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de Albuquerque PPLF, Santos LHS, Antunes D, Caffarena ER, Figueiredo AS. Structural insights into NS5B protein of novel equine hepaciviruses and pegiviruses complexed with polymerase inhibitors. Virus Res 2020; 278:197867. [PMID: 31972246 DOI: 10.1016/j.virusres.2020.197867] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 01/09/2023]
Abstract
Infections produced by hepaciviruses have been associated with liver disease in horses. Currently, at least three viruses belonging to the Flaviviridae family are capable of producing a chronic infection in equines: non-primate hepacivirus (NPHV), Theiler's disease-associated virus (TDAV), and equine pegivirus (EPgV). The RNA-dependent RNA polymerases of viruses (RdRp) (NS5 protein), from the flavivirus family, use de novo RNA synthesis to initiate synthesis. The two antiviral drugs currently used to treat hepatitis C (HCV), sofosbuvir and dasabuvir, act on the viral NS5B polymerase as nucleoside and non-nucleoside inhibitors, respectively. Both drugs have shown significant clinical inhibition of viral response. In this work, we aimed to model the NS5B polymerase of the equine hepacivirus (EHCV) subtypes 1 and 2, TDAV and EPgV, to assess whether current direct-acting antiviral drugs against HCV interact with these proteins. Crystal structures of HCV-NS5B were used as templates for modeling target sequences in both conformations (open and closed). Also, molecular docking of sofosbuvir and dasabuvir were performed to predict their possible binding modes at the modeled NS5B polymerase binding sites. We observed that the NS5B models of the EHCV and EPgV shared well-conserved 3D structures to HCV-NS5B and other RdRps, suggesting functional conservation. Interactions of EHCV subtypes 1, 2 and TDAV polymerases with sofosbuvir showed a similar molecular interaction pattern compared to HCV-NS5B, while interactions with dasabuvir were less conserved. In silico studies of molecular interactions between these modeled structures and sofosbuvir suggest that this compound could be efficient in combating equine pathogens, thus contributing to animal welfare.
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Affiliation(s)
| | - Lucianna H S Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Deborah Antunes
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Ernesto Raul Caffarena
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brazil
| | - Andreza Soriano Figueiredo
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
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Bakshi A, Savithri HS. Functional insights into the role of C-terminal disordered domain of Sesbania mosaic virus RNA-dependent RNA polymerase and the coat protein in viral replication in vivo. Virus Res 2019; 267:26-35. [PMID: 31054934 DOI: 10.1016/j.virusres.2019.05.003] [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: 02/15/2019] [Revised: 04/24/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022]
Abstract
The C-terminal disordered domain of sesbania mosaic virus (SeMV) RNA-dependent RNA polymerase (RdRp) interacts with the viral protein P10. The functional significance of this interaction in viral replication was examined by a comparative analysis of genomic and sub-genomic RNA levels (obtained by quantitative real time PCR) in the total RNA extracted from Cyamopsis plants agro-infiltrated with wild-type or mutant forms of SeMV infectious cDNA (icDNA). The sgRNA copy numbers were found to be significantly higher than those of gRNA in the wild-type icDNA transfected plants. Transfection of a mutant icDNA expressing an RdRp lacking the C-terminal disordered domain led to a drastic reduction in the copy numbers of both forms of viral RNA. This could be due to the loss of interaction between the disordered domain of RdRp and P10 and possibly other viral/host proteins that might be required for the assembly of viral replicase. The C-terminal disordered domain also harbours the motif E which is essential for the catalytic function of RdRp. Mutation of the conserved tyrosine within this motif in the full length icDNA resulted in complete inhibition of progeny RNA synthesis in the transfected plants confirming the importance of motif E in the polymerase function in vivo. The role of coat protein (CP) in viral infection was also investigated by agro-infiltration of a CP start codon mutant icDNA which suggested that CP is essential for the encapsidation of viral progeny RNAs at later stages of infection.
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Affiliation(s)
- Arindam Bakshi
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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de Macêdo Mendes C, Teixeira DG, Lima JPMS, Lanza DCF. Characterization of putative proteins encoded by variable ORFs in white spot syndrome virus genome. BMC STRUCTURAL BIOLOGY 2019; 19:8. [PMID: 30999895 PMCID: PMC6474068 DOI: 10.1186/s12900-019-0106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/28/2019] [Indexed: 01/07/2023]
Abstract
Background White Spot Syndrome Virus (WSSV) is an enveloped double-stranded DNA virus which causes mortality of several species of shrimp, being considered one of the main pathogens that affects global shrimp farming. This virus presents a complex genome of ~ 300 kb and viral isolates that present genomes with great identity. Despite this conservation, some variable regions in the WSSV genome occur in coding regions, and these putative proteins may have some relationship with viral adaptation and virulence mechanisms. Until now, the functions of these proteins were little studied. In this work, sequences and putative proteins encoded by WSSV variable regions were characterized in silico. Results The in silico approach enabled determining the variability of some sequences, as well as the identification of some domains resembling the Formin homology 2, RNA recognition motif, Xeroderma pigmentosum group D repair helicase, Hemagglutinin and Ankyrin motif. The information obtained from the sequences and the analysis of secondary and tertiary structure models allow to infer that some of these proteins possibly have functions related to protein modulation/degradation, intracellular transport, recombination and endosome fusion events. Conclusions The bioinformatics approaches were efficient in generating three-dimensional models and to identify domains, thereby enabling to propose possible functions for the putative polypeptides produced by the ORFs wsv129, wsv178, wsv249, wsv463a, wsv477, wsv479, wsv492, and wsv497. Electronic supplementary material The online version of this article (10.1186/s12900-019-0106-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cayro de Macêdo Mendes
