-open conformational changes involving the membrane proximal domain (MPD) linker, the outer pore, and the TRP helix, which are accompanied by breaking/forming of a network of closed/open-state specific hydrogen bonds. By comparing the closed-state simulations at 30°C and 60°C, we observed heat-activated conformational changes in the MPD linker, the outer pore, and the TRP helix that resemble the closed-to-open conformational changes, along with partial formation of the open-state specific hydrogen bonds. Some of the residues involved in the above key hydrogen bonds were validated by previous mutational studies. Taken together, our MD simulations have offered rich structural and dynamic details beyond the static structures of TRPV1, and promising targets for future mutagenesis and functional studies of the TRPV1 channel. Proteins 2016; 84:1938-1949. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Han Wen
- Department of Physics, State University of New York at Buffalo, Buffalo, New York, 14260
| | - Feng Qin
- Department of Physiology and Biophysical Sciences, State University of New York at Buffalo, Buffalo, New York, 14260
| | - Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, New York, 14260
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29
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Chen D. A New Poisson–Nernst–Planck Model with Ion–Water Interactions for Charge Transport in Ion Channels. Bull Math Biol 2016; 78:1703-26. [DOI: 10.1007/s11538-016-0196-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
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30
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Harris BJ, Cheng X, Frymier P. Structure and Function of Photosystem I–[FeFe] Hydrogenase Protein Fusions: An All-Atom Molecular Dynamics Study. J Phys Chem B 2016; 120:599-609. [DOI: 10.1021/acs.jpcb.5b07812] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bradley J. Harris
- College
of Engineering and Computer Science, University of Tennessee, Chattanooga, Tennessee 37403, United States
| | - Xiaolin Cheng
- Center for
Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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31
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Ma QL, Xia H, Zhang ST, Qin DD, Devaramani S, Shan DL, Lu XQ. Investigation of proton-driven amine functionalized tube array as ion responsive biomimetic nanochannels. RSC Adv 2016. [DOI: 10.1039/c5ra25114a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A simple amine embellished tube array was assembled at the liquid–liquid interface to study ion transfer behavior.
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Affiliation(s)
- Qiao-Ling Ma
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Hong Xia
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Shou-Ting Zhang
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Dong-Dong Qin
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Samrat Devaramani
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Duo-Liang Shan
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Xiao-Quan Lu
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
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32
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Probing binding sites and mechanisms of action of an I(Ks) activator by computations and experiments. Biophys J 2015; 108:62-75. [PMID: 25564853 DOI: 10.1016/j.bpj.2014.10.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/06/2014] [Accepted: 10/27/2014] [Indexed: 01/08/2023] Open
Abstract
The slow delayed rectifier (IKs) channel is composed of the KCNQ1 channel and KCNE1 auxiliary subunit, and functions to repolarize action potentials in the human heart. IKs activators may provide therapeutic efficacy for treating long QT syndromes. Here, we show that a new KCNQ1 activator, ML277, can enhance IKs amplitude in adult guinea pig and canine ventricular myocytes. We probe its binding site and mechanism of action by computational analysis based on our recently reported KCNQ1 and KCNQ1/KCNE1 3D models, followed by experimental validation. Results from a pocket analysis and docking exercise suggest that ML277 binds to a side pocket in KCNQ1 and the KCNE1-free side pocket of KCNQ1/KCNE1. Molecular-dynamics (MD) simulations based on the most favorable channel/ML277 docking configurations reveal a well-defined ML277 binding space surrounded by the S2-S3 loop and S4-S5 helix on the intracellular side, and by S4-S6 transmembrane helices on the lateral sides. A detailed analysis of MD trajectories suggests two mechanisms of ML277 action. First, ML277 restricts the conformational dynamics of the KCNQ1 pore, optimizing K(+) ion coordination in the selectivity filter and increasing current amplitudes. Second, ML277 binding induces global motions in the channel, including regions critical for KCNQ1 gating transitions. We conclude that ML277 activates IKs by binding to an intersubunit space and allosterically influencing pore conductance and gating transitions. KCNE1 association protects KCNQ1 from an arrhythmogenic (constitutive current-inducing) effect of ML277, but does not preclude its current-enhancing effect.
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33
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Pluhackova K, Böckmann RA. Biomembranes in atomistic and coarse-grained simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015. [PMID: 26194872 DOI: 10.1088/0953-8984/27/32/323103] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.
