1
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Lee CH, Korvink JG, Jouda M. Frequency multiplexing enables parallel multi-sample EPR. Sci Rep 2024; 14:11815. [PMID: 38783051 PMCID: PMC11116391 DOI: 10.1038/s41598-024-62564-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024] Open
Abstract
Electron paramagnetic resonance (EPR) spectroscopy stands out as a powerful analytical technique with extensive applications in the fields of biology, chemistry, physics, and material sciences. It proves invaluable for investigating the molecular structure and reaction mechanisms of substances containing unpaired electrons, such as metal complexes, organic and inorganic radicals, and intermediate states in chemical reactions. However, despite their remarkable capabilities, EPR systems face significant limitations in terms of sample throughput, as current commercial systems only target the analysis of one sample at a time. Here we introduce a novel scheme for conducting ultra-high frequency continuous-wave EPR (CW EPR) targeting the EPR spectroscopy of multiple microliter volume samples in parallel. Our proof-of-principle prototype involves two decoupled detection cells equipped with high qualty factor Q = 104 solenoidal coils tuned to 488 and 589 MHz, ensuring a significant frequency gap for effective radio frequency (RF) decoupling between the channels. To further enhance electromagnetic decoupling, an orthogonal alignment of the coils was adopted. The paper further presents an innovative radiofrequency circuit concept that utilizes a single physical RF channel to simultaneously conduct parallel EPR on up to eight cells. Parallel EPR experiments on two BDPA samples, each with a sample volume of 18.3 μL, registered signal-to-noise ratios of 255 and 252 for the two EPR measurement cells, with no observable coupling. The showcased prototype, built using cost-effective commercially available fabrication technology, is readily scalable and represents an initial step with promising potential for advancing sample screening with high-throughput parallel EPR.
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Affiliation(s)
- Chun Him Lee
- Karlsruhe Institute of Technology, Institute of Microstructure Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | - Jan G Korvink
- Karlsruhe Institute of Technology, Institute of Microstructure Technology, 76344, Eggenstein-Leopoldshafen, Germany.
| | - Mazin Jouda
- Karlsruhe Institute of Technology, Institute of Microstructure Technology, 76344, Eggenstein-Leopoldshafen, Germany.
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2
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Lee Y, Fracassi A, Devaraj NK. Control of giant vesicle assemblies by stimuli-responsive lipids. Chem Commun (Camb) 2024; 60:3930-3933. [PMID: 38497420 DOI: 10.1039/d4cc00322e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We describe a bottom-up synthesis of giant vesicles (GVs) utilizing an artificial stimuli-responsive diazobenzene lipid building block. Controlled by light, the GVs can exhibit dynamic behaviors, including reversible formation, the generation of highly multilamellar assemblies, and vesicle capturing and releasing events.
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Affiliation(s)
- Youngjun Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
| | - Alessandro Fracassi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
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3
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Farias KS, Ferreira MM, Amaral GV, Zugaib M, Santos AS, Gomes FP, Rezende RP, Gramacho KP, Aguiar ERGR, Pirovani CP. BASIDIN as a New Protein Effector of the Phytopathogen Causing Witche's Broom Disease in Cocoa. Int J Mol Sci 2023; 24:11714. [PMID: 37511472 PMCID: PMC10380501 DOI: 10.3390/ijms241411714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The fungus Moniliophthora perniciosa secretes protein effectors that manipulate the physiology of the host plant, but few effectors of this fungus have had their functions confirmed. We performed functional characterization of a promising candidate effector of M. perniciosa. The inoculation of rBASIDIN at 4 µmol L-1 in the mesophyll of leaflets of Solanum lycopersicum caused symptoms of shriveling within 6 h without the presence of necrosis. However, when sprayed on the plant at a concentration of 11 µmol L-1, it caused wilting symptoms only 2 h after application, followed by necrosis and cell death at 48 h. rBASIDIN applied to Theobroma cacao leaves at the same concentration caused milder symptoms. rBASIDIN caused hydrogen peroxide production in leaf tissue, damaging the leaf membrane and negatively affecting the photosynthetic rate of Solanum lycopersicum plants. Phylogenetic analysis indicated that BASIDIN has orthologs in other phytopathogenic basidiomycetes. Analysis of the transcripts revealed that BASIDIN and its orthologs are expressed in different fungal species, suggesting that this protein is differentially regulated in these basidiomycetes. Therefore, the results of applying BASIDIN allow the inference that it is an effector of the fungus M. perniciosa, with a strong potential to interfere in the defense system of the host plant.
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Affiliation(s)
- Keilane Silva Farias
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus 45662-900, Bahia, Brazil
| | - Monaliza Macêdo Ferreira
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus 45662-900, Bahia, Brazil
| | - Geiseane Veloso Amaral
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus 45662-900, Bahia, Brazil
| | - Maria Zugaib
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus 45662-900, Bahia, Brazil
| | - Ariana Silva Santos
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus 45662-900, Bahia, Brazil
| | - Fábio Pinto Gomes
- Fisiologia Vegetal, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus 45662-900, Bahia, Brazil
| | - Rachel Passos Rezende
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus 45662-900, Bahia, Brazil
| | - Karina Peres Gramacho
- Comissão Executiva do Plano da Lavoura Cacaueira, Centro de Pesquisas do Cacau-MAPA, Laboratório de Fitopatologia Molecular, km 22 Rodovia Ilhéus Itabuna, Ilhéus 45600-970, Bahia, Brazil
| | - Eric Roberto Guimarães Rocha Aguiar
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus 45662-900, Bahia, Brazil
| | - Carlos Priminho Pirovani
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus 45662-900, Bahia, Brazil
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4
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Azimi FC, Dean TT, Minari K, Basso LGM, Vance TDR, Serrão VHB. A Frame-by-Frame Glance at Membrane Fusion Mechanisms: From Viral Infections to Fertilization. Biomolecules 2023; 13:1130. [PMID: 37509166 PMCID: PMC10377500 DOI: 10.3390/biom13071130] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Viral entry and fertilization are distinct biological processes that share a common mechanism: membrane fusion. In viral entry, enveloped viruses attach to the host cell membrane, triggering a series of conformational changes in the viral fusion proteins. This results in the exposure of a hydrophobic fusion peptide, which inserts into the host membrane and brings the viral and host membranes into close proximity. Subsequent structural rearrangements in opposing membranes lead to their fusion. Similarly, membrane fusion occurs when gametes merge during the fertilization process, though the exact mechanism remains unclear. Structural biology has played a pivotal role in elucidating the molecular mechanisms underlying membrane fusion. High-resolution structures of the viral and fertilization fusion-related proteins have provided valuable insights into the conformational changes that occur during this process. Understanding these mechanisms at a molecular level is essential for the development of antiviral therapeutics and tools to influence fertility. In this review, we will highlight the biological importance of membrane fusion and how protein structures have helped visualize both common elements and subtle divergences in the mechanisms behind fusion; in addition, we will examine the new tools that recent advances in structural biology provide researchers interested in a frame-by-frame understanding of membrane fusion.
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Affiliation(s)
- Farshad C Azimi
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Trevor T Dean
- Pharmaceutical Sciences, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Karine Minari
- Biomolecular Cryo-Electron Microscopy Facility, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Luis G M Basso
- Laboratório de Ciências Físicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Tyler D R Vance
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vitor Hugo B Serrão
- Biomolecular Cryo-Electron Microscopy Facility, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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5
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Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B. Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane. Nature 2023; 619:403-409. [PMID: 37285872 DOI: 10.1038/s41586-023-06273-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The entry of SARS-CoV-2 into host cells depends on the refolding of the virus-encoded spike protein from a prefusion conformation, which is metastable after cleavage, to a lower-energy stable postfusion conformation1,2. This transition overcomes kinetic barriers for fusion of viral and target cell membranes3,4. Here we report a cryogenic electron microscopy (cryo-EM) structure of the intact postfusion spike in a lipid bilayer that represents the single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membrane-interacting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.
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Affiliation(s)
- Wei Shi
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yongfei Cai
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- CSL Seqirus, Waltham, MA, USA
| | - Haisun Zhu
- Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Jewel Voyer
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | - Hong Cao
- Codex BioSolutions, Rockville, MD, USA
| | - Megan L Mayer
- The Harvard Cryo-EM Center for Structural Biology, Boston, MA, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chen Xu
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jianming Lu
- Codex BioSolutions, Rockville, MD, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Jun Zhang
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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6
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Zhao Y, Zhao Y, Xie L, Li Q, Zhang Y, Zang Y, Li X, Zhang L, Yang Z. Identification of Potential Lead Compounds Targeting Novel Druggable Cavity of SARS-CoV-2 Spike Trimer by Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:ijms24076281. [PMID: 37047254 PMCID: PMC10094189 DOI: 10.3390/ijms24076281] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/07/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become an urgent public health problem. Spike (S) protein mediates the fusion between the virus and the host cell membranes, consequently emerging as an important target of drug design. The lack of comparisons of in situ full-length S homotrimer structures in different states hinders understanding the structures and revealing the function, thereby limiting the discovery and development of therapeutic agents. Here, the steady-state structures of the in situ full-length S trimer in closed and open states (Sclosed and Sopen) were modeled with the constraints of density maps, associated with the analysis of the dynamic structural differences. Subsequently, we identified various regions with structure and property differences as potential binding pockets for ligands that promote the formation of inactive trimeric protein complexes. By using virtual screening strategy and a newly defined druggable cavity, five ligands were screened with potential bioactivities. Then molecular dynamic (MD) simulations were performed on apo protein structures and ligand bound complexes to reveal the conformational changes upon ligand binding. Our simulation results revealed that sulforaphane (SFN), which has the best binding affinity, could inhibit the conformational changes of S homotrimer that would occur during the viral membrane fusion. Our results could aid in the understanding of the regulation mechanism of S trimer aggregation and the structure-activity relationship, facilitating the development of potential antiviral agents.
