1
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Kurakin S, Badreeva D, Dushanov E, Shutikov A, Efimov S, Timerova A, Mukhametzyanov T, Murugova T, Ivankov O, Mamatkulov K, Arzumanyan G, Klochkov V, Kučerka N. Arrangement of lipid vesicles and bicelle-like structures formed in the presence of Aβ(25-35) peptide. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184237. [PMID: 37820938 DOI: 10.1016/j.bbamem.2023.184237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/31/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Our complementary experimental data and molecular dynamics (MD) simulations results reveal the structure of previously observed lipid bicelle-like structures (BLSs) formed in the presence of amyloid-beta peptide Aβ(25-35) below the main phase transition temperature (Tm) of saturated phosphatidylcholine lipids and small unilamellar vesicles (SUVs) above this temperature. First, we show by using solid-state 31P nuclear magnetic resonance (NMR) spectroscopy that our BLSs being in the lipid gel phase demonstrate magnetic alignment along the magnetic field of NMR spectrometer and undergo a transition to SUVs in the lipid fluid phase when heated through the Tm. Secondly, thanks to the BLS alignment we present their lipid structure. Lipids are found located not only in the flat bilayered part but also around its perimeter, which is corroborated by the results of coarse-grained (CG) MD simulations. Finally, peptides appear to mix randomly with lipids in SUVs while assuming predominantly unordered secondary structures revealed by circular dichroism (CD), Raman spectroscopy, and all-atom MD simulations. Importantly, the former is changing little when the system undergoes morphological transitions between BLSs and SUVs. Our structural results then offer a platform for studying and understanding mechanisms of morphological transformations caused by the disruptive effect of amyloid-beta peptides on the lipid bilayer.
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Affiliation(s)
- Sergei Kurakin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia.
| | - Dina Badreeva
- Meshcheryakov Laboratory of Information Technologies, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Ermuhammad Dushanov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Artyom Shutikov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Sergey Efimov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Ayzira Timerova
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Timur Mukhametzyanov
- Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Tatiana Murugova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Oleksandr Ivankov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Kahramon Mamatkulov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Grigory Arzumanyan
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Vladimir Klochkov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Odbojárov 10, Bratislava 832 32, Slovakia.
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2
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Dregni AJ, McKay MJ, Surya W, Queralt-Martin M, Medeiros-Silva J, Wang HK, Aguilella V, Torres J, Hong M. The Cytoplasmic Domain of the SARS-CoV-2 Envelope Protein Assembles into a β-Sheet Bundle in Lipid Bilayers. J Mol Biol 2023; 435:167966. [PMID: 36682677 PMCID: PMC9851921 DOI: 10.1016/j.jmb.2023.167966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/23/2022] [Accepted: 01/11/2023] [Indexed: 01/21/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein forms a pentameric ion channel in the lipid membrane of the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of the infected cell. The cytoplasmic domain of E interacts with host proteins to cause virus pathogenicity and may also mediate virus assembly and budding. To understand the structural basis of these functions, here we investigate the conformation and dynamics of an E protein construct (residues 8-65) that encompasses the transmembrane domain and the majority of the cytoplasmic domain using solid-state NMR. 13C and 15N chemical shifts indicate that the cytoplasmic domain adopts a β-sheet-rich conformation that contains three β-strands separated by turns. The five subunits associate into an umbrella-shaped bundle that is attached to the transmembrane helices by a disordered loop. Water-edited NMR spectra indicate that the third β-strand at the C terminus of the protein is well hydrated, indicating that it is at the surface of the β-bundle. The structure of the cytoplasmic domain cannot be uniquely determined from the inter-residue correlations obtained here due to ambiguities in distinguishing intermolecular and intramolecular contacts for a compact pentameric assembly of this small domain. Instead, we present four structural topologies that are consistent with the measured inter-residue contacts. These data indicate that the cytoplasmic domain of the SARS-CoV-2 E protein has a strong propensity to adopt β-sheet conformations when the protein is present at high concentrations in lipid bilayers. The equilibrium between the β-strand conformation and the previously reported α-helical conformation may underlie the multiple functions of E in the host cell and in the virion.
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Affiliation(s)
- Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Matthew J McKay
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Maria Queralt-Martin
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I. 12080 Castellón, Spain
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Harrison K Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Vicente Aguilella
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I. 12080 Castellón, Spain
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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3
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Madsen JJ, Rossman JS. Cholesterol and M2 Rendezvous in Budding and Scission of Influenza A Virus. Subcell Biochem 2023; 106:441-459. [PMID: 38159237 DOI: 10.1007/978-3-031-40086-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The cholesterol of the host cell plasma membrane and viral M2 protein plays a crucial role in multiple stages of infection and replication of the influenza A virus. Cholesterol is required for the formation of heterogeneous membrane microdomains (or rafts) in the budozone of the host cell that serves as assembly sites for the viral components. The raft microstructures act as scaffolds for several proteins. Cholesterol may further contribute to the mechanical forces necessary for membrane scission in the last stage of budding and help to maintain the stability of the virus envelope. The M2 protein has been shown to cause membrane scission in model systems by promoting the formation of curved lipid bilayer structures that, in turn, can lead to membrane vesicles budding off or scission intermediates. Membrane remodeling by M2 is intimately linked with cholesterol as it affects local lipid composition, fluidity, and stability of the membrane. Thus, both cholesterol and M2 protein contribute to the efficient and proper release of newly formed influenza viruses from the virus-infected cells.
