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Crampon E, Covernton E, Vaney MC, Dellarole M, Sommer S, Sharma A, Haouz A, England P, Lepault J, Duquerroy S, Rey FA, Barba-Spaeth G. New insight into flavivirus maturation from structure/function studies of the yellow fever virus envelope protein complex. mBio 2023; 14:e0070623. [PMID: 37607061 PMCID: PMC10653854 DOI: 10.1128/mbio.00706-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/16/2023] [Indexed: 08/24/2023] Open
Abstract
IMPORTANCE All enveloped viruses enter cells by fusing their envelope with a target cell membrane while avoiding premature fusion with membranes of the producer cell-the latter being particularly important for viruses that bud at internal membranes. Flaviviruses bud in the endoplasmic reticulum, are transported through the TGN to reach the external milieu, and enter other cells via receptor-mediated endocytosis. The trigger for membrane fusion is the acidic environment of early endosomes, which has a similar pH to the TGN of the producer cell. The viral particles therefore become activated to react to mildly acidic pH only after their release into the neutral pH extracellular environment. Our study shows that for yellow fever virus (YFV), the mechanism of activation involves actively knocking out the fusion brake (protein pr) through a localized conformational change of the envelope protein upon exposure to the neutral pH external environment. Our study has important implications for understanding the molecular mechanism of flavivirus fusion activation in general and points to an alternative way of interfering with this process as an antiviral treatment.
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Affiliation(s)
- E. Crampon
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - E. Covernton
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - M. C. Vaney
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - M. Dellarole
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - S. Sommer
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - A. Sharma
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - A. Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Plateforme de Cristallographie-C2RT, Paris, France
| | - P. England
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Plateforme de Biophysique Moléculaire-C2RT, Paris, France
| | - J. Lepault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - S. Duquerroy
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
- Université Paris-Saclay, Faculté des Sciences, Orsay, France
| | - F. A. Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - G. Barba-Spaeth
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
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2
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Vollmer B, Pražák V, Vasishtan D, Jefferys EE, Hernandez-Duran A, Vallbracht M, Klupp BG, Mettenleiter TC, Backovic M, Rey FA, Topf M, Grünewald K. The prefusion structure of herpes simplex virus glycoprotein B. Sci Adv 2020; 6:eabc1726. [PMID: 32978151 PMCID: PMC7518877 DOI: 10.1126/sciadv.abc1726] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/12/2020] [Indexed: 05/03/2023]
Abstract
Cell entry of enveloped viruses requires specialized viral proteins that mediate fusion with the host membrane by substantial structural rearrangements from a metastable pre- to a stable postfusion conformation. This metastability renders the herpes simplex virus 1 (HSV-1) fusion glycoprotein B (gB) highly unstable such that it readily converts into the postfusion form, thereby precluding structural elucidation of the pharmacologically relevant prefusion conformation. By identification of conserved sequence signatures and molecular dynamics simulations, we devised a mutation that stabilized this form. Functionally locking gB allowed the structural determination of its membrane-embedded prefusion conformation at sub-nanometer resolution and enabled the unambiguous fit of all ectodomains. The resulting pseudo-atomic model reveals a notable conservation of conformational domain rearrangements during fusion between HSV-1 gB and the vesicular stomatitis virus glycoprotein G, despite their very distant phylogeny. In combination with our comparative sequence-structure analysis, these findings suggest common fusogenic domain rearrangements in all class III viral fusion proteins.
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Affiliation(s)
- B Vollmer
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
- Centre for Structural Systems Biology, Heinrich-Pette-Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
| | - V Pražák
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
| | - D Vasishtan
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
| | - E E Jefferys
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - M Vallbracht
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Germany
| | - B G Klupp
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Germany
| | - T C Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Germany
| | - M Backovic
- Institut Pasteur, Structural Virology Unit, Department of Virology, Paris, France
| | - F A Rey
- Institut Pasteur, Structural Virology Unit, Department of Virology, Paris, France
| | - M Topf
- Institute of Structural and Molecular Biology, Birkbeck, London, UK
| | - K Grünewald
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK.