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Affiliation(s)
- Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yifan Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Linke Xie
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Qian Li
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yuze Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Correspondence:
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7
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Baek JM, Jung WH, Yu ES, Ahn DJ, Ryu YS. In Vitro Membrane Platform for the Visualization of Water Impermeability across the Liquid-Ordered Phase under Hypertonic Conditions. J Am Chem Soc 2022; 144:21887-21896. [PMID: 36367984 DOI: 10.1021/jacs.2c06626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Passive water penetration across the cell membrane by osmotic diffusion is essential for the homeostasis of cell volume, in addition to the protein-assisted active transportation of water. Since membrane components can regulate water permeability, controlling compositional variation during the volume regulatory process is a prerequisite for investigating the underlying mechanisms of water permeation and related membrane dynamics. However, the lack of a viable in vitro membrane platform in hypertonic solutions impedes advanced knowledge of cell volume regulation processes, especially cholesterol-enriched lipid domains called lipid rafts. By reconstituting the liquid-ordered (Lo) domain as a likeness of lipid rafts, we verified suppressed water permeation across the Lo domains, which had yet to be confirmed with experimental demonstrations despite a simulation approach. With the help of direct transfer of the Lo domains from vesicles to supported lipid membranes, the biological roles of lipid composition in suppressed water translocation were experimentally confirmed. Additionally, the improvement in membrane stability under hypertonic conditions was demonstrated based on molecular dynamics simulations.
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Affiliation(s)
- Ji Min Baek
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woo Hyuk Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Eui-Sang Yu
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Dong June Ahn
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Yong-Sang Ryu
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
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8
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Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B. Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.05.519151. [PMID: 36523411 PMCID: PMC9753783 DOI: 10.1101/2022.12.05.519151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells depends on refolding of the virus-encoded spike protein from a prefusion conformation, metastable after cleavage, to a lower energy, stable postfusion conformation. This transition overcomes kinetic barriers for fusion of viral and target cell membranes. We report here a cryo-EM structure of the intact postfusion spike in a lipid bilayer that represents single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membraneinteracting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.
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9
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Rahman MM, Garudadri T, Das S. Role of Surface Tension in Microrobot Penetration in Membranes. ... INTERNATIONAL CONFERENCE ON MANIPULATION AUTOMATION AND ROBOTICS AT SMALL SCALES (MARSS). INTERNATIONAL CONFERENCE ON MANIPULATION AUTOMATION AND ROBOTICS AT SMALL SCALES 2022; 2022:10.1109/marss55884.2022.9870474. [PMID: 37521089 PMCID: PMC10387354 DOI: 10.1109/marss55884.2022.9870474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
cell-membrane fusion using microrobots can be a useful technique for delivering bioactive compounds to cellular systems. The role of membrane curvature and lipid ordering in the cell membrane penetration process is well known. However, once the fusion into the cell membrane is already initiated, the fluid dynamics of microrobot penetration based on tension difference of the microrobot solution and membrane curvature at the fusion pore has not been explored yet. Here, we demonstrate how surface tension difference among merging interfaces plays role in microrobot droplet penetration into a liquid bath, mimicking cell membrane fusion. The maximum penetration of a microrobot droplet into a liquid bath depends on the positive difference of surface tension between the droplet and liquid bath, longitudinal curvature of the bridge region, and the size of the droplet.
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Affiliation(s)
- Md Mahmudur Rahman
- Department of Mechanical Engineering, University of Delaware, Newark, DE 19716 USA. He is now with Department of Mechanical Engineering, Georgia Southern University, Statesboro, GA 30458 USA
| | | | - Sambeeta Das
- Department of Mechanical Engineering, University of Delaware, Newark, DE 19716 USA
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10
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Rath SL, Tripathy M, Mandal N. How Does Temperature Affect the Dynamics of SARS-CoV-2 M Proteins? Insights from Molecular Dynamics Simulations. J Membr Biol 2022; 255:341-356. [PMID: 35552785 PMCID: PMC9101995 DOI: 10.1007/s00232-022-00244-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Enveloped viruses, in general, have several transmembrane proteins and glycoproteins, which assist the virus in entry and attachment onto the host cells. These proteins also play a significant role in determining the shape and size of the newly formed virus particles. The lipid membrane and the embedded proteins affect each other in non-trivial ways during the course of the viral life cycle. Unraveling the nature of the protein-protein and protein-lipid interactions, under various environmental and physiological conditions, could therefore prove to be crucial in development of therapeutics. Here, we study the M protein of SARS-CoV-2 to understand the effect of temperature on the properties of the protein-membrane system. The membrane-embedded dimeric M proteins were studied using atomistic and coarse-grained molecular dynamics simulations at temperatures ranging between 10 and 50 °C. While temperature-induced fluctuations are expected to be monotonic, we observe a steady rise in the protein dynamics up to 40 °C, beyond which it surprisingly reverts back to the low-temperature behavior. Detailed investigation reveals disordering of the membrane lipids in the presence of the protein, which induces additional curvature around the transmembrane region. Coarse-grained simulations indicate temperature-dependent aggregation of M protein dimers. Our study clearly indicates that the dynamics of membrane lipids and integral M protein of SARS-CoV-2 enables it to better associate and aggregate only at a certain temperature range (i.e., ~ 30-40 °C). This can have important implications in the protein aggregation and subsequent viral budding/fission processes.
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Affiliation(s)
- Soumya Lipsa Rath
- Department of Biotechnology, National Institute of Technology Warangal (NITW), Telangana, 506004, India.
| | - Madhusmita Tripathy
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.
| | - Nabanita Mandal
- Department of Biotechnology, National Institute of Technology Warangal (NITW), Telangana, 506004, India
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11
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Functional Peptides from SARS-CoV-2 Binding with Cell Membrane: From Molecular Dynamics Simulations to Cell Demonstration. Cells 2022; 11:cells11111738. [PMID: 35681433 PMCID: PMC9179371 DOI: 10.3390/cells11111738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 12/03/2022] Open
Abstract
Herein, we have verified the interaction between the functional peptides from the SARS-CoV-2 and cell membrane, and we further proved that peptides exhibit little membrane disruption. The specific amino acids (Lys, Ile, Glu, Asn, Gln, etc.) with charge or hydrophobic residues play a significant role during the functional-peptide binding to membrane. The findings could provide the hints related to viral infection and also might pave the way for development of new materials based on peptides with membrane-binding activity, which would enable functional peptides further as peptide adjuvants, in order to help deliver the cancer drug into tumor cells for the efficient tumor therapy.
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12
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Valério M, Mendonça DA, Morais J, Buga CC, Cruz CH, Castanho MA, Melo MN, Soares CM, Veiga AS, Lousa D. Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures. ACS Chem Biol 2022; 17:1831-1843. [PMID: 35500279 PMCID: PMC9295702 DOI: 10.1021/acschembio.2c00208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Paramyxoviruses are enveloped viruses harboring a negative-sense RNA genome that must enter the host's cells to replicate. In the case of the parainfluenza virus, the cell entry process starts with the recognition and attachment to target receptors, followed by proteolytic cleavage of the fusion glycoprotein (F) protein, exposing the fusion peptide (FP) region. The FP is responsible for binding to the target membrane, and it is believed to play a crucial role in the fusion process, but the mechanism by which the parainfluenza FP (PIFP) promotes membrane fusion is still unclear. To elucidate this matter, we performed biophysical experimentation of the PIFP in membranes, together with coarse grain (CG) and atomistic (AA) molecular dynamics (MD) simulations. The simulation results led to the pinpointing of the most important PIFP amino acid residues for membrane fusion and show that, at high concentrations, the peptide induces the formation of a water-permeable porelike structure. This structure promotes lipid head intrusion and lipid tail protrusion, which facilitates membrane fusion. Biophysical experimental results validate these findings, showing that, depending on the peptide/lipid ratio, the PIFP can promote fusion and/or membrane leakage. Our work furthers the understanding of the PIFP-induced membrane fusion process, which might help foster development in the field of viral entry inhibition.
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Affiliation(s)
- Mariana Valério
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Diogo A. Mendonça
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - João Morais
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Carolina C. Buga
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Carlos H. Cruz
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel A.R.B. Castanho
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cláudio M. Soares
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana Salomé Veiga
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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13
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Joardar A, Pattnaik GP, Chakraborty H. Mechanism of Membrane Fusion: Interplay of Lipid and Peptide. J Membr Biol 2022; 255:211-224. [PMID: 35435451 PMCID: PMC9014786 DOI: 10.1007/s00232-022-00233-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/25/2022] [Indexed: 11/26/2022]
Abstract
Membrane fusion is an essential process for the survival of eukaryotes and the entry of enveloped viruses into host cells. A proper understanding of the mechanism of membrane fusion would provide us a handle to manipulate several biological pathways, and design efficient vaccines against emerging and re-emerging viral infections. Although fusion proteins take the central stage in catalyzing the process, role of lipid composition is also of paramount importance. Lipid composition modulates membrane organization and dynamics and impacts the lipid–protein (peptide) interaction. Moreover, the intrinsic curvature of lipids has strong impact on the formation of stalk and hemifusion diaphragm. Detection of transiently stable intermediates remains the bottleneck in the understanding of fusion mechanism. In order to circumvent this challenge, analytical methods can be employed to determine the kinetic parameters from ensemble average measurements of observables, such as lipid mixing, content mixing, and content leakage. The current review aims to present an analytical method that would aid our understanding of the fusion mechanism, provides a better insight into the role of lipid shape, and discusses the interplay of lipid and peptide in membrane fusion.
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Affiliation(s)
- Ankita Joardar
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768019, India
| | | | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768019, India.