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Affiliation(s)
- Jesper J Madsen
- Global and Planetary Health, Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, FL, USA.
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Jeremy S Rossman
- School of Biosciences, University of Kent, Canterbury, Kent, UK
- Research-Aid Networks, Chicago, IL, USA
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4
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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. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 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] [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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5
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Borcik C, Eason IR, Vanderloop B, Wylie BJ. 2H, 13C-Cholesterol for Dynamics and Structural Studies of Biological Membranes. ACS OMEGA 2022; 7:17151-17160. [PMID: 35647452 PMCID: PMC9134247 DOI: 10.1021/acsomega.2c00796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/08/2022] [Indexed: 05/19/2023]
Abstract
We present a cost-effective means of 2H and 13C enrichment of cholesterol. This method exploits the metabolism of 2H,13C-acetate into acetyl-CoA, the first substrate in the mevalonate pathway. We show that growing the cholesterol producing strain RH6827 of Saccharomyces cerevisiae in 2H,13C-acetate-enriched minimal media produces a skip-labeled pattern of deuteration. We characterize this cholesterol labeling pattern by mass spectrometry and solid-state nuclear magnetic resonance spectroscopy. It is confirmed that most 2H nuclei retain their original 2H-13C bonds from acetate throughout the biosynthetic pathway. We then quantify the changes in 13C chemical shifts brought by deuteration and the impact upon 13C-13C spin diffusion. Finally, using adiabatic rotor echo short pulse irradiation cross-polarization (RESPIRATIONCP), we acquire the 2H-13C correlation spectra to site specifically quantify cholesterol dynamics in two model membranes as a function of temperature. These measurements show that cholesterol acyl chains at physiological temperatures in mixtures of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), sphingomyelin, and cholesterol are more dynamic than cholesterol in POPC. However, this overall change in motion is not uniform across the cholesterol molecule. This result establishes that this cholesterol labeling pattern will have great utility in reporting on cholesterol dynamics and orientation in a variety of environments and with different membrane bilayer components, as well as monitoring the mevalonate pathway product interactions within the bilayer. Finally, the flexibility and universality of acetate labeling will allow this technique to be widely applied to a large range of lipids and other natural products.
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6
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Deciphering the Assembly of Enveloped Viruses Using Model Lipid Membranes. MEMBRANES 2022; 12:membranes12050441. [PMID: 35629766 PMCID: PMC9142974 DOI: 10.3390/membranes12050441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/01/2022] [Accepted: 04/09/2022] [Indexed: 01/09/2023]
Abstract
The cell plasma membrane is mainly composed of phospholipids, cholesterol and embedded proteins, presenting a complex interface with the environment. It maintains a barrier to control matter fluxes between the cell cytosol and its outer environment. Enveloped viruses are also surrounded by a lipidic membrane derived from the host-cell membrane and acquired while exiting the host cell during the assembly and budding steps of their viral cycle. Thus, model membranes composed of selected lipid mixtures mimicking plasma membrane properties are the tools of choice and were used to decipher the first step in the assembly of enveloped viruses. Amongst these viruses, we choose to report the three most frequently studied viruses responsible for lethal human diseases, i.e., Human Immunodeficiency Type 1 (HIV-1), Influenza A Virus (IAV) and Ebola Virus (EBOV), which assemble at the host-cell plasma membrane. Here, we review how model membranes such as Langmuir monolayers, bicelles, large and small unilamellar vesicles (LUVs and SUVs), supported lipid bilayers (SLBs), tethered-bilayer lipid membranes (tBLM) and giant unilamellar vesicles (GUVs) contribute to the understanding of viral assembly mechanisms and dynamics using biophysical approaches.
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7
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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] [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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8
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Kolokouris D, Kalenderoglou IE, Kolocouris A. Inside and Out of the Pore: Comparing Interactions and Molecular Dynamics of Influenza A M2 Viroporin Complexes in Standard Lipid Bilayers. J Chem Inf Model 2021; 61:5550-5568. [PMID: 34714655 DOI: 10.1021/acs.jcim.1c00264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion channels located at viral envelopes (viroporins) have a critical function for the replication of infectious viruses and are important drug targets. Over the last decade, the number and duration of molecular dynamics (MD) simulations of the influenza A M2 ion channel owing to the increased computational efficiency. Here, we aimed to define the system setup and simulation conditions for the correct description of the protein-pore and the protein-lipid interactions for influenza A M2 in comparison with experimental data. We performed numerous MD simulations of the influenza A M2 protein in complex with adamantane blockers in standard lipid bilayers using OPLS2005 and CHARMM36 (C36) force fields. We explored the effect of varying the M2 construct (M2(22-46) and M2(22-62)), the lipid buffer size and type (stiffer DMPC or softer POPC with or without 20% cholesterol), the simulation time, the H37 protonation site (Nδ or Νε), the conformational state of the W41 channel gate, and M2's cholesterol binding sites (BSs). We report that the 200 ns MD with M2(22-62) (having Nε Η37) in the 20 Å lipid buffer with the C36 force field accurately describe: (a) the M2 pore structure and interactions inside the pore, that is, adamantane channel blocker location, water clathrate structure, and water or chloride anion blockage/passage from the M2 pore in the presence of a channel blocker and (b) interactions between M2 and the membrane environment as reflected by the calculation of the M2 bundle tilt, folding of amphipathic helices, and cholesterol BSs. Strikingly, we also observed that the C36 1 μs MD simulations using M2(22-62) embedded in a 20 Å POPC:cholesterol (5:1) scrambled membrane produced frequent interactions with cholesterol, which when combined with computational kinetic analysis, revealed the experimentally observed BSs of cholesterol and suggested three similarly long-interacting positions in the top leaflet that have previously not been observed experimentally. These findings promise to be useful for other viroporin systems.