- Centre for Structural Systems Biology, Heinrich-Pette-Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
- Department of Chemistry, MIN Faculty, Universität Hamburg, Hamburg, Germany
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3
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Guardado-Calvo P, Atkovska K, Jeffers SA, Grau N, Backovic M, Pérez-Vargas J, de Boer SM, Tortorici MA, Pehau-Arnaudet G, Lepault J, England P, Rottier PJ, Bosch BJ, Hub JS, Rey FA. A glycerophospholipid-specific pocket in the RVFV class II fusion protein drives target membrane insertion. Science 2018; 358:663-667. [PMID: 29097548 DOI: 10.1126/science.aal2712] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 07/20/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022]
Abstract
The Rift Valley fever virus (RVFV) is transmitted by infected mosquitoes, causing severe disease in humans and livestock across Africa. We determined the x-ray structure of the RVFV class II fusion protein Gc in its postfusion form and in complex with a glycerophospholipid (GPL) bound in a conserved cavity next to the fusion loop. Site-directed mutagenesis and molecular dynamics simulations further revealed a built-in motif allowing en bloc insertion of the fusion loop into membranes, making few nonpolar side-chain interactions with the aliphatic moiety and multiple polar interactions with lipid head groups upon membrane restructuring. The GPL head-group recognition pocket is conserved in the fusion proteins of other arthropod-borne viruses, such as Zika and chikungunya viruses, which have recently caused major epidemics worldwide.
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Affiliation(s)
- P Guardado-Calvo
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France. .,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - K Atkovska
- Institute for Microbiology and Genetics, University of Goettingen, Justus-von-Liebig weg 11, 37077 Göttingen, Germany
| | - S A Jeffers
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - N Grau
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - M Backovic
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - J Pérez-Vargas
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - S M de Boer
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - M A Tortorici
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - G Pehau-Arnaudet
- UMR 3528, CNRS, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France
| | - J Lepault
- Institut de Biologie Intégrative de la Cellule, CNRS (UMR 9198), Gif-sur-Yvette, France
| | - P England
- UMR 3528, CNRS, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France.,Proteopole, Plateforme de Biophysique des Macromolécules et de leurs Interactions (PFBMI), Institut Pasteur, 25-28 rue du Dr Roux, F-75724 Paris Cedex 15, France
| | - P J Rottier
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - B J Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - J S Hub
- Institute for Microbiology and Genetics, University of Goettingen, Justus-von-Liebig weg 11, 37077 Göttingen, Germany.
| | - F A Rey
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France. .,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
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4
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Pronost S, Hue E, Fortier C, Foursin M, Fortier G, Desbrosse F, Rey FA, Pitel PH, Richard E, Saunier B. Prevalence of Equine Hepacivirus Infections in France and Evidence for Two Viral Subtypes Circulating Worldwide. Transbound Emerg Dis 2016; 64:1884-1897. [PMID: 27882682 DOI: 10.1111/tbed.12587] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Indexed: 12/20/2022]
Abstract
Like hepatitis C virus (HCV) in humans, the newly identified equine hepacivirus (NPHV) displays a predominating liver tropism that may evolve into chronic infections. The genomes of the two viruses share several organizational and functional features and are phylogenetically closest amongst the Hepacivirus genus. A limited amount of data is available regarding the spread of hepacivirus infections in horses. In this study, we asked whether in a more representative sample the prevalence and distribution of NPHV infections in France would resemble that reported so far in other countries. A total of 1033 horses sera from stud farms throughout France were analysed by qRT-PCR to determine the prevalence of ongoing NPHV infections and viral loads; in positive samples, partial sequences of NPHV's genome (5'UTR, NS3 and NS5B genes) were determined. Serum concentrations of biliary acids, glutamate dehydrogenase (GLDH) and L-gamma-glutamyl transferase (γ-GT) were measured for most horses. We detected NPHV infections in 6.2% of the horses, a prevalence that reached 8.3% in thoroughbreds and was significantly higher than in other breeds. The presence of circulating virus was neither significantly associated with biological disturbances nor with clinical hepatic impairment. Our phylogenetic analysis was based on both neighbour-joining and maximum-likelihood approaches. Its result shows that, like almost everywhere else in the world so far, two major groups of NPHV strains infect French domestic horses. Based on genetic distances, we propose a classification into two separate NPHV subtypes. Viral loads in the serum of horses infected by the main subtype were, in average, four times higher than in those infected by the second subtype. We hypothesize that amino acid substitutions in the palm domain of NS5B between NPHV subtypes could underlie viral phenotypes that explain this result.
