1
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Ding W, Zhao X, Wang H, Wang Y, Liu Y, Gong L, Lin S, Liu C, Li Y. Effect of Terahertz Electromagnetic Field on the Permeability of Potassium Channel Kv1.2. Int J Mol Sci 2023; 24:10271. [PMID: 37373419 DOI: 10.3390/ijms241210271] [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: 04/18/2023] [Revised: 06/10/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
In this paper, the influence of external terahertz electromagnetic fields with different frequencies of 4 THz, 10 THz, 15 THz, and 20 THz on the permeability of the Kv1.2 voltage-gated potassium ion channel on the nerve cell membrane was studied using the combined model of the "Constant Electric Field-Ion Imbalance" method by molecular dynamics. We found that although the applied terahertz electric field does not produce strong resonance with the -C=O groups of the conservative sequence T-V-G-Y-G amino acid residue of the selective filter (SF) of the channel, it would affect the stability of the electrostatic bond between potassium ions and the carbonyl group of T-V-G-Y-G of SF, and it would affect the stability of the hydrogen bond between water molecules and oxygen atoms of the hydroxyl group of the 374THR side chain at the SF entrance, changing the potential and occupied states of ions in the SF and the occurrence probability of the permeation mode of ions and resulting in the change in the permeability of the channel. Compared with no external electric field, when the external electric field with 15 THz frequency is applied, the lifetime of the hydrogen bond is reduced by 29%, the probability of the "soft knock on" mode is decreased by 46.9%, and the ion flux of the channel is activated by 67.7%. Our research results support the view that compared to "direct knock-on", "soft knock-on" is a slower permeation mode.
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Affiliation(s)
- Wen Ding
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- School of Electronic Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiaofei Zhao
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- School of Electronic Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Hongguang Wang
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- School of Electronic Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yize Wang
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- School of Electronic Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yanjiang Liu
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- School of Electronic Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lirong Gong
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- School of Electronic Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shu Lin
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- School of Electronic Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Chunliang Liu
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- School of Electronic Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yongdong Li
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, China
- School of Electronic Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
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2
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Wang Y, Wang H, Ding W, Zhao X, Li Y, Liu C. Regulation of Ion Permeation of the KcsA Channel by Applied Midinfrared Field. Int J Mol Sci 2022; 24:ijms24010556. [PMID: 36613998 PMCID: PMC9820211 DOI: 10.3390/ijms24010556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022] Open
Abstract
Ion transport molecules are involved in many physiological and pathological processes and are considered potential targets for cancer treatment. In the large family of ion transport molecules, potassium (K) ion channels, as surface-expressed proteins, show the highest variability and most frequent expression changes in many tumor types. The key to exploring the permeation of K+ through potassium channels lies in the conserved sequence TVGYG, which is common in the selectivity filter (SF) region of all potassium channels. We found that the K+ flux significantly increased with the help of a specific frequency terahertz electromagnetic wave (51.87 THz) in the KcsA channel using a molecular dynamics combined model through the combined simulation of the constant electric field method and ion imbalance method. This frequency has the strongest absorption peak in the infrared spectrum of -C=O groups in the SF region. With the applied electric field of 51.87 THz, the Y78 residue at the S1 site of the SF has a smaller vibration amplitude and a more stable structure, which enables the K+ to bind closely with the carbonyl oxygen atoms in the SF and realize ion conduction in a more efficient direct Coulomb knock-on.
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Affiliation(s)
- Yize Wang
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Hongguang Wang
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
- Correspondence: ; Tel.: +86-18191765263
| | - Wen Ding
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiaofei Zhao
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yongdong Li
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Chunliang Liu
- Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
- School of Electronic Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
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3
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Bergh C, Heusser SA, Howard R, Lindahl E. Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel. eLife 2021; 10:68369. [PMID: 34652272 PMCID: PMC8635979 DOI: 10.7554/elife.68369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 10/14/2021] [Indexed: 01/03/2023] Open
Abstract
Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels, the details of gating remain unclear, partly due to limited structural data and simulation timescales. Here, we used enhanced sampling to simulate the pH-gated channel GLIC, and construct Markov state models (MSMs) of gating. Consistent with new functional recordings, we report in oocytes, our analysis revealed differential effects of protonation and mutation on free-energy wells. Clustering of closed- versus open-like states enabled estimation of open probabilities and transition rates, while higher-order clustering affirmed conformational trends in gating. Furthermore, our models uncovered state- and protonation-dependent symmetrization. This demonstrates the applicability of MSMs to map energetic and conformational transitions between ion-channel functional states, and how they reproduce shifts upon activation or mutation, with implications for modeling neuronal function and developing state-selective drugs.
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Affiliation(s)
- Cathrine Bergh
- Science for Life Laboratory and Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Stephanie A Heusser
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Rebecca Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Erik Lindahl
- Science for Life Laboratory and Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
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4
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Lefebvre SN, Taly A, Menny A, Medjebeur K, Corringer PJ. Mutational analysis to explore long-range allosteric couplings involved in a pentameric channel receptor pre-activation and activation. eLife 2021; 10:60682. [PMID: 34590583 PMCID: PMC8504973 DOI: 10.7554/elife.60682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/29/2021] [Indexed: 01/23/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate chemical signaling through a succession of allosteric transitions that are yet not completely understood as intermediate states remain poorly characterized by structural approaches. In a previous study on the prototypic bacterial proton-gated channel GLIC, we generated several fluorescent sensors of the protein conformation that report a fast transition to a pre-active state, which precedes the slower process of activation with pore opening. Here, we explored the phenotype of a series of allosteric mutations, using simultaneous steady-state fluorescence and electrophysiological measurements over a broad pH range. Our data, fitted to a three-state Monod-Wyman-Changeux model, show that mutations at the subunit interface in the extracellular domain (ECD) principally alter pre-activation, while mutations in the lower ECD and in the transmembrane domain principally alter activation. We also show that propofol alters both transitions. Data are discussed in the framework of transition pathways generated by normal mode analysis (iModFit). It further supports that pre-activation involves major quaternary compaction of the ECD, and suggests that activation involves principally a reorganization of a ‘central gating region’ involving a contraction of the ECD β-sandwich and the tilt of the channel lining M2 helix.