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Affiliation(s)
- Dimitrios Kolokouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Iris E Kalenderoglou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
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9
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Solid-State NMR for Studying the Structure and Dynamics of Viral Assemblies. Viruses 2020; 12:v12101069. [PMID: 32987909 PMCID: PMC7599928 DOI: 10.3390/v12101069] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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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10
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Li M, Heller WT, Liu CH, Gao CY, Cai Y, Hou Y, Nieh MP. Effects of fluidity and charge density on the morphology of a bicellar mixture - A SANS study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183315. [PMID: 32304755 DOI: 10.1016/j.bbamem.2020.183315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 01/28/2023]
Abstract
The spontaneously formed structures of physiologically relevant lipid model membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) and 1,2-hexanoyl-sn-glycero-3-phosphocholine have been evaluated in depth using small angle neutron scattering. Although a common molar ratio of long- to short- chain phospholipids (~4) as reported in many bicellar mixtures was used, discoidal bicelles were not found as the major phase throughout the range of lipid concentration and temperature studied, indicating that the required condition for the formation of bicelle is the immiscibility between the long- and short- chain lipids, which were in the gel and Lα phases, respectively, in previous reports. In this study, all lipids are in the Lα phase. The characterization outcome suggests that the spontaneous structures tie strongly with the physical parameters of the system such as melting transition temperature of the long-chain lipid, total lipid concentration and charge density of the system. Multilamellar vesicles, unilamellar vesicles, ribbons and perforated lamellae can be obtained based on the analysis of the small angle neutron scattering results, leading to the construction of structural diagrams. This report provides the important map to choose suitable lipid systems for the structural study of membrane-associated proteins, design of theranostic nanocarriers or other related research fields.
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Affiliation(s)
- Ming Li
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, 06269, USA
| | - William T Heller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Hao Liu
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, 06269, USA
| | - Carrie Y Gao
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yutian Cai
- Department of Polymer Material Science and Engineering, College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410000, China
| | - Yiming Hou
- Department of Polymer Material Science and Engineering, College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410000, China
| | - Mu-Ping Nieh
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, 06269, USA; Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs 06269, USA; Department of Biomedical Engineering, University of Connecticut, Storrs 06269, USA.
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11
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Martyna A, Bahsoun B, Madsen JJ, Jackson FSJS, Badham MD, Voth GA, Rossman JS. Cholesterol Alters the Orientation and Activity of the Influenza Virus M2 Amphipathic Helix in the Membrane. J Phys Chem B 2020; 124:6738-6747. [PMID: 32644803 PMCID: PMC7515559 DOI: 10.1021/acs.jpcb.0c03331] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The
influenza virus M2 amphipathic helix (M2AH) alters membrane
curvature in a cholesterol-dependent manner, mediating viral membrane
scission during influenza virus budding. Here, we have investigated
the biophysical effects of cholesterol on the ability of an M2AH peptide
to manipulate membrane properties. We see that the ability of the
M2AH to interact with membranes and form an α-helix is independent
of membrane cholesterol concentration; however, cholesterol affects
the angle of the M2AH peptide within the membrane. This change in
membrane orientation affects the ability of the M2AH to alter lipid
order. In low-cholesterol membranes, the M2AH is inserted near the
level of the lipid head groups, increasing lipid order, which may
contribute to generation of the membrane curvature. As the cholesterol
content increases, the M2AH insertion becomes flatter and slightly
deeper in the membrane below the lipid headgroups, where the polar
face can continue to interact with the headgroups while the hydrophobic
face binds cholesterol. This changed orientation minimizes lipid packing
defects and lipid order changes, likely reducing the generation of
membrane curvature. Thus, cholesterol regulates M2 membrane scission
by precisely modulating M2AH positioning within the membrane. This
has implications for the understanding of many of amphipathic-helix-driven
cellular budding processes that occur in specific lipid environments.
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Affiliation(s)
- Agnieszka Martyna
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Basma Bahsoun
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Jesper J Madsen
- Department of Chemistry and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | | | - Matthew D Badham
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Gregory A Voth
- Department of Chemistry and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jeremy S Rossman
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
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12
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Chakraborty A, Deligey F, Quach J, Mentink-Vigier F, Wang P, Wang T. Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy. Biochem Soc Trans 2020; 48:1089-1099. [PMID: 32379300 PMCID: PMC7565284 DOI: 10.1042/bst20191084] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 01/07/2023]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) is an indispensable tool for elucidating the structure and dynamics of insoluble and non-crystalline biomolecules. The recent advances in the sensitivity-enhancing technique magic-angle spinning dynamic nuclear polarization (MAS-DNP) have substantially expanded the territory of ssNMR investigations and enabled the detection of polymer interfaces in a cellular environment. This article highlights the emerging MAS-DNP approaches and their applications to the analysis of biomolecular composites and intact cells to determine the folding pathway and ligand binding of proteins, the structural polymorphism of low-populated biopolymers, as well as the physical interactions between carbohydrates, proteins, and lignin. These structural features provide an atomic-level understanding of many cellular processes, promoting the development of better biomaterials and inhibitors. It is anticipated that the capabilities of MAS-DNP in biomolecular and biomaterial research will be further enlarged by the rapid development of instrumentation and methodology.