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14
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Silva CC, Bichara CNC, Carneiro FRO, Palacios VRDCM, Berg AVSVD, Quaresma JAS, Magno Falcão LF. Muscle dysfunction in the long coronavirus disease 2019 syndrome: Pathogenesis and clinical approach. Rev Med Virol 2022; 32:e2355. [PMID: 35416359 PMCID: PMC9111061 DOI: 10.1002/rmv.2355] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/20/2022] [Accepted: 04/01/2022] [Indexed: 01/08/2023]
Abstract
In long coronavirus disease 2019 (long COVID‐19), involvement of the musculoskeletal system is characterised by the persistence or appearance of symptoms such as fatigue, muscle weakness, myalgia, and decline in physical and functional performance, even at 4 weeks after the onset of acute symptoms of COVID‐19. Muscle injury biomarkers are altered during the acute phase of the disease. The cellular damage and hyperinflammatory state induced by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection may contribute to the persistence of symptoms, hypoxaemia, mitochondrial damage, and dysregulation of the renin‐angiotensin system. In addition, the occurrence of cerebrovascular diseases, involvement of the peripheral nervous system, and harmful effects of hospitalisation, such as the use of drugs, immobility, and weakness acquired in the intensive care unit, all aggravate muscle damage. Here, we review the multifactorial mechanisms of muscle tissue injury, aggravating conditions, and associated sequelae in long COVID‐19.
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Affiliation(s)
- Camilla Costa Silva
- Center for Biological and Health Sciences, State University of Para, Belém, Brazil
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15
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Santamaria A, Batchu KC, Matsarskaia O, Prévost SF, Russo D, Natali F, Seydel T, Hoffmann I, Laux V, Haertlein M, Darwish TA, Russell RA, Corucci G, Fragneto G, Maestro A, Zaccai NR. Strikingly Different Roles of SARS-CoV-2 Fusion Peptides Uncovered by Neutron Scattering. J Am Chem Soc 2022; 144:2968-2979. [PMID: 35157798 PMCID: PMC8862744 DOI: 10.1021/jacs.1c09856] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 02/02/2023]
Abstract
Coronavirus disease-2019 (COVID-19), a potentially lethal respiratory illness caused by the coronavirus SARS-CoV-2, emerged in the end of 2019 and has since spread aggressively across the globe. A thorough understanding of the molecular mechanisms of cellular infection by coronaviruses is therefore of utmost importance. A critical stage in infection is the fusion between viral and host membranes. Here, we present a detailed investigation of the role of selected SARS-CoV-2 Spike fusion peptides, and the influence of calcium and cholesterol, in this fusion process. Structural information from specular neutron reflectometry and small angle neutron scattering, complemented by dynamics information from quasi-elastic and spin-echo neutron spectroscopy, revealed strikingly different functions encoded in the Spike fusion domain. Calcium drives the N-terminal of the Spike fusion domain to fully cross the host plasma membrane. Removing calcium, however, reorients the peptide back to the lipid leaflet closest to the virus, leading to significant changes in lipid fluidity and rigidity. In conjunction with other regions of the fusion domain, which are also positioned to bridge and dehydrate viral and host membranes, the molecular events leading to cell entry by SARS-CoV-2 are proposed.
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Affiliation(s)
- Andreas Santamaria
- Institut
Laue-Langevin, 38042 Grenoble, France
- Departamento
de Química Física, Universidad
Complutense de Madrid, 28040 Madrid, Spain
| | | | | | | | - Daniela Russo
- Institut
Laue-Langevin, 38042 Grenoble, France
- CNR-IOM
& INSIDE@ILL, 38042 Grenoble, France
| | - Francesca Natali
- Institut
Laue-Langevin, 38042 Grenoble, France
- CNR-IOM
& INSIDE@ILL, 38042 Grenoble, France
| | - Tilo Seydel
- Institut
Laue-Langevin, 38042 Grenoble, France
| | | | | | | | - Tamim A. Darwish
- National
Deuteration Facility, ANSTO-Sidney, Lucas Heights, NSW 2234, Australia
| | - Robert A. Russell
- National
Deuteration Facility, ANSTO-Sidney, Lucas Heights, NSW 2234, Australia
| | - Giacomo Corucci
- Institut
Laue-Langevin, 38042 Grenoble, France
- École
Doctorale de Physique, Université
Grenoble Alpes, 38400 Saint-Martin-d’Héres, France
| | - Giovanna Fragneto
- Institut
Laue-Langevin, 38042 Grenoble, France
- École
Doctorale de Physique, Université
Grenoble Alpes, 38400 Saint-Martin-d’Héres, France
| | - Armando Maestro
- Institut
Laue-Langevin, 38042 Grenoble, France
- Centro
de Física de Materiales (CSIC, UPV/EHU) − Materials
Physics Center MPC, Paseo
Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- IKERBASQUE
− Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
| | - Nathan R. Zaccai
- Cambridge
Institute for Medical Research, University
of Cambridge, Cambridge CB22 7QQ, United Kingdom
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16
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Sigalov AB. SARS-CoV-2 may affect the immune response via direct inhibition of T cell receptor: Mechanistic hypothesis and rationale. Biochimie 2021; 195:86-89. [PMID: 34793886 PMCID: PMC8591858 DOI: 10.1016/j.biochi.2021.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/27/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022]
Abstract
During co-evolution with their hosts, many viruses have evolved a membrane fusion mechanism to facilitate host cell entry. Examples are human immunodeficiency virus type 1 (HIV-1) and severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2). These viruses can also infect immune cells (e.g., T cells), providing one of the possible mechanisms for the T cell lymphopenia observed in patients with these infections. Previously, we hypothesized and confirmed in vivo that like HIV-1, SARS-CoV-1 can use its fusion domain not only to enter the T cell but also to directly inhibit T cell receptor signaling. Here, based on the analysis of available structural and clinical data, we hypothesize that SARS-CoV-2 may use a similar "disarm the alarm" strategy to suppress immune responses. We also discuss the implications of this hypothesis for better understanding coronavirus disease 2019 (COVID-19) pathology, developing effective COVID-19 vaccines and improving clinical outcomes for COVID-19 patients.
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17
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Basso LGM, Zeraik AE, Felizatti AP, Costa-Filho AJ. Membranotropic and biological activities of the membrane fusion peptides from SARS-CoV spike glycoprotein: The importance of the complete internal fusion peptide domain. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183697. [PMID: 34274319 PMCID: PMC8280623 DOI: 10.1016/j.bbamem.2021.183697] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/05/2021] [Accepted: 07/10/2021] [Indexed: 11/28/2022]
Abstract
Fusion peptides (FP) are prominent hydrophobic segments of viral fusion proteins that play critical roles in viral entry. FPs interact with and insert into the host lipid membranes, triggering conformational changes in the viral protein that leads to the viral-cell fusion. Multiple membrane-active domains from the severe acute respiratory syndrome (SARS) coronavirus (CoV) spike protein have been reported to act as the functional fusion peptide such as the peptide sequence located between the S1/S2 and S2' cleavage sites (FP1), the S2'-adjacent fusion peptide domain (FP2), and the internal FP sequence (cIFP). Using a combined biophysical approach, we demonstrated that the α-helical coiled-coil-forming internal cIFP displayed the highest membrane fusion and permeabilizing activities along with membrane ordering effect in phosphatidylcholine (PC)/phosphatidylglycerol (PG) unilamellar vesicles compared to the other two N-proximal fusion peptide counterparts. While the FP1 sequence displayed intermediate membranotropic activities, the well-conserved FP2 peptide was substantially less effective in promoting fusion, leakage, and membrane ordering in PC/PG model membranes. Furthermore, Ca2+ did not enhance the FP2-induced lipid mixing activity in PC/phosphatidylserine/cholesterol lipid membranes, despite its strong erythrocyte membrane perturbation. Nonetheless, we found that the three putative SARS-CoV membrane-active fusion peptide sequences here studied altered the physical properties of model and erythrocyte membranes to different extents. The importance of the distinct membranotropic and biological activities of all SARS-CoV fusion peptide domains and the pronounced effect of the internal fusion peptide sequence to the whole spike-mediated membrane fusion process are discussed.
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Affiliation(s)
- Luis Guilherme Mansor Basso
- Laboratório de Ciências Físicas, Centro de Ciência e Tecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, 14040-901 Ribeirão Preto, SP, Brazil.
| | - Ana Eliza Zeraik
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Grupo de Biofísica e Biologia Estrutural "Sérgio Mascarenhas", Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Centro, São Carlos, SP, Brazil
| | - Ana Paula Felizatti
- Laboratório de Produtos Naturais, Departamento de Química, Centro de Ciências Exatas e de Tecnologia, Universidade Federal de São Carlos, Rod. Washington Luiz, Km 235, Monjolinho, 13565905, São Carlos, SP, Brazil; Grupo de Biofísica e Biologia Estrutural "Sérgio Mascarenhas", Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Centro, São Carlos, SP, Brazil
| | - Antonio José Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, 14040-901 Ribeirão Preto, SP, Brazil.
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18
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Dodero-Rojas E, Onuchic JN, Whitford PC. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. eLife 2021; 10:70362. [PMID: 34463614 PMCID: PMC8456623 DOI: 10.7554/elife.70362] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, and transmission involves a series of processes that may be targeted by vaccines and therapeutics. During transmission, host cell invasion is controlled by a large-scale (200–300 Å) conformational change of the Spike protein. This conformational rearrangement leads to membrane fusion, which creates transmembrane pores through which the viral genome is passed to the host. During Spike-protein-mediated fusion, the fusion peptides must be released from the core of the protein and associate with the host membrane. While infection relies on this transition between the prefusion and postfusion conformations, there has yet to be a biophysical characterization reported for this rearrangement. That is, structures are available for the endpoints, though the intermediate conformational processes have not been described. Interestingly, the Spike protein possesses many post-translational modifications, in the form of branched glycans that flank the surface of the assembly. With the current lack of data on the pre-to-post transition, the precise role of glycans during cell invasion has also remained unclear. To provide an initial mechanistic description of the pre-to-post rearrangement, an all-atom model with simplified energetics was used to perform thousands of simulations in which the protein transitions between the prefusion and postfusion conformations. These simulations indicate that the steric composition of the glycans can induce a pause during the Spike protein conformational change. We additionally show that this glycan-induced delay provides a critical opportunity for the fusion peptides to capture the host cell. In contrast, in the absence of glycans, the viral particle would likely fail to enter the host. This analysis reveals how the glycosylation state can regulate infectivity, while providing a much-needed structural framework for studying the dynamics of this pervasive pathogen.