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Affiliation(s)
- S Pronost
- Unité de Recherche Risques Microbiens (U2RM), EA 4655, Université de Caen Basse-Normandie, Caen, France.,LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - E Hue
- Unité de Recherche Risques Microbiens (U2RM), EA 4655, Université de Caen Basse-Normandie, Caen, France.,LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - C Fortier
- LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - M Foursin
- Clinique Equine de la Boisrie, Chailloué, France
| | - G Fortier
- Unité de Recherche Risques Microbiens (U2RM), EA 4655, Université de Caen Basse-Normandie, Caen, France.,LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - F Desbrosse
- Clinique Equine Desbrosse, Saint Lambert, France
| | - F A Rey
- Structural Virology Unit - CNRS UMR 3569, Institut Pasteur, Paris, France
| | - P-H Pitel
- LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - E Richard
- LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - B Saunier
- Structural Virology Unit - CNRS UMR 3569, Institut Pasteur, Paris, France
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5
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Rey FA, Perez-Vargas J, Krey T, Podbilewicz B. The cell fusion proteins of the 'FF' family are homologous to class II viral fusion proteins. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311098151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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6
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Navaza J, Lepault J, Rey FA, Alvarez-Rúa C, Borge J. On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation. Acta Crystallogr D Biol Crystallogr 2002; 58:1820-5. [PMID: 12351826 DOI: 10.1107/s0907444902013707] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2002] [Accepted: 07/30/2002] [Indexed: 11/10/2022]
Abstract
A fast method for fitting model electron densities into EM reconstructions is presented. The methodology was inspired by the molecular-replacement technique, adapted to take into account phase information and the symmetry imposed during the EM reconstruction. Calculations are performed in reciprocal space, which enables the selection of large volumes of the EM maps, thus avoiding the bias introduced when defining the boundaries of the target density.
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Affiliation(s)
- J Navaza
- LVMS, CNRS-GIF, 91198 Gif-sur-Yvette, France.
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7
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Lescar J, Roussel A, Wien MW, Navaza J, Fuller SD, Wengler G, Wengler G, Rey FA. The Fusion glycoprotein shell of Semliki Forest virus: an icosahedral assembly primed for fusogenic activation at endosomal pH. Cell 2001; 105:137-48. [PMID: 11301009 DOI: 10.1016/s0092-8674(01)00303-8] [Citation(s) in RCA: 402] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Semliki Forest virus (SFV) has been extensively studied as a model for analyzing entry of enveloped viruses into target cells. Here we describe the trace of the polypeptide chain of the SFV fusion glycoprotein, E1, derived from an electron density map at 3.5 A resolution and describe its interactions at the surface of the virus. E1 is unexpectedly similar to the flavivirus envelope protein, with three structural domains disposed in the same primary sequence arrangement. These results introduce a new class of membrane fusion proteins which display lateral interactions to induce the necessary curvature and direct budding of closed particles. The resulting surface protein lattice is primed to cause membrane fusion when exposed to the acidic environment of the endosome.