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Affiliation(s)
- Arnab Chakraborty
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jenny Quach
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Ping Wang
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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13
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Konstantinidi A, Chountoulesi M, Naziris N, Sartori B, Amenitsch H, Mali G, Čendak T, Plakantonaki M, Triantafyllakou I, Tselios T, Demetzos C, Busath DD, Mavromoustakos T, Kolocouris A. The boundary lipid around DMPC-spanning influenza A M2 transmembrane domain channels: Its structure and potential for drug accommodation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183156. [PMID: 31846647 DOI: 10.1016/j.bbamem.2019.183156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 10/25/2022]
Abstract
We have investigated the perturbation of influenza A M2TM in DMPC bilayers. We have shown that (a) DSC and SAXS detect changes in membrane organization caused by small changes (micromolar) in M2TM or aminoadamantane concentration and aminoadamantane structure, by comparison of amantadine and spiro[pyrrolidine-2,2'-adamantane] (AK13), (b) that WAXS and MD can suggest details of ligand topology. DSC and SAXS show that at a low M2TM micromolar concentration in DPMC bilayers, two lipid domains are observed, which likely correspond to M2TM boundary lipids and bulk-like lipids. At higher M2TM concentrations, one domain only is identified, which constitutes essentially all of the lipid molecules behaving as boundary lipids. According to SAXS, WAXS, and DSC in the absence of M2TM, both aminoadamantane drugs exert a similar perturbing effect on the bilayer at low concentrations. At the same concentrations of the drug when M2TM is present, amantadine and, to a lesser extent, AK13 cause, according to WAXS, a significant disordering of chain-stacking, which also leads to the formation of two lipid domains. This effect is likely due, according to MD simulations, to the preference of the more lipophilic AK13 to locate closer to the lateral surfaces of M2TM when compared to amantadine, which forms stronger ionic interactions with phosphate groups. The preference of AK13 to concentrate inside the lipid bilayer close to the exterior of the hydrophobic M2TM helices may contribute to its higher binding affinity compared to amantadine.
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Affiliation(s)
- Athina Konstantinidi
- Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Maria Chountoulesi
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Nikolaos Naziris
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, A-8010 Graz, Austria
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, A-8010 Graz, Austria
| | - Gregor Mali
- Department of Inorganic Chemistry and Technology, National Institute of Chemistry, Ljubljana SI-1001, Slovenia
| | - Tomaž Čendak
- Department of Inorganic Chemistry and Technology, National Institute of Chemistry, Ljubljana SI-1001, Slovenia
| | - Maria Plakantonaki
- Department of Chemistry, School of Natural Sciences, University of Patras, Rion, Patras 26500, Greece
| | - Iro Triantafyllakou
- Department of Chemistry, School of Natural Sciences, University of Patras, Rion, Patras 26500, Greece
| | - Theodore Tselios
- Department of Chemistry, School of Natural Sciences, University of Patras, Rion, Patras 26500, Greece
| | - Costas Demetzos
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - David D Busath
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Thomas Mavromoustakos
- Section of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece.
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece.
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14
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Kang X, Elson C, Penfield J, Kirui A, Chen A, Zhang L, Wang T. Integrated solid-state NMR and molecular dynamics modeling determines membrane insertion of human β-defensin analog. Commun Biol 2019; 2:402. [PMID: 31701030 PMCID: PMC6825183 DOI: 10.1038/s42003-019-0653-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/15/2019] [Indexed: 12/11/2022] Open
Abstract
Human β-defensins (hBD) play central roles in antimicrobial activities against various microorganisms and in immune-regulation. These peptides perturb phospholipid membranes for function, but it is not well understood how defensins approach, insert and finally disrupt membranes on the molecular level. Here we show that hBD-3 analogs interact with lipid bilayers through a conserved surface that is formed by two adjacent loops in the solution structure. By integrating a collection of 13C, 1H and 31P solid-state NMR methods with long-term molecular dynamic simulations, we reveal that membrane-binding rigidifies the peptide, enhances structural polymorphism, and promotes β-strand conformation. The peptide colocalizes with negatively charged lipids, confines the headgroup motion, and deforms membrane into smaller, ellipsoidal vesicles. This study designates the residue-specific, membrane-bound topology of hBD-3 analogs, serves as the basis for further elucidating the function-relevant structure and dynamics of other defensins, and facilitates the development of defensin-mimetic antibiotics, antifungals, and anti-inflammatories.