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Affiliation(s)
- Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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34
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Unraveling the mechanism of selective ion transport in hydrophobic subnanometer channels. Proc Natl Acad Sci U S A 2015; 112:10851-6. [PMID: 26283377 DOI: 10.1073/pnas.1513718112] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently reported synthetic organic nanopore (SONP) can mimic a key feature of natural ion channels, i.e., selective ion transport. However, the physical mechanism underlying the K(+)/Na(+) selectivity for the SONPs is dramatically different from that of natural ion channels. To achieve a better understanding of the selective ion transport in hydrophobic subnanometer channels in general and SONPs in particular, we perform a series of ab initio molecular dynamics simulations to investigate the diffusivity of aqua Na(+) and K(+) ions in two prototype hydrophobic nanochannels: (i) an SONP with radius of 3.2 Å, and (ii) single-walled carbon nanotubes (CNTs) with radii of 3-5 Å (these radii are comparable to those of the biological potassium K(+) channels). We find that the hydration shell of aqua Na(+) ion is smaller than that of aqua K(+) ion but notably more structured and less yielding. The aqua ions do not lower the diffusivity of water molecules in CNTs, but in SONP the diffusivity of aqua ions (Na(+) in particular) is strongly suppressed due to the rugged inner surface. Moreover, the aqua Na(+) ion requires higher formation energy than aqua K(+) ion in the hydrophobic nanochannels. As such, we find that the ion (K(+) vs. Na(+)) selectivity of the (8, 8) CNT is ∼20× higher than that of SONP. Hence, the (8, 8) CNT is likely the most efficient artificial K(+) channel due in part to its special interior environment in which Na(+) can be fully solvated, whereas K(+) cannot. This work provides deeper insights into the physical chemistry behind selective ion transport in nanochannels.
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35
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Ruiz L, Benjamin A, Sullivan M, Keten S. Regulating Ion Transport in Peptide Nanotubes by Tailoring the Nanotube Lumen Chemistry. J Phys Chem Lett 2015; 6:1514-1520. [PMID: 26263305 DOI: 10.1021/acs.jpclett.5b00252] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We use atomistic nonequilibrium molecular dynamics simulations to demonstrate how specific ionic flux in peptide nanotubes can be regulated by tailoring the lumen chemistry through single amino acid substitutions. By varying the size and polarity of the functional group inserted into the nanotube interior, we are able to adjust the Na(+) flux by over an order of magnitude. Cl(-) is consistently denied passage. Bulky, nonpolar groups encourage interactions between the Na(+) and the peptide backbone carbonyl groups, disrupting the Na(+) solvation shell and slowing the transport of Na(+). Small groups have the opposite effect and accelerate flow. These results suggest that relative ion flux and selectivity can be precisely regulated in subnanometer pores by molecularly defining the lumen according to biological principles.
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Affiliation(s)
- Luis Ruiz
- †Department of Mechanical Engineering and ‡Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Ari Benjamin
- †Department of Mechanical Engineering and ‡Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Matthew Sullivan
- †Department of Mechanical Engineering and ‡Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Sinan Keten
- †Department of Mechanical Engineering and ‡Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
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36
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Li Y, Gong H. Theoretical and simulation studies on voltage-gated sodium channels. Protein Cell 2015; 6:413-22. [PMID: 25894089 PMCID: PMC4444806 DOI: 10.1007/s13238-015-0152-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/05/2015] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated sodium (Nav) channels are indispensable membrane elements for the generation and propagation of electric signals in excitable cells. The successes in the crystallographic studies on prokaryotic Nav channels in recent years greatly promote the mechanistic investigation of these proteins and their eukaryotic counterparts. In this paper, we mainly review the progress in computational studies, especially the simulation studies, on these proteins in the past years.