- Applied Molecular Biology Lab - LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Postgraduate Program in Bioinformatics, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Diego Gomes Teixeira
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - João Paulo Matos Santos Lima
- Postgraduate Program in Bioinformatics, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Daniel Carlos Ferreira Lanza
- Applied Molecular Biology Lab - LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil. .,Postgraduate Program in Bioinformatics, Federal University of Rio Grande do Norte, Natal, RN, Brazil. .,Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
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4
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Nncube NB, Ramharack P, Soliman MES. Using bioinformatics tools for the discovery of Dengue RNA-dependent RNA polymerase inhibitors. PeerJ 2018; 6:e5068. [PMID: 30280009 PMCID: PMC6161702 DOI: 10.7717/peerj.5068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/04/2018] [Indexed: 12/29/2022] Open
Abstract
Background Dengue fever has rapidly manifested into a serious global health concern. The emergence of various viral serotypes has prompted the urgent need for innovative drug design techniques. Of the viral non-structural enzymes, the NS5 RNA-dependent RNA polymerase has been established as a promising target due to its lack of an enzymatic counterpart in mammalian cells and its conserved structure amongst all serotypes. The onus is now on scientists to probe further into understanding this enzyme and its mechanism of action. The field of bioinformatics has evolved greatly over recent decades, with updated drug design tools now being publically available. Methods In this study, bioinformatics tools were used to provide a comprehensive sequence and structural analysis of the two most prominent serotypes of Dengue RNA-dependent RNA polymerase. A list of popular flavivirus inhibitors were also chosen to dock to the active site of the enzyme. The best docked compound was then used as a template to generate a pharmacophore model that may assist in the design of target-specific Dengue virus inhibitors. Results Comparative sequence alignment exhibited similarity between all three domains of serotype 2 and 3.Sequence analysis revealed highly conserved regions at residues Meth530, Thr543 Asp597, Glu616, Arg659 and Pro671. Mapping of the active site demonstrated two highly conserved residues: Ser710 and Arg729. Of the active site interacting residues, Ser796 was common amongst all ten docked compounds, indicating its importance in the drug design process. Of the ten docked flavivirus inhibitors, NITD-203 showed the best binding affinity to the active site. Further pharmacophore modeling of NITD-203 depicted significant pharmacophoric elements that are necessary for stable binding to the active site. Discussion This study utilized publically available bioinformatics tools to provide a comprehensive framework on Dengue RNA-dependent RNA polymerase. Based on docking studies, a pharmacophore model was also designed to unveil the crucial pharmacophoric elements that are required when constructing an efficacious DENV inhibitor. We believe that this study will be a cornerstone in paving the road toward the design of target-specific inhibitors against DENV RdRp.
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Affiliation(s)
- Nomagugu B Nncube
- Molecular Bio-computation and Drug Design laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Pritika Ramharack
- Molecular Bio-computation and Drug Design laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
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Sacramento CQ, de Melo GR, de Freitas CS, Rocha N, Hoelz LVB, Miranda M, Fintelman-Rodrigues N, Marttorelli A, Ferreira AC, Barbosa-Lima G, Abrantes JL, Vieira YR, Bastos MM, de Mello Volotão E, Nunes EP, Tschoeke DA, Leomil L, Loiola EC, Trindade P, Rehen SK, Bozza FA, Bozza PT, Boechat N, Thompson FL, de Filippis AMB, Brüning K, Souza TML. The clinically approved antiviral drug sofosbuvir inhibits Zika virus replication. Sci Rep 2017; 7:40920. [PMID: 28098253 PMCID: PMC5241873 DOI: 10.1038/srep40920] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/13/2016] [Indexed: 12/18/2022] Open
Abstract
Zika virus (ZIKV) is a member of the Flaviviridae family, along with other agents of clinical significance such as dengue (DENV) and hepatitis C (HCV) viruses. Since ZIKV causes neurological disorders during fetal development and in adulthood, antiviral drugs are necessary. Sofosbuvir is clinically approved for use against HCV and targets the protein that is most conserved among the members of the Flaviviridae family, the viral RNA polymerase. Indeed, we found that sofosbuvir inhibits ZIKV RNA polymerase, targeting conserved amino acid residues. Sofosbuvir inhibited ZIKV replication in different cellular systems, such as hepatoma (Huh-7) cells, neuroblastoma (SH-Sy5y) cells, neural stem cells (NSC) and brain organoids. In addition to the direct inhibition of the viral RNA polymerase, we observed that sofosbuvir also induced an increase in A-to-G mutations in the viral genome. Together, our data highlight a potential secondary use of sofosbuvir, an anti-HCV drug, against ZIKV.
