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Sučec I, Pankratova Y, Parasar M, Hong M. Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63. Protein Sci 2024; 33:e4923. [PMID: 38501465 PMCID: PMC10949323 DOI: 10.1002/pro.4923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 03/20/2024]
Abstract
The envelope (E) proteins of coronaviruses (CoVs) form cation-conducting channels that are associated with the pathogenicity of these viruses. To date, high-resolution structural information about these viroporins is limited to the SARS-CoV E protein. To broaden our structural knowledge of other members of this family of viroporins, we now investigate the conformation of the E protein of the human coronavirus (hCoV), NL63. Using two- and three-dimensional magic-angle-spinning NMR, we have measured 13 C and 15 N chemical shifts of the transmembrane domain of E (ETM), which yielded backbone (ϕ, ψ) torsion angles. We further measured the water accessibility of NL63 ETM at neutral pH versus acidic pH in the presence of Ca2+ ions. These data show that NL63 ETM adopts a regular α-helical conformation that is unaffected by pH and the N-terminal ectodomain. Interestingly, the water accessibility of NL63 ETM increases only modestly at acidic pH in the presence of Ca2+ compared to neutral pH, in contrast to SARS ETM, which becomes much more hydrated at acidic pH. This difference suggests a structural basis for the weaker channel conductance of α-CoV compared to β-CoV E proteins. The weaker E channel activity may in turn contribute to the reduced virulence of hCoV-NL63 compared to SARS-CoV viruses.
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Affiliation(s)
- Iva Sučec
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Yanina Pankratova
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mriganka Parasar
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mei Hong
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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2
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Yadav Y, Singh K, Sharma S, Mishra VK, Sagar R. Recent Efforts in Identification of Privileged Scaffolds as Antiviral Agents. Chem Biodivers 2023; 20:e202300921. [PMID: 37589569 DOI: 10.1002/cbdv.202300921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 08/18/2023]
Abstract
Viral infections are the most important health concern nowadays to mankind, which is unexpectedly increasing the health complications and fatality rate worldwide. The recent viral infection outbreak developed a pressing need for small molecules that can be quickly deployed for the control/treatment of re-emerging or new emerging viral infections. Numerous viruses, including the human immunodeficiency virus (HIV), hepatitis, influenza, SARS-CoV-1, SARS-CoV-2, and others, are still challenging due to emerging resistance to known drugs. Therefore, there is always a need to search for new antiviral small molecules that can combat viral infection with new modes of action. This review highlighted recent progress in developing new antiviral molecules based on natural product-inspired scaffolds. Herein, the structure-activity relationship of the FDA-approved drugs along with the molecular docking studies of selected compounds have been discussed against several target proteins. The findings of new small molecules as neuraminidase inhibitors, other than known drug scaffolds, Anti-HIV and SARS-CoV are incorporated in this review paper.
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Affiliation(s)
- Yogesh Yadav
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Kavita Singh
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sunil Sharma
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Vinay Kumar Mishra
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Ram Sagar
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
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3
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Sutherland M, Tran N, Hong M. Clustering of tetrameric influenza M2 peptides in lipid bilayers investigated by 19F solid-state NMR. Biochim Biophys Acta Biomembr 2022; 1864:183909. [PMID: 35276226 DOI: 10.1016/j.bbamem.2022.183909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/08/2022] [Accepted: 03/05/2022] [Indexed: 11/19/2022]
Abstract
The influenza M2 protein forms a drug-targeted tetrameric proton channel to mediate virus uncoating, and carries out membrane scission to enable virus release. While the proton channel function of M2 has been extensively studied, the mechanism by which M2 catalyzes membrane scission is still not well understood. Previous fluorescence and electron microscopy studies indicated that M2 tetramers concentrate at the neck of the budding virus in the host plasma membrane. However, molecular evidence for this clustering is scarce. Here, we use 19F solid-state NMR to investigate M2 clustering in phospholipid bilayers. By mixing equimolar amounts of 4F-Phe47 labeled M2 peptide and CF3-Phe47 labeled M2 peptide and measuring F-CF3 cross peaks in 2D 19F19F correlation spectra, we show that M2 tetramers form nanometer-scale clusters in lipid bilayers. This clustering is stronger in cholesterol-containing membranes and phosphatidylethanolamine (PE) membranes than in cholesterol-free phosphatidylcholine and phosphatidylglycerol membranes. The observed correlation peaks indicate that Phe47 sidechains from different tetramers are less than ~2 nm apart. 1H19F correlation peaks between lipid chain protons and fluorinated Phe47 indicate that Phe47 is more deeply inserted into the lipid bilayer in the presence of cholesterol than in its absence, suggesting that Phe47 preferentially interacts with cholesterol. Static 31P NMR spectra indicate that M2 induces negative Gaussian curvature in the PE membrane. These results suggest that M2 tetramers cluster at cholesterol- and PE-rich regions of cell membranes to cause membrane curvature, which in turn can facilitate membrane scission in the last step of virus budding and release.
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Affiliation(s)
- Madeleine Sutherland
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America.
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4
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Avdeeva VV, Garaev TM, Breslav NV, Burtseva EI, Grebennikova TV, Zhdanov AP, Zhizhin KY, Malinina EA, Kuznetsov NT. New type of RNA virus replication inhibitor based on decahydro-closo-decaborate anion containing amino acid ester pendant group. J Biol Inorg Chem 2022. [PMID: 35332377 DOI: 10.1007/s00775-022-01937-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/03/2022] [Indexed: 12/04/2022]
Abstract
In this work, a synthetic approach to prepare an example of new class of the derivatives of the closo-decaborate anion with amino acids detached from the boron cluster by pendant group has been proposed and implemented. Compound Na2[B10H9–O(CH2)4C(O)–His–OMe] was isolated and characterized. This compound has an inorganic hydrophobic core which is the 10-vertex boron cage and the –O(CH2)4C(O)–His–OMe organic substituent. It has been shown to possess strong antiviral activity in vitro against modern strains of A/H1N1 virus at 10 and 5 µg/mL. The compound has been found to be non-cytotoxic up to 160 µg/mL. At the same time, the compound has been found to be inactive against SARS-CoV-2, indicating specific activity against RNA virus replication. Molecular docking of the target derivative of the closo-decaborate anion with a model of the transmembrane region of the M2 protein has been performed and the mechanism of its antiviral action is discussed.
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5
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Aledavood E, Selmi B, Estarellas C, Masetti M, Luque FJ. From Acid Activation Mechanisms of Proton Conduction to Design of Inhibitors of the M2 Proton Channel of Influenza A Virus. Front Mol Biosci 2022; 8:796229. [PMID: 35096969 PMCID: PMC8795881 DOI: 10.3389/fmolb.2021.796229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/24/2021] [Indexed: 11/26/2022] Open
Abstract
With an estimated 1 billion people affected across the globe, influenza is one of the most serious health concerns worldwide. Therapeutic treatments have encompassed a number of key functional viral proteins, mainly focused on the M2 proton channel and neuraminidase. This review highlights the efforts spent in targeting the M2 proton channel, which mediates the proton transport toward the interior of the viral particle as a preliminary step leading to the release of the fusion peptide in hemagglutinin and the fusion of the viral and endosomal membranes. Besides the structural and mechanistic aspects of the M2 proton channel, attention is paid to the challenges posed by the development of efficient small molecule inhibitors and the evolution toward novel ligands and scaffolds motivated by the emergence of resistant strains.
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Affiliation(s)
- Elnaz Aledavood
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Beatrice Selmi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Carolina Estarellas
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
| | - F. Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
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Abstract
Techniques for atomic-resolution structural biology have evolved during the past several decades. Breakthroughs in instrumentation, sample preparation, and data analysis that occurred in the past decade have enabled characterization of viruses with an unprecedented level of detail. Here we review the recent advances in magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy for structural analysis of viruses and viral assemblies. MAS NMR is a powerful method that yields information on 3D structures and dynamics in a broad range of experimental conditions. After a brief introduction, we discuss recent structural and functional studies of several viruses investigated with atomic resolution at various levels of structural organization, from individual domains of a membrane protein reconstituted into lipid bilayers to virus-like particles and intact viruses. We present examples of the unique information revealed by MAS NMR about drug binding, conduction mechanisms, interactions with cellular host factors, and DNA packaging in biologically relevant environments that are inaccessible by other methods.