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Affiliation(s)
- Yang Li
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084 China
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37
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Li P, Song LF, Merz KM. Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model. J Chem Theory Comput 2015; 11:1645-57. [PMID: 26574374 DOI: 10.1021/ct500918t] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Monovalent ions play fundamental roles in many biological processes in organisms. Modeling these ions in molecular simulations continues to be a challenging problem. The 12-6 Lennard-Jones (LJ) nonbonded model is widely used to model monovalent ions in classical molecular dynamics simulations. A lot of parameterization efforts have been reported for these ions with a number of experimental end points. However, some reported parameter sets do not have a good balance between the two Lennard-Jones parameters (the van der Waals (VDW) radius and potential well depth), which affects their transferability. In the present work, via the use of a noble gas curve we fitted in former work (J. Chem. Theory Comput. 2013, 9, 2733), we reoptimized the 12-6 LJ parameters for 15 monovalent ions (11 positive and 4 negative ions) for three extensively used water models (TIP3P, SPC/E, and TIP4P(EW)). Since the 12-6 LJ nonbonded model performs poorly in some instances for these ions, we have also parameterized the 12-6-4 LJ-type nonbonded model (J. Chem. Theory Comput. 2014, 10, 289) using the same three water models. The three derived parameter sets focused on reproducing the hydration free energies (the HFE set) and the ion-oxygen distance (the IOD set) using the 12-6 LJ nonbonded model and the 12-6-4 LJ-type nonbonded model (the 12-6-4 set) overall give improved results. In particular, the final parameter sets showed better agreement with quantum mechanically calculated VDW radii and improved transferability to ion-pair solutions when compared to previous parameter sets.
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Affiliation(s)
- Pengfei Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| | - Lin Frank Song
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
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38
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Keerthana SP, Kolandaivel P. Interaction between dimer interface residues of native and mutated SOD1 protein: a theoretical study. J Biol Inorg Chem 2015; 20:509-22. [PMID: 25578810 DOI: 10.1007/s00775-014-1235-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/27/2014] [Indexed: 01/01/2023]
Abstract
Cu-Zn superoxide dismutase 1 (SOD1) is a highly conserved bimetallic protein enzyme, used for the scavenging the superoxide radicals (O2 (-)) produced due to aerobic metabolism in the mitochondrial respiratory chain. Over 100 mutations have been identified and found to be in the homodimeric structure of SOD1. The enzyme has to be maintained in its dimeric state for the structural stability and enzymatic activity. From our investigation, we found that the mutations apart from the dimer interface residues are found to affect the dimer stability of protein and hence enhancing the aggregation and misfolding tendency of mutated protein. The homodimeric state of SOD1 is found to be held together by the non-covalent interactions. The molecular dynamics simulation has been used to study the hydrogen bond interactions between the dimer interface residues of the monomers in native and mutated forms of SOD1 in apo- and holo-states. The results obtained by this analysis reveal the fact that the loss of hydrogen bond interactions between the monomers of the dimer is responsible for the reduced stability of the apo- and holo-mutant forms of SOD1. The conformers with dimer interface residues in native and mutated protein obtained by the molecular dynamics simulation is subjected to quantum mechanical study using M052X/6-31G(d) level of theory. The charge transfer between N-H···O interactions in the dimer interface residues were studied. The weak interaction between the monomers of the dimer accounts for the reduced dimerization and enhanced deformation energy in the mutated SOD1 protein.
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Affiliation(s)
- S P Keerthana
- Department of Physics, Bharathiar University, Coimbatore, 641 046, India
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39
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40
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Horn R, Roux B, Åqvist J. Permeation redux: thermodynamics and kinetics of ion movement through potassium channels. Biophys J 2014; 106:1859-63. [PMID: 24806917 DOI: 10.1016/j.bpj.2014.03.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/14/2014] [Accepted: 03/27/2014] [Indexed: 10/25/2022] Open
Abstract
The fundamental biophysics underlying the selective movement of ions through ion channels was launched by George Eisenman in the 1960s, using glass electrodes. This minireview examines the insights from these early studies and the explosive progress made since then.
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Affiliation(s)
- Richard Horn
- Department of Molecular Physiology and Biophysics, Jefferson Medical College, Philadelphia, Pennsylvania.
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
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41
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Köpfer DA, Song C, Gruene T, Sheldrick GM, Zachariae U, de Groot BL. Ion permeation in K⁺ channels occurs by direct Coulomb knock-on. Science 2014; 346:352-5. [PMID: 25324389 DOI: 10.1126/science.1254840] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Potassium channels selectively conduct K(+) ions across cellular membranes with extraordinary efficiency. Their selectivity filter exhibits four binding sites with approximately equal electron density in crystal structures with high K(+) concentrations, previously thought to reflect a superposition of alternating ion- and water-occupied states. Consequently, cotranslocation of ions with water has become a widely accepted ion conduction mechanism for potassium channels. By analyzing more than 1300 permeation events from molecular dynamics simulations at physiological voltages, we observed instead that permeation occurs via ion-ion contacts between neighboring K(+) ions. Coulomb repulsion between adjacent ions is found to be the key to high-efficiency K(+) conduction. Crystallographic data are consistent with directly neighboring K(+) ions in the selectivity filter, and our model offers an intuitive explanation for the high throughput rates of K(+) channels.
