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Kephart SM, Hom N, Lee KK. Visualizing intermediate stages of viral membrane fusion by cryo-electron tomography. Trends Biochem Sci 2024:S0968-0004(24)00160-9. [PMID: 39054240 DOI: 10.1016/j.tibs.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
Protein-mediated membrane fusion is the dynamic process where specialized protein machinery undergoes dramatic conformational changes that drive two membrane bilayers together, leading to lipid mixing and opening of a fusion pore between previously separate membrane-bound compartments. Membrane fusion is an essential stage of enveloped virus entry that results in viral genome delivery into host cells. Recent studies applying cryo-electron microscopy techniques in a time-resolved fashion provide unprecedented glimpses into the interaction of viral fusion proteins and membranes, revealing fusion intermediate states from the initiation of fusion to release of the viral genome. In combination with complementary structural, biophysical, and computation modeling approaches, these advances are shedding new light on the mechanics and dynamics of protein-mediated membrane fusion.
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Affiliation(s)
- Sally M Kephart
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Nancy Hom
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA; Biological Structure Physics and Design Graduate Program, University of Washington, Seattle, WA, USA.
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2
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Abstract
There are at least 21 families of enveloped viruses that infect mammals, and many contain members of high concern for global human health. All enveloped viruses have a dedicated fusion protein or fusion complex that enacts the critical genome-releasing membrane fusion event that is essential before viral replication within the host cell interior can begin. Because all enveloped viruses enter cells by fusion, it behooves us to know how viral fusion proteins function. Viral fusion proteins are also major targets of neutralizing antibodies, and hence they serve as key vaccine immunogens. Here we review current concepts about viral membrane fusion proteins focusing on how they are triggered, structural intermediates between pre- and postfusion forms, and their interplay with the lipid bilayers they engage. We also discuss cellular and therapeutic interventions that thwart virus-cell membrane fusion.
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Affiliation(s)
- Judith M White
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA;
| | - Amanda E Ward
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Laura Odongo
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Lukas K Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
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3
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Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FKM, Acuna C, Lozach PY. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathog 2023; 19:e1011562. [PMID: 37578957 PMCID: PMC10449198 DOI: 10.1371/journal.ppat.1011562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/24/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells.
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Affiliation(s)
- Jana Koch
- Center for Integrative Infectious Diseases Research (CIID), University Hospital Heidelberg, Heidelberg, Germany
- CellNetworks–Cluster of Excellence, Heidelberg, Germany
- Univ. Lyon, INRAE, EPHE, IVPC, Lyon, France
| | - Qilin Xin
- Univ. Lyon, INRAE, EPHE, IVPC, Lyon, France
| | - Martin Obr
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Alicia Schäfer
- Center for Integrative Infectious Diseases Research (CIID), University Hospital Heidelberg, Heidelberg, Germany
- CellNetworks–Cluster of Excellence, Heidelberg, Germany
| | - Nina Rolfs
- Center for Integrative Infectious Diseases Research (CIID), University Hospital Heidelberg, Heidelberg, Germany
- CellNetworks–Cluster of Excellence, Heidelberg, Germany
| | - Holda A. Anagho
- Center for Integrative Infectious Diseases Research (CIID), University Hospital Heidelberg, Heidelberg, Germany
- CellNetworks–Cluster of Excellence, Heidelberg, Germany
| | - Aiste Kudulyte
- Center for Integrative Infectious Diseases Research (CIID), University Hospital Heidelberg, Heidelberg, Germany
- CellNetworks–Cluster of Excellence, Heidelberg, Germany
| | - Lea Woltereck
- Center for Integrative Infectious Diseases Research (CIID), University Hospital Heidelberg, Heidelberg, Germany
- CellNetworks–Cluster of Excellence, Heidelberg, Germany
| | - Susann Kummer
- Center for Integrative Infectious Diseases Research (CIID), University Hospital Heidelberg, Heidelberg, Germany
| | - Joaquin Campos
- Chica and Heinz Schaller Research Group, Institute of Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Zina M. Uckeley
- Center for Integrative Infectious Diseases Research (CIID), University Hospital Heidelberg, Heidelberg, Germany
- CellNetworks–Cluster of Excellence, Heidelberg, Germany
| | - Lesley Bell-Sakyi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United-Kingdom
| | - Hans-Georg Kräusslich
- Center for Integrative Infectious Diseases Research (CIID), University Hospital Heidelberg, Heidelberg, Germany
| | - Florian KM. Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Claudio Acuna
- Chica and Heinz Schaller Research Group, Institute of Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Pierre-Yves Lozach
- Center for Integrative Infectious Diseases Research (CIID), University Hospital Heidelberg, Heidelberg, Germany
- CellNetworks–Cluster of Excellence, Heidelberg, Germany
- Univ. Lyon, INRAE, EPHE, IVPC, Lyon, France
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4
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Gao J, Gui M, Xiang Y. Structural intermediates in the low pH-induced transition of influenza hemagglutinin. PLoS Pathog 2020; 16:e1009062. [PMID: 33253316 PMCID: PMC7728236 DOI: 10.1371/journal.ppat.1009062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/10/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
The hemagglutinin (HA) glycoproteins of influenza viruses play a key role in binding host cell receptors and in mediating virus-host cell membrane fusion during virus infection. Upon virus entry, HA is triggered by low pH and undergoes large structural rearrangements from a prefusion state to a postfusion state. While structures of prefusion state and postfusion state of HA have been reported, the intermediate structures remain elusive. Here, we report two distinct low pH intermediate conformations of the influenza virus HA using cryo-electron microscopy (cryo-EM). Our results show that a decrease in pH from 7.8 to 5.2 triggers the release of fusion peptides from the binding pockets and then causes a dramatic conformational change in the central helices, in which the membrane-proximal ends of the central helices unwind to an extended form. Accompanying the conformational changes of the central helices, the stem region of the HA undergoes an anticlockwise rotation of 9.5 degrees and a shift of 15 Å. The HA head, after being stabilized by an antibody, remains unchanged compared to the neutral pH state. Thus, the conformational change of the HA stem region observed in our research is likely to be independent of the HA head. These results provide new insights into the structural transition of HA during virus entry.