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Affiliation(s)
- Solène N Lefebvre
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France.,Sorbonne Université, Collège doctoral, Paris, France
| | - Antoine Taly
- Institut de Biologie Physico-chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.,Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France
| | - Anaïs Menny
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France.,Sorbonne Université, Collège doctoral, Paris, France
| | - Karima Medjebeur
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France
| | - Pierre-Jean Corringer
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France
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5
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Elephants in the Dark: Insights and Incongruities in Pentameric Ligand-gated Ion Channel Models. J Mol Biol 2021; 433:167128. [PMID: 34224751 DOI: 10.1016/j.jmb.2021.167128] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
The superfamily of pentameric ligand-gated ion channels (pLGICs) comprises key players in electrochemical signal transduction across evolution, including historic model systems for receptor allostery and targets for drug development. Accordingly, structural studies of these channels have steadily increased, and now approach 250 depositions in the protein data bank. This review contextualizes currently available structures in the pLGIC family, focusing on morphology, ligand binding, and gating in three model subfamilies: the prokaryotic channel GLIC, the cation-selective nicotinic acetylcholine receptor, and the anion-selective glycine receptor. Common themes include the challenging process of capturing and annotating channels in distinct functional states; partially conserved gating mechanisms, including remodeling at the extracellular/transmembrane-domain interface; and diversity beyond the protein level, arising from posttranslational modifications, ligands, lipids, and signaling partners. Interpreting pLGIC structures can be compared to describing an elephant in the dark, relying on touch alone to comprehend the many parts of a monumental beast: each structure represents a snapshot in time under specific experimental conditions, which must be integrated with further structure, function, and simulations data to build a comprehensive model, and understand how one channel may fundamentally differ from another.
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6
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Barabash M, Gibby WAT, Guardiani C, Luchinsky DG, Luan B, Smolyanitsky A, McClintock PVE. Field-Dependent Dehydration and Optimal Ionic Escape Paths for C 2N Membranes. J Phys Chem B 2021; 125:7044-7059. [PMID: 34115497 PMCID: PMC8279548 DOI: 10.1021/acs.jpcb.1c03255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/29/2021] [Indexed: 11/28/2022]
Abstract
Most analytic theories describing electrostatically driven ion transport through water-filled nanopores assume that the corresponding permeation barriers are bias-independent. While this assumption may hold for sufficiently wide pores under infinitely small bias, transport through subnanometer pores under finite bias is difficult to interpret analytically. Given recent advances in subnanometer pore fabrication and the rapid progress in detailed computer simulations, it is important to identify and understand the specific field-induced phenomena arising during ion transport. Here we consider an atomistic model of electrostatically driven ion permeation through subnanoporous C2N membranes. We analyze probability distributions of ionic escape trajectories and show that the optimal escape path switches between two different configurations depending on the bias magnitude. We identify two distinct mechanisms contributing to field-induced changes in transport-opposing barriers: a weak one arising from field-induced ion dehydration and a strong one due to the field-induced asymmetry of the hydration shells. The simulated current-voltage characteristics are compared with the solution of the 1D Nernst-Planck model. Finally, we show that the deviation of simulated currents from analytic estimates for large fields is consistent with the field-induced barriers and the observed changes in the optimal ion escape path.
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Affiliation(s)
| | - William A. T. Gibby
- Department
of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Carlo Guardiani
- Department
of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
- Department
of Mechanical and Aerospace Engineering, Sapienza University, 00184 Rome, Italy
| | - Dmitry G. Luchinsky
- Department
of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
- Ames
Research Center, KBR, Inc., Moffett Field, California 94035, United States
| | - Binquan Luan
- Computational
Biological Center, IBM Thomas J. Watson
Research, Yorktown
Heights, New York 10598, United States
| | - Alex Smolyanitsky
- Applied
Chemicals and Materials Division, National
Institute of Standards and Technology, Boulder, Colorado 80305, United States
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7
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Li Y, Chang C, Zhu Z, Sun L, Fan C. Terahertz Wave Enhances Permeability of the Voltage-Gated Calcium Channel. J Am Chem Soc 2021; 143:4311-4318. [PMID: 33625851 DOI: 10.1021/jacs.0c09401] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A deficiency of Ca2+ fluxes arising from dysfunctional voltage-gated calcium channels has been associated with a list of calcium channelopathies such as epilepsy, hypokalemic periodic paralysis, episodic ataxia, etc. Apart from analyzing the pathogenic channel mutations, understanding how the channel regulates the ion conduction would be instructive to the treatment as well. In the present work, in relating the free energetics of Ca2+ transport to the calcium channel, we demonstrate the importance of bridging Ca2+ hydration waters, which form hydrogen bonds with channel -COO- and -C═O groups and enable a long-distance effect on the Ca2+ permeation. By firing a terahertz wave which resonates with the stretching mode of either the -COO- or the -C═O group, we obtain significantly enhanced selectivity and conductance of Ca2+. The Ca2+ free energy negatively grows nearly 5-fold. The direct evidence is the reinforced hydrogen bonds. In addition, thanks to forced vibrations, -COO- contributes to raised permeation as well even under a field in resonance with -C═O, and vice versa. Since the resonant terahertz field could manipulate the conduction of calcium channels, it has potential applications in therapeutic intervention such as rectifying a Ca2+ deficiency in degraded calcium channels, inducing apoptosis of tumor cells with overloaded calcium etc.
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Affiliation(s)
- Yangmei Li
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, People's Republic of China
| | - Chao Chang
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, People's Republic of China.,Key Laboratory of Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Zhi Zhu
- School of Optical-Electrical Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Lan Sun
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, People's Republic of China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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8
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Cottone G, Chiodo L, Maragliano L. Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor. J Chem Inf Model 2020; 60:5045-5056. [PMID: 32803965 PMCID: PMC8011927 DOI: 10.1021/acs.jcim.0c00549] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Molecular
studies of human pentameric ligand-gated ion channels
(LGICs) expressed in neurons and at neuromuscular junctions are of
utmost importance in the development of therapeutic strategies for
neurological disorders. We focus here on the nicotinic acetylcholine
receptor nAChR-α7, a homopentameric channel widely expressed
in the human brain, with a proven role in a wide spectrum of disorders
including schizophrenia and Alzheimer’s disease. By exploiting
an all-atom structural model of the full (transmembrane and extracellular)
protein in the open, agonist-bound conformation we recently developed,
we evaluate the free energy and the mean first passage time of single-ion
permeation using molecular dynamics simulations and the milestoning
method with Voronoi tessellation. The results for the wild-type channel
provide the first available mapping of the potential of mean force
in the full-length α7 nAChR, reveal its expected cationic nature,
and are in good agreement with simulation data for other channels
of the LGIC family and with experimental data on nAChRs. We then investigate
the role of a specific mutation directly related to ion selectivity
in LGICs, the E-1′ → A-1′ substitution at the
cytoplasmatic selectivity filter. We find that the mutation strongly
affects sodium and chloride permeation in opposite directions, leading
to a complete inversion of selectivity, at variance with the limited
experimental results available that classify this mutant as cationic.
We thus provide structural determinants for the observed cationic-to-anionic
inversion, revealing a key role of the protonation state of residue
rings far from the mutation, in the proximity of the hydrophobic channel
gate.