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Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA;
| | - Amir Goldbourt
- School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA; .,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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7
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Tompa DR, Immanuel A, Srikanth S, Kadhirvel S. Trends and strategies to combat viral infections: A review on FDA approved antiviral drugs. Int J Biol Macromol 2021; 172:524-541. [PMID: 33454328 PMCID: PMC8055758 DOI: 10.1016/j.ijbiomac.2021.01.076] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 12/12/2022]
Abstract
The infectious microscopic viruses invade living cells to reproduce themselves, and causes chronic infections such as HIV/AIDS, hepatitis B and C, flu, etc. in humans which may lead to death if not treated. Different strategies have been utilized to develop new and superior antiviral drugs to counter the viral infections. The FDA approval of HIV nucleoside reverse transcriptase inhibitor, zidovudine in 1987 boosted the development of antiviral agents against different viruses. Currently, there are a number of combination drugs developed against various viral infections to arrest the activity of same or different viral macromolecules at multiple stages of its life cycle; among which majority are targeted to interfere with the replication of viral genome. Besides these, other type of antiviral molecules includes entry inhibitors, integrase inhibitors, protease inhibitors, interferons, immunomodulators, etc. The antiviral drugs can be toxic to human cells, particularly in case of administration of combination drugs, and on the other hand viruses can grow resistant to the antiviral drugs. Furthermore, emergence of new viruses like Ebola, coronaviruses (SARS-CoV, SARS-CoV-2) emphasizes the need for more innovative strategies to develop better antiviral drugs to fight the existing and the emerging viral infections. Hence, we reviewed the strategic enhancements in developing antiviral drugs for the treatment of different viral infections over the years.
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Affiliation(s)
- Dharma Rao Tompa
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India
| | - Aruldoss Immanuel
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India
| | - Srimari Srikanth
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India
| | - Saraboji Kadhirvel
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India.
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8
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Lecoq L, Fogeron ML, Meier BH, Nassal M, Böckmann A. Solid-State NMR for Studying the Structure and Dynamics of Viral Assemblies. Viruses 2020; 12:E1069. [PMID: 32987909 DOI: 10.3390/v12101069] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Structural virology reveals the architecture underlying infection. While notably electron microscopy images have provided an atomic view on viruses which profoundly changed our understanding of these assemblies incapable of independent life, spectroscopic techniques like NMR enter the field with their strengths in detailed conformational analysis and investigation of dynamic behavior. Typically, the large assemblies represented by viral particles fall in the regime of biological high-resolution solid-state NMR, able to follow with high sensitivity the path of the viral proteins through their interactions and maturation steps during the viral life cycle. We here trace the way from first solid-state NMR investigations to the state-of-the-art approaches currently developing, including applications focused on HIV, HBV, HCV and influenza, and an outlook to the possibilities opening in the coming years.
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9
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Schledorn M, Malär AA, Torosyan A, Penzel S, Klose D, Oss A, Org M, Wang S, Lecoq L, Cadalbert R, Samoson A, Böckmann A, Meier BH. Protein NMR Spectroscopy at 150 kHz Magic-Angle Spinning Continues To Improve Resolution and Mass Sensitivity. Chembiochem 2020; 21:2540-2548. [PMID: 32501630 PMCID: PMC7497035 DOI: 10.1002/cbic.202000341] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 12/21/2022]
Abstract
Spectral resolution is the key to unleashing the structural and dynamic information contained in NMR spectra. Fast magic-angle spinning (MAS) has recently revolutionized the spectroscopy of biomolecular solids. Herein, we report a further remarkable improvement in the resolution of the spectra of four fully protonated proteins and a small drug molecule by pushing the MAS rotation frequency higher (150 kHz) than the more routinely used 100 kHz. We observed a reduction in the average homogeneous linewidth by a factor of 1.5 and a decrease in the observed linewidth by a factor 1.25. We conclude that even faster MAS is highly attractive and increases mass sensitivity at a moderate price in overall sensitivity.
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Affiliation(s)
| | | | | | | | - Daniel Klose
- Physical ChemistryETH Zürich8093ZürichSwitzerland
| | - Andres Oss
- Institute of Health TechnologiesTallinn University of TechnologyAkadeemia tee 15a12618TallinnEstonia
| | - Mai‐Liis Org
- Institute of Health TechnologiesTallinn University of TechnologyAkadeemia tee 15a12618TallinnEstonia
| | - Shishan Wang
- Institut de Biologie et Chimie des Protéines MMSB UMR 5086 CNRS/Université de Lyon, Labex Ecofect7 passage du Vercors69367LyonFrance
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines MMSB UMR 5086 CNRS/Université de Lyon, Labex Ecofect7 passage du Vercors69367LyonFrance
| | | | - Ago Samoson
- Institute of Health TechnologiesTallinn University of TechnologyAkadeemia tee 15a12618TallinnEstonia
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines MMSB UMR 5086 CNRS/Université de Lyon, Labex Ecofect7 passage du Vercors69367LyonFrance
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10
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Jalily PH, Duncan MC, Fedida D, Wang J, Tietjen I. Put a cork in it: Plugging the M2 viral ion channel to sink influenza. Antiviral Res 2020; 178:104780. [PMID: 32229237 PMCID: PMC7102647 DOI: 10.1016/j.antiviral.2020.104780] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/12/2020] [Accepted: 03/20/2020] [Indexed: 12/17/2022]
Abstract
The ongoing threat of seasonal and pandemic influenza to human health requires antivirals that can effectively supplement existing vaccination strategies. The M2 protein of influenza A virus (IAV) is a proton-gated, proton-selective ion channel that is required for virus replication and is an established antiviral target. While licensed adamantane-based M2 antivirals have been historically used, M2 mutations that confer major adamantane resistance are now so prevalent in circulating virus strains that these drugs are no longer recommended. Here we review the current understanding of IAV M2 structure and function, mechanisms of inhibition, the rise of drug resistance mutations, and ongoing efforts to develop new antivirals that target resistant forms of M2.
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Affiliation(s)
- Pouria H Jalily
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - David Fedida
- Department of Anesthesiology, Pharmacology, and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tuscon, AZ, USA
| | - Ian Tietjen
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; The Wistar Institute, Philadelphia, PA, USA.
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11
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12
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Abstract
Design of a drug compound that can effectively bind to the M2 ion channel and block the diffusion of hydrogen ions (H+) through and inhibit influenza A virus replication is an important task. Known anti-influenza drugs amantadine and rimantadine have a weak effect on influenza A virus. A new class of positively charged, +2 e.u., molecules is proposed here to block diffusion of H+ ion through the M2 channel. Several drug candidates, derivatives of a lead compound (diazabicyclooctane), were proposed and investigated. Molecular dynamics of thermal fluctuations of M2 protein structure and ionization-conformation coupling of all the ionizable residues were simulated at physiological pH. The influence of the most probable mutations of key drug-binding amino acid residues in the M2 ion channel were investigated too. It is shown that the suggested new blocker has high binding affinity for the M2 channel. There are two in-channel binding sites of high affinity, the first one has H-bonds with two of four serine residues Ser-31A (B) or Ser-31C(D), and the second one has H-bonds with two of four histidine residues His-37A (B), or His-37C(D). The main advantage of the new drug molecule is the positive charge, +2 e.u., which creates a positive electrostatic potential barrier (in addition to a steric one) for a transfer of H+ ion through M2 channel and may serve as an effective anti-influenza A virus drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yury N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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13
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Movellan K, Wegstroth M, Overkamp K, Leonov A, Becker S, Andreas LB. Imidazole-Imidazole Hydrogen Bonding in the pH-Sensing Histidine Side Chains of Influenza A M2. J Am Chem Soc 2020; 142:2704-2708. [PMID: 31970979 PMCID: PMC7307898 DOI: 10.1021/jacs.9b10984] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Indexed: 12/28/2022]
Abstract
The arrangement of histidine side chains in influenza A M2 tetramer determines their pKa values, which define pH-controlled proton conduction critical to the virus lifecycle. Both water-associated and hydrogen-bonded imidazole-imidazolium histidine quaternary structures have been proposed, based on crystal structures and NMR chemical shifts, respectively. Here we show, using the conduction domain construct of M2 in lipid bilayers, that the imidazole rings are hydrogen bonded even at a pH of 7.8 in the neutral charge state. An intermolecular 8.9 ± 0.3 Hz 2hJNN hydrogen bond is observed between H37 Nε and Nδ recorded in a fully protonated sample with 100 kHz magic-angle spinning. This interaction could not be detected in the drug-bound sample.