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Affiliation(s)
- Jingjing Gao
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Miao Gui
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- * E-mail: (MG); (YX)
| | - Ye Xiang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- * E-mail: (MG); (YX)
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5
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Belot L, Ouldali M, Roche S, Legrand P, Gaudin Y, Albertini AA. Crystal structure of Mokola virus glycoprotein in its post-fusion conformation. PLoS Pathog 2020; 16:e1008383. [PMID: 32150590 PMCID: PMC7082061 DOI: 10.1371/journal.ppat.1008383] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/19/2020] [Accepted: 02/05/2020] [Indexed: 01/08/2023] Open
Abstract
Mokola virus (MOKV) belongs to the lyssavirus genus. As other genus members-including rabies virus (RABV)-it causes deadly encephalitis in mammals. MOKV entry into host cells is mediated by its transmembrane glycoprotein G. First, G binds cellular receptors, triggering virion endocytosis. Then, in the acidic endosomal environment, G undergoes a conformational change from its pre- toward its post-fusion state that catalyzes the merger of the viral and endosomal membranes. Here, we have determined the crystal structure of a soluble MOKV G ectodomain in which the hydrophobic fusion loops have been replaced by more hydrophilic sequences. The crystal structure corresponds to a monomer that is similar to the protomer of the trimeric post-fusion state of vesicular stomatitis virus (VSV) G. However, by electron microscopy, we show that, at low pH, at the surface of pseudotyped VSV, MOKV spikes adopt the trimeric post-fusion conformation and have a tendency to reorganize into regular arrays. Sequence alignment between MOKV G and RABV G allows a precise location of RABV G antigenic sites. Repositioning MOKV G domains on VSV G pre-fusion structure reveals that antigenic sites are located in the most exposed part of the molecule in its pre-fusion conformation and are therefore very accessible to antibodies. Furthermore, the structure allows the identification of pH-sensitive molecular switches. Specifically, the long helix, which constitutes the core of the post-fusion trimer for class III fusion glycoproteins, contains many acidic residues located at the trimeric interface. Several of them, aligned along the helix, point toward the trimer axis. They have to be protonated for the post-fusion trimer to be stable. At high pH, when they are negatively charged, they destabilize the interface, which explains the conformational change reversibility. Finally, the present structure will be of great help to perform rational mutagenesis on lyssavirus glycoproteins.
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Affiliation(s)
- Laura Belot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, France
| | - Malika Ouldali
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, France
| | - Stéphane Roche
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, France
| | | | - Yves Gaudin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, France
- * E-mail: (YG); (AAA)
| | - Aurélie A. Albertini
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, France
- * E-mail: (YG); (AAA)
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6
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Gilman MSA, Furmanova-Hollenstein P, Pascual G, B van 't Wout A, Langedijk JPM, McLellan JS. Transient opening of trimeric prefusion RSV F proteins. Nat Commun 2019; 10:2105. [PMID: 31068578 PMCID: PMC6506550 DOI: 10.1038/s41467-019-09807-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/02/2019] [Indexed: 01/19/2023] Open
Abstract
The respiratory syncytial virus (RSV) F glycoprotein is a class I fusion protein that mediates viral entry and is a major target of neutralizing antibodies. Structures of prefusion forms of RSV F, as well as other class I fusion proteins, have revealed compact trimeric arrangements, yet whether these trimeric forms can transiently open remains unknown. Here, we perform structural and biochemical studies on a recently isolated antibody, CR9501, and demonstrate that it enhances the opening of prefusion-stabilized RSV F trimers. The 3.3 Å crystal structure of monomeric RSV F bound to CR9501, combined with analysis of over 25 previously determined RSV F structures, reveals a breathing motion of the prefusion conformation. We also demonstrate that full-length RSV F trimers transiently open and dissociate on the cell surface. Collectively, these findings have implications for the function of class I fusion proteins, as well as antibody prophylaxis and vaccine development for RSV.