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Affiliation(s)
- Grazia Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Letizia Chiodo
- Department of Engineering, Campus Bio-Medico University of Rome, Via Á. del Portillo 21, 00128 Rome, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132 Genova, Italy
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9
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Faulkner C, Plant DF, de Leeuw NH. Modulation of the Gloeobacter violaceus Ion Channel by Fentanyl: A Molecular Dynamics Study. Biochemistry 2019; 58:4804-4808. [PMID: 31718178 DOI: 10.1021/acs.biochem.9b00881] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fentanyl is an opioid analgesic, which is routinely used in general surgery to suppress the sensation of pain and as the analgesic component in the induction and maintenance of anesthesia. Fentanyl is also used as the main component to induce anesthesia and as a potentiator to the general anesthetic propofol. The mechanism by which fentanyl induces its anesthetic action is still unclear, and we have therefore employed fully atomistic molecular dynamics simulations to probe this process by simulating the interactions of fentanyl with the Gloeobacter violaceus ligand-gated ion channel (GLIC). In this paper, we identify multiple extracellular fentanyl binding sites, which are different from the transmembrane general anesthetic binding sites observed for propofol and other general anesthetics. Our simulations identify a novel fentanyl binding site within the GLIC that results in conformational changes that inhibit conduction through the channel.
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Affiliation(s)
- Christopher Faulkner
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff CF10 3AT , United Kingdom
| | - David F Plant
- Atomic Weapons Establishment (AWE) , Aldermaston, Reading RG7 4PR , United Kingdom
| | - Nora H de Leeuw
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff CF10 3AT , United Kingdom
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10
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Oakes V, Domene C. Capturing the Molecular Mechanism of Anesthetic Action by Simulation Methods. Chem Rev 2018; 119:5998-6014. [DOI: 10.1021/acs.chemrev.8b00366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Victoria Oakes
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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11
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Gonzalez-Gutierrez G, Wang Y, Cymes GD, Tajkhorshid E, Grosman C. Chasing the open-state structure of pentameric ligand-gated ion channels. J Gen Physiol 2017; 149:1119-1138. [PMID: 29089419 PMCID: PMC5715906 DOI: 10.1085/jgp.201711803] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 09/14/2017] [Accepted: 10/05/2017] [Indexed: 11/25/2022] Open
Abstract
Members of the pentameric ligand-gated ion channel family have been crystallized in different conformations, including one in which the transmembrane pore is surprisingly wide. Gonzalez-Gutierrez et al. show that the open-channel conformation of animal members is more similar to the models with narrow pores. Remarkable advances have been made toward the structural characterization of ion channels in the last two decades. However, the unambiguous assignment of well-defined functional states to the obtained structural models has proved challenging. In the case of the superfamily of nicotinic-receptor channels (also referred to as pentameric ligand-gated ion channels [pLGICs]), for example, two different types of model of the open-channel conformation have been proposed on the basis of structures solved to resolutions better than 4.0 Å. At the level of the transmembrane pore, the open-state models of the proton-gated pLGIC from Gloeobacter violaceus (GLIC) and the invertebrate glutamate-gated Cl– channel (GluCl) are very similar to each other, but that of the glycine receptor (GlyR) is considerably wider. Indeed, the mean distances between the axis of ion permeation and the Cα atoms at the narrowest constriction of the pore (position −2′) differ by ∼2 Å in these two classes of model, a large difference when it comes to understanding the physicochemical bases of ion conduction and charge selectivity. Here, we take advantage of the extreme open-channel stabilizing effect of mutations at pore-facing position 9′. We find that the I9′A mutation slows down entry into desensitization of GLIC to the extent that macroscopic currents decay only slightly by the end of pH 4.5 solution applications to the extracellular side for several minutes. We crystallize (at pH 4.5) two variants of GLIC carrying this mutation and solve their structures to resolutions of 3.12 Å and 3.36 Å. Furthermore, we perform all-atom molecular dynamics simulations of ion permeation and picrotoxinin block, using the different open-channel structural models. On the basis of these results, we favor the notion that the open-channel structure of pLGICs from animals is much closer to that of the narrow models (of GLIC and GluCl) than it is to that of the GlyR.
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Affiliation(s)
| | - Yuhang Wang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Gisela D Cymes
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Claudio Grosman
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL .,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL
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12
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Chen D. Fractional Poisson-Nernst-Planck Model for Ion Channels I: Basic Formulations and Algorithms. Bull Math Biol 2017; 79:2696-2726. [PMID: 28940114 DOI: 10.1007/s11538-017-0349-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/15/2017] [Indexed: 11/28/2022]
Abstract
In this work, we propose a fractional Poisson-Nernst-Planck model to describe ion permeation in gated ion channels. Due to the intrinsic conformational changes, crowdedness in narrow channel pores, binding and trapping introduced by functioning units of channel proteins, ionic transport in the channel exhibits a power-law-like anomalous diffusion dynamics. We start from continuous-time random walk model for a single ion and use a long-tailed density distribution function for the particle jump waiting time, to derive the fractional Fokker-Planck equation. Then, it is generalized to the macroscopic fractional Poisson-Nernst-Planck model for ionic concentrations. Necessary computational algorithms are designed to implement numerical simulations for the proposed model, and the dynamics of gating current is investigated. Numerical simulations show that the fractional PNP model provides a more qualitatively reasonable match to the profile of gating currents from experimental observations. Meanwhile, the proposed model motivates new challenges in terms of mathematical modeling and computations.
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Affiliation(s)
- Duan Chen
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC, USA.
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13
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Ion BF, Wells MM, Chen Q, Xu Y, Tang P. Ketamine Inhibition of the Pentameric Ligand-Gated Ion Channel GLIC. Biophys J 2017; 113:605-612. [PMID: 28793215 DOI: 10.1016/j.bpj.2017.06.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/14/2017] [Accepted: 06/22/2017] [Indexed: 12/11/2022] Open
Abstract
Ketamine inhibits pentameric ligand-gated ion channels (pLGICs), including the bacterial pLGIC from Gloeobacter violaceus (GLIC). The crystal structure of GLIC shows R-ketamine bound to an extracellular intersubunit cavity. Here, we performed molecular dynamics simulations of GLIC in the absence and presence of R- or S-ketamine. No stable binding of S-ketamine in the original cavity was observed in the simulations, largely due to its unfavorable access to residue D154, which provides important electrostatic interactions to stabilize R-ketamine binding. Contrary to the symmetric binding shown in the crystal structure, R-ketamine moved away from some of the binding sites and was bound to GLIC asymmetrically at the end of simulations. The asymmetric binding is consistent with the experimentally measured negative cooperativity of ketamine binding to GLIC. In the presence of R-ketamine, all subunits showed changes in structure and dynamics, irrespective of binding stability; the extracellular intersubunit cavity expanded and intersubunit electrostatic interactions involved in channel activation were altered. R-ketamine binding promoted a conformational shift toward closed GLIC. Conformational changes near the ketamine-binding site were propagated to the interface between the extracellular and transmembrane domains, and further to the pore-lining TM2 through two pathways: pre-TM1 and the β1-β2 loop. Both signaling pathways have been predicted previously using the perturbation-based Markovian transmission model. The study provides a structural and dynamics basis for the inhibitory modulation of ketamine on pLGICs.