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Affiliation(s)
- Xue Kang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Christopher Elson
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505 USA
| | - Jackson Penfield
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505 USA
| | - Alex Kirui
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Adrian Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Liqun Zhang
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505 USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
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15
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Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding. Proc Natl Acad Sci U S A 2018; 115:E8595-E8603. [PMID: 30150411 DOI: 10.1073/pnas.1805443115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The influenza A matrix 2 (M2) transmembrane protein facilitates virion release from the infected host cell. In particular, M2 plays a role in the induction of membrane curvature and/or in the scission process whereby the envelope is cut upon virion release. Here we show using coarse-grained computer simulations that various M2 assembly geometries emerge due to an entropic driving force, resulting in compact clusters or linearly extended aggregates as a direct consequence of the lateral membrane stresses. Conditions under which these protein assemblies will cause the lipid membrane to curve are explored, and we predict that a critical cluster size is required for this to happen. We go on to demonstrate that under the stress conditions taking place in the cellular membrane as it undergoes large-scale membrane remodeling, the M2 protein will, in principle, be able to both contribute to curvature induction and sense curvature to line up in manifolds where local membrane line tension is high. M2 is found to exhibit linactant behavior in liquid-disordered-liquid-ordered phase-separated lipid mixtures and to be excluded from the liquid-ordered phase, in near-quantitative agreement with experimental observations. Our findings support a role for M2 in membrane remodeling during influenza viral budding both as an inducer and a sensor of membrane curvature, and they suggest a mechanism by which localization of M2 can occur as the virion assembles and releases from the host cell, independent of how the membrane curvature is produced.
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16
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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] [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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17
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Mandala VS, Gelenter MD, Hong M. Transport-Relevant Protein Conformational Dynamics and Water Dynamics on Multiple Time Scales in an Archetypal Proton Channel: Insights from Solid-State NMR. J Am Chem Soc 2018; 140:1514-1524. [PMID: 29303574 DOI: 10.1021/jacs.7b12464] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The influenza M2 protein forms a tetrameric proton channel that conducts protons from the acidic endosome into the virion by shuttling protons between water and a transmembrane histidine. Previous NMR studies have shown that this histidine protonates and deprotonates on the microsecond time scale. However, M2's proton conduction rate is 10-1000 s-1, more than 2 orders of magnitude slower than the histidine-water proton-exchange rate. M2 is also known to be conformationally plastic. To address the disparity between the functional time scale and the time scales of protein conformational dynamics and water dynamics, we have now investigated a W41F mutant of the M2 transmembrane domain using solid-state NMR. 13C chemical shifts of the membrane-bound peptide indicate the presence of two distinct tetramer conformations, whose concentrations depend exclusively on pH and hence the charge-state distribution of the tetramers. High-temperature 2D correlation spectra indicate that these two conformations interconvert at a rate of ∼400 s-1 when the +2 and +3 charge states dominate, which gives the first experimental evidence of protein conformational motion on the transport time scale. Protein 13C-detected water 1H T2 relaxation measurements show that channel water relaxes an order of magnitude faster than bulk water and membrane-associated water, indicating that channel water undergoes nanosecond motion in a pH-independent fashion. These results connect motions on three time scales to explain M2's proton-conduction mechanism: picosecond-to-nanosecond motions of water molecules facilitate proton Grotthuss hopping, microsecond motions of the histidine side chain allow water-histidine proton transfer, while millisecond motions of the entire four-helix bundle constitute the rate-limiting step, dictating the number of protons released into the virion.
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Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology , 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Martin D Gelenter
- 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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18
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Elkins MR, Williams JK, Gelenter MD, Dai P, Kwon B, Sergeyev IV, Pentelute BL, Hong M. Cholesterol-binding site of the influenza M2 protein in lipid bilayers from solid-state NMR. Proc Natl Acad Sci U S A 2017; 114:12946-12951. [PMID: 29158386 PMCID: PMC5724280 DOI: 10.1073/pnas.1715127114] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The influenza M2 protein not only forms a proton channel but also mediates membrane scission in a cholesterol-dependent manner to cause virus budding and release. The atomic interaction of cholesterol with M2, as with most eukaryotic membrane proteins, has long been elusive. We have now determined the cholesterol-binding site of the M2 protein in phospholipid bilayers using solid-state NMR spectroscopy. Chain-fluorinated cholesterol was used to measure cholesterol proximity to M2 while sterol-deuterated cholesterol was used to measure bound-cholesterol orientation in lipid bilayers. Carbon-fluorine distance measurements show that at a cholesterol concentration of 17 mol%, two cholesterol molecules bind each M2 tetramer. Cholesterol binds the C-terminal transmembrane (TM) residues, near an amphipathic helix, without requiring a cholesterol recognition sequence motif. Deuterium NMR spectra indicate that bound cholesterol is approximately parallel to the bilayer normal, with the rough face of the sterol rings apposed to methyl-rich TM residues. The distance- and orientation-restrained cholesterol-binding site structure shows that cholesterol is stabilized by hydrophobic interactions with the TM helix and polar and aromatic interactions with neighboring amphipathic helices. At the 1:2 binding stoichiometry, lipid 31P spectra show an isotropic peak indicative of high membrane curvature. This M2-cholesterol complex structure, together with previously observed M2 localization at phase boundaries, suggests that cholesterol mediates M2 clustering to the neck of the budding virus to cause the necessary curvature for membrane scission. The solid-state NMR approach developed here is generally applicable for elucidating the structural basis of cholesterol's effects on membrane protein function.