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Affiliation(s)
- Kumar
Tekwani Movellan
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Melanie Wegstroth
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Kerstin Overkamp
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Andrei Leonov
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Stefan Becker
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Loren B. Andreas
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, Göttingen 37077, Germany
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14
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Fu R, Miao Y, Qin H, Cross TA. Observation of the Imidazole-Imidazolium Hydrogen Bonds Responsible for Selective Proton Conductance in the Influenza A M2 Channel. J Am Chem Soc 2020; 142:2115-2119. [PMID: 31970982 DOI: 10.1021/jacs.9b09985] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The integral membrane M2 protein is a 97-residue membrane protein that assembles as a tetramer to conduct protons at a slow rate (102-103/s) when activated by low pH. The proton conductance mechanism has been extensively debated in the literature, but it is accepted that the proton conductance is facilitated by hydrogen bonds involving the His37 residues. However, the hydrogen bonding partnership remains unresolved. Here, we report on the measurement of 15N-15N J-couplings of 15N His37-labeled full length M2 (M2FL) protein from Influenza A virus embedded in synthetic liquid crystalline lipid bilayers using two-dimensional J-resolved NMR spectroscopy. We experimentally observed the hydrogen-bond mediated J-couplings between Nδ1 and Nε2 of adjacent His37 imidazole rings, providing direct evidence for the existence of various imidazolium-imidazole hydrogen-bonding geometries in the histidine tetrad at low pH, thus validating the proton conduction mechanism in the M2FL protein by which the proton is transferred through the breaking and reforming of the hydrogen bonds between pairs of His37 residues.
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Affiliation(s)
- Riqiang Fu
- National High Magnet Field Lab , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Yimin Miao
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
| | - Huajun Qin
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
| | - Timothy A Cross
- National High Magnet Field Lab , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States.,Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
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15
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Hasan M, Patel D, Ellis N, Brown SP, Lewandowski JR, Dixon AM. Modulation of Transmembrane Domain Interactions in Neu Receptor Tyrosine Kinase by Membrane Fluidity and Cholesterol. J Membr Biol 2019; 252:357-369. [DOI: 10.1007/s00232-019-00075-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/09/2019] [Indexed: 01/06/2023]
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16
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Santner P, Martins JMDS, Kampmeyer C, Hartmann-Petersen R, Laursen JS, Stein A, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K. Random Mutagenesis Analysis of the Influenza A M2 Proton Channel Reveals Novel Resistance Mutants. Biochemistry 2018; 57:5957-5968. [PMID: 30230310 DOI: 10.1021/acs.biochem.8b00722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influenza M2 proton channel is a major drug target, but unfortunately, the acquisition of resistance mutations greatly reduces the functional life span of a drug in influenza treatment. New M2 inhibitors that inhibit mutant M2 channels otherwise resistant to the early adamantine-based drugs have been reported, but it remains unclear whether and how easy resistance could arise to such inhibitors. We have combined a newly developed proton conduction assay with an established method for selection and screening, both Escherichia coli-based, to enable the study of M2 function and inhibition. Combining this platform with two groups of structurally different M2 inhibitors allowed us to isolate drug resistant M2 channels from a mutant library. Two groups of M2 variants emerged from this analysis. A first group appeared almost unaffected by the inhibitor, M_089 (N13I, I35L, and F47L) and M_272 (G16C and D44H), and the single-substitution variants derived from these (I35L, L43P, D44H, and L46P). Functionally, these resemble the known drug resistant M2 channels V27A, S31N, and swine flu. In addition, a second group of tested M2 variants were all still inhibited by drugs but to a lesser extent than wild type M2. Molecular dynamics simulations aided in distinguishing the two groups where drug binding to the wild type and the less resistant M2 group showed a stable positioning of the ligand in the canonical binding pose, as opposed to the drug resistant group in which the ligand rapidly dissociated from the complex during the simulations.
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Affiliation(s)
- Paul Santner
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - João Miguel da Silva Martins
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Caroline Kampmeyer
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Jonas S Laursen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Amelie Stein
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Christian A Olsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark.,Center for Biopharmaceuticals, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Isaiah T Arkin
- Department of Biological Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Givat-Ram, Jerusalem 91904 , Israel
| | - Jakob R Winther
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Martin Willemoës
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
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17
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Thomaston JL, Polizzi NF, Konstantinidi A, Wang J, Kolocouris A, DeGrado WF. Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters. J Am Chem Soc 2018; 140:15219-15226. [PMID: 30165017 DOI: 10.1021/jacs.8b06741] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Water-mediated interactions play key roles in drug binding. In protein sites with sparse polar functionality, a small-molecule approach is often viewed as insufficient to achieve high affinity and specificity. Here we show that small molecules can enable potent inhibition by targeting key waters. The M2 proton channel of influenza A is the target of the antiviral drugs amantadine and rimantadine. Structural studies of drug binding to the channel using X-ray crystallography have been limited because of the challenging nature of the target, with the one previously solved crystal structure limited to 3.5 Å resolution. Here we describe crystal structures of amantadine bound to M2 in the Inwardclosed conformation (2.00 Å), rimantadine bound to M2 in both the Inwardclosed (2.00 Å) and Inwardopen (2.25 Å) conformations, and a spiro-adamantyl amine inhibitor bound to M2 in the Inwardclosed conformation (2.63 Å). These X-ray crystal structures of the M2 proton channel with bound inhibitors reveal that ammonium groups bind to water-lined sites that are hypothesized to stabilize transient hydronium ions formed in the proton-conduction mechanism. Furthermore, the ammonium and adamantyl groups of the adamantyl-amine class of drugs are free to rotate in the channel, minimizing the entropic cost of binding. These drug-bound complexes provide the first high-resolution structures of drugs that interact with and disrupt networks of hydrogen-bonded waters that are widely utilized throughout nature to facilitate proton diffusion within proteins.
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Affiliation(s)
- Jessica L Thomaston
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Nicholas F Polizzi
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Athina Konstantinidi
- Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , 15771 Athens , Greece
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy , University of Arizona , Tucson , Arizona 85721 , United States
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , 15771 Athens , Greece
| | - William F DeGrado
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
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18
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Drakopoulos A, Tzitzoglaki C, McGuire K, Hoffmann A, Konstantinidi A, Kolokouris D, Ma C, Freudenberger K, Hutterer J, Gauglitz G, Wang J, Schmidtke M, Busath DD, Kolocouris A. Unraveling the Binding, Proton Blockage, and Inhibition of Influenza M2 WT and S31N by Rimantadine Variants. ACS Med Chem Lett 2018. [PMID: 29541360 DOI: 10.1021/acsmedchemlett.7b00458] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recently, the binding kinetics of a ligand-target interaction, such as the residence time of a small molecule on its protein target, are seen as increasingly important for drug efficacy. Here, we investigate these concepts to explain binding and proton blockage of rimantadine variants bearing progressively larger alkyl groups to influenza A virus M2 wild type (WT) and M2 S31N protein proton channel. We showed that resistance of M2 S31N to rimantadine analogues compared to M2 WT resulted from their higher koff rates compared to the kon rates according to electrophysiology (EP) measurements. This is due to the fact that, in M2 S31N, the loss of the V27 pocket for the adamantyl cage resulted in low residence time inside the M2 pore. Both rimantadine enantiomers have similar channel blockage and binding kon and koff against M2 WT. To compare the potency between the rimantadine variants against M2, we applied approaches using different mimicry of M2, i.e., isothermal titration calorimetry and molecular dynamics simulation, EP, and antiviral assays. It was also shown that a small change in an amino acid at site 28 of M2 WT, which does not line the pore, seriously affects M2 WT blockage kinetics.
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Affiliation(s)
- Antonios Drakopoulos
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Greece
| | - Christina Tzitzoglaki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Greece
| | - Kelly McGuire
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah 84602, United States
| | - Anja Hoffmann
- Department of Medicinal Microbiology, Section Experimental Virology, Jena University Hospital, Hans Knoell Str. 2, D-07745 Jena, Germany
| | - Athina Konstantinidi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Greece
| | - Dimitrios Kolokouris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Greece
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Kathrin Freudenberger
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität Tübingen, 72074 Tübingen, Germany
| | - Johanna Hutterer
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität Tübingen, 72074 Tübingen, Germany
| | - Günter Gauglitz
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität Tübingen, 72074 Tübingen, Germany
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Michaela Schmidtke
- Department of Medicinal Microbiology, Section Experimental Virology, Jena University Hospital, Hans Knoell Str. 2, D-07745 Jena, Germany
| | - David D. Busath
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah 84602, United States
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Greece
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19
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Liao SY, Lee M, Hong M. Interplay between membrane curvature and protein conformational equilibrium investigated by solid-state NMR. J Struct Biol 2018; 206:20-28. [PMID: 29501472 DOI: 10.1016/j.jsb.2018.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/19/2018] [Accepted: 02/26/2018] [Indexed: 11/28/2022]
Abstract
Many membrane proteins sense and induce membrane curvature for function, but structural information about how proteins modulate their structures to cause membrane curvature is sparse. We review our recent solid-state NMR studies of two virus membrane proteins whose conformational equilibrium is tightly coupled to membrane curvature. The influenza M2 proton channel has a drug-binding site in the transmembrane (TM) pore. Previous chemical shift data indicated that this pore-binding site is lost in an M2 construct that contains the TM domain and a curvature-inducing amphipathic helix. We have now obtained chemical shift perturbation, protein-drug proximity, and drug orientation data that indicate that the pore-binding site is restored when the full cytoplasmic domain is present. This finding indicates that the curvature-inducing amphipathic helix distorts the TM structure to interfere with drug binding, while the cytoplasmic tail attenuates this effect. In the second example, we review our studies of a parainfluenza virus fusion protein that merges the cell membrane and the virus envelope during virus entry. Chemical shifts of two hydrophobic domains of the protein indicate that both domains have membrane-dependent backbone conformations, with the β-strand structure dominating in negative-curvature phosphatidylethanolamine (PE) membranes. 31P NMR spectra and 1H-31P correlation spectra indicate that the β-strand-rich conformation induces saddle-splay curvature to PE membranes and dehydrates them, thus stabilizing the hemifusion state. These results highlight the indispensable role of solid-state NMR to simultaneously determine membrane protein structures and characterize the membrane curvature in which these protein structures exist.