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Affiliation(s)
- J Lescar
- Laboratoire de Génétique des Virus, CNRS-UPR 9053, 1, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
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8
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Ferlenghi I, Clarke M, Ruttan T, Allison SL, Schalich J, Heinz FX, Harrison SC, Rey FA, Fuller SD. Molecular organization of a recombinant subviral particle from tick-borne encephalitis virus. Mol Cell 2001; 7:593-602. [PMID: 11463384 DOI: 10.1016/s1097-2765(01)00206-4] [Citation(s) in RCA: 219] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The tick-borne encephalitis (TBE) flavivirus contains two transmembrane proteins, E and M. Coexpression of E and the M precursor (prM) leads to secretion of recombinant subviral particles (RSPs). In the most common form of these RSPs, analyzed at a 19 A resolution by cryo-electron microscopy (cryo-EM), 60 copies of E pack as dimers in a T = 1 icosahedral surface lattice (outer diameter, 315 A). Fitting the high-resolution structure of a soluble E fragment into the RSP density defines interaction sites between E dimers, positions M relative to E, and allows assignment of transmembrane regions of E and M. Lateral interactions among the glycoproteins stabilize this capsidless particle; similar interactions probably contribute to assembly of virions. The structure suggests a picture for trimer association under fusion-inducing conditions.
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Affiliation(s)
- I Ferlenghi
- The Structural Biology Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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9
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Duarte dos Santos CN, Frenkiel MP, Courageot MP, Rocha CF, Vazeille-Falcoz MC, Wien MW, Rey FA, Deubel V, Desprès P. Determinants in the envelope E protein and viral RNA helicase NS3 that influence the induction of apoptosis in response to infection with dengue type 1 virus. Virology 2000; 274:292-308. [PMID: 10964773 DOI: 10.1006/viro.2000.0457] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One mechanism by which dengue (DEN) virus may cause cell death is apoptosis. In this study, we investigated whether the genetic determinants responsible for acquisition by DEN type 1 (DEN-1) virus of mouse neurovirulence interfere with the induction of apoptosis. Neurovirulent variant FGA/NA d1d was generated during the adaptation of the human isolate of DEN-1 virus strain FGA/89 to grow in newborn mouse brains and mosquito cells in vitro [Desprès, P. Frenkiel, M. -P. Ceccaldi, P.-E. Duarte Dos Santos, C. and Deubel, V. (1998) J. Virol., 72: 823-829]. Genetic determinants possibly responsible for mouse neurovirulence were studied by sequencing the entire genomes of both DEN-1 viruses. Three amino acid differences in the envelope E protein and one in the nonstructural NS3 protein were found. The cytotoxicity of the mouse-neurovirulent DEN-1 variant was studied in different target cells in vitro and compared with the parental strain. FGA/NA d1d was more pathogenic for mouse neuroblastoma cells and attenuated for human hepatoma cells. Changes in virus replicative functions and virus assembly may account, in a large part, for the differences in the induction of apoptosis. Our data suggest that identified amino acid substitutions in the envelope E protein and viral RNA helicase NS3 may influence DEN-1 virus pathogenicity by altering viral growth.
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Affiliation(s)
- C N Duarte dos Santos
- Departmento de Bioquimica e Biologia Molecular, Laboratorio de Expressao e Regulaçao Genica, Rio de Janeiro, R.J., Brazil
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10
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Mathieu M, Petipas I, Lepault J, Erk I, Navaza J, Prasad V, Cohen J, Rey FA. Structural Plasticity in the major capsid protein VP6 of rotaviruses revealed by combined X-ray crystallography and electron cryo-microscopy analyses. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300022662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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11
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Bressanelli S, Tomei L, Roussel A, Incitti I, Vitale RL, Mathieu M, De Francesco R, Rey FA. The RNA-dependent RNA polymerase of hepatitis C virus: 3D structure and implications for viral replication. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300022315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Bressanelli S, Tomei L, Roussel A, Incitti I, Vitale RL, Mathieu M, De Francesco R, Rey FA. Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proc Natl Acad Sci U S A 1999; 96:13034-9. [PMID: 10557268 PMCID: PMC23895 DOI: 10.1073/pnas.96.23.13034] [Citation(s) in RCA: 488] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We report the crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus, a major human pathogen, to 2.8-A resolution. This enzyme is a key target for developing specific antiviral therapy. The structure of the catalytic domain contains 531 residues folded in the characteristic fingers, palm, and thumb subdomains. The fingers subdomain contains a region, the "fingertips," that shares the same fold with reverse transcriptases. Superposition to the available structures of the latter shows that residues from the palm and fingertips are structurally equivalent. In addition, it shows that the hepatitis C virus polymerase was crystallized in a closed fingers conformation, similar to HIV-1 reverse transcriptase in ternary complex with DNA and dTTP [Huang H., Chopra, R., Verdine, G. L. & Harrison, S. C. (1998) Science 282, 1669-1675]. This superposition reveals the majority of the amino acid residues of the hepatitis C virus enzyme that are likely to be implicated in binding to the replicating RNA molecule and to the incoming NTP. It also suggests a rearrangement of the thumb domain as well as a possible concerted movement of thumb and fingertips during translocation of the RNA template-primer in successive polymerization rounds.
