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Stampolaki Μ, Hoffmann A, Tekwani K, Georgiou K, Tzitzoglaki C, Ma C, Becker S, Schmerer P, Döring K, Stylianakis I, Turcu AL, Wang J, Vázquez S, Andreas LB, Schmidtke M, Kolocouris A. A Study of the Activity of Adamantyl Amines against Mutant Influenza A M2 Channels Identified a Polycyclic Cage Amine Triple Blocker, Explored by Molecular Dynamics Simulations and Solid-State NMR. ChemMedChem 2023; 18:e202300182. [PMID: 37377066 DOI: 10.1002/cmdc.202300182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 06/29/2023]
Abstract
We compared the anti-influenza potencies of 57 adamantyl amines and analogs against influenza A virus with serine-31 M2 proton channel, usually termed as WT M2 channel, which is amantadine sensitive. We also tested a subset of these compounds against viruses with the amantadine-resistant L26F, V27A, A30T, G34E M2 mutant channels. Four compounds inhibited WT M2 virus in vitro with mid-nanomolar potency, with 27 compounds showing sub-micromolar to low micromolar potency. Several compounds inhibited L26F M2 virus in vitro with sub-micromolar to low micromolar potency, but only three compounds blocked L26F M2-mediated proton current as determined by electrophysiology (EP). One compound was found to be a triple blocker of WT, L26F, V27A M2 channels by EP assays, but did not inhibit V27A M2 virus in vitro, and one compound inhibited WT, L26F, V27A M2 in vitro without blocking V27A M2 channel. One compound blocked only L26F M2 channel by EP, but did not inhibit virus replication. The triple blocker compound is as long as rimantadine, but could bind and block V27A M2 channel due to its larger girth as revealed by molecular dynamics simulations, while MAS NMR informed on the interaction of the compound with M2(18-60) WT or L26F or V27A.
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Affiliation(s)
- Μarianna Stampolaki
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Anja Hoffmann
- Department of Medical Microbiology, Jena University Hospital, CMB Building, R. 443, Hans Knoell Str. 2, 07745, Jena (Germany), Germany
| | - Kumar Tekwani
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Kyriakos Georgiou
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
| | - Christina Tzitzoglaki
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
| | - Chunlong Ma
- Department of Medicinal Chemistry, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Patrick Schmerer
- Department of Medical Microbiology, Jena University Hospital, CMB Building, R. 443, Hans Knoell Str. 2, 07745, Jena (Germany), Germany
| | - Kristin Döring
- Department of Medical Microbiology, Jena University Hospital, CMB Building, R. 443, Hans Knoell Str. 2, 07745, Jena (Germany), Germany
| | - Ioannis Stylianakis
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
| | - Andreea L Turcu
- Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Jun Wang
- Department of Medicinal Chemistry, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
| | - Santiago Vázquez
- Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Michaela Schmidtke
- Department of Medical Microbiology, Jena University Hospital, CMB Building, R. 443, Hans Knoell Str. 2, 07745, Jena (Germany), Germany
| | - Antonios Kolocouris
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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3
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Tryptophan-mediated Dimerization of the TssL Transmembrane Anchor Is Required for Type VI Secretion System Activity. J Mol Biol 2018; 430:987-1003. [DOI: 10.1016/j.jmb.2018.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/29/2018] [Accepted: 02/11/2018] [Indexed: 11/23/2022]
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4
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Gu RX, Liu LA, Wei DQ, Du JG, Liu L, Liu H. Free energy calculations on the two drug binding sites in the M2 proton channel. J Am Chem Soc 2011; 133:10817-25. [PMID: 21711026 DOI: 10.1021/ja1114198] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Two alternative binding sites of adamantane-type drugs in the influenza A M2 channel have been suggested, one with the drug binding inside the channel pore and the other with four drug molecule S-binding to the C-terminal surface of the transmembrane domain. Recent computational and experimental studies have suggested that the pore binding site is more energetically favorable but the external surface binding site may also exist. Nonetheless, which drug binding site leads to channel inhibition in vivo and how drug-resistant mutations affect these sites are not completely understood. We applied molecular dynamics simulations and potential of mean force calculations to examine the structures and the free energies associated with these putative drug binding sites in an M2-lipid bilayer system. We found that, at biological pH (~7.4), the pore binding site is more thermodynamically favorable than the surface binding site by ~7 kcal/mol and, hence, would lead to more stable drug binding and channel inhibition. This result is in excellent agreement with several recent studies. More importantly, a novel finding of ours is that binding to the channel pore requires overcoming a much higher energy barrier of ~10 kcal/mol than binding to the C-terminal channel surface, indicating that the latter site is more kinetically favorable. Our study is the first computational work that provides both kinetic and thermodynamic energy information on these drug binding sites. Our results provide a theoretical framework to interpret and reconcile existing and often conflicting results regarding these two binding sites, thus helping to expand our understanding of M2-drug binding, and may help guide the design and screening of novel drugs to combat the virus.