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Affiliation(s)
- David A Köpfer
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Chen Song
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Tim Gruene
- Department of Structural Chemistry, University of Göttingen, 37077 Göttingen, Germany
| | - George M Sheldrick
- Department of Structural Chemistry, University of Göttingen, 37077 Göttingen, Germany
| | - Ulrich Zachariae
- School of Engineering, Physics and Mathematics, University of Dundee, Dundee DD1 4HN, UK. College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Bert L de Groot
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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42
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Harris BJ, Cheng X, Frymier P. All-atom molecular dynamics simulation of a photosystem i/detergent complex. J Phys Chem B 2014; 118:11633-45. [PMID: 25233289 DOI: 10.1021/jp507157e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.
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Affiliation(s)
- Bradley J Harris
- Department of Chemical and Biomolecular Engineering, ‡Department of Biochemistry and Cellular and Molecular Biology, §Sustainable Energy Education and Research Center, and ∥Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee , Knoxville, Tennessee 37996, United States
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43
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Kiani MJ, Harun FKC, Ahmadi MT, Rahmani M, Saeidmanesh M, Zare M. Conductance modulation of charged lipid bilayer using electrolyte-gated graphene-field effect transistor. NANOSCALE RESEARCH LETTERS 2014; 9:371. [PMID: 25114659 PMCID: PMC4125348 DOI: 10.1186/1556-276x-9-371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 07/09/2014] [Indexed: 05/28/2023]
Abstract
Graphene is an attention-grabbing material in electronics, physics, chemistry, and even biology because of its unique properties such as high surface-area-to-volume ratio. Also, the ability of graphene-based materials to continuously tune charge carriers from holes to electrons makes them promising for biological applications, especially in lipid bilayer-based sensors. Furthermore, changes in charged lipid membrane properties can be electrically detected by a graphene-based electrolyte-gated graphene field effect transistor (GFET). In this paper, a monolayer graphene-based GFET with a focus on the conductance variation caused by membrane electric charges and thickness is studied. Monolayer graphene conductance as an electrical detection platform is suggested for neutral, negative, and positive electric-charged membrane. The electric charge and thickness of the lipid bilayer (Q LP and L LP) as a function of carrier density are proposed, and the control parameters are defined. Finally, the proposed analytical model is compared with experimental data which indicates good overall agreement.
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Affiliation(s)
- Mohammad Javad Kiani
- Faculty of Electrical Engineering, Universiti Teknologi Malaysia, Skudai, Johor 81310, Malaysia
- Department of Electrical Engineering, Islamic Azad University, Yasooj branch, Yasooj 75916, Iran
| | - Fauzan Khairi Che Harun
- Faculty of Electrical Engineering, Universiti Teknologi Malaysia, Skudai, Johor 81310, Malaysia
| | | | - Meisam Rahmani
- Faculty of Electrical Engineering, Universiti Teknologi Malaysia, Skudai, Johor 81310, Malaysia
| | - Mahdi Saeidmanesh
- Faculty of Electrical Engineering, Universiti Teknologi Malaysia, Skudai, Johor 81310, Malaysia
| | - Moslem Zare
- Department of Physics, Yasouj University, Yasouj 75914-353, Iran
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
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44
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Abstract
Ion channels are membrane-bound enzymes whose catalytic sites are ion-conducting pores that open and close (gate) in response to specific environmental stimuli. Ion channels are important contributors to cell signaling and homeostasis. Our current understanding of gating is the product of 60 plus years of voltage-clamp recording augmented by intervention in the form of environmental, chemical, and mutational perturbations. The need for good phenomenological models of gating has evolved in parallel with the sophistication of experimental technique. The goal of modeling is to develop realistic schemes that not only describe data, but also accurately reflect mechanisms of action. This review covers three areas that have contributed to the understanding of ion channels: traditional Eyring kinetic theory, molecular dynamics analysis, and statistical thermodynamics. Although the primary emphasis is on voltage-dependent channels, the methods discussed here are easily generalized to other stimuli and could be applied to any ion channel and indeed any macromolecule.