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Affiliation(s)
- S Bressanelli
- Virologie Moléculaire Structurale, Laboratoire de Génétique des Virus, Centre National de la Recherche Scientifique/Unité Propre de Recherche 9053 1, Avenue de la Terrasse, F-91198 Gif-sur-Yvette Cedex, France
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13
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Flamand M, Megret F, Mathieu M, Lepault J, Rey FA, Deubel V. Dengue virus type 1 nonstructural glycoprotein NS1 is secreted from mammalian cells as a soluble hexamer in a glycosylation-dependent fashion. J Virol 1999; 73:6104-10. [PMID: 10364366 PMCID: PMC112675 DOI: 10.1128/jvi.73.7.6104-6110.1999] [Citation(s) in RCA: 241] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nonstructural glycoprotein NS1, specified by dengue virus type 1 (Den-1), is secreted from infected green monkey kidney (Vero) cells in a major soluble form characterized by biochemical and biophysical means as a unique hexameric species. This noncovalently bound oligomer is formed by three dimeric subunits and has a molecular mass of 310 kDa and a Stokes radius of 64.4 A. During protein export, one of the two oligosaccharides of NS1 is processed into an endo-beta-N-acetylglucosaminidase F-resistant complex-type sugar while the other remains of the polymannose type, protected in the dimeric subunit from the action of maturation enzymes. Complete processing of the complex-type sugar appears to be required for efficient release of soluble NS1 into the culture fluid of infected cells, as suggested by the repressive effects of the N-glycan processing inhibitors swainsonine and deoxymannojyrimicin. These results, together with observations related to the absence of secretion of NS1 from Den-infected insect cells, suggest that maturation and secretion of hexameric NS1 depend on the glycosylation status of the host cell.
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Affiliation(s)
- M Flamand
- Unité des Arbovirus et Virus des Fièvres Hémorragiques, Institut Pasteur, 75724 Paris Cedex 15, 91198 Gif-sur-Yvette Cedex, France.
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14
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Abstract
Alphaviruses are isometric enveloped viruses approximately 70 nm in diameter. The viral surface contains 80 glycoprotein spikes arranged in a T = 4 lattice. Each of these spikes consists of three heterodimers of the viral membrane proteins E1 (approximately 49 kDa) and E2 (approximately 51 kDa). Cryoelectron microscopic analyses have shown that the spikes form a protein shell on the viral surface. We have made an attempt to isolate biologically active protein fragments from this surface and to grow crystals from such fragments. To this end membrane proteins were extracted with Nonidet-P40 from the Semliki Forest alphavirus and the proteins were separated from detergent by centrifugation. A protein complex containing the E1 and E2 molecules in quantitative yield was obtained by this procedure. This complex has the following properties: It sediments at approximately 30S, it chromatographs with an apparent molecular mass of approximately 580,000 Da during gel filtration, it cannot be dissociated by either nonionic detergents or 6 M urea, and at acid pH it is a highly active hemagglutinin. The data indicate that this 30S hemagglutinin complex, which has not been hitherto described for alphaviruses, may represent a variant form of the protein lattice present on the alphavirus surface. Cleavage of this complex by subtilisin selectively removes carboxy-terminal sequences from the E1 and E2 proteins, which contain the cytoplasmic and transmembrane segments of the proteins and a small part of their ectodomain. The remaining ectodomains are called E1DeltaS and E2DeltaS. This proteolysis also leads to dissociation of the 30S complex. The cleavage products accumulate in the form of a heterodimer of the E1DeltaS and E2DeltaS proteins. Treatment of the heterodimer with PNGase F leads to rapid removal of carbohydrate from the E2DeltaS protein and a dissociation of the complex into the constituent molecules, which can be separated by chromatography. The finding that the heterodimer and the purified E1DeltaS protein both function as hemagglutinin at acid pH indicates that the E1 protein represents the alphavirus hemagglutinin. We have obtained crystals of the E1DeltaS protein and are currently in the process of determining the atomic structure of this protein by the isomorphous replacement method.