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Affiliation(s)
- Carolina Q Sacramento
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Gabrielle R de Melo
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Caroline S de Freitas
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Natasha Rocha
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Milene Miranda
- Laboratório de Vírus Respiratório e do Sarampo, IOC, Fiocruz, Rio de Janeiro, RJ, Brazil.,Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Andressa Marttorelli
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - André C Ferreira
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Giselle Barbosa-Lima
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Juliana L Abrantes
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Yasmine Rangel Vieira
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Mônica M Bastos
- Instituto de Tecnologia de Fármacos (Farmanguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | | | - Diogo A Tschoeke
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,SAGE -COPPE, UFRJ, Rio de Janeiro, RJ, Brazil.,Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Luciana Leomil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,SAGE -COPPE, UFRJ, Rio de Janeiro, RJ, Brazil
| | | | - Pablo Trindade
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, RJ, Brazil
| | - Stevens K Rehen
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,D'Or Institute for Research and Education (IDOR), Rio de Janeiro, RJ, Brazil
| | - Fernando A Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Patrícia T Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Nubia Boechat
- Instituto de Tecnologia de Fármacos (Farmanguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,SAGE -COPPE, UFRJ, Rio de Janeiro, RJ, Brazil
| | | | - Karin Brüning
- BMK Consortium: Blanver Farmoquímica Ltda; Microbiológica Química e FarmacêuticaLtda; Karin Bruning &Cia, Ltda, Brazil
| | - Thiago Moreno L Souza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
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Potisopon S, Ferron F, Fattorini V, Selisko B, Canard B. Substrate selectivity of Dengue and Zika virus NS5 polymerase towards 2'-modified nucleotide analogues. Antiviral Res 2016; 140:25-36. [PMID: 28041959 DOI: 10.1016/j.antiviral.2016.12.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 12/28/2016] [Accepted: 12/29/2016] [Indexed: 12/11/2022]
Abstract
In targeting the essential viral RNA-dependent RNA-polymerase (RdRp), nucleotide analogues play a major role in antiviral therapies. In the Flaviviridae family, the hepatitis C virus (HCV) can be eradicated from chronically infected patients using a combination of drugs which generally include the 2'-modified uridine analogue Sofosbuvir, delivered as nucleotide prodrug. Dengue and Zika viruses are emerging flaviviruses whose RdRp is closely related to that of HCV, yet no nucleoside drug has been clinically approved for these acute infections. We have purified dengue and Zika virus full-length NS5, the viral RdRps, and used them to assemble a stable binary complex made of NS5 and virus-specific RNA primer/templates. The complex was used to assess the selectivity of NS5 towards nucleotide analogues bearing modifications at the 2'-position. We show that dengue and Zika virus RdRps exhibit the same discrimination pattern: 2'-O-Me > 2'-C-Me-2'-F > 2'-C-Me nucleoside analogues, unlike HCV RdRp for which the presence of the 2'-F is beneficial rendering the discrimination pattern 2'-O-Me > 2'-C-Me ≥ 2'-C-Me-2'-F. Both 2'-C-Me and 2'-C-Me-2'-F analogues act as non-obligate RNA chain terminators. The dengue and Zika NS5 nucleotide selectivity towards 2'-modified NTPs mirrors potency of the corresponding analogues in infected cell cultures.
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Affiliation(s)
- Supanee Potisopon
- Aix-Marseille Université, AFMB (Laboratoire d'Architecture et Fonction de Macromolécules Biologiques) UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France
| | - François Ferron
- Aix-Marseille Université, AFMB (Laboratoire d'Architecture et Fonction de Macromolécules Biologiques) UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France
| | - Véronique Fattorini
- Aix-Marseille Université, AFMB (Laboratoire d'Architecture et Fonction de Macromolécules Biologiques) UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France
| | - Barbara Selisko
- Aix-Marseille Université, AFMB (Laboratoire d'Architecture et Fonction de Macromolécules Biologiques) UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France.
| | - Bruno Canard
- Aix-Marseille Université, AFMB (Laboratoire d'Architecture et Fonction de Macromolécules Biologiques) UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille, France.
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7
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Fang D, Gan H, Lee JH, Han J, Wang Z, Riester SM, Jin L, Chen J, Zhou H, Wang J, Zhang H, Yang N, Bradley EW, Ho TH, Rubin BP, Bridge JA, Thibodeau SN, Ordog T, Chen Y, van Wijnen AJ, Oliveira AM, Xu RM, Westendorf JJ, Zhang Z. The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas. Science 2016; 352:1344-8. [PMID: 27229140 PMCID: PMC5460624 DOI: 10.1126/science.aae0065] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 05/16/2016] [Indexed: 12/18/2022]
Abstract
More than 90% of chondroblastomas contain a heterozygous mutation replacing lysine-36 with methionine-36 (K36M) in the histone H3 variant H3.3. Here we show that H3K36 methylation is reduced globally in human chondroblastomas and in chondrocytes harboring the same genetic mutation, due to inhibition of at least two H3K36 methyltransferases, MMSET and SETD2, by the H3.3K36M mutant proteins. Genes with altered expression as well as H3K36 di- and trimethylation in H3.3K36M cells are enriched in cancer pathways. In addition, H3.3K36M chondrocytes exhibit several hallmarks of cancer cells, including increased ability to form colonies, resistance to apoptosis, and defects in differentiation. Thus, H3.3K36M proteins reprogram the H3K36 methylation landscape and contribute to tumorigenesis, in part through altering the expression of cancer-associated genes.
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Affiliation(s)
- Dong Fang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Haiyun Gan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA. Epigenomics Program, Center of Individualized Medicine, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Jing Han
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Zhiquan Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Scott M Riester
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Long Jin
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Jianji Chen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Hui Zhou
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Jinglong Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 5 Datun Road, Beijing 100101, China. University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Honglian Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Na Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 5 Datun Road, Beijing 100101, China
| | - Elizabeth W Bradley
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Thai H Ho
- Division of Hematology/Oncology, Mayo Clinic Arizona, 13400 East Shea B., Scottsdale, AZ 85259, USA
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute and Department of Cancer Biology, Cleveland Clinic and Lerner Research Institute, L2 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Julia A Bridge
- Departments of Pathology and Microbiology, Pediatrics, and Orthopaedic Surgery and Rehabilitation
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Tamas Ordog
- Epigenomics Program, Center of Individualized Medicine, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA. Department of Physiology and Biomedical Engineering, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA. Interdisciplinary Health Science Initiative, 1110 Micro and Nanotechnology Laboratory, M/C 249, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Andre J van Wijnen
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA. Department of Orthopedic Surgery, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Andre M Oliveira
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA. Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 5 Datun Road, Beijing 100101, China. University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jennifer J Westendorf
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA. Department of Orthopedic Surgery, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Zhiguo Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA. Epigenomics Program, Center of Individualized Medicine, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.