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Affiliation(s)
- Shu Y Liao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Myungwoon Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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20
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Ramsey J, Mukhopadhyay S. Disentangling the Frames, the State of Research on the Alphavirus 6K and TF Proteins. Viruses 2017; 9:v9080228. [PMID: 28820485 PMCID: PMC5580485 DOI: 10.3390/v9080228] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 08/03/2017] [Accepted: 08/16/2017] [Indexed: 01/04/2023] Open
Abstract
For 30 years it was thought the alphavirus 6K gene encoded a single 6 kDa protein. However, through a bioinformatics search 10 years ago, it was discovered that there is a frameshifting event and two proteins, 6K and transframe (TF), are translated from the 6K gene. Thus, many functions attributed to the 6K protein needed reevaluation to determine if they properly belong to 6K, TF, or both proteins. In this mini-review, we reevaluate the past research on 6K and put those results in context where there are two proteins, 6K and TF, instead of one. Additionally, we discuss the most cogent outstanding questions for 6K and TF research, including their collective importance in alphavirus budding and their potential importance in disease based on the latest virulence data.
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Affiliation(s)
- Jolene Ramsey
- Department of Biology at Indiana University, Bloomington, IN 47405, USA.
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21
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Nováková L, Pavlík J, Chrenková L, Martinec O, Červený L. Current antiviral drugs and their analysis in biological materials-Part I: Antivirals against respiratory and herpes viruses. J Pharm Biomed Anal 2017; 147:400-416. [PMID: 28755849 DOI: 10.1016/j.jpba.2017.06.071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 02/07/2023]
Abstract
This review article is the first in the series providing an overview of currently used antiviral drugs and presenting contemporary approaches to their analysis. Large number of available antivirals and their structural variability makes this task very challenging. Trying to cover this topic comprehensively while maintaining reasonable size of the article, the review is presented in two parts. For the purpose of the overall review, antivirals were divided into four groups: (i) antivirals against herpes viruses, (ii) antivirals against respiratory viruses, (iii) antivirals against hepatitis viruses, and (iv) antivirals against HIV. Part one is devoted to the groups (i) and (ii) and also concerns the key features of the bioanalytical method. The mechanisms of action of antivirals against respiratory and herpes viruses and their use in clinical practice are briefly outlined, and the analytical methods for selected representatives of each class are described in more detail. The methods developed for the determination of drugs from these classes mostly include conventional procedures. In contrast, current trends such as UHPLC are used rarely and proper method validation based on requirements of bioanalytical guidelines can be often considered insufficient.
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Affiliation(s)
- Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic.
| | - Jakub Pavlík
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Lucia Chrenková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Ondřej Martinec
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Lukáš Červený
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
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22
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Mandala VS, Liao SY, Kwon B, Hong M. Structural Basis for Asymmetric Conductance of the Influenza M2 Proton Channel Investigated by Solid-State NMR Spectroscopy. J Mol Biol 2017; 429:2192-210. [PMID: 28535993 DOI: 10.1016/j.jmb.2017.05.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/21/2017] [Accepted: 05/16/2017] [Indexed: 12/25/2022]
Abstract
The influenza M2 protein forms an acid-activated proton channel that is essential for virus replication. The transmembrane H37 selects for protons under low external pH while W41 ensures proton conduction only from the N terminus to the C terminus and prevents reverse current under low internal pH. Here, we address the molecular basis for this asymmetric conduction by investigating the structure and dynamics of a mutant channel, W41F, which permits reverse current under low internal pH. Solid-state NMR experiments show that W41F M2 retains the pH-dependent α-helical conformations and tetrameric structure of the wild-type (WT) channel but has significantly altered protonation and tautomeric equilibria at H37. At high pH, the H37 structure is shifted toward the π tautomer and less cationic tetrads, consistent with faster forward deprotonation to the C terminus. At low pH, the mutant channel contains more cationic tetrads than the WT channel, consistent with faster reverse protonation from the C terminus. 15N NMR spectra allow the extraction of four H37 pKas and show that the pKas are more clustered in the mutant channel compared to WT M2. Moreover, binding of the antiviral drug, amantadine, at the N-terminal pore at low pH did not convert all histidines to the neutral state, as seen in WT M2, but left half of all histidines cationic, unambiguously demonstrating C-terminal protonation of H37 in the mutant. These results indicate that asymmetric conduction in WT M2 is due to W41 inhibition of C-terminal acid activation by H37. When Trp is replaced by Phe, protons can be transferred to H37 bidirectionally with distinct rate constants.
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23
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Qin H, Miao Y, Cross TA, Fu R. Beyond Structural Biology to Functional Biology: Solid-State NMR Experiments and Strategies for Understanding the M2 Proton Channel Conductance. J Phys Chem B 2017; 121:4799-4809. [PMID: 28425709 DOI: 10.1021/acs.jpcb.7b02468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In terms of structural biology, solid-state NMR experiments and strategies have been well established for resonance assignments, leading to the determination of three-dimensional structures of insoluble membrane proteins in their native-like environment. It is also known that NMR has the unique capabilities to characterize structure-function relationships of membrane-bound biological systems beyond structural biology. Here, we report on solid-state NMR experiments and strategies for extracting functional activities on a sub-millisecond time scale. Specifically, we use the His37-labeled full length M2 (M2FL) protein of the Influenza A virus embedded in synthetic lipid bilayers as an example to characterize the proton conduction mechanism and kinetics. The integral membrane M2 protein assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH and is essential for the viral lifecycle. Our results present convincing evidence for the formation of imidazolium-imidazole hydrogen bonds in the His37 tetrad at low pH and that these hydrogen bonds have a low barrier that facilitates the proton conduction mechanism in the M2FL protein. Moreover, it has been possible to measure hydronium ion exchange between water and the protons in the His37 NH bonds based on chemical exchange spectroscopy with minimized spin diffusion. The results identify an exchange rate constant of ∼4000 s-1 for pH 5.8 at -10 °C.
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Affiliation(s)
- Huajun Qin
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Yimin Miao
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Timothy A Cross
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States.,National High Magnet Field Lab , 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Riqiang Fu
- National High Magnet Field Lab , 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
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24
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Abstract
Since the first antiviral drug, idoxuridine, was approved in 1963, 90 antiviral drugs categorized into 13 functional groups have been formally approved for the treatment of the following 9 human infectious diseases: (i) HIV infections (protease inhibitors, integrase inhibitors, entry inhibitors, nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and acyclic nucleoside phosphonate analogues), (ii) hepatitis B virus (HBV) infections (lamivudine, interferons, nucleoside analogues, and acyclic nucleoside phosphonate analogues), (iii) hepatitis C virus (HCV) infections (ribavirin, interferons, NS3/4A protease inhibitors, NS5A inhibitors, and NS5B polymerase inhibitors), (iv) herpesvirus infections (5-substituted 2'-deoxyuridine analogues, entry inhibitors, nucleoside analogues, pyrophosphate analogues, and acyclic guanosine analogues), (v) influenza virus infections (ribavirin, matrix 2 protein inhibitors, RNA polymerase inhibitors, and neuraminidase inhibitors), (vi) human cytomegalovirus infections (acyclic guanosine analogues, acyclic nucleoside phosphonate analogues, pyrophosphate analogues, and oligonucleotides), (vii) varicella-zoster virus infections (acyclic guanosine analogues, nucleoside analogues, 5-substituted 2'-deoxyuridine analogues, and antibodies), (viii) respiratory syncytial virus infections (ribavirin and antibodies), and (ix) external anogenital warts caused by human papillomavirus infections (imiquimod, sinecatechins, and podofilox). Here, we present for the first time a comprehensive overview of antiviral drugs approved over the past 50 years, shedding light on the development of effective antiviral treatments against current and emerging infectious diseases worldwide.