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Affiliation(s)
- Esteban Dodero-Rojas
- Center for Theoretical Biological Physics, Rice University, Houston, United States
| | - Jose N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, United States.,Department of Physics and Astronomy, Rice University, Houston, United States.,Department of Chemistry, Rice University, Houston, United States.,Department of Biosciences, Rice University, Houston, United States
| | - Paul Charles Whitford
- Center for Theoretical Biological Physics, Northeastern University, Boston, United States.,Department of Physics, Northeastern University, Boston, United States
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19
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Lee D, Jung WH, Lee S, Yu ES, Lee T, Kim JH, Song HS, Lee KH, Lee S, Han SK, Choi MC, Ahn DJ, Ryu YS, Kim C. Ionic contrast across a lipid membrane for Debye length extension: towards an ultimate bioelectronic transducer. Nat Commun 2021; 12:3741. [PMID: 34145296 PMCID: PMC8213817 DOI: 10.1038/s41467-021-24122-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/03/2021] [Indexed: 11/09/2022] Open
Abstract
Despite technological advances in biomolecule detections, evaluation of molecular interactions via potentiometric devices under ion-enriched solutions has remained a long-standing problem. To avoid severe performance degradation of bioelectronics by ionic screening effects, we cover probe surfaces of field effect transistors with a single film of the supported lipid bilayer, and realize respectable potentiometric signals from receptor-ligand bindings irrespective of ionic strength of bulky solutions by placing an ion-free water layer underneath the supported lipid bilayer. High-energy X-ray reflectometry together with the circuit analysis and molecular dynamics simulation discovered biochemical findings that effective electrical signals dominantly originated from the sub-nanoscale conformational change of lipids in the course of receptor-ligand bindings. Beyond thorough analysis on the underlying mechanism at the molecular level, the proposed supported lipid bilayer-field effect transistor platform ensures the world-record level of sensitivity in molecular detection with excellent reproducibility regardless of molecular charges and environmental ionic conditions.
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Affiliation(s)
- Donggeun Lee
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea.,Department of Electrical & Electronic Engineering, Yonsei University, Seoul, Republic of Korea
| | - Woo Hyuk Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul, Republic of Korea
| | - Suho Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Eui-Sang Yu
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Taikjin Lee
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Jae Hun Kim
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Hyun Seok Song
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Kwan Hyi Lee
- Center for Biomaterials, Korea Institute of Science and Technology, Seoul, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea
| | - Seok Lee
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Sang-Kook Han
- Department of Electrical & Electronic Engineering, Yonsei University, Seoul, Republic of Korea
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Dong June Ahn
- Department of Chemical and Biological Engineering, Korea University, Seoul, Republic of Korea. .,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea.
| | - Yong-Sang Ryu
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea. .,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea.
| | - Chulki Kim
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea.
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20
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Nishima W, Kulik M. Full-Length Computational Model of the SARS-CoV-2 Spike Protein and Its Implications for a Viral Membrane Fusion Mechanism. Viruses 2021; 13:v13061126. [PMID: 34208191 PMCID: PMC8230804 DOI: 10.3390/v13061126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 12/22/2022] Open
Abstract
The SARS-CoV-2 virus has now become one of the greatest causes of infectious death and morbidity since the 1918 flu pandemic. Substantial and unprecedented progress has been made in the elucidation of the viral infection process in a short time; however, our understanding of the structure–function dynamics of the spike protein during the membrane fusion process and viral uptake remains incomplete. Employing computational approaches, we use full-length structural models of the SARS-CoV-2 spike protein integrating Cryo-EM images and biophysical properties, which fill the gaps in our understanding. We propose a membrane fusion model incorporating structural transitions associated with the proteolytic processing of the spike protein, which initiates and regulates a series of events to facilitate membrane fusion and viral genome uptake. The membrane fusion mechanism highlights the notable role of the S1 subunit and eventual mature spike protein uptake through the host membrane. Our comprehensive view accounts for distinct neutralizing antibody binding effects targeting the spike protein and the enhanced infectivity of the SARS-CoV-2 variant.
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Affiliation(s)
- Wataru Nishima
- New Mexico Consortium, Los Alamos, NM 87545, USA
- University of New Mexico, Albuquerque, NM 87131, USA
- Correspondence:
| | - Marta Kulik
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-839 Warsaw, Poland;
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21
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Beale DJ, Shah R, Karpe AV, Hillyer KE, McAuley AJ, Au GG, Marsh GA, Vasan SS. Metabolic Profiling from an Asymptomatic Ferret Model of SARS-CoV-2 Infection. Metabolites 2021; 11:327. [PMID: 34069591 PMCID: PMC8160988 DOI: 10.3390/metabo11050327] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/06/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Coronavirus disease (COVID-19) is a contagious respiratory disease that is causing significant global morbidity and mortality. Understanding the impact of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection on the host metabolism is still in its infancy but of great importance. Herein, we investigated the metabolic response during viral shedding and post-shedding in an asymptomatic SARS-CoV-2 ferret model (n = 6) challenged with two SARS-CoV-2 isolates. Virological and metabolic analyses were performed on (minimally invasive) collected oral swabs, rectal swabs, and nasal washes. Fragments of SARS-CoV-2 RNA were only found in the nasal wash samples in four of the six ferrets, and in the samples collected 3 to 9 days post-infection (referred to as viral shedding). Central carbon metabolism metabolites were analyzed during viral shedding and post-shedding periods using a dynamic Multiple Reaction Monitoring (dMRM) database and method. Subsequent untargeted metabolomics and lipidomics of the same samples were performed using a Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry (LC-QToF-MS) methodology, building upon the identified differentiated central carbon metabolism metabolites. Multivariate analysis of the acquired data identified 29 significant metabolites and three lipids that were subjected to pathway enrichment and impact analysis. The presence of viral shedding coincided with the challenge dose administered and significant changes in the citric acid cycle, purine metabolism, and pentose phosphate pathways, amongst others, in the host nasal wash samples. An elevated immune response in the host was also observed between the two isolates studied. These results support other metabolomic-based findings in clinical observational studies and indicate the utility of metabolomics applied to ferrets for further COVID-19 research that advances early diagnosis of asymptomatic and mild clinical COVID-19 infections, in addition to assessing the effectiveness of new or repurposed drug therapies.
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Affiliation(s)
- David J. Beale
- Land & Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia or (R.S.); (A.V.K.); (K.E.H.)
| | - Rohan Shah
- Land & Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia or (R.S.); (A.V.K.); (K.E.H.)
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Avinash V. Karpe
- Land & Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia or (R.S.); (A.V.K.); (K.E.H.)
| | - Katie E. Hillyer
- Land & Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia or (R.S.); (A.V.K.); (K.E.H.)
| | - Alexander J. McAuley
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (A.J.M.); (G.G.A.); (G.A.M.); (S.S.V.)
| | - Gough G. Au
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (A.J.M.); (G.G.A.); (G.A.M.); (S.S.V.)
| | - Glenn A. Marsh
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (A.J.M.); (G.G.A.); (G.A.M.); (S.S.V.)
| | - Seshadri S. Vasan
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (A.J.M.); (G.G.A.); (G.A.M.); (S.S.V.)
- Department of Health Sciences, University of York, York YO10 5DD, UK
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22
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Shaath H, Alajez NM. Identification of PBMC-based molecular signature associational with COVID-19 disease severity. Heliyon 2021; 7:e06866. [PMID: 33898797 PMCID: PMC8057768 DOI: 10.1016/j.heliyon.2021.e06866] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/10/2021] [Accepted: 04/16/2021] [Indexed: 12/18/2022] Open
Abstract
The longevity of COVID-19 as a global pandemic, and the devastating effects it has had on certain subsets of individuals thus far has highlighted the importance of identifying blood-based biomarkers associated with disease severity. We employed computational and transcriptome analyses of publicly available datasets from PBMCs from 126 patients with COVID-19 admitted to ICU (n = 50), COVID-19 not admitted to ICU (n = 50), non-COVID-19 admitted to ICU (n = 16) and non-COVID-19 not admitted to ICU (n = 10), and utilized the Gencode V33 assembly to analyze protein coding mRNA and long noncoding RNA (lncRNA) transcriptomes in the context of disease severity. Our data identified several aberrantly expressed mRNA and lncRNA based biomarkers associated with SARS-CoV-2 severity, which in turn significantly affected canonical, upstream, and disease functions in each group of patients. Immune, interferon, and antiviral responses were severely suppressed in COVID-19 patients admitted to ICU versus those who were not admitted to ICU. Our data suggests a possible therapeutic approach for severe COVID-19 through administration of interferon therapy. Delving further into these biomarkers, roles and their implications on the onset and disease severity of COVID-19 could play a crucial role in patient stratification and identifying varied therapeutic options with diverse clinical implications.