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Affiliation(s)
- Matthew R Elkins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jonathan K Williams
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139;
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19
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Iijima T, Shimizu T. Deuterium off-magic-angle spinning NMR spectroscopy for pure-quadrupole spectra of paramagnetic solids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 84:234-241. [PMID: 28676276 DOI: 10.1016/j.ssnmr.2017.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 06/07/2023]
Abstract
We examined a simple two-dimensional 2H nuclear magnetic resonance spectroscopy for paramagnetic solids utilizing off-magic-angle spinning (OMAS). By adding a rotor-synchronized 180° pulse to rotational echo (RE) measurement, the effect of the shift interaction was removed from the indirect dimension. The obtained pure-quadrupole spectrum could be simulated by calculating a quasi-one-dimensional NMR signal without considering the shift interaction. The sensitivity of the proposed method was compared with that of previous static NMR methods.
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Affiliation(s)
- Takahiro Iijima
- Institute of Arts and Sciences, Yamagata University, Yamagata 990-8560, Japan.
| | - Tadashi Shimizu
- National Institute for Materials Science, Tsukuba 305-0003, Japan
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20
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Lateral Organization of Influenza Virus Proteins in the Budozone Region of the Plasma Membrane. J Virol 2017; 91:JVI.02104-16. [PMID: 28202765 DOI: 10.1128/jvi.02104-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/12/2017] [Indexed: 12/24/2022] Open
Abstract
Influenza virus assembles and buds at the plasma membrane of virus-infected cells. The viral proteins assemble at the same site on the plasma membrane for budding to occur. This involves a complex web of interactions among viral proteins. Some proteins, like hemagglutinin (HA), NA, and M2, are integral membrane proteins. M1 is peripherally membrane associated, whereas NP associates with viral RNA to form an RNP complex that associates with the cytoplasmic face of the plasma membrane. Furthermore, HA and NP have been shown to be concentrated in cholesterol-rich membrane raft domains, whereas M2, although containing a cholesterol binding motif, is not raft associated. Here we identify viral proteins in planar sheets of plasma membrane using immunogold staining. The distribution of these proteins was examined individually and pairwise by using the Ripley K function, a type of nearest-neighbor analysis. Individually, HA, NA, M1, M2, and NP were shown to self-associate in or on the plasma membrane. HA and M2 are strongly coclustered in the plasma membrane; however, in the case of NA and M2, clustering depends upon the expression system used. Despite both proteins being raft resident, HA and NA occupy distinct but adjacent membrane domains. M2 and M1 strongly cocluster, but the association of M1 with HA or NA is dependent upon the means of expression. The presence of HA and NP at the site of budding depends upon the coexpression of other viral proteins. Similarly, M2 and NP occupy separate compartments, but an association can be bridged by the coexpression of M1.IMPORTANCE The complement of influenza virus proteins necessary for the budding of progeny virions needs to accumulate at budozones. This is complicated by HA and NA residing in lipid raft-like domains, whereas M2, although an integral membrane protein, is not raft associated. Other necessary protein components such as M1 and NP are peripherally associated with the membrane. Our data define spatial relationships between viral proteins in the plasma membrane. Some proteins, such as HA and M2, inherently cocluster within the membrane, although M2 is found mostly at the periphery of regions of HA, consistent with the proposed role of M2 in scission at the end of budding. The association between some pairs of influenza virus proteins, such as M2 and NP, appears to be brokered by additional influenza virus proteins, in this case M1. HA and NA, while raft associated, reside in distinct domains, reflecting their distributions in the viral membrane.
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21
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Liang R, Swanson JMJ, Madsen JJ, Hong M, DeGrado WF, Voth GA. Acid activation mechanism of the influenza A M2 proton channel. Proc Natl Acad Sci U S A 2016; 113:E6955-E6964. [PMID: 27791184 PMCID: PMC5111692 DOI: 10.1073/pnas.1615471113] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The homotetrameric influenza A M2 channel (AM2) is an acid-activated proton channel responsible for the acidification of the influenza virus interior, an important step in the viral lifecycle. Four histidine residues (His37) in the center of the channel act as a pH sensor and proton selectivity filter. Despite intense study, the pH-dependent activation mechanism of the AM2 channel has to date not been completely understood at a molecular level. Herein we have used multiscale computer simulations to characterize (with explicit proton transport free energy profiles and their associated calculated conductances) the activation mechanism of AM2. All proton transfer steps involved in proton diffusion through the channel, including the protonation/deprotonation of His37, are explicitly considered using classical, quantum, and reactive molecular dynamics methods. The asymmetry of the proton transport free energy profile under high-pH conditions qualitatively explains the rectification behavior of AM2 (i.e., why the inward proton flux is allowed when the pH is low in viral exterior and high in viral interior, but outward proton flux is prohibited when the pH gradient is reversed). Also, in agreement with electrophysiological results, our simulations indicate that the C-terminal amphipathic helix does not significantly change the proton conduction mechanism in the AM2 transmembrane domain; the four transmembrane helices flanking the channel lumen alone seem to determine the proton conduction mechanism.