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Affiliation(s)
- Bogdan F Ion
- Departments of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Marta M Wells
- Departments of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Qiang Chen
- Departments of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yan Xu
- Departments of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Pei Tang
- Departments of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
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14
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Arcario MJ, Mayne CG, Tajkhorshid E. A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the Gloeobacter violaceus ion channel. J Biol Chem 2017; 292:9480-9492. [PMID: 28420728 PMCID: PMC5465477 DOI: 10.1074/jbc.m117.780197] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/10/2017] [Indexed: 12/30/2022] Open
Abstract
General anesthetics exert their effects on the central nervous system by acting on ion channels, most notably pentameric ligand-gated ion channels. Although numerous studies have focused on pentameric ligand-gated ion channels, the details of anesthetic binding and channel modulation are still debated. A better understanding of the anesthetic mechanism of action is necessary for the development of safer and more efficacious drugs. Herein, we present a computational study identifying two anesthetic binding sites in the transmembrane domain of the Gloeobacter violaceus ligand-gated ion channel (GLIC) channel, characterize the putative binding pathway, and observe structural changes associated with channel function. Molecular simulations of desflurane reveal a binding pathway to GLIC via a membrane-embedded tunnel using an intrasubunit protein lumen as the conduit, an observation that explains the Meyer-Overton hypothesis, or why the lipophilicity of an anesthetic and its potency are generally proportional. Moreover, employing high concentrations of ligand led to the identification of a second transmembrane site (TM2) that inhibits dissociation of anesthetic from the TM1 site and is consistent with the high concentrations of anesthetics required to achieve clinical effects. Finally, asymmetric binding patterns of anesthetic to the channel were found to promote an iris-like conformational change that constricts and dehydrates the ion pore, creating a 13.5 kcal/mol barrier to ion translocation. Together with previous studies, the simulations presented herein demonstrate a novel anesthetic binding site in GLIC that is accessed through a membrane-embedded tunnel and interacts with a previously known site, resulting in conformational changes that produce a non-conductive state of the channel.
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Affiliation(s)
- Mark J Arcario
- From the Center for Biophysics and Quantitative Biology.,Department of Biochemistry, College of Medicine, and.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Christopher G Mayne
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Emad Tajkhorshid
- From the Center for Biophysics and Quantitative Biology, .,Department of Biochemistry, College of Medicine, and.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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15
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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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16
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Jun I, Cheng MH, Sim E, Jung J, Suh BL, Kim Y, Son H, Park K, Kim CH, Yoon JH, Whitcomb DC, Bahar I, Lee MG. Pore dilatation increases the bicarbonate permeability of CFTR, ANO1 and glycine receptor anion channels. J Physiol 2016; 594:2929-55. [PMID: 26663196 DOI: 10.1113/jp271311] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 12/06/2015] [Indexed: 01/30/2023] Open
Abstract
KEY POINTS Cellular stimuli can modulate the ion selectivity of some anion channels, such as CFTR, ANO1 and the glycine receptor (GlyR), by changing pore size. Ion selectivity of CFTR, ANO1 and GlyR is critically affected by the electric permittivity and diameter of the channel pore. Pore size change affects the energy barriers of ion dehydration as well as that of size-exclusion of anion permeation. Pore dilatation increases the bicarbonate permeability (P HC O3/ Cl ) of CFTR, ANO1 and GlyR. Dynamic change in P HC O3/ Cl may mediate many physiological and pathological processes. ABSTRACT Chloride (Cl(-) ) and bicarbonate (HCO3 (-) ) are two major anions and their permeation through anion channels plays essential roles in our body. However, the mechanism of ion selection by the anion channels is largely unknown. Here, we provide evidence that pore dilatation increases the bicarbonate permeability (P HC O3/ Cl ) of anion channels by reducing energy barriers of size-exclusion and ion dehydration of HCO3 (-) permeation. Molecular, physiological and computational analyses of major anion channels, such as cystic fibrosis transmembrane conductance regulator (CFTR), anoctamin-1(ANO1/TMEM16A) and the glycine receptor (GlyR), revealed that the ion selectivity of anion channels is basically determined by the electric permittivity and diameter of the pore. Importantly, cellular stimuli dynamically modulate the anion selectivity of CFTR and ANO1 by changing the pore size. In addition, pore dilatation by a mutation in the pore-lining region alters the anion selectivity of GlyR. Changes in pore size affected not only the energy barriers of size exclusion but that of ion dehydration by altering the electric permittivity of water-filled cavity in the pore. The dynamic increase in P HC O3/ Cl by pore dilatation may have many physiological and pathophysiological implications ranging from epithelial HCO3 (-) secretion to neuronal excitation.
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Affiliation(s)
- Ikhyun Jun
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 120-752, Korea.,Department of Ophthalmology, Yonsei University College of Medicine, Seoul, 120-752, Korea
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eunji Sim
- Department of Chemistry, Yonsei University College of Science, Seoul, 120-749, Korea
| | - Jinsei Jung
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 120-752, Korea.,Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, 120-752, Korea
| | - Bong Lim Suh
- Department of Chemistry, Yonsei University College of Science, Seoul, 120-749, Korea
| | - Yonjung Kim
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 120-752, Korea
| | - Hankil Son
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 120-752, Korea
| | - Kyungsoo Park
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 120-752, Korea
| | - Chul Hoon Kim
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 120-752, Korea
| | - Joo-Heon Yoon
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, 120-752, Korea
| | - David C Whitcomb
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Min Goo Lee
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 120-752, Korea
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17
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An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels. Nat Commun 2016; 7:8770. [PMID: 26753910 PMCID: PMC4730032 DOI: 10.1038/ncomms9770] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 10/01/2015] [Indexed: 01/07/2023] Open
Abstract
Gap junction channels mediate intercellular signalling that is crucial in tissue development, homeostasis and pathologic states such as cardiac arrhythmias, cancer and trauma. To explore the mechanism by which Ca(2+) blocks intercellular communication during tissue injury, we determined the X-ray crystal structures of the human Cx26 gap junction channel with and without bound Ca(2+). The two structures were nearly identical, ruling out both a large-scale structural change and a local steric constriction of the pore. Ca(2+) coordination sites reside at the interfaces between adjacent subunits, near the entrance to the extracellular gap, where local, side chain conformational rearrangements enable Ca(2+)chelation. Computational analysis revealed that Ca(2+)-binding generates a positive electrostatic barrier that substantially inhibits permeation of cations such as K(+) into the pore. Our results provide structural evidence for a unique mechanism of channel regulation: ionic conduction block via an electrostatic barrier rather than steric occlusion of the channel pore.