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25
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Llabrés S, Juárez-Jiménez J, Masetti M, Leiva R, Vázquez S, Gazzarrini S, Moroni A, Cavalli A, Luque FJ. Mechanism of the Pseudoirreversible Binding of Amantadine to the M2 Proton Channel. J Am Chem Soc 2016; 138:15345-15358. [DOI: 10.1021/jacs.6b07096] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Salomé Llabrés
- Department
of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and
Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Avgda. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
| | - Jordi Juárez-Jiménez
- Department
of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and
Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Avgda. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
| | - Matteo Masetti
- Department
of Pharmacy and Biotecnology (FaBit), Alma Mater Studiorum, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Rosana Leiva
- Laboratori
de Química Farmacèutica (Unitat Associada al CSIC),
Facultat de Farmàcia i Ciències de l’Alimentació,
and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan
XXIII 27-31, 08028 Barcelona, Spain
| | - Santiago Vázquez
- Laboratori
de Química Farmacèutica (Unitat Associada al CSIC),
Facultat de Farmàcia i Ciències de l’Alimentació,
and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan
XXIII 27-31, 08028 Barcelona, Spain
| | - Sabrina Gazzarrini
- Department
of Biosciences and National Research Council (CNR) Biophysics Institute
(IBF), University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Anna Moroni
- Department
of Biosciences and National Research Council (CNR) Biophysics Institute
(IBF), University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Andrea Cavalli
- Department
of Pharmacy and Biotecnology (FaBit), Alma Mater Studiorum, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
- CompuNet, Istituto Italiano di Tecnologia (IIT), via Morego 30, 16163 Genova,Italy
| | - F. Javier Luque
- Department
of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and
Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Avgda. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
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26
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Markiewicz BN, Lemmin T, Zhang W, Ahmed IA, Jo H, Fiorin G, Troxler T, DeGrado WF, Gai F. Infrared and fluorescence assessment of the hydration status of the tryptophan gate in the influenza A M2 proton channel. Phys Chem Chem Phys 2016; 18:28939-28950. [PMID: 27725984 PMCID: PMC5157935 DOI: 10.1039/c6cp03426h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The M2 proton channel of the influenza A virus has been the subject of extensive studies because of its critical role in viral replication. As such, we now know a great deal about its mechanism of action, especially how it selects and conducts protons in an asymmetric fashion. The conductance of this channel is tuned to conduct protons at a relatively low biologically useful rate, which allows acidification of the viral interior of a virus entrapped within an endosome, but not so great as to cause toxicity to the infected host cell prior to packaging of the virus. The dynamic, structural and chemical features that give rise to this tuning are not fully understood. Herein, we use a tryptophan (Trp) analog, 5-cyanotryptophan, and various methods, including linear and nonlinear infrared spectroscopies, static and time-resolved fluorescence techniques, and molecular dynamics simulations, to site-specifically interrogate the structure and hydration dynamics of the Trp41 gate in the transmembrane domain of the M2 proton channel. Our results suggest that the Trp41 sidechain adopts the t90 rotamer, the χ2 dihedral angle of which undergoes an increase of approximately 35° upon changing the pH from 7.4 to 5.0. Furthermore, we find that Trp41 is situated in an environment lacking bulk-like water, and somewhat surprisingly, the water density and dynamics do not show a measurable difference between the high (7.4) and low (5.0) pH states. Since previous studies have shown that upon channel opening water flows into the cavity above the histidine tetrad (His37), the present finding thus provides evidence indicating that the lack of sufficient water molecules near Trp41 needed to establish a continuous hydrogen bonding network poses an additional energetic bottleneck for proton conduction.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, USA.
| | - Wenkai Zhang
- Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ismail A Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, USA.
| | - Giacomo Fiorin
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Thomas Troxler
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. and Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. and Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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27
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Abstract
Proton-coupled transmembrane proteins play important roles in human health and diseases; however, detailed mechanisms are often elusive. Experimentally resolving proton positions and structural details is challenging, and conventional molecular dynamics simulations are performed with preassigned and fixed protonation states. To address this challenge, here we illustrate the use of the state-of-the-art continuous constant pH molecular dynamics (CpHMD) to directly describe the activation of the M2 channel of influenza virus, for which abundant experimental data are available. Starting from the closed crystal structure, simulation reveals a pH-dependent conformational switch to an activated state that resembles the open crystal structure. Importantly, simulation affords the free energy of channel opening coupled to the titration of a histidine tetrad, thereby providing a thermodynamic mechanism for M2 activation, that is consistent with NMR data and resolves the controversy with crystal structures obtained at different pH values. This work illustrates the utility of CpHMD in offering previously unattainable conformational details and thermodynamic information for proton-coupled transmembrane channels and transporters.
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Affiliation(s)
- Wei Chen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Yandong Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
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Kwon B, Hong M. The Influenza M2 Ectodomain Regulates the Conformational Equilibria of the Transmembrane Proton Channel: Insights from Solid-State Nuclear Magnetic Resonance. Biochemistry 2016; 55:5387-97. [PMID: 27571210 PMCID: PMC5257201 DOI: 10.1021/acs.biochem.6b00727] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The influenza M2 protein is the target of the amantadine family of antiviral drugs, and its transmembrane (TM) domain structure and dynamics have been extensively studied. However, little is known about the structure of the highly conserved N-terminal ectodomain, which contains epitopes targeted by influenza vaccines. In this study, we synthesized an M2 construct containing the N-terminal ectodomain and the TM domain, to understand the site-specific conformation and dynamics of the ectodomain and to investigate the effect of the ectodomain on the TM structure. We incorporated (13)C- and (15)N-labeled residues into both domains and measured their chemical shifts and line widths using solid-state nuclear magnetic resonance. The data indicate that the entire ectodomain is unstructured and dynamic, but the motion is slower for residues closer to the TM domain. (13)C line shapes indicate that this ecto-TM construct undergoes fast uniaxial rotational diffusion, like the isolated TM peptide, but drug binding increases the motional rates of the TM helix while slowing the local motion of the ectodomain residues that are close to the TM domain. Moreover, (13)C and (15)N chemical shifts indicate that the ectodomain shifts the conformational equilibria of the TM residues toward the drug-bound state even in the absence of amantadine, thus providing a molecular structural basis for the lower inhibitory concentration of full-length M2 compared to that of the ectodomain-truncated M2. We propose that this conformational selection may result from electrostatic repulsion between negatively charged ectodomain residues in the tetrameric protein. Together with the recent study of the M2 cytoplasmic domain, these results show that intrinsically disordered extramembrane domains in membrane proteins can regulate the functionally relevant conformation and dynamics of the structurally ordered TM domains.
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Affiliation(s)
- Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
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29
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30
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Fischer WB, Kalita MM, Heermann D. Viral channel forming proteins--How to assemble and depolarize lipid membranes in silico. Biochim Biophys Acta 2016; 1858:1710-21. [PMID: 26806161 PMCID: PMC7094687 DOI: 10.1016/j.bbamem.2016.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 01/23/2023]
Abstract
Viral channel forming proteins (VCPs) have been discovered in the late 70s and are found in many viruses to date. Usually they are small and have to assemble to form channels which depolarize the lipid membrane of the host cells. Structural information is just about to emerge for just some of them. Thus, computational methods play a pivotal role in generating plausible structures which can be used in the drug development process. In this review the accumulation of structural data is introduced from a historical perspective. Computational performances and their predictive power are reported guided by biological questions such as the assembly, mechanism of function and drug–protein interaction of VCPs. An outlook of how coarse grained simulations can contribute to yet unexplored issues of these proteins is given. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Early references about the discovery of viral channel forming proteins. Latest structural information about the class of proteins. Identification of structural motifs, assembly mechanism of function and drug action using computational methods. Outlook for the use of coarse grained techniques to address assembly and integration into cellular processes.