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8
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Lin X, Thorne L, Jin Z, Hammad LA, Li S, Deval J, Goodfellow IG, Kao CC. Subgenomic promoter recognition by the norovirus RNA-dependent RNA polymerases. Nucleic Acids Res 2014; 43:446-60. [PMID: 25520198 PMCID: PMC4288183 DOI: 10.1093/nar/gku1292] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The replication enzyme of RNA viruses must preferentially recognize their RNAs in an environment that contains an abundance of cellular RNAs. The factors responsible for specific RNA recognition are not well understood, in part because viral RNA synthesis takes place within enzyme complexes associated with modified cellular membrane compartments. Recombinant RNA-dependent RNA polymerases (RdRps) from the human norovirus and the murine norovirus (MNV) were found to preferentially recognize RNA segments that contain the promoter and a short template sequence for subgenomic RNA synthesis. Both the promoter and template sequence contribute to stable RdRp binding, accurate initiation of the subgenomic RNAs and efficient RNA synthesis. Using a method that combines RNA crosslinking and mass spectrometry, residues near the template channel of the MNV RdRp were found to contact the hairpin RNA motif. Mutations in the hairpin contact site in the MNV RdRp reduced MNV replication and virus production in cells. This work demonstrates that the specific recognition of the norovirus subgenomic promoter is through binding by the viral RdRp.
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Affiliation(s)
- Xiaoyan Lin
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Lucy Thorne
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Hills Road CB2 2QQ, UK
| | - Zhinan Jin
- Alios BioPharma, Inc., 260 East Grand Avenue South, San Francisco, CA 94080, USA
| | - Loubna A Hammad
- Laboratory for Biological Mass Spectrometry, Indiana University, Bloomington, IN 47405, USA
| | - Serena Li
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jerome Deval
- Alios BioPharma, Inc., 260 East Grand Avenue South, San Francisco, CA 94080, USA
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Hills Road CB2 2QQ, UK
| | - C Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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9
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Hydrophobic and charged residues in the C-terminal arm of hepatitis C virus RNA-dependent RNA polymerase regulate initiation and elongation. J Virol 2014; 89:2052-63. [PMID: 25428878 DOI: 10.1128/jvi.01106-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED The RNA-dependent RNA polymerase (RdRp) of hepatitis C virus (HCV) is essential for viral genome replication. Crystal structures of the HCV RdRp reveal two C-terminal features, a β-loop and a C-terminal arm, suitably located for involvement in positioning components of the initiation complex. Here we show that these two elements intimately regulate template and nucleotide binding, initiation, and elongation. We constructed a series of β-loop and C-terminal arm mutants, which were used for in vitro analysis of RdRp de novo initiation and primer extension activities. All mutants showed a substantial decrease in initiation activities but a marked increase in primer extension activities, indicating an ability to form more stable elongation complexes with long primer-template RNAs. Structural studies of the mutants indicated that these enzyme properties might be attributed to an increased flexibility in the C-terminal features resulting in a more open polymerase cleft, which likely favors the elongation process but hampers the initiation steps. A UTP cocrystal structure of one mutant shows, in contrast to the wild-type protein, several alternate conformations of the substrate, confirming that even subtle changes in the C-terminal arm result in a more loosely organized active site and flexible binding modes of the nucleotide. We used a subgenomic replicon system to assess the effects of the same mutations on viral replication in cells. Even the subtlest mutations either severely impaired or completely abolished the ability of the replicon to replicate, further supporting the concept that the correct positioning of both the β-loop and C-terminal arm plays an essential role during initiation and in HCV replication in general. IMPORTANCE HCV RNA polymerase is a key target for the development of directly acting agents to cure HCV infections, which necessitates a thorough understanding of the functional roles of the various structural features of the RdRp. Here we show that even highly conservative changes, e.g., Tyr→Phe or Asp→Glu, in these seemingly peripheral structural features have profound effects on the initiation and elongation properties of the HCV polymerase.
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10
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Li C, Wu A, Peng Y, Wang J, Guo Y, Chen Z, Zhang H, Wang Y, Dong J, Wang L, Qin FXF, Cheng G, Deng T, Jiang T. Integrating computational modeling and functional assays to decipher the structure-function relationship of influenza virus PB1 protein. Sci Rep 2014; 4:7192. [PMID: 25424584 PMCID: PMC4244630 DOI: 10.1038/srep07192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/03/2014] [Indexed: 11/12/2022] Open
Abstract
The influenza virus PB1 protein is the core subunit of the heterotrimeric polymerase complex (PA, PB1 and PB2) in which PB1 is responsible for catalyzing RNA polymerization and binding to the viral RNA promoter. Among the three subunits, PB1 is the least known subunit so far in terms of its structural information. In this work, by integrating template-based structural modeling approach with all known sequence and functional information about the PB1 protein, we constructed a modeled structure of PB1. Based on this model, we performed mutagenesis analysis for the key residues that constitute the RNA template binding and catalytic (TBC) channel in an RNP reconstitution system. The results correlated well with the model and further identified new residues of PB1 that are critical for RNA synthesis. Moreover, we derived 5 peptides from the sequence of PB1 that form the TBC channel and 4 of them can inhibit the viral RNA polymerase activity. Interestingly, we found that one of them named PB1(491–515) can inhibit influenza virus replication by disrupting viral RNA promoter binding activity of polymerase. Therefore, this study has not only deepened our understanding of structure-function relationship of PB1, but also promoted the development of novel therapeutics against influenza virus.