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MESH Headings
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- B-Lymphocytes/virology
- Chlorocebus aethiops
- Computer Simulation
- Crystallography, X-Ray
- Drug Development
- HEK293 Cells
- HeLa Cells
- Humans
- Models, Molecular
- Protein Multimerization/physiology
- Respiratory Syncytial Virus Infections/immunology
- Respiratory Syncytial Virus Infections/prevention & control
- Respiratory Syncytial Virus Infections/virology
- Respiratory Syncytial Virus Vaccines/immunology
- Respiratory Syncytial Virus, Human/isolation & purification
- Respiratory Syncytial Virus, Human/physiology
- Vero Cells
- Viral Fusion Proteins/chemistry
- Viral Fusion Proteins/immunology
- Viral Fusion Proteins/metabolism
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Affiliation(s)
- Morgan S A Gilman
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Gabriel Pascual
- Janssen Immunosciences, World Without Disease Accelerator, San Diego, CA, 92121, USA
| | - Angélique B van 't Wout
- Janssen Prevention Center, Janssen Vaccines & Prevention B.V, Leiden, CN, 2333, The Netherlands
- AlphaBiomics, London, SW4 0PA, United Kingdom
| | | | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
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7
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Abstract
Rhabdoviruses are enveloped viruses with a negative-sense single strand RNA genome and are widespread among a great variety of organisms. In their membrane, they have a single glycoprotein (G) that mediates both virus attachment to cellular receptors and fusion between viral and endosomal membranes allowing viral genome release in the cytoplasm. We present structural and cellular aspects of Rhabdovirus entry into their host cell with a focus on vesicular stomatitis virus (VSV) and rabies virus (RABV) for which the early events of the viral cycle have been extensively studied. Recent data have shown that the only VSV receptors are the members of the LDL-R family. This is in contrast with RABV for which multiple receptors belonging to unrelated families have been identified. Despite having different receptors, after attachment, rhabdovirus internalization occurs through clathrin-mediated endocytosis (CME) in an actin-dependent manner. There are still debates about the exact endocytic pathway of VSV in the cell and on RABV transport in the neuronal axon. In any case, fusion is triggered in the endosomal vesicle via a low-pH induced structural rearrangement of G from its pre- to its postfusion conformation. Vesiculovirus G is one of the best characterized fusion glycoproteins as the previously reported crystal structures of the pre- and postfusion states have been recently completed by those of intermediates during the structural transition. Understanding the entry pathway of rhabdoviruses may have strong impact in biotechnologies as, for example, VSV G is used for pseudotyping lentiviruses to promote efficient transduction, and VSV is a promising oncolytic virus.
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8
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Ranaweera A, Ratnayake PU, Weliky DP. The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Biochemistry 2018; 57:5480-5493. [PMID: 30141905 DOI: 10.1021/acs.biochem.8b00764] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellular entry of influenza virus is mediated by the viral protein hemagglutinin (HA), which forms an initial complex of three HA1 and three HA2 subunits. Each HA2 includes a fusion peptide (FP), a soluble ectodomain (SE), and a transmembrane domain. HA1 binds to cellular sialic acids, followed by virus endocytosis, pH reduction, dissociation of HA1, and structural rearrangement of HA2 into a final trimer-of-SE hairpins. A decrease in pH also triggers HA2-mediated virus/endosome membrane fusion. SE hairpins have an interior parallel helical bundle and C-terminal strands in the grooves of the exterior of the bundle. FPs are separate helical hairpins. This study compares wild-type HA2 (WT-HA2) with G1E(FP) and I173E(SE strand) mutants. WT-HA2 induces vesicle fusion at pH 5.0, whereas the extent of fusion is greatly reduced for both mutants. Circular dichroism for HA2 and FHA2≡FP+SE constructs shows dramatic losses of stability for the mutants, including a Tm reduced by 40 °C for I173E-FHA2. This is evidence of destabilization of SE hairpins via dissociation of strands from the helical bundle, which is also supported by larger monomer fractions for mutant versus WT proteins. The G1E mutant may have disrupted FP hairpins, with consequent non-native FP binding to dissociated SE strands. It is commonly proposed that free energy released by the HA2 structural rearrangement catalyzes HA-mediated fusion. This study supports an alternate mechanistic model in which fusion is preceded by FP insertion in the target membrane and formation of the final SE hairpin. Less fusion by the mutants is due to the loss of hairpin stability and consequent reduced level of membrane apposition of the virus and target membranes.
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Affiliation(s)
- Ahinsa Ranaweera
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Punsisi U Ratnayake
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - David P Weliky
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
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Affiliation(s)
- Pierre-Yves Lozach
- CellNetworks-Cluster of Excellence and Center for Integrative Infectious Disease Research, University Hospital Heidelberg, Heidelberg, Germany.
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