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Affiliation(s)
- Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan.
| | - Monoj Mon Kalita
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
| | - Dieter Heermann
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
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31
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Ward ME, Wang S, Munro R, Ritz E, Hung I, Gor'kov PL, Jiang Y, Liang H, Brown LS, Ladizhansky V. In situ structural studies of Anabaena sensory rhodopsin in the E. coli membrane. Biophys J 2016; 108:1683-1696. [PMID: 25863060 DOI: 10.1016/j.bpj.2015.02.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/18/2014] [Accepted: 02/12/2015] [Indexed: 01/06/2023] Open
Abstract
Magic-angle spinning nuclear magnetic resonance is well suited for the study of membrane proteins in the nativelike lipid environment. However, the natural cellular membrane is invariably more complex than the proteoliposomes most often used for solid-state NMR (SSNMR) studies, and differences may affect the structure and dynamics of the proteins under examination. In this work we use SSNMR and other biochemical and biophysical methods to probe the structure of a seven-transmembrane helical photoreceptor, Anabaena sensory rhodopsin (ASR), prepared in the Escherichia coli inner membrane, and compare it to that in a bilayer formed by DMPC/DMPA lipids. We find that ASR is organized into trimers in both environments but forms two-dimensional crystal lattices of different symmetries. It favors hexagonal packing in liposomes, but may form a square lattice in the E. coli membrane. To examine possible changes in structure site-specifically, we perform two- and three-dimensional SSNMR experiments and analyze the differences in chemical shifts and peak intensities. Overall, this analysis reveals that the structure of ASR is largely conserved in the inner membrane of E. coli, with many of the important structural features of rhodopsins previously observed in ASR in proteoliposomes being preserved. Small, site-specific perturbations in protein structure that occur as a result of the membrane changes indicate that the protein can subtly adapt to its environment without large structural rearrangement.
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Affiliation(s)
- Meaghan E Ward
- Department of Physics, University of Guelph, Guelph, Ontario, Canada; Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Shenlin Wang
- Department of Physics, University of Guelph, Guelph, Ontario, Canada; Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Rachel Munro
- Department of Physics, University of Guelph, Guelph, Ontario, Canada; Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Emily Ritz
- Department of Physics, University of Guelph, Guelph, Ontario, Canada
| | - Ivan Hung
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida
| | - Peter L Gor'kov
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida
| | - Yunjiang Jiang
- Department of Metallurgical and Materials Engineering, Colorado School of Mines, Golden, Colorado
| | - Hongjun Liang
- Department of Metallurgical and Materials Engineering, Colorado School of Mines, Golden, Colorado
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, Ontario, Canada; Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada.
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, Guelph, Ontario, Canada; Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada.
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Van Nguyen H, Nguyen HT, Le LT. Investigation of the free energy profiles of amantadine and rimantadine in the AM2 binding pocket. Eur Biophys J 2016; 45:63-70. [PMID: 26391902 DOI: 10.1007/s00249-015-1077-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/20/2015] [Accepted: 08/30/2015] [Indexed: 01/29/2023]
Abstract
The purpose of this work was to study the mechanism of drug resistance of M2 channel proteins by analyzing the interactions between the drugs amantadine and rimantadine and M2 channel proteins (including the wild type and the three mutants V27A, S31N, and G34A) and the drug binding pathways, by use of a computational approach. Our results showed that multiple drug-binding sites were present in the M2 channel, and the trajectory of the drugs through the M2 channel was determined. A novel method was developed to investigate of free energy profiles of the ligand-protein complexes. Our work provides a new explanation of the large amount of experimental data on drug efficacy.
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Kwon B, Tietze D, White PB, Liao SY, Hong M. Chemical ligation of the influenza M2 protein for solid-state NMR characterization of the cytoplasmic domain. Protein Sci 2015; 24:1087-99. [PMID: 25966817 PMCID: PMC4500309 DOI: 10.1002/pro.2690] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 04/13/2015] [Accepted: 04/24/2015] [Indexed: 12/17/2022]
Abstract
Solid-state NMR-based structure determination of membrane proteins and large protein complexes faces the challenge of limited spectral resolution when the proteins are uniformly (13)C-labeled. A strategy to meet this challenge is chemical ligation combined with site-specific or segmental labeling. While chemical ligation has been adopted in NMR studies of water-soluble proteins, it has not been demonstrated for membrane proteins. Here we show chemical ligation of the influenza M2 protein, which contains a transmembrane (TM) domain and two extra-membrane domains. The cytoplasmic domain, which contains an amphipathic helix (AH) and a cytoplasmic tail, is important for regulating virus assembly, virus budding, and the proton channel activity. A recent study of uniformly (13)C-labeled full-length M2 by spectral simulation suggested that the cytoplasmic tail is unstructured. To further test this hypothesis, we conducted native chemical ligation of the TM segment and part of the cytoplasmic domain. Solid-phase peptide synthesis of the two segments allowed several residues to be labeled in each segment. The post-AH cytoplasmic residues exhibit random-coil chemical shifts, low bond order parameters, and a surface-bound location, thus indicating that this domain is a dynamic random coil on the membrane surface. Interestingly, the protein spectra are similar between a model membrane and a virus-mimetic membrane, indicating that the structure and dynamics of the post-AH segment is insensitive to the lipid composition. This chemical ligation approach is generally applicable to medium-sized membrane proteins to provide site-specific structural constraints, which complement the information obtained from uniformly (13)C, (15)N-labeled proteins.
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Affiliation(s)
- Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Daniel Tietze
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Paul B White
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Shu Y Liao
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
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Abstract
The channel-forming activity of a family of small, hydrophobic integral membrane proteins termed 'viroporins' is essential to the life cycles of an increasingly diverse range of RNA and DNA viruses, generating significant interest in targeting these proteins for antiviral development. Viroporins vary greatly in terms of their atomic structure and can perform multiple functions during the virus life cycle, including those distinct from their role as oligomeric membrane channels. Recent progress has seen an explosion in both the identification and understanding of many such proteins encoded by highly significant pathogens, yet the prototypic M2 proton channel of influenza A virus remains the only example of a viroporin with provenance as an antiviral drug target. This review attempts to summarize our current understanding of the channel-forming functions for key members of this growing family, including recent progress in structural studies and drug discovery research, as well as novel insights into the life cycles of many viruses revealed by a requirement for viroporin activity. Ultimately, given the successes of drugs targeting ion channels in other areas of medicine, unlocking the therapeutic potential of viroporins represents a valuable goal for many of the most significant viral challenges to human and animal health.
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Affiliation(s)
- Claire Scott
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
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35
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Liao SY, Yang Y, Tietze D, Hong M. The influenza m2 cytoplasmic tail changes the proton-exchange equilibria and the backbone conformation of the transmembrane histidine residue to facilitate proton conduction. J Am Chem Soc 2015; 137:6067-77. [PMID: 25892574 DOI: 10.1021/jacs.5b02510] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The influenza M2 protein forms an acid-activated tetrameric proton channel important for the virus lifecycle. Residue His37 in the transmembrane domain is responsible for channel activation and proton selectivity. While the structure and dynamics of His37 have been well studied in TM peptide constructs, it has not been investigated in the presence of the full cytoplasmic domain, which increases the proton conductivity by 2-fold compared to the TM peptide. We report here (13)C and (15)N chemical shifts of His37 in the cytoplasmic-containing M2(21-97) and show that cationic histidines are already present at neutral pH, in contrast to the TM peptide, indicating that the cytoplasmic domain shifts the protonation equilibria. Quantification of the imidazole (15)N intensities yielded two resolved proton dissociation constants (pKa's) of 7.1 and 5.4, which differ from the TM result but resemble the M2(18-60) result, suggesting cooperative proton binding. The average His37 pKa is higher for M2(21-97) than for the shorter constructs. We attribute this higher pKa to direct and indirect effects of the cytoplasmic domain, which is rich in acidic residues. 2D (13)C-(13)C correlation spectra reveal seven His37 Cα-Cβ cross peaks at different pH, some of which are unique to the cytoplasmic-containing M2 and correspond to more ideal α-helical conformations. Based on the pH at which these chemical shifts appear and their side chain structures, we assign these conformations to His37 in differently charged tetramers. Thus, the cytoplasmic domain facilitates proton conduction through the transmembrane pore by modifying the His37-water proton exchange equilibria and the His37 backbone conformational distribution.