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Affiliation(s)
- Hibah Shaath
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Nehad M Alajez
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
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23
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Gorgun D, Lihan M, Kapoor K, Tajkhorshid E. Binding mode of SARS-CoV-2 fusion peptide to human cellular membrane. Biophys J 2021; 120:2914-2926. [PMID: 33675757 PMCID: PMC7929786 DOI: 10.1016/j.bpj.2021.02.041] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/29/2021] [Accepted: 02/15/2021] [Indexed: 01/08/2023] Open
Abstract
Infection of human cells by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) relies on its binding to a specific receptor and subsequent fusion of the viral and host cell membranes. The fusion peptide (FP), a short peptide segment in the spike protein, plays a central role in the initial penetration of the virus into the host cell membrane, followed by the fusion of the two membranes. Here, we use an array of molecular dynamics simulations that take advantage of the highly mobile membrane mimetic model to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level and to characterize the membrane-bound form of the peptide. Six independent systems were generated by changing the initial positioning and orientation of the FP with respect to the membrane, and each system was simulated in five independent replicas, each for 300 ns. In 73% of the simulations, the FP reaches a stable, membrane-bound configuration, in which the peptide deeply penetrated into the membrane. Clustering of the results reveals three major membrane-binding modes (binding modes 1-3), in which binding mode 1 populates over half of the data points. Taking into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, the significant depth of penetration of the whole peptide, and the dense population of the respective cluster, we propose that the most deeply inserted membrane-bound form (binding mode 1) represents more closely the biologically relevant form. Analysis of FP-lipid interactions shows the involvement of specific residues, previously described as the "fusion-active core residues," in membrane binding. Taken together, the results shed light on a key step involved in SARS-CoV2 infection, with potential implications in designing novel inhibitors.
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Affiliation(s)
- Defne Gorgun
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Muyun Lihan
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Karan Kapoor
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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Extracellular Vesicles in Viral Pathogenesis: A Case of Dr. Jekyll and Mr. Hyde. Life (Basel) 2021; 11:life11010045. [PMID: 33450847 PMCID: PMC7828316 DOI: 10.3390/life11010045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 02/06/2023] Open
Abstract
Secretion of extracellular vesicles (EVs) is a fundamental property of living cells. EVs are known to transfer biological signals between cells and thus regulate the functional state of recipient cells. Such vesicles mediate the intercellular transport of many biologically active molecules (proteins, nucleic acids, specific lipids) and participate in regulation of key physiological processes. In addition, EVs are involved in the pathogenesis of multiple diseases: infectious, neurodegenerative, and oncological. The current EV classification into microvesicles, apoptotic bodies, and exosomes is based on their size, pathways of cellular biogenesis, and molecular composition. This review is focused on analysis of the role of EVs (mainly exosomes) in the pathogenesis of viral infection. We briefly characterize the biogenesis and molecular composition of various EV types. Then, we consider EV-mediated pro- and anti-viral mechanisms. EV secretion by infected cells can be an important factor of virus spread in target cell populations, or a protective factor limiting viral invasion. The data discussed in this review, on the effect of EV secretion by infected cells on processes in neighboring cells and on immune cells, are of high significance in the search for new therapeutic approaches and for design of new generations of vaccines.
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25
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Liposomal Encapsulation of Oleuropein and an Olive Leaf Extract: Molecular Interactions, Antioxidant Effects and Applications in Model Food Systems. FOOD BIOPHYS 2020. [DOI: 10.1007/s11483-020-09650-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractThe influence of actively/passively encapsulated oleuropein on DPPC liposomes thermal and structural properties, and its antioxidant capacity against lipid peroxidation were investigated. Also, an oleuropein-rich olive leaf extract was encapsulated in soy phosphatidylcholine (PL-90 g) and incorporated in model and commercial drinks. Oleuropein induced a concentration-dependent broadening and splitting of the gel-to-liquid phase transition temperature. Fluorescence measurements revealed a fluidizing effect on liposomes below their gel-to-liquid phase transition temperature, and a higher lipid ordering above, especially to active encapsulation. Oleuropein also showed an antioxidant effect against lipid peroxidation in PL-90 g liposomes. PL-90 g Liposomes with olive leaf extract showed a mean diameter of 405 ± 4 nm and oleuropein encapsulation efficiency of 34% and delayed oleuropein degradation at pH 2.0 and 2.8 model drinks. In conclusion, greater effects were observed on the structure and fluidity of DPPC liposomes when oleuropein was actively encapsulated, while its incorporation into acidic foods in encapsulated form could enhance its stability.
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Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics. Biophys Chem 2020; 265:106438. [PMID: 32721790 PMCID: PMC7375304 DOI: 10.1016/j.bpc.2020.106438] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 01/04/2023]
Abstract
The emerging and re-emerging viral diseases are continuous threats to the wellbeing of human life. Previous outbreaks of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS had evidenced potential threats of coronaviruses in human health. The recent pandemic due to SARS-CoV-2 is overwhelming and has been going beyond control. Vaccines and antiviral drugs are ungently required to mitigate the pandemic. Therefore, it is important to comprehend the mechanistic details of viral infection process. The fusion between host cell and virus being the first step of infection, understanding the fusion mechanism could provide crucial information to intervene the infection process. Interestingly, all enveloped viruses contain fusion protein on their envelope that acts as fusion machine. For coronaviruses, the spike or S glycoprotein mediates successful infection through receptor binding and cell fusion. The cell fusion process requires merging of virus and host cell membranes, and that is essentially performed by the S2 domain of the S glycoprotein. In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. We have further discussed about the cell fusion of SARS-CoV-2 in the context of present pandemic situation.
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27
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Poon WCK, Brown AT, Direito SOL, Hodgson DJM, Le Nagard L, Lips A, MacPhee CE, Marenduzzo D, Royer JR, Silva AF, Thijssen JHJ, Titmuss S. Soft matter science and the COVID-19 pandemic. SOFT MATTER 2020; 16:8310-8324. [PMID: 32909024 DOI: 10.1039/d0sm01223h] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Much of the science underpinning the global response to the COVID-19 pandemic lies in the soft matter domain. Coronaviruses are composite particles with a core of nucleic acids complexed to proteins surrounded by a protein-studded lipid bilayer shell. A dominant route for transmission is via air-borne aerosols and droplets. Viral interaction with polymeric body fluids, particularly mucus, and cell membranes controls their infectivity, while their interaction with skin and artificial surfaces underpins cleaning and disinfection and the efficacy of masks and other personal protective equipment. The global response to COVID-19 has highlighted gaps in the soft matter knowledge base. We survey these gaps, especially as pertaining to the transmission of the disease, and suggest questions that can (and need to) be tackled, both in response to COVID-19 and to better prepare for future viral pandemics.
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Affiliation(s)
- Wilson C K Poon
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Aidan T Brown
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Susana O L Direito
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Daniel J M Hodgson
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Lucas Le Nagard
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Alex Lips
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Cait E MacPhee
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Davide Marenduzzo
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - John R Royer
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Andreia F Silva
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Job H J Thijssen
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
| | - Simon Titmuss
- Edinburgh Complex Fluids Partnership (ECFP), SUPA and School of Physics & Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
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Mandal SM, Panda S. Inhaler with electrostatic sterilizer and use of cationic amphiphilic peptides may accelerate recovery from COVID-19. Biotechniques 2020; 69:206-210. [PMID: 32929995 PMCID: PMC7299243 DOI: 10.2144/btn-2020-0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We explore the design of a smart inhaler with electrostatic sterilizer and propose the utilization of cationic amphiphilic peptides, independently or in conjunction with a bronchodilator, for COVID-19 patients to quickly improve wellbeing while maintaining a strategic distance to protect healthcare personnel from virus-containing aerosol or droplets during the process of inhalation.
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Affiliation(s)
- Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Souvik Panda
- Kachua, Tagaria, Contai, 721433, Purba Medinipur, West Bengal, India
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29
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Balgoma D, Gil-de-Gómez L, Montero O. Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update. Metabolites 2020; 10:E356. [PMID: 32878290 PMCID: PMC7569815 DOI: 10.3390/metabo10090356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022] Open
Abstract
The pathogenic mechanisms underlying the Biology and Biochemistry of viral infections are known to depend on the lipid metabolism of infected cells. From a lipidomics viewpoint, there are a variety of mechanisms involving virus infection that encompass virus entry, the disturbance of host cell lipid metabolism, and the role played by diverse lipids in regard to the infection effectiveness. All these aspects have currently been tackled separately as independent issues and focused on the function of proteins. Here, we review the role of cholesterol and other lipids in ssRNA+ infection.
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Affiliation(s)
- David Balgoma
- Analytical Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, Husarg. 3, 75123 Uppsala, Sweden;
| | - Luis Gil-de-Gómez
- Center of Childhood Cancer Center, Children’s Hospital of Philadelphia, Colket Translational Research Center, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA;
| | - Olimpio Montero
- Spanish National Research Council (CSIC), Boecillo’s Technological Park Bureau, Av. Francisco Vallés 8, 47151 Boecillo, Spain
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30
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Ftiha F, Shalom M, Jradeh H. Neurological symptoms due to Coronavirus disease 2019. Neurol Int 2020; 12:8639. [PMID: 32874447 PMCID: PMC7445577 DOI: 10.4081/ni.2020.8639] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 01/01/2023] Open
Abstract
In this review, we focus on summarizing everything that is known about the neurological effects of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2). It has been shown that Coronavirus Disease 2019 (Covid-19) may result in neuromuscular disorders or damage to nerves outside of the brain and spinal cord, which may lead to weakness, numbness, and pain. Published literature has stated that SARS-COV-1 may infect the central nervous system and due to its similarities to SARS-COV-2, we suspect that SARS-COV-2 has the same potential. We conclude that Covid-19 has neurological manifestations. Further research should be done in this field to understand the full extent of this virus.
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31
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Navarese EP, Musci RL, Frediani L, Gurbel PA, Kubica J. Ion channel inhibition against COVID-19: A novel target for clinical investigation. Cardiol J 2020; 27:421-424. [PMID: 32643141 DOI: 10.5603/cj.a2020.0090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Eliano P Navarese
- Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Rita L Musci
- Department of Cardiology, Azienda Ospedaliera Bonomo, Andria, Italy, Andria, Italy
| | - Lara Frediani
- Department of Cardiology, Azienda Usl Toscana Nord-Ovest Cardiologia UTIC-Ospedali Riuniti di Livorno, Italy, Livorno, Italy
| | - Paul A Gurbel
- Sinai Center for Cardiovascular Research, Sinai Hospital of Baltimore, LifeBridgehealth, Baltimore, MD, USA., Baltimore, United States
| | - Jacek Kubica
- Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland.