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Affiliation(s)
- Chunfeng Li
- 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China
| | - Aiping Wu
- 1] Suzhou Institute of Systems Medicine, Suzhou. 215123, China [2] Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China
| | - Yousong Peng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha. 410082, China
| | - Jingfeng Wang
- Suzhou Institute of Systems Medicine, Suzhou. 215123, China
| | - Yang Guo
- MOH Key Laboratory of Systems Biology of Pahogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, 100730, China
| | - Zhigao Chen
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China
| | - Hong Zhang
- Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China
| | - Yongqiang Wang
- Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China
| | - Jiuhong Dong
- Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China
| | - Lulan Wang
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China
| | - F Xiao-Feng Qin
- 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China
| | - Genhong Cheng
- 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China [3] Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Tao Deng
- MOH Key Laboratory of Systems Biology of Pahogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, 100730, China
| | - Taijiao Jiang
- 1] Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing. 100005, China [2] Suzhou Institute of Systems Medicine, Suzhou. 215123, China [3] Key Laboratory of Protein &Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing. 100101, China
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11
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Zhang B, Chen K, Ni E. Comparison of three methods for extraction of HCV RNA in sera collected from individuals with hyperlipidemia, hyperbilirubinemia and hyperglobulinemia. J Virol Methods 2014; 212:44-6. [PMID: 25445797 DOI: 10.1016/j.jviromet.2014.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 10/30/2014] [Accepted: 11/06/2014] [Indexed: 12/12/2022]
Abstract
Efficient detection of HCV RNA in serum is critical for the diagnosis of hepatitis C virus (HCV) infection. Various nucleic acid extraction methods have been used to extract viral RNA for real-time reverse transcription PCR (RT-PCR). However, the efficiencies of extraction methods for HCV RNA in sera collected from individuals with hyperlipidemia, hyperbilirubinemia and hyperglobulinemia have not been investigated. In the present study, the efficiencies of three extraction methods, i.e., Trizol, guanidine isothiocyanate and silica nanoparticles, were evaluated and compared. All serum samples were collected from HCV-infected patients. For serum samples in which bilirubin, lipids and globulins were all within the normal range, the medians of HCV RNA concentration with Trizol, guanidine isothiocyanate and silica method were 2.25×10(4), 2.80×10(4) and 3.26×10(5)IU/ml HCV RNA respectively (n=180). For hyperlipidemia serum samples, the medians were 6.70×10(3), 8.79×10(3) and 1.10×10(6) respectively (n=158). For hyperbilirubinemia serum samples, the medians were 5.71×10(4), 1.59×10(5) and 1.09×10(6) respectively (n=107). For hyperglobulinemia serum samples, the medians were 3.44×10(4), 3.10×10(4) and 3.06×10(5) respectively (n=71). The medians were highest with silica method from all these types of serum samples. The silica method is, therefore, efficient for HCV RNA extraction even for sera from hyperlipidemia, hyperbilirubinemia and hyperglobulinemia patients.
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Affiliation(s)
- Baohua Zhang
- Clinical Laboratory, Fuzhou Dongfang Hospital, Fuzhou, China
| | - Kun Chen
- Clinical Laboratory, Fuzhou Dongfang Hospital, Fuzhou, China
| | - Erru Ni
- Clinical Laboratory, Fuzhou Dongfang Hospital, Fuzhou, China.
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12
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Maruyama SR, Castro-Jorge LA, Ribeiro JMC, Gardinassi LG, Garcia GR, Brandão LG, Rodrigues AR, Okada MI, Abrão EP, Ferreira BR, Fonseca BALD, Miranda-Santos IKFD. Characterisation of divergent flavivirus NS3 and NS5 protein sequences detected in Rhipicephalus microplus ticks from Brazil. Mem Inst Oswaldo Cruz 2013; 109:38-50. [PMID: 24626302 PMCID: PMC4005522 DOI: 10.1590/0074-0276130166] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/16/2013] [Indexed: 01/19/2023] Open
Abstract
Transcripts similar to those that encode the nonstructural (NS) proteins NS3 and NS5
from flaviviruses were found in a salivary gland (SG) complementary DNA (cDNA)
library from the cattle tick Rhipicephalus microplus. Tick extracts
were cultured with cells to enable the isolation of viruses capable of replicating in
cultured invertebrate and vertebrate cells. Deep sequencing of the viral RNA isolated
from culture supernatants provided the complete coding sequences for the NS3 and NS5
proteins and their molecular characterisation confirmed similarity with the NS3 and
NS5 sequences from other flaviviruses. Despite this similarity, phylogenetic analyses
revealed that this potentially novel virus may be a highly divergent member of the
genus Flavivirus. Interestingly, we detected the divergent NS3 and NS5 sequences in
ticks collected from several dairy farms widely distributed throughout three regions
of Brazil. This is the first report of flavivirus-like transcripts in R.
microplus ticks. This novel virus is a potential arbovirus because it
replicated in arthropod and mammalian cells; furthermore, it was detected in a cDNA
library from tick SGs and therefore may be present in tick saliva. It is important to
determine whether and by what means this potential virus is transmissible and to
monitor the virus as a potential emerging tick-borne zoonotic pathogen.