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Affiliation(s)
- Ruo-Xu Gu
- State Key Laboratory of Microbial Metabolism, Luc Montagnier Biomedical Research Institute, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai Minhang District, China 200240
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5
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Wang J, Qiu JX, Soto C, DeGrado WF. Structural and dynamic mechanisms for the function and inhibition of the M2 proton channel from influenza A virus. Curr Opin Struct Biol 2011; 21:68-80. [PMID: 21247754 PMCID: PMC3039100 DOI: 10.1016/j.sbi.2010.12.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 12/09/2010] [Indexed: 12/11/2022]
Abstract
The M2 proton channel from influenza A virus, a prototype for a class of viral ion channels known as viroporins, conducts protons along a chain of water molecules and ionizable sidechains, including His37. Recent studies highlight a delicate interplay between protein folding, proton binding, and proton conduction through the channel. Drugs inhibit proton conduction by binding to an aqueous cavity adjacent to M2's proton-selective filter, thereby blocking access of proton to the filter, and altering the energetic landscape of the channel and the energetics of proton-binding to His37.
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Affiliation(s)
- Jun Wang
- Department of Chemistry, School of Medicine, University of Pennsylvania, 422 Curvie Blvd, Philadelphia, PA, 19104, USA
| | - Jade Xiaoyan Qiu
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, 422 Curvie Blvd, Philadelphia, PA, 19104, USA
| | - Cinque Soto
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, 422 Curvie Blvd, Philadelphia, PA, 19104, USA
| | - William F. DeGrado
- Department of Chemistry, School of Medicine, University of Pennsylvania, 422 Curvie Blvd, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, 422 Curvie Blvd, Philadelphia, PA, 19104, USA
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6
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Cady SD, Luo W, Hu F, Hong M. Structure and function of the influenza A M2 proton channel. Biochemistry 2009; 48:7356-64. [PMID: 19601584 DOI: 10.1021/bi9008837] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The M2 protein of influenza A viruses forms a tetrameric pH-activated proton-selective channel that is targeted by the amantadine class of antiviral drugs. Its ion channel function has been extensively studied by electrophysiology and mutagenesis; however, the molecular mechanism of proton transport is still elusive, and the mechanism of inhibition by amantadine is controversial. We review the functional data on proton channel activity, molecular dynamics simulations of the proton conduction mechanism, and high-resolution structural and dynamical information of this membrane protein in lipid bilayers and lipid-mimetic detergents. These studies indicate that elucidation of the structural basis of M2 channel activity and inhibition requires thorough examination of the complex dynamics and conformational plasticity of the protein in different lipid bilayers and lipid-mimetic environments.