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45
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K(+) and Na(+) conduction in selective and nonselective ion channels via molecular dynamics simulations. Biophys J 2014; 105:1737-45. [PMID: 24138849 DOI: 10.1016/j.bpj.2013.08.049] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 08/24/2013] [Accepted: 08/30/2013] [Indexed: 12/23/2022] Open
Abstract
Generations of scientists have been captivated by ion channels and how they control the workings of the cell by admitting ions from one side of the cell membrane to the other. Elucidating the molecular determinants of ion conduction and selectivity are two of the most fundamental issues in the field of biophysics. Combined with ongoing progress in structural studies, modeling and simulation have been an integral part of the development of the field. As of this writing, the relentless growth in computational power, the development of new algorithms to tackle the so-called rare events, improved force-field parameters, and the concomitant increasing availability of membrane protein structures, allow simulations to contribute even further, providing more-complete models of ion conduction and selectivity in ion channels. In this report, we give an overview of the recent progress made by simulation studies on the understanding of ion permeation in selective and nonselective ion channels.
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46
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Keerthana S, Kolandaivel P. Study on the disulfide bond and disulfide loop of native and mutated SOD1 protein. J Mol Graph Model 2014; 50:78-89. [DOI: 10.1016/j.jmgm.2014.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 02/03/2023]
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47
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Keerthana S, Kolandaivel P. Study of mutation and misfolding of Cu-Zn SOD1 protein. J Biomol Struct Dyn 2013; 33:167-83. [DOI: 10.1080/07391102.2013.865104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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48
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Arcangeletti M, Marchesi A, Mazzolini M, Torre V. Multiple mechanisms underlying rectification in retinal cyclic nucleotide-gated (CNGA1) channels. Physiol Rep 2013; 1:e00148. [PMID: 24400150 PMCID: PMC3871463 DOI: 10.1002/phy2.148] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 10/03/2013] [Indexed: 11/29/2022] Open
Abstract
In cyclic nucleotide-gated (CNGA1) channels, in the presence of symmetrical ionic conditions, current–voltage (I-V) relationship depends, in a complex way, on the radius of permeating ion. It has been suggested that both the pore and S4 helix contribute to the observed rectification. In the present manuscript, using tail and gating current measurements from homotetrameric CNGA1 channels expressed in Xenopus oocytes, we clarify and quantify the role of the pore and of the S4 helix. We show that in symmetrical Rb+ and Cs+ single-channel current rectification dominates macroscopic currents while voltage-dependent gating becomes larger in symmetrical ethylammonium and dimethylammonium, where the open probability strongly depends on voltage. Isochronal tail currents analysis in dimethylammonium shows that at least two voltage-dependent transitions underlie the observed rectification. Only the first voltage-dependent transition is sensible to mutation of charge residues in the S4 helix. Moreover, analysis of tail and gating currents indicates that the number of elementary charges per channel moving across the membrane is less than 2, when they are about 12 in K+ channels. These results indicate the existence of distinct mechanisms underlying rectification in CNG channels. A restricted motion of the S4 helix together with an inefficient coupling to the channel gate render CNGA1 channels poorly sensitive to voltage in the presence of physiological Na+ and K+.