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Affiliation(s)
| | | | | | - Luiz Gustavo Gardinassi
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, RockvilleMD, USA
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13
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Space constrained homology modelling: the paradigm of the RNA-dependent RNA polymerase of dengue (type II) virus. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:108910. [PMID: 23986788 PMCID: PMC3748430 DOI: 10.1155/2013/108910] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 07/08/2013] [Indexed: 11/18/2022]
Abstract
Protein structure is more conserved than sequence in nature. In this direction we developed a novel methodology that significantly improves conventional homology modelling when sequence identity is low, by taking into consideration 3D structural features of the template, such as size and shape. Herein, our new homology modelling approach was applied to the homology modelling of the RNA-dependent RNA polymerase (RdRp) of dengue (type II) virus. The RdRp of dengue was chosen due to the low sequence similarity shared between the dengue virus polymerase and the available templates, while purposely avoiding to use the actual X-ray structure that is available for the dengue RdRp. The novel approach takes advantage of 3D space corresponding to protein shape and size by creating a 3D scaffold of the template structure. The dengue polymerase model built by the novel approach exhibited all features of RNA-dependent RNA polymerases and was almost identical to the X-ray structure of the dengue RdRp, as opposed to the model built by conventional homology modelling. Therefore, we propose that the space-aided homology modelling approach can be of a more general use to homology modelling of enzymes sharing low sequence similarity with the template structures.
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14
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Vlachakis D, Koumandou VL, Kossida S. A holistic evolutionary and structural study of flaviviridae provides insights into the function and inhibition of HCV helicase. PeerJ 2013; 1:e74. [PMID: 23678398 PMCID: PMC3646357 DOI: 10.7717/peerj.74] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 04/24/2013] [Indexed: 01/16/2023] Open
Abstract
Viral RNA helicases are involved in duplex unwinding during the RNA replication of the virus. It is suggested that these helicases represent very promising antiviral targets. Viruses of the flaviviridae family are the causative agents of many common and devastating diseases, including hepatitis, yellow fever and dengue fever. As there is currently no available anti-Flaviviridae therapy, there is urgent need for the development of efficient anti-viral pharmaceutical strategies. Herein, we report the complete phylogenetic analysis across flaviviridae alongside a more in-depth evolutionary study that revealed a series of conserved and invariant amino acids that are predicted to be key to the function of the helicase. Structural molecular modelling analysis revealed the strategic significance of these residues based on their relative positioning on the 3D structures of the helicase enzymes, which may be used as pharmacological targets. We previously reported a novel series of highly potent HCV helicase inhibitors, and we now re-assess their antiviral potential using the 3D structural model of the invariant helicase residues. It was found that the most active compound of the series, compound C4, exhibited an IC50 in the submicromolar range, whereas its stereoisomer (compound C12) was completely inactive. Useful insights were obtained from molecular modelling and conformational search studies via molecular dynamics simulations. C12 tends to bend and lock in an almost “U” shape conformation, failing to establish vital interactions with the active site of HCV. On the contrary, C4 spends most of its conformational time in a straight, more rigid formation that allows it to successfully block the passage of the oligonucleotide in the ssRNA channel of the HCV helicase. This study paves the way and provides the necessary framework for the in-depth analysis required to enable the future design of new and potent anti-viral agents.
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Affiliation(s)
- Dimitrios Vlachakis
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens , Athens , Greece
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15
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Bussetta C, Choi KH. Dengue virus nonstructural protein 5 adopts multiple conformations in solution. Biochemistry 2012; 51:5921-31. [PMID: 22757685 PMCID: PMC3448003 DOI: 10.1021/bi300406n] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dengue virus (DENV) nonstructural protein 5 (NS5) is composed of two globular domains separated by a 10-residue linker. The N-terminal domain participates in the synthesis of a mRNA cap 1 structure ((7Me)GpppA(2'OMe)) at the 5' end of the viral genome and possesses guanylyltransferase, guanine-N7-methyltransferase, and nucleoside-2'O-methyltransferase activities. The C-terminal domain is an RNA-dependent RNA polymerase responsible for viral RNA synthesis. Although crystal structures of the two isolated domains have been obtained, there are no structural data for full-length NS5. It is also unclear whether the two NS5 domains interact with each other to form a stable structure in which the relative orientation of the two domains is fixed. To investigate the structure and dynamics of DENV type 3 NS5 in solution, we conducted small-angle X-ray scattering experiments with the full-length protein. NS5 was found to be monomeric and well-folded under the conditions tested. The results of these experiments also suggest that NS5 adopts multiple conformations in solution, ranging from compact to more extended forms in which the two domains do not seem to interact with each other. We interpret the multiple conformations of NS5 observed in solution as resulting from weak interactions between the two NS5 domains and flexibility of the linker in the absence of other components of the replication complex.
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Affiliation(s)
- Cécile Bussetta
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX 77555-0647
| | - Kyung H. Choi
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX 77555-0647
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16
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Nucleoside analog inhibitors of hepatitis C viral replication: recent advances, challenges and trends. Future Med Chem 2011; 1:1429-52. [PMID: 21426058 DOI: 10.4155/fmc.09.88] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infection is a global health problem, with over 170 million people infected worldwide. The current therapy, pegylated interferon (PEG-IFN) plus ribavirin (RBV), provides only approximately a 40% sustained virological response (undetectable HCV RNA for greater than 24 weeks after cessation of therapy), in genotype 1-infected individuals. In addition to the limited sustained virological response, PEG-IFN/RBV treatment is associated with serious adverse effects. Nucleosides have long been the cornerstone of antiviral therapy because of their proven efficacy and high barrier to resistance. Through the use of surrogate viruses or the HCV subgenomic replicon, several classes of nucleoside analogs or their monophosphate prodrugs have been identified that inhibit HCV RNA replication. Nucleoside analogs that possess the 2´-C-methyl modification vary in their ability to be phosphorylated and to act as alternative substrate inhibitors of the HCV RNA polymerase. Herein, we discuss various classes of nucleoside inhibitors, with a focus on available structure-activity relationships, their mode of action and resistance profile.