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18
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Arcario MJ, Mayne CG, Tajkhorshid E. Atomistic models of general anesthetics for use in in silico biological studies. J Phys Chem B 2014; 118:12075-86. [PMID: 25303275 PMCID: PMC4207551 DOI: 10.1021/jp502716m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
While small molecules have been used
to induce anesthesia in a
clinical setting for well over a century, a detailed understanding
of the molecular mechanism remains elusive. In this study, we utilize
ab initio calculations to develop a novel set of CHARMM-compatible
parameters for the ubiquitous modern anesthetics desflurane, isoflurane,
sevoflurane, and propofol for use in molecular dynamics (MD) simulations.
The parameters generated were rigorously tested against known experimental
physicochemical properties including dipole moment, density, enthalpy
of vaporization, and free energy of solvation. In all cases, the anesthetic
parameters were able to reproduce experimental measurements, signifying
the robustness and accuracy of the atomistic models developed. The
models were then used to study the interaction of anesthetics with
the membrane. Calculation of the potential of mean force for inserting
the molecules into a POPC bilayer revealed a distinct energetic minimum
of 4–5 kcal/mol relative to aqueous solution at the level of
the glycerol backbone in the membrane. The location of this minimum
within the membrane suggests that anesthetics partition to the membrane
prior to binding their ion channel targets, giving context to the
Meyer–Overton correlation. Moreover, MD simulations of these
drugs in the membrane give rise to computed membrane structural parameters,
including atomic distribution, deuterium order parameters, dipole
potential, and lateral stress profile, that indicate partitioning
of anesthetics into the membrane at the concentration range studied
here, which does not appear to perturb the structural integrity of
the lipid bilayer. These results signify that an indirect, membrane-mediated
mechanism of channel modulation is unlikely.
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Affiliation(s)
- Mark J Arcario
- Center for Biophysics and Computational Biology, Department of Biochemistry, College of Medicine, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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19
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Turchenkov DA, Bystrov VS. Conductance simulation of the purinergic P2X2, P2X4, and P2X7 ionic channels using a combined Brownian dynamics and molecular dynamics approach. J Phys Chem B 2014; 118:9119-27. [PMID: 25006754 DOI: 10.1021/jp501177d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper investigates the application of an original combined approach of molecular and Brownian dynamic methods with quantum chemistry calculations for modeling the process of conductance of ion channels using purinergic P2X family receptors P2X2, P2X4, and P2X7 as a case study. A simplified model of the ionic channel in the lipid bilayer has been developed. A high level of conductance (30 pS) of P2X2 ionic channel together with the key role of Asp349 in forming the selectivity filter of P2X2 has been shown by using this approach. Calculated P2X2 permeability to monovalent cations Li(+), Na(+), and K(+) conforms to the free diffusion coefficient of these ions, which shows the low selectivity of P2X2 ionic channel.
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20
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Sun H, Li Y, Tian S, Wang J, Hou T. P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape. PLoS Comput Biol 2014; 10:e1003729. [PMID: 25033171 PMCID: PMC4102447 DOI: 10.1371/journal.pcbi.1003729] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/02/2014] [Indexed: 01/04/2023] Open
Abstract
Tyrosine kinases are regarded as excellent targets for chemical drug therapy of carcinomas. However, under strong purifying selection, drug resistance usually occurs in the cancer cells within a short term. Many cases of drug resistance have been found to be associated with secondary mutations in drug target, which lead to the attenuated drug-target interactions. For example, recently, an acquired secondary mutation, G2032R, has been detected in the drug target, ROS1 tyrosine kinase, from a crizotinib-resistant patient, who responded poorly to crizotinib within a very short therapeutic term. It was supposed that the mutation was located at the solvent front and might hinder the drug binding. However, a different fact could be uncovered by the simulations reported in this study. Here, free energy surfaces were characterized by the drug-target distance and the phosphate-binding loop (P-loop) conformational change of the crizotinib-ROS1 complex through advanced molecular dynamics techniques, and it was revealed that the more rigid P-loop region in the G2032R-mutated ROS1 was primarily responsible for the crizotinib resistance, which on one hand, impaired the binding of crizotinib directly, and on the other hand, shortened the residence time induced by the flattened free energy surface. Therefore, both of the binding affinity and the drug residence time should be emphasized in rational drug design to overcome the kinase resistance. Cancers can eventually confer drug resistance to the continued medication. In most cases, mutations occurred in a drug target can attenuate the binding affinity of the drugs. Here, we studied the drug resistance mechanisms of the mutations G2032R in the ROS1 tyrosine kinase in fusion-type NSCLC. It is well known that the phosphate-binding loop (P-loop) plays a vital role in the binding of competitive inhibitors in tyrosine kinases, and numerous mutations have been found occurred around the P-loop, which may affect the binding/unbinding process of a drug. Free energy surfaces were constructed to characterize the impact of the mutation to the binding/unbinding process of a well-known NSCLC drug, crizotinib. Two advanced free energy calculation methods, namely funnel based well-tempered metadynamics and umbrella sampling based absolute binding free energy calculation achieved consistent results with the experimental data, suggesting that the rigid P-loop of the mutated target was mainly responsible for the crizotinib resistance to ROS1 tyrosine kinase.
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Affiliation(s)
- Huiyong Sun
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Sheng Tian
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Junmei Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Tingjun Hou
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail:
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21
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Salari R, Murlidaran S, Brannigan G. Pentameric Ligand-gated Ion Channels : Insights from Computation. MOLECULAR SIMULATION 2014; 40:821-829. [PMID: 25931676 PMCID: PMC4412168 DOI: 10.1080/08927022.2014.896462] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Pentameric ligand-gated ion channels (pLGICs) conduct upon the binding of an agonist and are fundamental to neurotransmission. New insights into the complex mechanisms underlying pLGIC gating, ion selectivity, and modulation have recently been gained via a series of crystal structures in prokaryotes and C .elegans, as well as computational studies relying on these structures. Here we review contributions from a variety of computational approaches, including normal mode analysis, automated docking, and fully atomistic molecular dynamics simulation. Examples from our own research, particularly concerning interactions with general anesthetics and lipids, are used to illustrate predictive results complementary to crystallographic studies.
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Affiliation(s)
- Reza Salari
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
- Department of Physics, Rutgers University, Camden, NJ
| | - Sruthi Murlidaran
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
- Department of Physics, Rutgers University, Camden, NJ
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22
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Laghaei R, Kowallis W, Evans DG, Coalson RD. Calculation of Iron Transport through Human H-chain Ferritin. J Phys Chem A 2014; 118:7442-53. [DOI: 10.1021/jp500198u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rozita Laghaei
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - William Kowallis
- Department
of Chemistry, Carlow University, Pittsburgh, Pennsylvania 15213, United States
| | - Deborah G. Evans
- The
Nanoscience and Microsystems Program and the Department of Chemistry
and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Rob D. Coalson
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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23
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Wei GW. Multiscale Multiphysics and Multidomain Models I: Basic Theory. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013; 12:10.1142/S021963361341006X. [PMID: 25382892 PMCID: PMC4220694 DOI: 10.1142/s021963361341006x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field.