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Affiliation(s)
- Shu Y Liao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yu Yang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel Tietze
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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36
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Quinn CM, Lu M, Suiter CL, Hou G, Zhang H, Polenova T. Magic angle spinning NMR of viruses. Prog Nucl Magn Reson Spectrosc 2015; 86-87:21-40. [PMID: 25919197 PMCID: PMC4413014 DOI: 10.1016/j.pnmrs.2015.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/27/2015] [Accepted: 02/08/2015] [Indexed: 05/02/2023]
Abstract
Viruses, relatively simple pathogens, are able to replicate in many living organisms and to adapt to various environments. Conventional atomic-resolution structural biology techniques, X-ray crystallography and solution NMR spectroscopy provided abundant information on the structures of individual proteins and nucleic acids comprising viruses; however, viral assemblies are not amenable to analysis by these techniques because of their large size, insolubility, and inherent lack of long-range order. In this article, we review the recent advances in magic angle spinning NMR spectroscopy that enabled atomic-resolution analysis of structure and dynamics of large viral systems and give examples of several exciting case studies.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Christopher L Suiter
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Huilan Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
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37
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Wang T, Hong M. Investigation of the curvature induction and membrane localization of the influenza virus M2 protein using static and off-magic-angle spinning solid-state nuclear magnetic resonance of oriented bicelles. Biochemistry 2015; 54:2214-26. [PMID: 25774685 DOI: 10.1021/acs.biochem.5b00127] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A wide variety of membrane proteins induce membrane curvature for function; thus, it is important to develop new methods to simultaneously determine membrane curvature and protein binding sites in membranes with multiple curvatures. We introduce solid-state nuclear magnetic resonance (NMR) methods based on magnetically oriented bicelles and off-magic-angle spinning (OMAS) to measure membrane curvature and the binding site of proteins in mixed-curvature membranes. We demonstrate these methods on the influenza virus M2 protein, which not only acts as a proton channel but also mediates virus assembly and membrane scission. An M2 peptide encompassing the transmembrane (TM) domain and an amphipathic helix, M2(21-61), was studied and compared with the TM peptide (M2TM). Static (31)P NMR spectra of magnetically oriented 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) bicelles exhibit a temperature-independent isotropic chemical shift in the presence of M2(21-61) but not M2TM, indicating that the amphipathic helix confers the ability to generate a high-curvature phase. Two-dimensional (2D) (31)P spectra indicate that this high-curvature phase is associated with the DHPC bicelle edges, suggestive of the structure of budding viruses from the host cell. (31)P- and (13)C-detected (1)H relaxation times of the lipids indicate that the majority of M2(21-61) is bound to the high-curvature phase. Using OMAS experiments, we resolved the (31)P signals of lipids with identical headgroups based on their distinct chemical shift anisotropies. On the basis of this resolution, 2D (1)H-(31)P correlation spectra show that the amide protons in M2(21-61) correlate with the DMPC but not DHPC (31)P signal of the bicelle, indicating that a small percentage of M2(21-61) partitions into the planar region of the bicelles. These results show that the amphipathic helix induces high membrane curvature and localizes the protein to this phase, in good agreement with the membrane scission function of the protein. These bicelle-based relaxation and OMAS solid-state NMR techniques are generally applicable to curvature-inducing membrane proteins such as those involved in membrane trafficking, membrane fusion, and cell division.
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Affiliation(s)
- Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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38
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Witter R, Möllhoff M, Koch F, Sternberg U. Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein. J CHEM-NY 2015; 2015:1-14. [DOI: 10.1155/2015/908204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT). Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges ofab initiocalculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation ofR=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angleχ1and small variations ofχ2of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.
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39
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Gleed ML, Busath DD. Why bound amantadine fails to inhibit proton conductance according to simulations of the drug-resistant influenza A M2 (S31N). J Phys Chem B 2014; 119:1225-31. [PMID: 25426702 PMCID: PMC4306489 DOI: 10.1021/jp508545d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The mechanisms responsible for drug resistance in the Asn31 variant of the M2 protein of influenza A are not well understood. Molecular dynamics simulations were performed on wild-type (Ser31) and S31N influenza A M2 in the homotetramer configuration. After evaluation of 13 published M2 structures, a solid-state NMR structure with amantadine bound was selected for simulations, an S31N mutant structure was developed and equilibrated, and the native and mutant structures were used to determine the binding behavior of amantadine and the dynamics of water in the two channels. Amantadine is stable in the plugging region of wild-type M2, with the adamantane in contact with the Val27 side chains, while amantadine in S31N M2 has more variable movement and orientation, and spontaneously moves lower into the central cavity of the channel. Free energy profiles from umbrella sampling support this observation. In this configuration, water surrounds the drug and can easily transport protons past it, so the drug binds without blocking proton transport in the S31N M2 channel.
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Affiliation(s)
- Mitchell L Gleed
- Department of Physiology and Developmental Biology, Brigham Young University , Provo, Utah 84602, United States
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40
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Williams JK, Hong M. Probing membrane protein structure using water polarization transfer solid-state NMR. J Magn Reson 2014; 247:118-127. [PMID: 25228502 PMCID: PMC4398059 DOI: 10.1016/j.jmr.2014.08.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/10/2014] [Accepted: 08/15/2014] [Indexed: 05/27/2023]
Abstract
Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected (1)H polarization transfer from water to biomolecules is a versatile approach for studying water-protein, water-membrane, and water-carbohydrate interactions in biology. We review radiofrequency pulse sequences for measuring water polarization transfer to biomolecules, the mechanisms of polarization transfer, and the application of this method to various biological systems. Three polarization transfer mechanisms, chemical exchange, spin diffusion and NOE, manifest themselves at different temperatures, magic-angle-spinning frequencies, and pulse irradiations. Chemical exchange is ubiquitous in all systems examined so far, and spin diffusion plays the key role in polarization transfer within the macromolecule. Tightly bound water molecules with long residence times are rare in proteins at ambient temperature. The water polarization-transfer technique has been used to study the hydration of microcrystalline proteins, lipid membranes, and plant cell wall polysaccharides, and to derive atomic-resolution details of the kinetics and mechanism of ion conduction in channels and pumps. Using this approach, we have measured the water polarization transfer to the transmembrane domain of the influenza M2 protein to obtain information on the structure of this tetrameric proton channel. At short mixing times, the polarization transfer rates are site-specific and depend on the pH, labile protons, sidechain conformation, as well as the radial position of the residues in this four-helix bundle. Despite the multiple dependences, the initial transfer rates reflect the periodic nature of the residue positions from the water-filled pore, thus this technique provides a way of gleaning secondary structure information, helix tilt angle, and the oligomeric structure of membrane proteins.
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Affiliation(s)
- Jonathan K Williams
- Department of Chemistry, Iowa State University, Ames, IA 50011, United States
| | - Mei Hong
- Department of Chemistry, Iowa State University, Ames, IA 50011, United States.
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41
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Liang R, Li H, Swanson JM, Voth GA. Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel. Proc Natl Acad Sci U S A 2014; 111:9396-401. [PMID: 24979779 DOI: 10.1073/pnas.1401997111] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The influenza A virus M2 channel (AM2) is crucial in the viral life cycle. Despite many previous experimental and computational studies, the mechanism of the activating process in which proton permeation acidifies the virion to release the viral RNA and core proteins is not well understood. Herein the AM2 proton permeation process has been systematically characterized using multiscale computer simulations, including quantum, classical, and reactive molecular dynamics methods. We report, to our knowledge, the first complete free-energy profiles for proton transport through the entire AM2 transmembrane domain at various pH values, including explicit treatment of excess proton charge delocalization and shuttling through the His37 tetrad. The free-energy profiles reveal that the excess proton must overcome a large free-energy barrier to diffuse to the His37 tetrad, where it is stabilized in a deep minimum reflecting the delocalization of the excess charge among the histidines and the cost of shuttling the proton past them. At lower pH values the His37 tetrad has a larger total charge that increases the channel width, hydration, and solvent dynamics, in agreement with recent 2D-IR spectroscopic studies. The proton transport barrier becomes smaller, despite the increased charge repulsion, due to backbone expansion and the more dynamic pore water molecules. The calculated conductances are in quantitative agreement with recent experimental measurements. In addition, the free-energy profiles and conductances for proton transport in several mutants provide insights for explaining our findings and those of previous experimental mutagenesis studies.
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42
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Deryabin PG, Garaev TM, Finogenova MP, Botikov AG, Shibnev VA. Amino Acid Derivatives of Adamantane Carbocycle are Capable of Inhibiting Replication of Highly Virulent Avian Influenza A/H5N1 Virus. Bull Exp Biol Med 2014; 157:62-5. [DOI: 10.1007/s10517-014-2492-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Indexed: 11/25/2022]
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43
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Murray DT, Hung I, Cross TA. Assignment of oriented sample NMR resonances from a three transmembrane helix protein. J Magn Reson 2014; 240:34-44. [PMID: 24509383 PMCID: PMC3980497 DOI: 10.1016/j.jmr.2013.12.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/21/2013] [Accepted: 12/28/2013] [Indexed: 06/03/2023]
Abstract
Oriented sample solid state NMR techniques have been routinely employed to determine the structures of membrane proteins with one or two transmembrane helices. For larger proteins the technique has been limited by spectral resolution and lack of assignment strategies. Here, a strategy for resonance assignment is devised and applied to a three transmembrane helix protein. Sequence specific assignments for all labeled transmembrane amino acid sites are obtained, which provide a set of orientational restraints and helix orientations in the bilayer. Our experiments expand the utility of solid state NMR in membrane protein structure characterization to three transmembrane helix proteins and represent a straightforward strategy for routinely characterizing multiple transmembrane helix protein structures.