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Affiliation(s)
- Sarah D Cady
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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7
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Nayak DP, Balogun RA, Yamada H, Zhou ZH, Barman S. Influenza virus morphogenesis and budding. Virus Res 2009; 143:147-61. [PMID: 19481124 PMCID: PMC2730999 DOI: 10.1016/j.virusres.2009.05.010] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 05/19/2009] [Indexed: 12/11/2022]
Abstract
Influenza viruses are enveloped, negative stranded, segmented RNA viruses belonging to Orthomyxoviridae family. Each virion consists of three major sub-viral components, namely (i) a viral envelope decorated with three transmembrane proteins hemagglutinin (HA), neuraminidase (NA) and M2, (ii) an intermediate layer of matrix protein (M1), and (iii) an innermost helical viral ribonucleocapsid [vRNP] core formed by nucleoprotein (NP) and negative strand viral RNA (vRNA). Since complete virus particles are not found inside the cell, the processes of assembly, morphogenesis, budding and release of progeny virus particles at the plasma membrane of the infected cells are critically important for the production of infectious virions and pathogenesis of influenza viruses as well. Morphogenesis and budding require that all virus components must be brought to the budding site which is the apical plasma membrane in polarized epithelial cells whether in vitro cultured cells or in vivo infected animals. HA and NA forming the outer spikes on the viral envelope possess apical sorting signals and use exocytic pathways and lipid rafts for cell surface transport and apical sorting. NP also has apical determinant(s) and is probably transported to the apical budding site similarly via lipid rafts and/or through cortical actin microfilaments. M1 binds the NP and the exposed RNAs of vRNPs, as well as to the cytoplasmic tails (CT) and transmembrane (TM) domains of HA, NA and M2, and is likely brought to the budding site on the piggy-back of vRNP and transmembrane proteins. Budding processes involve bud initiation, bud growth and bud release. The presence of lipid rafts and assembly of viral components at the budding site can cause asymmetry of lipid bilayers and outward membrane bending leading to bud initiation and bud growth. Bud release requires fusion of the apposing viral and cellular membranes and scission of the virus buds from the infected cellular membrane. The processes involved in bud initiation, bud growth and bud scission/release require involvement both viral and host components and can affect bud closing and virus release in both positive and negative ways. Among the viral components, M1, M2 and NA play important roles in bud release and M1, M2 and NA mutations all affect the morphology of buds and released viruses. Disassembly of host cortical actin microfilaments at the pinching-off site appears to facilitate bud fission and release. Bud scission is energy dependent and only a small fraction of virus buds present on the cell surface is released. Discontinuity of M1 layer underneath the lipid bilayer, absence of outer membrane spikes, absence of lipid rafts in the lipid bilayer, as well as possible presence of M2 and disassembly of cortical actin microfilaments at the pinching-off site appear to facilitate bud fission and bud release. We provide our current understanding of these important processes leading to the production of infectious influenza virus particles.
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Affiliation(s)
- Debi P Nayak
- Department of Microbiology, Immunology and Molecular Genetics, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
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8
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Affiliation(s)
- Philip Ball
- Nature, 4-6 Crinan Street, London N1 9XW, U.K
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9
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Moffat JC, Vijayvergiya V, Gao PF, Cross TA, Woodbury DJ, Busath DD. Proton transport through influenza A virus M2 protein reconstituted in vesicles. Biophys J 2007; 94:434-45. [PMID: 17827230 PMCID: PMC2157240 DOI: 10.1529/biophysj.107.109082] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza A virus M2 protein is known to form acid-activated, proton-selective, amantadine-sensitive channels. We directly measured proton uptake in vesicles containing reconstituted M2 by monitoring external pH after addition of valinomycin to vesicles with 100-fold-diluted external [K(+)]. External pH typically increased by a few tenths of a pH unit over a few minutes after valinomycin addition, but proton uptake was not significantly altered by acidification. Under neutral conditions, external addition of 1 mM amantadine produced a reduction in flux consistent with randomly ordered channels; however, experimental variation is high with this method and the block was not statistically significant. Amantadine block was reduced at pH 5.4. In accord with Lin and Schroeder's study of reconstituted M2 using a pH-sensitive dye to monitor intravesicular pH, we conclude that bath pH weakly affects or does not significantly affect proton flow in the pH range 5.4-7.0 for the reconstituted system, contrary to results from electrophysiological studies. Theoretical analysis of the relaxation to Donnan equilibrium utilized for such vesicle uptake assays illuminates the appropriate timescale of the initial slope and an important limitation that must be placed on inferences about channel ion selectivity. The rise in pH over 10 s after ionophore addition yielded time-averaged single-channel conductances of 0.35 +/- 0.20 aS and 0.72 +/- 0.42 aS at pH 5.4 and 7.0, respectively, an order of magnitude lower than previously reported in vesicles. Assuming complete membrane incorporation and tetramerization of the reconstituted protein, such a low time-averaged conductance in the face of previously observed single-channel conductance (6 pS at pH 3) implies an open channel probability of 10(-6)-10(-4). Based on leakage of potassium from M2-containing vesicles, compared to protein-free vesicles, we conclude that M2 exhibits approximately 10(7) selectivity for hydrogen over potassium.