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Affiliation(s)
- Ruibin Liang
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Jessica M J Swanson
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Jesper J Madsen
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of San Francisco, San Francisco, CA 94158
| | - Gregory A Voth
- Department of Chemistry, The University of Chicago, Chicago, IL 60637;
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- James Franck Institute, The University of Chicago, Chicago, IL 60637
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22
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Matsui R, Uchida N, Ohtani M, Yamada K, Shigeta A, Kawamura I, Aida T, Ishida Y. Magnetically Alignable Bicelles with Unprecedented Stability Using Tunable Surfactants Derived from Cholic Acid. Chemphyschem 2016; 17:3916-3922. [DOI: 10.1002/cphc.201600897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Ryoichi Matsui
- Department of Chemistry and Biotechnology; School of Engineering, the; University of Tokyo; Hongo 7-3-1, Bunkyo-ku Tokyo 113-8656 Japan
| | - Noriyuki Uchida
- Department of Chemistry and Biotechnology; School of Engineering, the; University of Tokyo; Hongo 7-3-1, Bunkyo-ku Tokyo 113-8656 Japan
| | - Masataka Ohtani
- RIKEN Center for Emergent Matter Science; Hirosawa 2-1, Wako Saitama 351-0198 Japan
| | - Kuniyo Yamada
- RIKEN Center for Emergent Matter Science; Hirosawa 2-1, Wako Saitama 351-0198 Japan
| | - Arisu Shigeta
- Graduate School of Engineering; Yokohama National University; Tokiwadai 79-5, Hodogaya-ku Yokohama 240-8501 Japan
| | - Izuru Kawamura
- Graduate School of Engineering; Yokohama National University; Tokiwadai 79-5, Hodogaya-ku Yokohama 240-8501 Japan
| | - Takuzo Aida
- RIKEN Center for Emergent Matter Science; Hirosawa 2-1, Wako Saitama 351-0198 Japan
- Department of Chemistry and Biotechnology; School of Engineering, the; University of Tokyo; Hongo 7-3-1, Bunkyo-ku Tokyo 113-8656 Japan
| | - Yasuhiro Ishida
- RIKEN Center for Emergent Matter Science; Hirosawa 2-1, Wako Saitama 351-0198 Japan
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23
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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] [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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24
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Ho CS, Khadka NK, She F, Cai J, Pan J. Influenza M2 Transmembrane Domain Senses Membrane Heterogeneity and Enhances Membrane Curvature. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:6730-6738. [PMID: 27285399 PMCID: PMC5131574 DOI: 10.1021/acs.langmuir.6b00150] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Targeting host cell membranes by M2 of influenza A virus is important for virus invasion and replication. We study the transmembrane domain of M2 (M2TM) interacting with mica-supported planar bilayers and free-standing giant unilamellar vesicles (GUVs). Using solution atomic force microscopy (AFM), we show that the size of M2TM oligomers is dependent on lipid composition. The addition of M2TM to lipid bilayers containing liquid-ordered (Lo) and liquid-disordered (Ld) phases reveals that M2TM preferentially partitions into the Ld phase; phase-dependent partitioning results in a larger rigidity of the Ld phase. We next use fluorescence microscopy to study the effects of M2TM on phase-coexisting GUVs. In particular, M2TM is found to increase GUVs' miscibility transition temperature Tmix. The augmented thermodynamic stability can be accounted for by considering an enhanced energy barrier of lipid mixing between coexisting phases. Our GUV study also shows that M2TM can elicit an array of vesicle shapes mimicking virus budding. M2TM enhanced membrane curvature is consistent with our AFM data, which show altered membrane rigidity and consequently line tension at domain edges. Together, our results highlight that in addition to conducting protons, M2TM can actively regulate membrane heterogeneity and augment membrane curvature.
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Affiliation(s)
- Chian Sing Ho
- Department of Physics, University of South Florida, Tampa, FL 33620, United States
| | - Nawal K. Khadka
- Department of Physics, University of South Florida, Tampa, FL 33620, United States
| | - Fengyu She
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, United States
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Martyna A, Gómez-Llobregat J, Lindén M, Rossman JS. Curvature Sensing by a Viral Scission Protein. Biochemistry 2016; 55:3493-6. [PMID: 27299375 DOI: 10.1021/acs.biochem.6b00539] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane scission is the final step in all budding processes wherein a membrane neck is sufficiently constricted so as to allow for fission and the release of the budded particle. For influenza viruses, membrane scission is mediated by an amphipathic helix (AH) domain in the viral M2 protein. While it is known that the M2AH alters membrane curvature, it is not known how the protein is localized to the center neck of budding virions where it would be able to cause membrane scission. Here, we use molecular dynamics simulations on buckled lipid bilayers to show that the M2AH senses membrane curvature and preferentially localizes to regions of high membrane curvature, comparable to that seen at the center neck of budding influenza viruses. These results were then validated using in vitro binding assays to show that the M2AH senses membrane curvature by detecting lipid packing defects in the membrane. Our results show that the M2AH senses membrane curvature and suggest that the AH domain may localize the protein at the viral neck where it can then mediate membrane scission and the release of budding viruses.