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Affiliation(s)
- D T Murray
- Institute for Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - I Hung
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - T A Cross
- Institute for Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
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44
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45
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Ma C, Fiorin G, Carnevale V, Wang J, Lamb RA, Klein ML, Wu Y, Pinto LH, DeGrado WF. Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. Structure 2013; 21:2033-41. [PMID: 24139991 DOI: 10.1016/j.str.2013.08.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/22/2013] [Accepted: 08/26/2013] [Indexed: 01/20/2023]
Abstract
Channel gating and proton conductance of the influenza A virus M2 channel result from complex pH-dependent interactions involving the pore-lining residues His37, Trp41, and Asp44. Protons diffusing from the outside of the virus protonate His37, which opens the Trp41 gate and allows one or more protons to move into the virus interior. The Trp41 gate gives rise to a strong asymmetry in the conductance, favoring rapid proton flux only when the outside is at acid pH. Here, we show that the proton currents recorded for mutants of Asp44, including D44N found in the A/FPV/Rostock/34 strain, lose this asymmetry. Moreover, NMR and MD simulations show that the mutations induce a conformational change similar to that induced by protonation of His37 at low pH, and decrease the structural stability of the hydrophobic seal associated with the Trp41 gate. Thus, Asp44 is able to determine two important properties of the M2 proton channel.
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46
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Liao SY, Fritzsching KJ, Hong M. Conformational analysis of the full-length M2 protein of the influenza A virus using solid-state NMR. Protein Sci 2013; 22:1623-38. [PMID: 24023039 DOI: 10.1002/pro.2368] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/04/2013] [Accepted: 09/04/2013] [Indexed: 12/24/2022]
Abstract
The influenza A M2 protein forms a proton channel for virus infection and mediates virus assembly and budding. While extensive structural information is known about the transmembrane helix and an adjacent amphipathic helix, the conformation of the N-terminal ectodomain and the C-terminal cytoplasmic tail remains largely unknown. Using two-dimensional (2D) magic-angle-spinning solid-state NMR, we have investigated the secondary structure and dynamics of full-length M2 (M2FL) and found them to depend on the membrane composition. In 2D (13)C DARR correlation spectra, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)-bound M2FL exhibits several peaks at β-sheet chemical shifts, which result from water-exposed extramembrane residues. In contrast, M2FL bound to cholesterol-containing membranes gives predominantly α-helical chemical shifts. Two-dimensional J-INADEQUATE spectra and variable-temperature (13)C spectra indicate that DMPC-bound M2FL is highly dynamic while the cholesterol-containing membranes significantly immobilize the protein at physiological temperature. Chemical-shift prediction for various secondary-structure models suggests that the β-strand is located at the N-terminus of the DMPC-bound protein, while the cytoplasmic domain is unstructured. This prediction is confirmed by the 2D DARR spectrum of the ectodomain-truncated M2(21-97), which no longer exhibits β-sheet chemical shifts in the DMPC-bound state. We propose that the M2 conformational change results from the influence of cholesterol, and the increased helicity of M2FL in cholesterol-rich membranes may be relevant for M2 interaction with the matrix protein M1 during virus assembly and budding. The successful determination of the β-strand location suggests that chemical-shift prediction is a promising approach for obtaining structural information of disordered proteins before resonance assignment.
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Affiliation(s)
- Shu Yu Liao
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011
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47
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Mote KR, Gopinath T, Veglia G. Determination of structural topology of a membrane protein in lipid bilayers using polarization optimized experiments (POE) for static and MAS solid state NMR spectroscopy. J Biomol NMR 2013; 57:91-102. [PMID: 23963722 PMCID: PMC3883141 DOI: 10.1007/s10858-013-9766-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 07/26/2013] [Indexed: 05/11/2023]
Abstract
The low sensitivity inherent to both the static and magic angle spinning techniques of solid-state NMR (ssNMR) spectroscopy has thus far limited the routine application of multidimensional experiments to determine the structure of membrane proteins in lipid bilayers. Here, we demonstrate the advantage of using a recently developed class of experiments, polarization optimized experiments, for both static and MAS spectroscopy to achieve higher sensitivity and substantial time-savings for 2D and 3D experiments. We used sarcolipin, a single pass membrane protein, reconstituted in oriented bicelles (for oriented ssNMR) and multilamellar vesicles (for MAS ssNMR) as a benchmark. The restraints derived by these experiments are then combined into a hybrid energy function to allow simultaneous determination of structure and topology. The resulting structural ensemble converged to a helical conformation with a backbone RMSD ~0.44 Å, a tilt angle of 24° ± 1°, and an azimuthal angle of 55° ± 6°. This work represents a crucial first step toward obtaining high-resolution structures of large membrane proteins using combined multidimensional oriented solid-state NMR and magic angle spinning solid-state NMR.
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Affiliation(s)
- Kaustubh R. Mote
- Department of Chemistry University of Minnesota, Minneapolis, MN 55455, USA
| | - T. Gopinath
- Department of Biochemistry, Molecular Biology & Biophysics University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianluigi Veglia
- Department of Chemistry University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology & Biophysics University of Minnesota, Minneapolis, MN 55455, USA
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48
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Gu RX, Liu LA, Wei DQ. Structural and energetic analysis of drug inhibition of the influenza A M2 proton channel. Trends Pharmacol Sci 2013; 34:571-80. [PMID: 24011996 DOI: 10.1016/j.tips.2013.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/09/2013] [Accepted: 08/12/2013] [Indexed: 01/07/2023]
Abstract
The type A influenza virus matrix protein 2 (M2) is a highly selective proton channel in the viral envelope. Because of its crucial role in viral infection and replication, the M2 channel has been a target of anti-influenza drugs. Due to the occurrence of drug-resistant mutations in the M2 channel, existing anti-influenza drugs that block the M2 channel, such as amantadine and rimantadine, have lost their efficacy against these mutant channels. Recent experimental and computational efforts have made great progress in understanding the drug resistance mechanisms of these mutations as well as designing novel drug candidates to block the mutant M2 channels. In this review, we briefly summarize the structural characteristics of the M2 channel, and then we discuss these recent studies on drug resistance and drug design of the mutant channels, focusing on the structures and energetics. We show that structural biology experiments and molecular modeling have led to the successful design of novel drugs targeting mutant M2 channels.
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Affiliation(s)
- Ruo-Xu Gu
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai Minhang District, 200240, China
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Nanda V, Cristian L, Toptygin D, Brand L, Degrado WF. Nanosecond Dynamics of InfluenzaA/M2TM and an Amantadine Resistant Mutant Probed by Time-Dependent Red Shifts of a Native Tryptophan. Chem Phys 2013; 422:10.1016/j.chemphys.2012.12.018. [PMID: 24273370 PMCID: PMC3833813 DOI: 10.1016/j.chemphys.2012.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Proteins involved in functions such as electron transfer or ion transport must be capable of stabilizing transient charged species on time scales ranging from picoseconds to microseconds. We study the influenza A M2 proton channel, containing a tryptophan residue that serves as an essential part of the proton conduction pathway. We induce a transition dipole in tryptophan by photoexcitation, and then probe the dielectric stabilization of its excited state. The magnitude of the stabilization over this time regime was larger than that generally found for tryptophan in membrane or protein environments. M2 achieves a water-like stabilization over a 25 nanosecond time scale, slower than that of bulk water, but sufficiently rapid to contribute to stabilization of charge as protons diffuse through the channel. These measurements should stimulate future MD studies to clarify the role of sidechain versus non-bulk water in defining the process of relaxation.
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Affiliation(s)
- Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School - UMDNJ, Piscataway, New Jersey 08854 ; Department of Biochemistry, Robert Wood Johnson Medical School - UMDNJ, Piscataway, New Jersey 08854
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50
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Bankura A, Klein ML, Carnevale V. Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from ab initio molecular dynamics. Chem Phys 2013; 422:156-164. [PMID: 25914436 PMCID: PMC4407280 DOI: 10.1016/j.chemphys.2013.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Ab initio molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the Nδ and Nε positions of the imidazole group to estimate the pKa's. Anticipating our results, we will see that the estimated pKa for the first protonation event of the M2 channel is in good agreement with experimental estimates. Surprisingly, despite the fact that the histidine is partially desolvated in the M2 channel, the affinity for protons is similar to that of a histidine in aqueous solution. Importantly, the electrostatic environment provided by the indoles is responsible for the stabilization of the charged imidazolium.
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Affiliation(s)
- Arindam Bankura
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Michael L. Klein
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
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