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Affiliation(s)
- J Craig Moffat
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah 84602, USA
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10
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Chen H, Wu Y, Voth GA. Proton transport behavior through the influenza A M2 channel: insights from molecular simulation. Biophys J 2007; 93:3470-9. [PMID: 17693473 PMCID: PMC2072055 DOI: 10.1529/biophysj.107.105742] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural properties of the influenza A virus M2 transmembrane channel in dimyristoylphosphatidylcholine bilayer for each of the four protonation states of the proton-gating His-37 tetrad and their effects on proton transport for this low-pH activated, highly proton-selective channel are studied by classical molecular dynamics with the multistate empirical valence-bond (MS-EVB) methodology. The excess proton permeation free energy profile and maximum ion conductance calculated from the MS-EVB simulation data combined with the Poisson-Nernst-Planck theory indicates that the triply protonated His-37 state is the most likely open state via a significant side-chain conformational change of the His-37 tetrad. This proposed open state of M2 has a calculated proton permeation free energy barrier of 7 kcal/mol and a maximum conductance of 53 pS compared to the experimental value of 6 pS. By contrast, the maximum conductance for Na(+) is calculated to be four orders of magnitude lower, in reasonable agreement with the experimentally observed proton selectivity. The pH value to activate the channel opening is estimated to be 5.5 from dielectric continuum theory, which is also consistent with experimental results. This study further reveals that the Ala-29 residue region is the primary binding site for the antiflu drug amantadine (AMT), probably because that domain is relatively spacious and hydrophobic. The presence of AMT is calculated to reduce the proton conductance by 99.8% due to a significant dehydration penalty of the excess proton in the vicinity of the channel-bound AMT.
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Affiliation(s)
- Hanning Chen
- Center for Biophysical Modeling and Simulation, Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
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11
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Qin Z, Tepper HL, Voth GA. Effect of Membrane Environment on Proton Permeation through Gramicidin A Channels. J Phys Chem B 2007; 111:9931-9. [PMID: 17672487 DOI: 10.1021/jp0708998] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multistate empirical valence bond simulations were employed to study proton transport through gramicidin A channels embedded in two different lipid bilayers, glycerol 1-monooleate (GMO) and diphytanolphosphatidylcholine (DiPhPC). Free energy barriers to proton permeation were derived using a new internal reaction coordinate describing the proton permeation process. The large quantitative and qualitative differences between the two systems are discussed in terms of local bilayer structures, ordering of interfacial water, and channel flexibility in the two environments.
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Affiliation(s)
- Zhen Qin
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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12
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Kolocouris A, Zikos C, Broadhurst RW. 19F NMR detection of the complex between amantadine and the receptor portion of the influenza A M2 ion channel in DPC micelles. Bioorg Med Chem Lett 2007; 17:3947-52. [PMID: 17502147 DOI: 10.1016/j.bmcl.2007.04.100] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 04/27/2007] [Accepted: 04/28/2007] [Indexed: 11/18/2022]
Abstract
(19)F NMR probes were used to follow interactions between ligands in the aminoadamantane series, amantadine (Am) 1 and 3-F-Am 2, and the 5-F-Trp20 transmembrane fragment of the influenza A M2 proton channel (F-M2TM 3) in dodecylphosphocholine micelles over the pH range 5-8. Above pH 7, when the peptide adopts a tetrameric state that is able to bind channel blocking ligands, (19)F-Trp signals from both the free and bound states of the M2TM tetramer are resolved. This differentiation of bound and unbound states of the M2TM receptor by (19)F NMR may provide a system for SAR studies.
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Affiliation(s)
- Antonios Kolocouris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Panepistimioupolis-Zografou, Athens 15 771, Greece
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13
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Swanson JMJ, Maupin CM, Chen H, Petersen MK, Xu J, Wu Y, Voth GA. Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. J Phys Chem B 2007; 111:4300-14. [PMID: 17429993 PMCID: PMC2548316 DOI: 10.1021/jp070104x] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The excess proton in aqueous media plays a pivotal role in many fundamental chemical (e.g., acid-base chemistry) and biological (e.g., bioenergetics and enzyme catalysis) processes. Understanding the hydrated proton is, therefore, crucial for chemistry, biology, and materials sciences. Although well studied for over 200 years, excess proton solvation and transport remains to this day mysterious, surprising, and perhaps even misunderstood. In this feature article, various efforts to address this problem through computer modeling and simulation will be described. Applications of computer simulations to a number of important and interesting systems will be presented, highlighting the roles of charge delocalization and Grotthuss shuttling, a phenomenon unique in many ways to the excess proton in water.