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17
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Epstein JH, Quan PL, Briese T, Street C, Jabado O, Conlan S, Ali Khan S, Verdugo D, Hossain MJ, Hutchison SK, Egholm M, Luby SP, Daszak P, Lipkin WI. Identification of GBV-D, a novel GB-like flavivirus from old world frugivorous bats (Pteropus giganteus) in Bangladesh. PLoS Pathog 2010; 6:e1000972. [PMID: 20617167 PMCID: PMC2895649 DOI: 10.1371/journal.ppat.1000972] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 05/27/2010] [Indexed: 11/19/2022] Open
Abstract
Bats are reservoirs for a wide range of zoonotic agents including lyssa-, henipah-, SARS-like corona-, Marburg-, Ebola-, and astroviruses. In an effort to survey for the presence of other infectious agents, known and unknown, we screened sera from 16 Pteropus giganteus bats from Faridpur, Bangladesh, using high-throughput pyrosequencing. Sequence analyses indicated the presence of a previously undescribed virus that has approximately 50% identity at the amino acid level to GB virus A and C (GBV-A and -C). Viral nucleic acid was present in 5 of 98 sera (5%) from a single colony of free-ranging bats. Infection was not associated with evidence of hepatitis or hepatic dysfunction. Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades.
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Affiliation(s)
- Jonathan H. Epstein
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Craig Street
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Omar Jabado
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Sean Conlan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Shahneaz Ali Khan
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
- Chittagong Veterinary & Animal Sciences University, Chittagong, Bangladesh
| | - Dawn Verdugo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - M. Jahangir Hossain
- Programme on Infectious Disease and Vaccine Sciences, International Centre for Diarrheal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | | | - Michael Egholm
- 454 Life Sciences, Branford, Connecticut, United States of America
| | - Stephen P. Luby
- Programme on Infectious Disease and Vaccine Sciences, International Centre for Diarrheal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Peter Daszak
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
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18
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Choi KH, Rossmann MG. RNA-dependent RNA polymerases from Flaviviridae. Curr Opin Struct Biol 2009; 19:746-51. [PMID: 19914821 DOI: 10.1016/j.sbi.2009.10.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 10/18/2009] [Accepted: 10/20/2009] [Indexed: 12/13/2022]
Abstract
Viral genome replication in Flaviviridae is carried out by a virally encoded RNA-dependent RNA polymerase (RdRp). These viruses initiate the RNA synthesis via a de novo mechanism that differs from the primer-dependent mechanism used by Picornaviridae. Like all polymerases, the structure of Flaviviridae RdRps resembles a right hand with characteristic fingers, palm, and thumb domains. Structural features that distinguish Flaviviridae RdRps from other polymerases are a large thumb domain and a C-terminal motif that encircles the active site. This domain arrangement restricts the volume of the template-binding channel, allowing only single-stranded RNA to enter the active site. While this closed form of the polymerase is ideal to stabilize a de novo initiation complex, significant conformational changes are expected to accommodate the elongation complex containing the RNA duplex product.
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Affiliation(s)
- Kyung H Choi
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, TX 77555-0647, USA.
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19
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1,5-benzodiazepines, a novel class of hepatitis C virus polymerase nonnucleoside inhibitors. Antimicrob Agents Chemother 2008; 52:4420-31. [PMID: 18852280 DOI: 10.1128/aac.00669-08] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The exogenous control of hepatitis C virus (HCV) replication can be mediated through the inhibition of the RNA-dependent RNA polymerase (RdRp) activity of NS5B. Small-molecule inhibitors of NS5B include nucleoside and nonnucleoside analogs. Here, we report the discovery of a novel class of HCV polymerase nonnucleoside inhibitors, 1,5-benzodiazepines (1,5-BZDs), identified by high-throughput screening of a library of small molecules. A fluorescence-quenching assay and X-ray crystallography revealed that 1,5-BZD 4a bound stereospecifically to NS5B next to the catalytic site. When introduced into replicons, mutations known to confer resistance against chemotypes that bind at this site were detrimental to inhibition by 1,5-BZD 7a. Using a panel of enzyme isolates that covered genotypes 1 to 6, we showed that compound 4a inhibited genotype 1 only. In mechanistic studies, 4a was found to inhibit the RdRp activity of NS5B noncompetitively with GTP and to inhibit the formation of the first phosphodiester bond during the polymerization cycle. The specificity for the HCV target was evaluated by profiling the 1,5-BZDs against other viral and human polymerases, as well as BZD receptors.
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20
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Malet H, Massé N, Selisko B, Romette JL, Alvarez K, Guillemot JC, Tolou H, Yap TL, Vasudevan S, Lescar J, Canard B. The flavivirus polymerase as a target for drug discovery. Antiviral Res 2008; 80:23-35. [PMID: 18611413 DOI: 10.1016/j.antiviral.2008.06.007] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 06/06/2008] [Accepted: 06/10/2008] [Indexed: 02/06/2023]
Abstract
Flaviviruses are emerging pathogens of increasingly important public health concern in the world. For most flaviviruses such as dengue virus (DENV) and West Nile virus (WNV) neither vaccine nor antiviral treatment is available. The viral RNA-dependent RNA polymerase (RdRp) non-structural protein 5 (NS5) has no equivalent in the host cell and is essential for viral replication. Here, we give an overview of the current knowledge regarding Flavivirus RdRp function and structure as it represents an attractive target for drug design. Flavivirus RdRp exhibits primer-independent activity, thus initiating RNA synthesis de novo. Following initiation, a conformational change must occur to allow the elongation process. Structure-function studies of Flavivirus RdRp are now facilitated by the crystal structures of DENV (serotype 3) and WNV RdRp domains. Both adopt a classic viral RdRp fold and present a closed pre-initiation conformation. The so-called priming loop is thought to provide the initiation platform stabilizing the de novo initiation complex. A zinc-ion binding site at the hinge between two subdomains might be involved in opening up the RdRp structure towards a conformation for elongation. Using two different programs we predicted common potential allosteric inhibitor binding sites on both structures. We also review ongoing approaches of in vitro and cell-based screening programs aiming at the discovery of nucleosidic and non-nucleosidic inhibitors targeting Flavivirus RdRps.