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Affiliation(s)
- Agnieszka Martyna
- School of Biosciences, University of Kent , Canterbury, Kent CT2 7NJ, United Kingdom
| | - Jordi Gómez-Llobregat
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Martin Lindén
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Jeremy S Rossman
- School of Biosciences, University of Kent , Canterbury, Kent CT2 7NJ, United Kingdom
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Chlanda P, Zimmerberg J. Protein-lipid interactions critical to replication of the influenza A virus. FEBS Lett 2016; 590:1940-54. [PMID: 26921878 DOI: 10.1002/1873-3468.12118] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/08/2016] [Accepted: 02/21/2016] [Indexed: 12/12/2022]
Abstract
Influenza A virus (IAV) assembles on the plasma membrane where viral proteins localize to form a bud encompassing the viral genome, which ultimately pinches off to give rise to newly formed infectious virions. Upon entry, the virus faces the opposite task-fusion with the endosomal membrane and disassembly to deliver the viral genome to the cytoplasm. There are at least four influenza proteins-hemagglutinin (HA), neuraminidase (NA), matrix 1 protein (M1), and the M2 ion channel-that are known to directly interact with the cellular membrane and modify membrane curvature in order to both assemble and disassemble membrane-enveloped virions. Here, we summarize and discuss current knowledge of the interactions of lipids and membrane proteins involved in the IAV replication cycle.
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Affiliation(s)
- Petr Chlanda
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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27
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Kim SS, Upshur MA, Saotome K, Sahu ID, McCarrick RM, Feix JB, Lorigan GA, Howard KP. Cholesterol-Dependent Conformational Exchange of the C-Terminal Domain of the Influenza A M2 Protein. Biochemistry 2015; 54:7157-67. [PMID: 26569023 PMCID: PMC4734095 DOI: 10.1021/acs.biochem.5b01065] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The C-terminal amphipathic helix of the influenza A M2 protein plays a critical cholesterol-dependent role in viral budding. To provide atomic-level detail on the impact cholesterol has on the conformation of M2 protein, we spin-labeled sites right before and within the C-terminal amphipathic helix of the M2 protein. We studied the spin-labeled M2 proteins in membranes both with and without cholesterol. We used a multipronged site-directed spin-label electron paramagnetic resonance (SDSL-EPR) approach and collected data on line shapes, relaxation rates, accessibility of sites to the membrane, and distances between symmetry-related sites within the tetrameric protein. We demonstrate that the C-terminal amphipathic helix of M2 populates at least two conformations in POPC/POPG 4:1 bilayers. Furthermore, we show that the conformational state that becomes more populated in the presence of cholesterol is less dynamic, less membrane buried, and more tightly packed than the other state. Cholesterol-dependent changes in M2 could be attributed to the changes cholesterol induces in bilayer properties and/or direct binding of cholesterol to the protein. We propose a model consistent with all of our experimental data that suggests that the predominant conformation we observe in the presence of cholesterol is relevant for the understanding of viral budding.
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Affiliation(s)
- Sangwoo S. Kim
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081
| | - Mary Alice Upshur
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081
| | - Kei Saotome
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081
| | - Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - Robert M. McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - Jimmy B. Feix
- Department of Biophysics, National Biomedical EPR Center, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - Kathleen P. Howard
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081
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28
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Martin RW, Kelly JE, Collier KA. Spatial reorientation experiments for NMR of solids and partially oriented liquids. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 90-91:92-122. [PMID: 26592947 PMCID: PMC6936739 DOI: 10.1016/j.pnmrs.2015.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/13/2015] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
Motional reorientation experiments are extensions of Magic Angle Spinning (MAS) where the rotor axis is changed in order to average out, reintroduce, or scale anisotropic interactions (e.g. dipolar couplings, quadrupolar interactions or chemical shift anisotropies). This review focuses on Variable Angle Spinning (VAS), Switched Angle Spinning (SAS), and Dynamic Angle Spinning (DAS), all of which involve spinning at two or more different angles sequentially, either in successive experiments or during a multidimensional experiment. In all of these experiments, anisotropic terms in the Hamiltonian are scaled by changing the orientation of the spinning sample relative to the static magnetic field. These experiments vary in experimental complexity and instrumentation requirements. In VAS, many one-dimensional spectra are collected as a function of spinning angle. In SAS, dipolar couplings and/or chemical shift anisotropies are reintroduced by switching the sample between two different angles, often 0° or 90° and the magic angle, yielding a two-dimensional isotropic-anisotropic correlation spectrum. Dynamic Angle Spinning (DAS) is a related experiment that is used to simultaneously average out the first- and second-order quadrupolar interactions, which cannot be accomplished by spinning at any unique rotor angle in physical space. Although motional reorientation experiments generally require specialized instrumentation and data analysis schemes, some are accessible with only minor modification of standard MAS probes. In this review, the mechanics of each type of experiment are described, with representative examples. Current and historical probe and coil designs are discussed from the standpoint of how each one accomplishes the particular objectives of the experiment(s) it was designed to perform. Finally, applications to inorganic materials and liquid crystals, which present very different experimental challenges, are discussed. The review concludes with perspectives on how motional reorientation experiments can be applied to current problems in chemistry, molecular biology, and materials science, given the many advances in high-field NMR magnets, fast spinning, and sample preparation realized in recent years.
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Affiliation(s)
- Rachel W Martin
- Department of Chemistry, University of California, Irvine 92697-2025, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine 92697-3900, United States.
| | - John E Kelly
- Department of Chemistry, University of California, Irvine 92697-2025, United States
| | - Kelsey A Collier
- Department of Physics and Astronomy, University of California, Irvine 92697-4575, United States
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