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Affiliation(s)
- Jessica M J Swanson
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112-0850, USA
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14
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Chen H, Ilan B, Wu Y, Zhu F, Schulten K, Voth GA. Charge delocalization in proton channels, I: the aquaporin channels and proton blockage. Biophys J 2006; 92:46-60. [PMID: 17056733 PMCID: PMC1697834 DOI: 10.1529/biophysj.106.091934] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The explicit contribution to the free energy barrier and proton conductance from the delocalized nature of the excess proton is examined in aquaporin channels using an accurate all-atom molecular dynamics computer simulation model. In particular, the channel permeation free energy profiles are calculated and compared for both a delocalized (fully Grotthuss shuttling) proton and a classical (nonshuttling) hydronium ion along two aquaporin channels, Aqp1 and GlpF. To elucidate the effects of the bipolar field thought to arise from two alpha-helical macrodipoles on proton blockage, free energy profiles were also calculated for computational mutants of the two channels where the bipolar field was eliminated by artificially discharging the backbone atoms. Comparison of the free energy profiles between the proton and hydronium cases indicates that the magnitude of the free energy barrier and position of the barrier peak for the fully delocalized and shuttling proton are somewhat different from the case of the (localized) classical hydronium. The proton conductance through the two aquaporin channels is also estimated using Poisson-Nernst-Planck theory for both the Grotthuss shuttling excess proton and the classical hydronium cation.
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Affiliation(s)
- Hanning Chen
- Center for Biophysical Modeling and Simulation, Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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15
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Hu J, Fu R, Nishimura K, Zhang L, Zhou HX, Busath DD, Vijayvergiya V, Cross TA. Histidines, heart of the hydrogen ion channel from influenza A virus: toward an understanding of conductance and proton selectivity. Proc Natl Acad Sci U S A 2006; 103:6865-70. [PMID: 16632600 PMCID: PMC1458985 DOI: 10.1073/pnas.0601944103] [Citation(s) in RCA: 210] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The heart of the H+ conductance mechanism in the homotetrameric M2 H+ channel from influenza A is a set of four histidine side chains. Here, we show that protonation of the third of these imidazoles coincides with acid activation of this transmembrane channel and that, at physiological pH, the channel is closed by two imidazole-imidazolium dimers, each sharing a low-barrier hydrogen bond. This unique construct succeeds in distributing a pair of charges over four rings and many atoms in a low dielectric environment to minimize charge repulsion. These dimers form with identical pKas of 8.2 +/- 0.2, suggesting cooperative H+ binding and clearly illustrating high H+ affinity for this channel. The protonation behavior of the histidine side chains has been characterized by using solid-state NMR spectroscopy on the M2 transmembrane domain in fully hydrated lipid bilayers where the tetrameric backbone structure is known. Furthermore, electrophysiological measurements of multichannel and single-channel experiments confirm that these protein constructs are functional.
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Affiliation(s)
- Jun Hu
- Departments of *Chemistry and Biochemistry and
- National High Magnetic Field Laboratory, and
| | - Riqiang Fu
- National High Magnetic Field Laboratory, and
| | - Katsuyuki Nishimura
- National High Magnetic Field Laboratory, and
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogayaku, Yokohama, Kanagawa 240-8501, Japan
| | - Li Zhang
- Departments of *Chemistry and Biochemistry and
- National High Magnetic Field Laboratory, and
- Amgen, 1 Amgen Center Drive, MS 18S-1-A, Thousand Oaks, CA 91320; and
| | - Huan-Xiang Zhou
- Physics
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32310
| | - David D. Busath
- **Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602
| | - Viksita Vijayvergiya
- **Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602
| | - Timothy A. Cross
- Departments of *Chemistry and Biochemistry and
- National High Magnetic Field Laboratory, and
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32310
- To whom correspondence should be addressed at:
National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310. E-mail:
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Wu Y, Voth GA. A computational study of the closed and open states of the influenza a M2 proton channel. Biophys J 2005; 89:2402-11. [PMID: 16040757 PMCID: PMC1366740 DOI: 10.1529/biophysj.105.066647] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, four possible conformations of the His-37 and Trp-41 residues for the closed state of the influenza M2 ion channel were identified by a conformation scan based on a solid-state NMR restraint. In the four conformations, the His-37 residue can be of either the t-160 or t60 rotamer, whereas Trp-41 can be of either the t-105 or t90 rotamer. These conformations were further analyzed by density functional theory calculations and molecular dynamics simulations, and the data indicate that the His-37 residue most likely adopts the t60 rotamer and should be monoprotonated at the delta-nitrogen site, whereas Trp-41 adopts the t90 rotamer. This result is consistent with published experimental data and points to a simple gating mechanism: in the closed state, the His-37 and Trp-41 residues adopt the (t60, t90) conformation, which nearly occludes the pore, preventing nonproton ions from passing through due to the steric and desolvation effects. Moreover, the His-37 tetrad interrupts the otherwise continuous hydrogen-bonding network of the pore water by forcing the water molecules above and below it to adopt opposite orientations, thus adding to the blockage of proton shuttling. The channel can be easily opened by rotating the His-37 chi2 angle from 60 to 0 degrees . This open structure allows pore water to penetrate the constrictive region and to form a continuous water wire for protons to shuttle through, while being still narrow enough to exclude other ions.