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Affiliation(s)
- Hélène Malet
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
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Beerens N, Selisko B, Ricagno S, Imbert I, van der Zanden L, Snijder EJ, Canard B. De novo initiation of RNA synthesis by the arterivirus RNA-dependent RNA polymerase. J Virol 2007; 81:8384-95. [PMID: 17537850 PMCID: PMC1951334 DOI: 10.1128/jvi.00564-07] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
All plus-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) that functions as the catalytic subunit of the viral replication/transcription complex, directing viral RNA synthesis in concert with other viral proteins and, sometimes, host proteins. RNA synthesis essentially can be initiated by two different mechanisms, de novo initiation and primer-dependent initiation. Most viral RdRps have been identified solely on the basis of comparative sequence analysis, and for many viruses the mechanism of initiation is unknown. In this study, using the family prototype equine arteritis virus (EAV), we address the mechanism of initiation of RNA synthesis in arteriviruses. The RdRp domains of the members of the arterivirus family, which are part of replicase subunit nsp9, were compared to coronavirus RdRps that belong to the same order of Nidovirales, as well as to other RdRps with known initiation mechanisms and three-dimensional structures. We report here the first successful expression and purification of an arterivirus RdRp that is catalytically active in the absence of other viral or cellular proteins. The EAV nsp9/RdRp initiates RNA synthesis by a de novo mechanism on homopolymeric templates in a template-specific manner. In addition, the requirements for initiation of RNA synthesis from the 3' end of the viral genome were studied in vivo using a reverse genetics approach. These studies suggest that the 3'-terminal nucleotides of the EAV genome play a critical role in viral RNA synthesis.
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Affiliation(s)
- Nancy Beerens
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, LUMC P4-26, 2300 RC Leiden, The Netherlands
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D'Abramo CM, Deval J, Cameron CE, Cellai L, Götte M. Control of template positioning during de novo initiation of RNA synthesis by the bovine viral diarrhea virus NS5B polymerase. J Biol Chem 2006; 281:24991-8. [PMID: 16831816 DOI: 10.1074/jbc.m600474200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The RNA-dependent RNA polymerase of the hepatitis C virus and the bovine viral diarrhea virus(BVDV)is able to initiate RNA synthesis denovo in the absence of a primer. Previous crystallographic data have pointed to the existence of a GTP-specific binding site (G-site) that is located in the vicinity of the active site of the BVDV enzyme. Here we have studied the functional role of the G-site and present evidence to show that specific GTP binding affects the positioning of the template during de novo initiation. Following the formation of the first phosphodiester bond, the polymerase translocates relative to the newly synthesized dinucleotide, which brings the 5'-end of the primer into the G-site, releasing the previously bound GTP. At this stage, the 3'-end of the template can remain opposite to the 5'-end of the primer or be repositioned to its original location before RNA synthesis proceeds. We show that the template can freely move between the two locations, and both complexes can isomerize to equilibrium. These data suggest that the bound GTP can stabilize the interaction between the 3'-end of the template and the priming nucleotide, preventing the template to overshoot and extend beyond the active site during de novo initiation. The hepatitis C virus enzyme utilizes a dinucleotide primer exclusively from the blunt end; the existence of a functionally equivalent G-site is therefore uncertain. For the BVDV polymerase we showed that de novo initiation is severely compromised by the T320A mutant that likely affects hydrogen bonding between the G-site and the guanine base. Dinucleotide-primed reactions are not influenced by this mutation, which supports the notion that the G-site is located in close proximity but not at the active site of the enzyme.
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Affiliation(s)
- Claudia M D'Abramo
- Department of Microbiology & Immunology, and Department of Medicine, McGill University, Montréal, Québec H3A 2B4, Canada
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Selisko B, Dutartre H, Guillemot JC, Debarnot C, Benarroch D, Khromykh A, Desprès P, Egloff MP, Canard B. Comparative mechanistic studies of de novo RNA synthesis by flavivirus RNA-dependent RNA polymerases. Virology 2006; 351:145-58. [PMID: 16631221 DOI: 10.1016/j.virol.2006.03.026] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 02/22/2006] [Accepted: 03/16/2006] [Indexed: 01/09/2023]
Abstract
Flavivirus protein NS5 harbors the RNA-dependent RNA polymerase (RdRp) activity. In contrast to the RdRps of hepaci- and pestiviruses, which belong to the same family of Flaviviridae, NS5 carries two activities, a methyltransferase (MTase) and a RdRp. RdRp domains of Dengue virus (DV) and West Nile virus (WNV) NS5 were purified in high yield relative to full-length NS5 and showed full RdRp activity. Steady-state enzymatic parameters were determined on homopolymeric template poly(rC). The presence of the MTase domain does not affect the RdRp activity. Flavivirus RdRp domains might bear more than one GTP binding site displaying positive cooperativity. The kinetics of RNA synthesis by four Flaviviridae RdRps were compared. In comparison to Hepatitis C RdRp, DV and WNV as well as Bovine Viral Diarrhea virus RdRps show less rate limitation by early steps of short-product formation. This suggests that they display a higher conformational flexibility upon the transition from initiation to elongation.
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Affiliation(s)
- Barbara Selisko
- Centre National de la Recherche Scientifique and Universités d'Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, AFMB-CNRS-ESIL, 13288 Marseille Cedex 9, France
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