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32
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Ma C, Su S, Wang J, Wei L, Du L, Jiang S. From SARS-CoV to SARS-CoV-2: safety and broad-spectrum are important for coronavirus vaccine development. Microbes Infect 2020; 22:245-253. [PMID: 32437926 PMCID: PMC7211703 DOI: 10.1016/j.micinf.2020.05.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/28/2022]
Abstract
The global pandemic of COVID-19 caused by SARS-CoV-2 (also known as 2019-nCoV and HCoV-19) has posed serious threats to public health and economic stability worldwide, thus calling for development of vaccines against SARS-CoV-2 and other emerging and reemerging coronaviruses. Since SARS-CoV-2 and SARS-CoV have high similarity of their genomic sequences and share the same cellular receptor (ACE2), it is essential to learn the lessons and experiences from the development of SARS-CoV vaccines for the development of SARS-CoV-2 vaccines. In this review, we summarized the current knowledge on the advantages and disadvantages of the SARS-CoV vaccine candidates and prospected the strategies for the development of safe, effective and broad-spectrum coronavirus vaccines for prevention of infection by currently circulating SARS-CoV-2 and other emerging and reemerging coronaviruses that may cause future epidemics or pandemics.
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Affiliation(s)
- Cuiqing Ma
- Department of Immunology, Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Hebei Medical University, 050017, Shijiazhuang, China
| | - Shan Su
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiachao Wang
- Department of Immunology, Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Hebei Medical University, 050017, Shijiazhuang, China
| | - Lin Wei
- Department of Immunology, Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Hebei Medical University, 050017, Shijiazhuang, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA.
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33
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The Role of Extracellular Vesicles as Allies of HIV, HCV and SARS Viruses. Viruses 2020; 12:v12050571. [PMID: 32456011 PMCID: PMC7291340 DOI: 10.3390/v12050571] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 12/16/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid bilayer-enclosed entities containing proteins and nucleic acids that mediate intercellular communication, in both physiological and pathological conditions. EVs resemble enveloped viruses in both structural and functional aspects. In full analogy with viral biogenesis, some of these vesicles are generated inside cells and, once released into the extracellular milieu, are called “exosomes”. Others bud from the plasma membrane and are generally referred to as “microvesicles”. In this review, we will discuss the state of the art of the current studies on the relationship between EVs and viruses and their involvement in three important viral infections caused by HIV, HCV and Severe Acute Respiratory Syndrome (SARS) viruses. HIV and HCV are two well-known pathogens that hijack EVs content and release to create a suitable environment for viral infection. SARS viruses are a new entry in the world of EVs studies, but are equally important in this historical framework. A thorough knowledge of the involvement of the EVs in viral infections could be helpful for the development of new therapeutic strategies to counteract different pathogens.
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34
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Felizatti AP, Zeraik AE, Basso LG, Kumagai PS, Lopes JL, Wallace B, Araujo AP, DeMarco R. Interactions of amphipathic α-helical MEG proteins from Schistosoma mansoni with membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183173. [DOI: 10.1016/j.bbamem.2019.183173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 02/04/2023]
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35
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Munusamy S, Conde R, Bertrand B, Munoz-Garay C. Biophysical approaches for exploring lipopeptide-lipid interactions. Biochimie 2020; 170:173-202. [PMID: 31978418 PMCID: PMC7116911 DOI: 10.1016/j.biochi.2020.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 01/19/2020] [Indexed: 02/07/2023]
Abstract
In recent years, lipopeptides (LPs) have attracted a lot of attention in the pharmaceutical industry due to their broad-spectrum of antimicrobial activity against a variety of pathogens and their unique mode of action. This class of compounds has enormous potential for application as an alternative to conventional antibiotics and for pest control. Understanding how LPs work from a structural and biophysical standpoint through investigating their interaction with cell membranes is crucial for the rational design of these biomolecules. Various analytical techniques have been developed for studying intramolecular interactions with high resolution. However, these tools have been barely exploited in lipopeptide-lipid interactions studies. These biophysical approaches would give precise insight on these interactions. Here, we reviewed these state-of-the-art analytical techniques. Knowledge at this level is indispensable for understanding LPs activity and particularly their potential specificity, which is relevant information for safe application. Additionally, the principle of each analytical technique is presented and the information acquired is discussed. The key challenges, such as the selection of the membrane model are also been briefly reviewed. A brief overview of topics to understand the generalities of lipopeptide (LP) science. Main analytical techniques used to reveal the interaction and the distorting effect of LP on artificial membranes. Guidelines for selecting of the most adequate membrane models for the given analytical technique.
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Affiliation(s)
- Sathishkumar Munusamy
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Renaud Conde
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico.
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36
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Sastre DE, Basso LGM, Trastoy B, Cifuente JO, Contreras X, Gueiros-Filho F, de Mendoza D, Navarro MVAS, Guerin ME. Membrane fluidity adjusts the insertion of the transacylase PlsX to regulate phospholipid biosynthesis in Gram-positive bacteria. J Biol Chem 2019; 295:2136-2147. [PMID: 31796629 DOI: 10.1074/jbc.ra119.011122] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/19/2019] [Indexed: 12/24/2022] Open
Abstract
PlsX plays a central role in the coordination of fatty acid and phospholipid biosynthesis in Gram-positive bacteria. PlsX is a peripheral membrane acyltransferase that catalyzes the conversion of acyl-ACP to acyl-phosphate, which is in turn utilized by the polytopic membrane acyltransferase PlsY on the pathway of bacterial phospholipid biosynthesis. We have recently studied the interaction between PlsX and membrane phospholipids in vivo and in vitro, and observed that membrane association is necessary for the efficient transfer of acyl-phosphate to PlsY. However, understanding the molecular basis of such a channeling mechanism remains a major challenge. Here, we disentangle the binding and insertion events of the enzyme to the membrane, and the subsequent catalysis. We show that PlsX membrane binding is a process mostly mediated by phospholipid charge, whereas fatty acid saturation and membrane fluidity remarkably influence the membrane insertion step. Strikingly, the PlsXL254E mutant, whose biological functionality was severely compromised in vivo but remains catalytically active in vitro, was able to superficially bind to phospholipid vesicles, nevertheless, it loses the insertion capacity, strongly supporting the importance of membrane insertion in acyl-phosphate delivery. We propose a mechanism in which membrane fluidity governs the insertion of PlsX and thus regulates the biosynthesis of phospholipids in Gram-positive bacteria. This model may be operational in other peripheral membrane proteins with an unprecedented impact in drug discovery/development strategies.
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Affiliation(s)
- Diego E Sastre
- Grupo de Biofísica Molecular "Sergio Mascarenhas," Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brasil.
| | - Luis G M Basso
- Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Beatriz Trastoy
- Structural Biology Unit, CIC bioGUNE Technological Park of Bizkaia, Derio, Vizcaya, Spain
| | - Javier O Cifuente
- Structural Biology Unit, CIC bioGUNE Technological Park of Bizkaia, Derio, Vizcaya, Spain
| | - Xabier Contreras
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain; Instituto Biofisika, Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, 48940 Bizkaia, Spain; Departamento de Bioquímica, Universidad del País Vasco, Leioa, 48940 Bizkaia, Spain
| | - Frederico Gueiros-Filho
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brasil
| | - Diego de Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR), Rosario, Santa Fe, Argentina
| | - Marcos V A S Navarro
- Grupo de Biofísica Molecular "Sergio Mascarenhas," Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brasil
| | - Marcelo E Guerin
- Structural Biology Unit, CIC bioGUNE Technological Park of Bizkaia, Derio, Vizcaya, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
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37
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Meher G, Chakraborty H. Membrane Composition Modulates Fusion by Altering Membrane Properties and Fusion Peptide Structure. J Membr Biol 2019; 252:261-272. [PMID: 31011762 PMCID: PMC7079885 DOI: 10.1007/s00232-019-00064-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/12/2019] [Indexed: 01/21/2023]
Abstract
Membrane fusion, one of the most essential processes in the life of eukaryotes, occurs when two separate lipid bilayers merge into a continuous bilayer and internal contents of two separated membranes mingle. There is a certain class of proteins that assist the binding of the viral envelope to the target host cell and catalyzing fusion. All class I viral fusion proteins contain a highly conserved 20–25 amino-acid amphipathic peptide at the N-terminus, which is essential for fusion activity and is termed as the ‘fusion peptide’. It has been shown that insertion of fusion peptides into the host membrane and the perturbation in the membrane generated thereby is crucial for membrane fusion. Significant efforts have been given in the last couple of decades to understand the lipid-dependence of structure and function of the fusion peptide in membranes to understand the role of lipid compositions in membrane fusion. In addition, the lipid compositions further change the membrane physical properties and alter the mechanism and extent of membrane fusion. Therefore, lipid compositions modulate membrane fusion by changing membrane physical properties and altering structure of the fusion peptide.
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Affiliation(s)
- Geetanjali Meher
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768 019, India
| | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768 019, India.