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Affiliation(s)
- G Wengler
- Institut für Virologie, Justus-Liebig-Universität Giessen, Giessen, 35392, Germany
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15
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Petitpas I, Lepault J, Vachette P, Charpilienne A, Mathieu M, Kohli E, Pothier P, Cohen J, Rey FA. Crystallization and preliminary X-Ray analysis of rotavirus protein VP6. J Virol 1998; 72:7615-9. [PMID: 9696863 PMCID: PMC110019 DOI: 10.1128/jvi.72.9.7615-7619.1998] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/1998] [Accepted: 05/19/1998] [Indexed: 12/31/2022] Open
Abstract
As a first step to gain insight into the structure of the rotavirus virion at atomic resolution, we report here the expression, purification, and crystallization of recombinant rotavirus protein VP6. This protein has the property of polymerizing in the form of tubular structures in solution which have hindered crystallization thus far. Using a combination of electron microscopy and small-angle X-ray scattering, we found that addition of Ca2+ at concentrations higher than 100 mM results in depolymerization of the tubes, leading to an essentially monodisperse solution of trimeric VP6 even at high protein concentrations (higher than 10 mg/ml), thereby enabling us to search for crystallization conditions. We have thus obtained crystals of VP6 which diffract to better than 2.4 A resolution and belong to the cubic space group P4132 with a cell dimension a of 160 A. The crystals contain a trimer of VP6 lying along the diagonal of the cubic unit cell, resulting in one VP6 monomer per asymmetric unit and a solvent content of roughly 70%.
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Affiliation(s)
- I Petitpas
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR 9063, 91198 Gif-sur-Yvette Cedex, France
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16
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Abstract
Analysis of the NF-kappa B p50 homodimer bound to different DNA sequences shows that the protein can recognize half-site spacings of either three or four base pairs. The protein can maintain most of its DNA contacts by a relative reorientation of its two domains.
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17
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Abstract
The crystallographically determined structure of a soluble fragment from the major envelope protein of a flavivirus reveals an unusual architecture. The flat, elongated dimer extends in a direction that would be parallel to the viral membrane. Residues that influence binding of monoclonal antibodies lie on the outward-facing surface of the protein. The clustering of mutations that affect virulence in various flaviviruses indicates a possible receptor binding site and, together with other mutational and biochemical data, suggests a picture for the fusion-activating, conformational change triggered by low pH.
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Affiliation(s)
- F A Rey
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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18
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Abstract
The structure of a large fragment of the p50 subunit of the human transcription factor NF-kappa B, bound as a homodimer to DNA, reveals that the Rel-homology region has two beta-barrel domains that grip DNA in the major groove. Both domains contact the DNA backbone. The amino-terminal specificity domain contains a recognition loop that interacts with DNA bases; the carboxy-terminal dimerization domain bears the site of I-kappa B interaction. The folds of these domains are related to immunoglobulin-like modules. The amino-terminal domain also resembles the core domain of p53.
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Affiliation(s)
- C W Müller
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02138
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19
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Abstract
We present an efficient algorithm to compute X-ray intensities scattered by macromolecules in solution, from atomic positions found in crystal structures. The algorithm applies the Fast Fourier Transform to an electron density map created from the atomic coordinates and corrected for solvent density. We compute scattering curves for both allosteric forms of E. coli aspartate carbamoyltransferase. Calculated intensities are in agreement with the ones measured by Moody et al. which shows that the structures observed in solution in the presence or in the absence of a substrate analogue do correspond to those of two crystal forms analyzed by Lipscomb and collaborators .
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