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Affiliation(s)
- Guo-Wei Wei
- Department of Mathematics Michigan State University, MI 48824, USA Department of Electrical and Computer Engineering Michigan State University, MI 48824, USA Department of Biochemistry and Molecular Biology Michigan State University, MI 48824, USA
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24
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Manson AC, Coalson RD. Overdamped Dynamics of Folded Protein Domains within a Locally Harmonic Basin Using Coarse Graining Based on a Partition of Compact Flexible Clusters. J Phys Chem B 2013; 117:6646-55. [DOI: 10.1021/jp4017147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anthony C. Manson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Rob D. Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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25
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Xie HB, Wang J, Sha Y, Cheng MS. Molecular dynamics investigation of Cl(-) transport through the closed and open states of the 2α12β2γ2 GABA(A) receptor. Biophys Chem 2013; 180-181:1-9. [PMID: 23771165 DOI: 10.1016/j.bpc.2013.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/18/2013] [Accepted: 05/20/2013] [Indexed: 01/16/2023]
Abstract
The α1β2γ2 gamma-aminobutyric type A receptor (GABA(A)R) is one of the most widely expressed GABA(A)R subtypes in the mammalian brain. GABA(A)Rsbelonging to the Cys-loop superfamily of ligand-gated ion channels have been identified as key targets for many clinical drugs, and the motions that govern the gating mechanism are still not well understood. In this study, an open-state GABA(A)R was constructed using the structure of the glutamate-gated chloride channel (GluCl), which has a high sequence identity to GABA(A)R. A closed-state model was constructed using the structure of the nicotinic acetylcholine receptor (nAChR). Molecular dynamics simulations of the open-state and closed-state GABA(A)R were performed. We calculated the electrostatic potential of the two conformations, the pore radius of the two ion channels and the root-mean-square fluctuation. We observed the presence of two positively charged girdles around the ion channel and found flexible regions in the GABA(A)R. Then, the free-energy of chloride ion permeations through the closed-state and open-state G GABA(A)R has been estimated using adaptive biasing force (ABF) simulation. For the closed-state G GABA(A)R, we observed two major energy barriers for chloride ion translocation in the transmembrane domain (TMD). For the open-state GABA(A)R, there was only one energy barrier formed by two Thr261 (α1), two Thr255 (β2) and one Thr271 (γ2). By using ABF simulation, the overall free-energy profile is obtained for Cl(-) transporting through GABA(A)R, which gives a complete map of the ion channel of Cl(-) permeation.
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Affiliation(s)
- Hong-Bo Xie
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, PR China
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26
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Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. EMBO J 2013; 32:728-41. [PMID: 23403925 PMCID: PMC3590989 DOI: 10.1038/emboj.2013.17] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 01/07/2013] [Indexed: 12/14/2022] Open
Abstract
To understand the molecular mechanism of ion permeation in pentameric ligand-gated ion channels (pLGIC), we solved the structure of an open form of GLIC, a prokaryotic pLGIC, at 2.4 Å. Anomalous diffraction data were used to place bound anions and cations. This reveals ordered water molecules at the level of two rings of hydroxylated residues (named Ser6' and Thr2') that contribute to the ion selectivity filter. Two water pentagons are observed, a self-stabilized ice-like water pentagon and a second wider water pentagon, with one sodium ion between them. Single-channel electrophysiology shows that the side-chain hydroxyl of Ser6' is crucial for ion translocation. Simulations and electrostatics calculations complemented the description of hydration in the pore and suggest that the water pentagons observed in the crystal are important for the ion to cross hydrophobic constriction barriers. Simulations that pull a cation through the pore reveal that residue Ser6' actively contributes to ion translocation by reorienting its side chain when the ion is going through the pore. Generalization of these findings to the pLGIC family is proposed.
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27
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Mowrey D, Cheng MH, Liu LT, Willenbring D, Lu X, Wymore T, Xu Y, Tang P. Asymmetric ligand binding facilitates conformational transitions in pentameric ligand-gated ion channels. J Am Chem Soc 2013; 135:2172-80. [PMID: 23339564 DOI: 10.1021/ja307275v] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The anesthetic propofol inhibits the currents of the homopentameric ligand-gated ion channel GLIC, yet the crystal structure of GLIC with five propofol molecules bound symmetrically shows an open-channel conformation. To address this dilemma and determine if the symmetry of propofol binding sites affects the channel conformational transition, we performed a total of 1.5 μs of molecular dynamics simulations for different GLIC systems with propofol occupancies of 0, 1, 2, 3, and 5. GLIC without propofol binding or with five propofol molecules bound symmetrically, showed similar channel conformation and hydration status over multiple replicates of 100-ns simulations. In contrast, asymmetric binding to one, two or three equivalent sites in different subunits accelerated the channel dehydration, increased the conformational heterogeneity of the pore-lining TM2 helices, and shifted the lateral and radial tilting angles of TM2 toward a closed-channel conformation. The results differentiate two groups of systems based on the propofol binding symmetry. The difference between symmetric and asymmetric groups is correlated with the variance in the propofol-binding cavity adjacent to the hydrophobic gate and the force imposed by the bound propofol. Asymmetrically bound propofol produced greater variance in the cavity size that could further elevate the conformation heterogeneity. The force trajectory generated by propofol in each subunit over the course of a simulation exhibits an ellipsoidal shape, which has the larger component tangential to the pore. Asymmetric propofol binding creates an unbalanced force that expedites the channel conformation transitions. The findings from this study not only suggest that asymmetric binding underlies the propofol functional inhibition of GLIC, but also advocate for the role of symmetry breaking in facilitating channel conformational transitions.
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Affiliation(s)
- David Mowrey
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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Tillman T, Cheng MH, Chen Q, Tang P, Xu Y. Reversal of ion-charge selectivity renders the pentameric ligand-gated ion channel GLIC insensitive to anaesthetics. Biochem J 2013; 449:61-8. [PMID: 22978431 PMCID: PMC3992983 DOI: 10.1042/bj20121072] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
pLGICs (pentameric ligand-gated ion channels) are a family of structurally homologous cation and anion channels involved in neurotransmission. Cation-selective members of the pLGIC family are typically inhibited by general anaesthetics, whereas anion-selective members are potentiated. GLIC is a prokaryotic cation pLGIC and can be inhibited by clinical concentrations of general anaesthetics. The introduction of three mutations, Y221A (Y-3'A), E222P (E-2'P) and N224R (N0'R), at the selectivity filter and one, A237T (A13'T), at the hydrophobic gate, converted GLIC into an anion channel. The mutated GLIC (GLIC4) became insensitive to the anaesthetics propofol and etomidate, as well as the channel blocker picrotoxin. MD (molecular dynamics) simulations revealed changes in the structure and dynamics of GLIC4 in comparison with GLIC, particularly in the tilting angles of the pore-lining helix [TM2 (transmembrane helix 2)] that consequently resulted in different pore radius and hydration profiles. Propofol binding to an intra-subunit site of GLIC shifted the tilting angles of TM2 towards closure at the hydrophobic gate region, consistent with propofol inhibition of GLIC. In contrast, the pore of GLIC4 was much more resilient to perturbation from propofol binding. The present study underscores the importance of pore dynamics and conformation to anaesthetic effects on channel functions.