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Crusca E, Basso LGM, Altei WF, Marchetto R. Biophysical characterization and antitumor activity of synthetic Pantinin peptides from scorpion's venom. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2155-2165. [DOI: 10.1016/j.bbamem.2018.08.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/24/2018] [Accepted: 08/19/2018] [Indexed: 01/30/2023]
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Shang J, Zheng Y, Yang Y, Liu C, Geng Q, Luo C, Zhang W, Li F. Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins. PLoS Pathog 2018; 14:e1007009. [PMID: 29684066 PMCID: PMC5933801 DOI: 10.1371/journal.ppat.1007009] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/03/2018] [Accepted: 04/03/2018] [Indexed: 01/08/2023] Open
Abstract
As cell-invading molecular machinery, coronavirus spike proteins pose an evolutionary conundrum due to their high divergence. In this study, we determined the cryo-EM structure of avian infectious bronchitis coronavirus (IBV) spike protein from the γ-genus. The trimeric IBV spike ectodomain contains three receptor-binding S1 heads and a trimeric membrane-fusion S2 stalk. While IBV S2 is structurally similar to those from the other genera, IBV S1 possesses structural features that are unique to different other genera, thereby bridging these diverse spikes into an evolutionary spectrum. Specifically, among different genera, the two domains of S1, the N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD), diverge from simpler tertiary structures and quaternary packing to more complex ones, leading to different functions of the spikes in receptor usage and membrane fusion. Based on the above structural and functional comparisons, we propose that the evolutionary spectrum of coronavirus spikes follows the order of α-, δ-, γ-, and β-genus. This study has provided insight into the evolutionary relationships among coronavirus spikes and deepened our understanding of their structural and functional diversity.
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Affiliation(s)
- Jian Shang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Yuan Zheng
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Yang Yang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Chang Liu
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Qibin Geng
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Chuming Luo
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Wei Zhang
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, United States of America
- Characterization Facility, College of Science and Engineering, University of Minnesota, Minneapolis, MN, United States of America
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States of America
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Cryo-Electron Microscopy Structure of Porcine Deltacoronavirus Spike Protein in the Prefusion State. J Virol 2018; 92:JVI.01556-17. [PMID: 29070693 DOI: 10.1128/jvi.01556-17] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Coronavirus spike proteins from different genera are divergent, although they all mediate coronavirus entry into cells by binding to host receptors and fusing viral and cell membranes. Here, we determined the cryo-electron microscopy structure of porcine deltacoronavirus (PdCoV) spike protein at 3.3-Å resolution. The trimeric protein contains three receptor-binding S1 subunits that tightly pack into a crown-like structure and three membrane fusion S2 subunits that form a stalk. Each S1 subunit contains two domains, an N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD). PdCoV S1-NTD has the same structural fold as alpha- and betacoronavirus S1-NTDs as well as host galectins, and it recognizes sugar as its potential receptor. PdCoV S1-CTD has the same structural fold as alphacoronavirus S1-CTDs, but its structure differs from that of betacoronavirus S1-CTDs. PdCoV S1-CTD binds to an unidentified receptor on host cell surfaces. PdCoV S2 is locked in the prefusion conformation by structural restraint of S1 from a different monomeric subunit. PdCoV spike possesses several structural features that may facilitate immune evasion by the virus, such as its compact structure, concealed receptor-binding sites, and shielded critical epitopes. Overall, this study reveals that deltacoronavirus spikes are structurally and evolutionally more closely related to alphacoronavirus spikes than to betacoronavirus spikes; it also has implications for the receptor recognition, membrane fusion, and immune evasion by deltacoronaviruses as well as coronaviruses in general.
IMPORTANCE
In this study, we determined the cryo-electron microscopy structure of porcine deltacoronavirus (PdCoV) spike protein at a 3.3-Å resolution. This is the first atomic structure of a spike protein from the deltacoronavirus genus, which is divergent in amino acid sequences from the well-studied alpha- and betacoronavirus spike proteins. Here, we described the overall structure of the PdCoV spike and the detailed structure of each of its structural elements. Moreover, we analyzed the functions of each of the structural elements. Based on the structures and functions of these structural elements, we discussed the evolution of PdCoV spike protein in relation to the spike proteins from other coronavirus genera. This study combines the structure, function, and evolution of PdCoV spike protein and provides many insights into its receptor recognition, membrane fusion, and immune evasion.
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Millet JK, Whittaker GR. Physiological and molecular triggers for SARS-CoV membrane fusion and entry into host cells. Virology 2017; 517:3-8. [PMID: 29275820 PMCID: PMC7112017 DOI: 10.1016/j.virol.2017.12.015] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 11/17/2022]
Abstract
During viral entry, enveloped viruses require the fusion of their lipid envelope with host cell membranes. For coronaviruses, this critical step is governed by the virally-encoded spike (S) protein, a class I viral fusion protein that has several unique features. Coronavirus entry is unusual in that it is often biphasic in nature, and can occur at or near the cell surface or in late endosomes. Recent advances in structural, biochemical and molecular biology of the coronavirus S protein has shed light on the intricacies of coronavirus entry, in particular the molecular triggers of coronavirus S-mediated membrane fusion. Furthermore, characterization of the coronavirus fusion peptide (FP), the segment of the fusion protein that inserts to a target lipid bilayer during membrane fusion, has revealed its particular attributes which imparts some of the unusual properties of the S protein, such as Ca2+-dependency. These unusual characteristics can explain at least in part the biphasic nature of coronavirus entry. In this review, using severe acute respiratory syndrome coronavirus (SARS-CoV) as model virus, we give an overview of advances in research on the coronavirus fusion peptide with an emphasis on its role and properties within the biological context of host cell entry.
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Affiliation(s)
- Jean Kaoru Millet
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
| | - Gary R Whittaker
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States.
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Vicente EF, Sahu ID, Crusca E, Basso LGM, Munte CE, Costa-Filho AJ, Lorigan GA, Cilli EM. HsDHODH Microdomain-Membrane Interactions Influenced by the Lipid Composition. J Phys Chem B 2017; 121:11085-11095. [PMID: 29148803 DOI: 10.1021/acs.jpcb.7b09642] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Human dihydroorotate dehydrogenase (HsDHODH) enzyme has been studied as selective target for inhibitors to block the enzyme activity, intending to prevent proliferative diseases. The N-terminal microdomain seems to play an important role in the enzyme function. However, the molecular mechanism of action and dynamics of this region are not totally understood yet. This study analyzes the interaction and conformation in model membranes of HsDHODH microdomain using peptide analogues containing the paramagnetic amino acid TOAC at strategic positions. In buffer solution, the analogues presented a disordered conformation, but acquired a high content of α-helical structure in membrane mimetics, which was found to be lipid dependent. The microdomain peptide structure in micelles showed a very different peptide conformation when compared to the reported crystal structure, displaying a conformational flexibility of its helices, promoted by the connecting loop, which might be functionally relevant. Electron spin resonance in membrane compositions containing POPC, POPE, and cardiolipin showed that interaction of the analogues was enhanced by the presence of cardiolipin, indicating that the microdomain preferentially interacts with cardiolipin-containing membranes. Therefore, the great flexibility of the microdomain and the cardiolipin affinity should be considered in further studies aimed at finding new inhibitory compounds to fight proliferative diseases.
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Affiliation(s)
- Eduardo F Vicente
- School of Science and Engineering, São Paulo State University (UNESP) , 17602-496, Tupã, SP Brazil
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Edson Crusca
- Institute of Chemistry, São Paulo State University (UNESP) , 14800-900, Araraquara, SP Brazil.,Instituto de Física de São Carlos, Universidade de São Paulo (USP) , 13566-590 - São Carlos, SP Brazil
| | - Luis G M Basso
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP) , 14040-901, Ribeirão Preto, SP Brazil
| | - Claudia E Munte
- Instituto de Física de São Carlos, Universidade de São Paulo (USP) , 13566-590 - São Carlos, SP Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP) , 14040-901, Ribeirão Preto, SP Brazil
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Eduardo M Cilli
- Institute of Chemistry, São Paulo State University (UNESP) , 14800-900, Araraquara, SP Brazil
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Lai AL, Millet JK, Daniel S, Freed JH, Whittaker GR. The SARS-CoV Fusion Peptide Forms an Extended Bipartite Fusion Platform that Perturbs Membrane Order in a Calcium-Dependent Manner. J Mol Biol 2017; 429:3875-3892. [PMID: 29056462 PMCID: PMC5705393 DOI: 10.1016/j.jmb.2017.10.017] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/02/2017] [Accepted: 10/12/2017] [Indexed: 01/12/2023]
Abstract
Coronaviruses (CoVs) are a major infectious disease threat and include the pathogenic human pathogens of zoonotic origin: severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV). Entry of CoVs into host cells is mediated by the viral spike (S) protein, which is structurally categorized as a class I viral fusion protein, within the same group as influenza virus and HIV. However, S proteins have two distinct cleavage sites that can be activated by a much wider range of proteases. The exact location of the CoV fusion peptide (FP) has been disputed. However, most evidence suggests that the domain immediately downstream of the S2' cleavage site is the FP (amino acids 798-818 SFIEDLLFNKVTLADAGFMKQY for SARS-CoV, FP1). In our previous electron spin resonance spectroscopic studies, the membrane-ordering effect of influenza virus, HIV, and Dengue virus FPs has been consistently observed. In this study, we used this effect as a criterion to identify and characterize the bona fide SARS-CoV FP. Our results indicate that both FP1 and the region immediately downstream (amino acids 816-835 KQYGECLGDINARDLICAQKF, FP2) induce significant membrane ordering. Furthermore, their effects are calcium dependent, which is consistent with in vivo data showing that calcium is required for SARS-CoV S-mediated fusion. Isothermal titration calorimetry showed a direct interaction between calcium cations and both FPs. This Ca2+-dependency membrane ordering was not observed with influenza FP, indicating that the CoV FP exhibits a mechanistically different behavior. Membrane-ordering effects are greater and penetrate deeper into membranes when FP1 and FP2 act in a concerted manner, suggesting that they form an extended fusion "platform."
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Affiliation(s)
- Alex L Lai
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
| | - Jean K Millet
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, United States
| | - Susan Daniel
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, United States.