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Affiliation(s)
- Yujie Wu
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
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Abstract
Influenza viruses are causative agents of an acute febrile respiratory disease called influenza (commonly known as "flu") and belong to the Orthomyxoviridae family. These viruses possess segmented, negative stranded RNA genomes (vRNA) and are enveloped, usually spherical and bud from the plasma membrane (more specifically, the apical plasma membrane of polarized epithelial cells). Complete virus particles, therefore, are not found inside infected cells. Virus particles consist of three major subviral components, namely the viral envelope, matrix protein (M1), and core (viral ribonucleocapsid [vRNP]). The viral envelope surrounding the vRNP consists of a lipid bilayer containing spikes composed of viral glycoproteins (HA, NA, and M2) on the outer side and M1 on the inner side. Viral lipids, derived from the host plasma membrane, are selectively enriched in cholesterol and glycosphingolipids. M1 forms the bridge between the viral envelope and the core. The viral core consists of helical vRNP containing vRNA (minus strand) and NP along with minor amounts of NEP and polymerase complex (PA, PB1, and PB2). For viral morphogenesis to occur, all three viral components, namely the viral envelope (containing lipids and transmembrane proteins), M1, and the vRNP must be brought to the assembly site, i.e. the apical plasma membrane in polarized epithelial cells. Finally, buds must be formed at the assembly site and virus particles released with the closure of buds. Transmembrane viral proteins are transported to the assembly site on the plasma membrane via the exocytic pathway. Both HA and NA possess apical sorting signals and use lipid rafts for cell surface transport and apical sorting. These lipid rafts are enriched in cholesterol, glycosphingolipids and are relatively resistant to neutral detergent extraction at low temperature. M1 is synthesized on free cytosolic polyribosomes. vRNPs are made inside the host nucleus and are exported into the cytoplasm through the nuclear pore with the help of M1 and NEP. How M1 and vRNPs are directed to the assembly site on the plasma membrane remains unclear. The likely possibilities are that they use a piggy-back mechanism on viral glycoproteins or cytoskeletal elements. Alternatively, they may possess apical determinants or diffuse to the assembly site, or a combination of these pathways. Interactions of M1 with M1, M1 with vRNP, and M1 with HA and NA facilitate concentration of viral components and exclusion of host proteins from the budding site. M1 interacts with the cytoplasmic tail (CT) and transmembrane domain (TMD) of glycoproteins, and thereby functions as a bridge between the viral envelope and vRNP. Lipid rafts function as microdomains for concentrating viral glycoproteins and may serve as a platform for virus budding. Virus bud formation requires membrane bending at the budding site. A combination of factors including concentration of and interaction among viral components, increased viscosity and asymmetry of the lipid bilayer of the lipid raft as well as pulling and pushing forces of viral and host components are likely to cause outward curvature of the plasma membrane at the assembly site leading to bud formation. Eventually, virus release requires completion of the bud due to fusion of the apposing membranes, leading to the closure of the bud, separation of the virus particle from the host plasma membrane and release of the virus particle into the extracellular environment. Among the viral components, M1 contains an L domain motif and plays a critical role in budding. Bud completion requires not only viral components but also host components. However, how host components facilitate bud completion remains unclear. In addition to bud completion, influenza virus requires NA to release virus particles from sialic acid residues on the cell surface and spread from cell to cell. Elucidation of both viral and host factors involved in viral morphogenesis and budding may lead to the development of drugs interfering with the steps of viral morphogenesis and in disease progression.
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Affiliation(s)
- Debi P Nayak
- Department of Microbiology, Immunology and Molecular Genetics, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
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