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Affiliation(s)
- Tommy Tillman
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Mary H. Cheng
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, PA 15261
- Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Qiang Chen
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Pei Tang
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, PA 15261
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261
- Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Yan Xu
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, PA 15261
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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30
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Cheng MH, Coalson RD. Energetics and ion permeation characteristics in a glutamate-gated chloride (GluCl) receptor channel. J Phys Chem B 2012; 116:13637-43. [PMID: 23088363 DOI: 10.1021/jp3074915] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
An invertebrate glutamate-gated chloride channel (GluCl) has recently been crystallized in an open-pore state. This channel is homologous to the human Cys-loop receptor family of pentameric ligand-gated ion channels, including anion-selective GlyR and GABAR and cation-selective nAChR and 5HT(3). We implemented molecular dynamics (MD) in conjunction with an elastic network model to perturb the X-ray structure of GluCl and investigated the open channel stability and its ion permeation characteristics. Our study suggests that TM2 helical tilting may close GluCl near the hydrophobic constriction L254 (L9'), similar to its cation-selective homologues. Ion permeation characteristics were determined by Brownian dynamics simulations using a hybrid MD/continuum electrostatics approach to evaluate the free energy profiles for ion transport. Near the selectivity filter region (P243 or P-2'), the free energy barrier for Na(+) transport is over 4 k(B)T higher than that for Cl(-), indicating anion selectivity of the channel. Furthermore, three layers of positivity charged rings in the extracellular domain also contribute to charge selectivity and facilitate Cl(-) permeability over Na(+). Collectively, the charge selectivity of GluCl may be determined by overall electrostatic and ion dehydration effects, perhaps not deriving from a single region of the channel (the selectivity filter region near the intracellular entrance).
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Affiliation(s)
- Mary Hongying Cheng
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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Abstract
Complex biological systems are intimately linked to their environment, a very crowded and equally complex solution compartmentalized by fluid membranes. Modeling such systems remains challenging and requires a suitable representation of these solutions and their interfaces. Here, we focus on particle-based modeling at an atomistic level using molecular dynamics (MD) simulations. As an example, we discuss important steps in modeling the solution chemistry of an ion channel of the ligand-gated ion channel receptor family, a major target of many drugs including anesthetics and addiction treatments. The bacterial pentameric ligand-gated ion channel (pLGIC) called GLIC provides clues about the functional importance of solvation, in particular for mechanisms such as permeation and gating. We present some current challenges along with promising novel modeling approaches.
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Murail S, Howard RJ, Broemstrup T, Bertaccini EJ, Harris RA, Trudell JR, Lindahl E. Molecular mechanism for the dual alcohol modulation of Cys-loop receptors. PLoS Comput Biol 2012; 8:e1002710. [PMID: 23055913 PMCID: PMC3464191 DOI: 10.1371/journal.pcbi.1002710] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 08/15/2012] [Indexed: 11/29/2022] Open
Abstract
Cys-loop receptors constitute a superfamily of pentameric ligand-gated ion channels (pLGICs), including receptors for acetylcholine, serotonin, glycine and γ-aminobutyric acid. Several bacterial homologues have been identified that are excellent models for understanding allosteric binding of alcohols and anesthetics in human Cys-loop receptors. Recently, we showed that a single point mutation on a prokaryotic homologue (GLIC) could transform it from a channel weakly potentiated by ethanol into a highly ethanol-sensitive channel. Here, we have employed molecular simulations to study ethanol binding to GLIC, and to elucidate the role of the ethanol-enhancing mutation in GLIC modulation. By performing 1-µs simulations with and without ethanol on wild-type and mutated GLIC, we observed spontaneous binding in both intra-subunit and inter-subunit transmembrane cavities. In contrast to the glycine receptor GlyR, in which we previously observed ethanol binding primarily in an inter-subunit cavity, ethanol primarily occupied an intra-subunit cavity in wild-type GLIC. However, the highly ethanol-sensitive GLIC mutation significantly enhanced ethanol binding in the inter-subunit cavity. These results demonstrate dramatic effects of the F(14′)A mutation on the distribution of ligands, and are consistent with a two-site model of pLGIC inhibition and potentiation. Communication from one nerve cell to the next is an essential process for brain and muscle function. Nerve impulses result in release of transmitter molecules from one cell that bind to receptors on the next cell. Transmitter binding opens a pore in each receptor and ions flow across the membrane, leading to either enhancement or inhibition of new nerve impulses. These receptors are modulated by numerous drugs, including alcohols and anesthetics; identifying the precise location of modulator binding is critical for drug development. We have used computer simulation methods to model alcohol diffusion and binding to a receptor. By modifying a single residue in the receptor, we were able to move the location of the binding site and dramatically alter alcohol modulation, which supports a model with two separate binding sites for enhancement and inhibition in this family of receptors.
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Affiliation(s)
- Samuel Murail
- Science for Life Laboratory, KTH Royal Institute of Technology & Stockholm University, Stockholm, Sweden
- Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden
| | - Rebecca J. Howard
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas, United States of America
| | - Torben Broemstrup
- Science for Life Laboratory, KTH Royal Institute of Technology & Stockholm University, Stockholm, Sweden
- Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden
| | - Edward J. Bertaccini
- Department of Anesthesia, Palo Alto Veterans Affairs Health Care System, Palo Alto, California, United States of America
- Department of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford University School of Medicine, Stanford, United States of America
| | - R. Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, Texas, United States of America
| | - James R. Trudell
- Department of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford University School of Medicine, Stanford, United States of America
| | - Erik Lindahl
- Science for Life Laboratory, KTH Royal Institute of Technology & Stockholm University, Stockholm, Sweden
- Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden
- * E-mail:
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Zhu F, Hummer G. Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction. Biophys J 2012; 103:219-27. [PMID: 22853899 DOI: 10.1016/j.bpj.2012.06.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 05/31/2012] [Accepted: 06/04/2012] [Indexed: 11/19/2022] Open
Abstract
The theoretical prediction of water drying transitions near nonpolar surfaces has stimulated an intensive search for biological processes exploiting this extreme form of hydrophobicity. Here we quantitatively demonstrate that drying of a hydrophobic constriction is the major determinant of ion conductance in the GLIC pentameric ion channel. Molecular-dynamics simulations show that in the closed state, the channel conductance is ∼12 orders-of-magnitude lower than in the open state. This large drop in conductance is remarkable because even in the functionally closed conformation the pore constriction remains wide enough for the passage of sodium ions, aided by a continuous bridge of ∼12 water molecules. However, we find that the free energy cost of hydrating the hydrophobic gate is large, accounting almost entirely for the energetic barrier blocking ion passage. The free energies of transferring a sodium ion into a prehydrated gate in functionally closed and open states differ by only 1.2 kcal/mol, compared to an 11 kcal/mol difference in the costs of hydrating the hydrophobic gate. Conversely, ion desolvation effects play only minor roles in GLIC ion channel gating. Our simulations help rationalize experiments probing the gating kinetics of the nicotinic acetylcholine receptor in response to mutations of pore-lining residues. The molecular character and phase behavior of water should thus be included in quantitative descriptions of ion channel gating.