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Nguyễn CH, Putaux JL, Santoni G, Tfaili S, Fourmentin S, Coty JB, Choisnard L, Gèze A, Wouessidjewe D, Barratt G, Lesieur S, Legrand FX. New nanoparticles obtained by co-assembly of amphiphilic cyclodextrins and nonlamellar single-chain lipids: Preparation and characterization. Int J Pharm 2017; 531:444-456. [PMID: 28698068 DOI: 10.1016/j.ijpharm.2017.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/30/2017] [Accepted: 07/02/2017] [Indexed: 01/04/2023]
Abstract
This work aimed at preparing new nanoscale assemblies based on an amphiphilic bio-esterified β-cyclodextrin (β-CD), substituted at the secondary face with n-decanoic fatty acid chains (β-CD-C10), and monoolein (MO) as new carriers for parenteral drug delivery. Stable binary (β-CD-C10/MO) and ternary (β-CD-C10/MO/stabilizer) nanoscale assemblies close to 100nm in size were successfully prepared in water by the solvent displacement method. The generated nanoparticles were fully characterized by dynamic light scattering, transmission electron microscopy, small-angle X-ray scattering, residual solvent analysis, complement activation and the contribution of each formulation parameter was determined by principal component analysis. The β-CD-C10 units were shown to self-organize into nanoparticles with a hexagonal supramolecular packing that was significantly modulated by the molar ratio of the constituents and the presence of a steric or electrostatic stabilizer (DOPE-PEG2000 or DOPA/POPA, respectively). Indeed, nanoparticles differing in morphology and in hexagonal lattice parameters were obtained while the co-existence of multiple mesophases was observed in some formulations, in particular for the β-CD-C10/MO/DOPA and β-CD-C10/MO/POPA systems. The mixed β-CD-C10/MO/DOPE-PEG2000 nanoparticles (49:49:2 in mol%) appeared to be the most suitable for use as a drug delivery system since they contained a very low amount of residual solvent and showed a low level of complement C3 activation.
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Affiliation(s)
- Cảnh Hưng Nguyễn
- Institut Galien Paris-Sud, CNRS UMR 8612, Univ. Paris-Sud, Université Paris-Saclay, 5 rue Jean-Baptiste Clément, F-92290 Châtenay-Malabry, France
| | - Jean-Luc Putaux
- Centre de Recherches sur les Macromolécules Végétales, CNRS UPR 5301, Univ. Grenoble Alpes, BP 53, F-38401 Grenoble Cedex 9, France
| | - Gianluca Santoni
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Sana Tfaili
- Lip(Sys)², EA 7357, Chimie Analytique Pharmaceutique, Univ. Paris-Sud, Université Paris-Saclay, 5 rue Jean-Baptiste Clément, F-92290 Châtenay-Malabry, France
| | - Sophie Fourmentin
- Unité de Chimie Environnementale et Interactions sur le Vivant, EA 4492, SFR Condorcet FR CNRS 3417, Université Littoral Côte d'Opale, 145 avenue Maurice Schumann, F-59140 Dunkerque, France
| | - Jean-Baptiste Coty
- Institut Galien Paris-Sud, CNRS UMR 8612, Univ. Paris-Sud, Université Paris-Saclay, 5 rue Jean-Baptiste Clément, F-92290 Châtenay-Malabry, France
| | - Luc Choisnard
- Département de Pharmacochimie Moléculaire, CNRS UMR 5063, Univ. Grenoble Alpes, F-38000 Grenoble, France
| | - Annabelle Gèze
- Département de Pharmacochimie Moléculaire, CNRS UMR 5063, Univ. Grenoble Alpes, F-38000 Grenoble, France
| | - Denis Wouessidjewe
- Département de Pharmacochimie Moléculaire, CNRS UMR 5063, Univ. Grenoble Alpes, F-38000 Grenoble, France
| | - Gillian Barratt
- Institut Galien Paris-Sud, CNRS UMR 8612, Univ. Paris-Sud, Université Paris-Saclay, 5 rue Jean-Baptiste Clément, F-92290 Châtenay-Malabry, France
| | - Sylviane Lesieur
- Institut Galien Paris-Sud, CNRS UMR 8612, Univ. Paris-Sud, Université Paris-Saclay, 5 rue Jean-Baptiste Clément, F-92290 Châtenay-Malabry, France
| | - François-Xavier Legrand
- Institut Galien Paris-Sud, CNRS UMR 8612, Univ. Paris-Sud, Université Paris-Saclay, 5 rue Jean-Baptiste Clément, F-92290 Châtenay-Malabry, France.
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Mahajan M, Chatterjee D, Bhuvaneswari K, Pillay S, Bhattacharjya S. NMR structure and localization of a large fragment of the SARS-CoV fusion protein: Implications in viral cell fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:407-415. [PMID: 28988778 PMCID: PMC7094225 DOI: 10.1016/j.bbamem.2017.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/16/2017] [Accepted: 10/03/2017] [Indexed: 01/20/2023]
Abstract
The lethal Coronaviruses (CoVs), Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV) and most recently Middle East Respiratory Syndrome Coronavirus, (MERS-CoV) are serious human health hazard. A successful viral infection requires fusion between virus and host cells carried out by the surface spike glycoprotein or S protein of CoV. Current models propose that the S2 subunit of S protein assembled into a hexameric helical bundle exposing hydrophobic fusogenic peptides or fusion peptides (FPs) for membrane insertion. The N-terminus of S2 subunit of SARS-CoV reported to be active in cell fusion whereby FPs have been identified. Atomic-resolution structure of FPs derived either in model membranes or in membrane mimic environment would glean insights toward viral cell fusion mechanism. Here, we have solved 3D structure, dynamics and micelle localization of a 64-residue long fusion peptide or LFP in DPC detergent micelles by NMR methods. Micelle bound structure of LFP is elucidated by the presence of discretely folded helical and intervening loops. The C-terminus region, residues F42-Y62, displays a long hydrophobic helix, whereas the N-terminus is defined by a short amphipathic helix, residues R4-Q12. The intervening residues of LFP assume stretches of loops and helical turns. The N-terminal helix is sustained by close aromatic and aliphatic sidechain packing interactions at the non-polar face. 15N{1H}NOE studies indicated dynamical motion, at ps-ns timescale, of the helices of LFP in DPC micelles. PRE NMR showed that insertion of several regions of LFP into DPC micelle core. Together, the current study provides insights toward fusion mechanism of SARS-CoV.
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Affiliation(s)
- Mukesh Mahajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Deepak Chatterjee
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Kannaian Bhuvaneswari
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Shubhadra Pillay
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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Micheletto MC, Mendes LFS, Basso LGM, Fonseca-Maldonado RG, Costa-Filho AJ. Lipid membranes and acyl-CoA esters promote opposing effects on acyl-CoA binding protein structure and stability. Int J Biol Macromol 2017; 102:284-296. [PMID: 28390829 DOI: 10.1016/j.ijbiomac.2017.03.197] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 12/21/2022]
Abstract
Acyl-CoA Binding Proteins (ACBP) form a housekeeping family of proteins that is responsible for the buffering of long chain acyl-coenzyme A esters (LCFA-CoA) inside the cell. Even though numerous studies have focused on the characterization of different members of the ACBP family, the knowledge about the impact of both LCFA-CoA and phospholipids on ACBP structure and stability remains scarce. Besides, there are still controversies regarding the possible interaction of ACBP with biological membranes, even though this might be essential for the cargo capture and delivery. In this study, we observed that LCFA-CoA and phospholipids play opposite roles on protein stability and that the interaction with the membrane is dictated by electrostatic interaction. Furthermore, the results support the hypothesis that the LCFA-CoA delivery is driven by the increase of the negative charge on the membrane surface. The combined influence played by the different molecules on ACBP structure is discussed on the light of cargo capture/delivery giving new insights about this important process.
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Affiliation(s)
- Mariana C Micheletto
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Luís F S Mendes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Luis G M Basso
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Raquel G Fonseca-Maldonado
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil; Instituto Federal de Educação, Ciência e Tecnologia de São Paulo/IFSP Campus Jacareí-Dept Gestão, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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47
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Non-linear van't Hoff behavior in pulmonary surfactant model membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1133-1143. [PMID: 28336314 DOI: 10.1016/j.bbamem.2017.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/14/2017] [Accepted: 03/18/2017] [Indexed: 11/22/2022]
Abstract
Pulmonary surfactant exhibits phase coexistence over a wide range of surface pressure and temperature. Less is known about the effect of temperature on pulmonary surfactant models. Given the lack of studies on this issue, we used electron paramagnetic resonance (EPR) and nonlinear least-squares (NLLS) simulations to investigate the thermotropic phase behavior of the matrix that mimics the pulmonary surfactant lipid complex, i.e., the lipid mixture composed of dipalmitoyl phosphatidylcholine (DPPC), palmitoyl-oleoyl phosphatidylcholine (POPC) and palmitoyl-oleoyl phosphatidylglycerol (POPG). Irrespective of pH, the EPR spectra recorded from 5°C to 25°C in the DPPC/POPC/POPG (4:3:1) model membrane contain two spectral components corresponding to lipids in gel-like and fluid-like phases, indicating a coexistence of two domains in that range. The temperature dependence of the distribution of spin labels between the domains yielded nonlinear van't Hoff plots. The thermodynamic parameters evaluated were markedly different for DPPC and for the ternary DPPC/POPC/POPG (4:3:1) membranes and exhibited a dependence on chemical environment. While enthalpy and entropy changes for DPPC were always positive and presented a quadratic behavior with temperature, those of the ternary mixture were linearly dependent on temperature and changed from negative to positive values. Despite that, enthalpy-entropy compensation takes place in the two systems. The thermotropic process associated with the coexistence of the two domains is entropically-driven in DPPC and either entropically- or enthalpically-driven in the pulmonary surfactant membrane depending on the pH, ionic strength and temperature. The significance of these results to the structure and function of the pulmonary surfactant lipid matrix is discussed.
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