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Affiliation(s)
- Manuel Arcangeletti
- Neuroscience Area, International School for Advanced Studies (SISSA) Trieste, Italy
| | - Arin Marchesi
- Neuroscience Area, International School for Advanced Studies (SISSA) Trieste, Italy
| | - Monica Mazzolini
- Neuroscience Area, International School for Advanced Studies (SISSA) Trieste, Italy ; CBM S.c.r.l., Area Science Park Basovizza, 34012, Trieste, Italy
| | - Vincent Torre
- Neuroscience Area, International School for Advanced Studies (SISSA) Trieste, Italy
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49
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Rossi M, Tkatchenko A, Rempe SB, Varma S. Role of methyl-induced polarization in ion binding. Proc Natl Acad Sci U S A 2013; 110:12978-83. [PMID: 23878238 PMCID: PMC3740884 DOI: 10.1073/pnas.1302757110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The chemical property of methyl groups that renders them indispensable to biomolecules is their hydrophobicity. Quantum mechanical studies undertaken here to understand the effect of point substitutions on potassium (K-) channels illustrate quantitatively how methyl-induced polarization also contributes to biomolecular function. K- channels regulate transmembrane salt concentration gradients by transporting K(+) ions selectively. One of the K(+) binding sites in the channel's selectivity filter, the S4 site, also binds Ba(2+) ions, which blocks K(+) transport. This inhibitory property of Ba(2+) ions has been vital in understanding K-channel mechanism. In most K-channels, the S4 site is composed of four threonine amino acids. The K channels that carry serine instead of threonine are significantly less susceptible to Ba(2+) block and have reduced stabilities. We find that these differences can be explained by the lower polarizability of serine compared with threonine, because serine carries one less branched methyl group than threonine. A T→S substitution in the S4 site reduces its polarizability, which, in turn, reduces ion binding by several kilocalories per mole. Although the loss in binding affinity is high for Ba(2+), the loss in K(+) binding affinity is also significant thermodynamically, which reduces channel stability. These results highlight, in general, how biomolecular function can rely on the polarization induced by methyl groups, especially those that are proximal to charged moieties, including ions, titratable amino acids, sulfates, phosphates, and nucleotides.
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Affiliation(s)
- Mariana Rossi
- Theory Department, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Alexandre Tkatchenko
- Theory Department, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Susan B. Rempe
- Biological and Materials Sciences Center, Sandia National Laboratories, Albuquerque, NM 87185; and
| | - Sameer Varma
- Biological and Materials Sciences Center, Sandia National Laboratories, Albuquerque, NM 87185; and
- Department of Cell Biology, Microbiology, and Molecular Biology, and Department of Physics, University of South Florida, Tampa, FL 33620
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50
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Montes J, Gomez E, Merchán-Pérez A, DeFelipe J, Peña JM. A machine learning method for the prediction of receptor activation in the simulation of synapses. PLoS One 2013; 8:e68888. [PMID: 23894367 PMCID: PMC3720878 DOI: 10.1371/journal.pone.0068888] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 06/01/2013] [Indexed: 11/18/2022] Open
Abstract
Chemical synaptic transmission involves the release of a neurotransmitter that diffuses in the extracellular space and interacts with specific receptors located on the postsynaptic membrane. Computer simulation approaches provide fundamental tools for exploring various aspects of the synaptic transmission under different conditions. In particular, Monte Carlo methods can track the stochastic movements of neurotransmitter molecules and their interactions with other discrete molecules, the receptors. However, these methods are computationally expensive, even when used with simplified models, preventing their use in large-scale and multi-scale simulations of complex neuronal systems that may involve large numbers of synaptic connections. We have developed a machine-learning based method that can accurately predict relevant aspects of the behavior of synapses, such as the percentage of open synaptic receptors as a function of time since the release of the neurotransmitter, with considerably lower computational cost compared with the conventional Monte Carlo alternative. The method is designed to learn patterns and general principles from a corpus of previously generated Monte Carlo simulations of synapses covering a wide range of structural and functional characteristics. These patterns are later used as a predictive model of the behavior of synapses under different conditions without the need for additional computationally expensive Monte Carlo simulations. This is performed in five stages: data sampling, fold creation, machine learning, validation and curve fitting. The resulting procedure is accurate, automatic, and it is general enough to predict synapse behavior under experimental conditions that are different to the ones it has been trained on. Since our method efficiently reproduces the results that can be obtained with Monte Carlo simulations at a considerably lower computational cost, it is suitable for the simulation of high numbers of synapses and it is therefore an excellent tool for multi-scale simulations.
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Affiliation(s)
- Jesus Montes
- Departamento de Arquitectura y Tecnología de Sistemas Informáticos, Facultad de Informática, Universidad Politécnica de Madrid, Madrid, Spain
| | - Elena Gomez
- Departamento de Arquitectura y Tecnología de Sistemas Informáticos, Facultad de Informática, Universidad Politécnica de Madrid, Madrid, Spain
| | - Angel Merchán-Pérez
- Departamento de Arquitectura y Tecnología de Sistemas Informáticos, Facultad de Informática, Universidad Politécnica de Madrid, Madrid, Spain
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
| | - Javier DeFelipe
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jose-Maria Peña
- Departamento de Arquitectura y Tecnología de Sistemas Informáticos, Facultad de Informática, Universidad Politécnica de Madrid, Madrid, Spain
- * E-mail:
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