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Affiliation(s)
- Fangqiang Zhu
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, USA.
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Zhu F, Hummer G. Theory and simulation of ion conduction in the pentameric GLIC channel. J Chem Theory Comput 2012; 8:3759-3768. [PMID: 23413364 DOI: 10.1021/ct2009279] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
GLIC is a bacterial member of the large family of pentameric ligand-gated ion channels. To study ion conduction through GLIC and other membrane channels, we combine the one-dimensional potential of mean force for ion passage with a Smoluchowski diffusion model, making it possible to calculate single-channel conductance in the regime of low ion concentrations from all-atom molecular dynamics (MD) simulations. We then perform MD simulations to examine sodium ion conduction through the GLIC transmembrane pore in two systems with different bulk ion concentrations. The ion potentials of mean force, calculated from umbrella sampling simulations with Hamiltonian replica exchange, reveal a major barrier at the hydrophobic constriction of the pore. The relevance of this barrier for ion transport is confirmed by a committor function that rises sharply in the barrier region. From the free evolution of Na(+) ions starting at the barrier top, we estimate the effective diffusion coefficient in the barrier region, and subsequently calculate the conductance of the pore. The resulting diffusivity compares well with the position-dependent ion diffusion coefficient obtained from restrained simulations. The ion conductance obtained from the diffusion model agrees with the value determined via a reactive-flux rate calculation. Our results show that the conformation in the GLIC crystal structure, with an estimated conductance of ~1 picosiemens at 140 mM ion concentration, is consistent with a physiologically open state of the channel.
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Affiliation(s)
- Fangqiang Zhu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
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35
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Wei GW, Zheng Q, Chen Z, Xia K. Variational multiscale models for charge transport. SIAM REVIEW. SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS 2012; 54:699-754. [PMID: 23172978 PMCID: PMC3501390 DOI: 10.1137/110845690] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle for chemo-electro-fluid systems. A number of computational algorithms is developed to implement the proposed new variational multiscale models in an efficient manner. A set of ten protein molecules and a realistic ion channel, Gramicidin A, are employed to confirm the consistency and verify the capability. Extensive numerical experiment is designed to validate the proposed variational multiscale models. A good quantitative agreement between our model prediction and the experimental measurement of current-voltage curves is observed for the Gramicidin A channel transport. This paper also provides a brief review of the field.
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Affiliation(s)
- Guo-Wei Wei
- Department of Mathematics Michigan State University, MI 48824, USA
- Department of Electrical and Computer Engineering Michigan State University, MI 48824, USA
- Address correspondences to Guo-Wei Wei.
| | - Qiong Zheng
- Department of Mathematics Michigan State University, MI 48824, USA
| | - Zhan Chen
- Department of Mathematics Michigan State University, MI 48824, USA
| | - Kelin Xia
- Department of Mathematics Michigan State University, MI 48824, USA
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36
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Song C, Corry B. Testing the applicability of Nernst-Planck theory in ion channels: comparisons with Brownian dynamics simulations. PLoS One 2011; 6:e21204. [PMID: 21731672 PMCID: PMC3121742 DOI: 10.1371/journal.pone.0021204] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 05/23/2011] [Indexed: 11/30/2022] Open
Abstract
The macroscopic Nernst-Planck (NP) theory has often been used for predicting ion channel currents in recent years, but the validity of this theory at the microscopic scale has not been tested. In this study we systematically tested the ability of the NP theory to accurately predict channel currents by combining and comparing the results with those of Brownian dynamics (BD) simulations. To thoroughly test the theory in a range of situations, calculations were made in a series of simplified cylindrical channels with radii ranging from 3 to 15 Å, in a more complex 'catenary' channel, and in a realistic model of the mechanosensitive channel MscS. The extensive tests indicate that the NP equation is applicable in narrow ion channels provided that accurate concentrations and potentials can be input as the currents obtained from the combination of BD and NP match well with those obtained directly from BD simulations, although some discrepancies are seen when the ion concentrations are not radially uniform. This finding opens a door to utilising the results of microscopic simulations in continuum theory, something that is likely to be useful in the investigation of a range of biophysical and nano-scale applications and should stimulate further studies in this direction.
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Affiliation(s)
- Chen Song
- School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Perth, Australia
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ben Corry
- School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Perth, Australia
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Zheng Q, Chen D, Wei GW. Second-order Poisson Nernst-Planck solver for ion channel transport. JOURNAL OF COMPUTATIONAL PHYSICS 2011; 230:5239-5262. [PMID: 21552336 PMCID: PMC3087981 DOI: 10.1016/j.jcp.2011.03.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The Poisson Nernst-Planck (PNP) theory is a simplified continuum model for a wide variety of chemical, physical and biological applications. Its ability of providing quantitative explanation and increasingly qualitative predictions of experimental measurements has earned itself much recognition in the research community. Numerous computational algorithms have been constructed for the solution of the PNP equations. However, in the realistic ion-channel context, no second order convergent PNP algorithm has ever been reported in the literature, due to many numerical obstacles, including discontinuous coefficients, singular charges, geometric singularities, and nonlinear couplings. The present work introduces a number of numerical algorithms to overcome the abovementioned numerical challenges and constructs the first second-order convergent PNP solver in the ion-channel context. First, a Dirichlet to Neumann mapping (DNM) algorithm is designed to alleviate the charge singularity due to the protein structure. Additionally, the matched interface and boundary (MIB) method is reformulated for solving the PNP equations. The MIB method systematically enforces the interface jump conditions and achieves the second order accuracy in the presence of complex geometry and geometric singularities of molecular surfaces. Moreover, two iterative schemes are utilized to deal with the coupled nonlinear equations. Furthermore, extensive and rigorous numerical validations are carried out over a number of geometries, including a sphere, two proteins and an ion channel, to examine the numerical accuracy and convergence order of the present numerical algorithms. Finally, application is considered to a real transmembrane protein, the Gramicidin A channel protein. The performance of the proposed numerical techniques is tested against a number of factors, including mesh sizes, diffusion coefficient profiles, iterative schemes, ion concentrations, and applied voltages. Numerical predictions are compared with experimental measurements.
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Affiliation(s)
- Qiong Zheng
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Duan Chen
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, MI 48824, USA
- Department of Electrical and Computer Engineering, Michigan State University, MI 48824, USA
- Please address correspondence to Guowei Wei.
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