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Mondal S, Sarvari G, Boehr DD. Picornavirus 3C Proteins Intervene in Host Cell Processes through Proteolysis and Interactions with RNA. Viruses 2023; 15:2413. [PMID: 38140654 PMCID: PMC10747604 DOI: 10.3390/v15122413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
The Picornaviridae family comprises a large group of non-enveloped viruses with enormous impact on human and animal health. The picornaviral genome contains one open reading frame encoding a single polyprotein that can be processed by viral proteases. The picornaviral 3C proteases share similar three-dimensional structures and play a significant role in the viral life cycle and virus-host interactions. Picornaviral 3C proteins also have conserved RNA-binding activities that contribute to the assembly of the viral RNA replication complex. The 3C protease is important for regulating the host cell response through the cleavage of critical host cell proteins, acting to selectively 'hijack' host factors involved in gene expression, promoting picornavirus replication, and inactivating key factors in innate immunity signaling pathways. The protease and RNA-binding activities of 3C are involved in viral polyprotein processing and the initiation of viral RNA synthesis. Most importantly, 3C modifies critical molecules in host organelles and maintains virus infection by subtly subverting host cell death through the blocking of transcription, translation, and nucleocytoplasmic trafficking to modulate cell physiology for viral replication. Here, we discuss the molecular mechanisms through which 3C mediates physiological processes involved in promoting virus infection, replication, and release.
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Affiliation(s)
| | | | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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2
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Selina PI, Karaseva MA, Komissarov AA, Safina DR, Lunina NA, Roschina MP, Sverdlov ED, Demidyuk IV, Kostrov SV. Embryotoxic activity of 3C protease of human hepatitis A virus in developing Danio rerio embryos. Sci Rep 2021; 11:18196. [PMID: 34521911 PMCID: PMC8440601 DOI: 10.1038/s41598-021-97641-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/27/2021] [Indexed: 11/23/2022] Open
Abstract
The 3C protease is a key factor in picornavirus-induced pathologies with a comprehensive action on cell targets. However, the effects induced by the enzyme have not been described at the organismic level. Here, the model of developing Danio rerio embryos was used to analyze possible toxic effects of the 3C protease of human hepatitis A virus (3Cpro) at the whole-body level. The transient 3Cpro expression had a notable lethal effect and induced a number of specific abnormalities in Danio rerio embryos within 24 h. These effects are due to the proteolytic activity of the enzyme. At the same time, the 3Cpro variant with reduced catalytic activity (3Cmut) increased the incidence of embryonic abnormalities; however, this effect was smaller compared to the native enzyme form. While the expression of 3Cmut increased the overall rate of abnormalities, no predominance of specific ones was observed. The data obtained point to a presence significant impact of picornavirus 3Cprotease at the whole-organism level and make contribution to the study of the infectious process caused by human hepatitis A virus.
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Affiliation(s)
- Polina I Selina
- Institute of Molecular Genetics of National Research Center, Kurchatov Institute, 123182, Moscow, Russia.
| | - Maria A Karaseva
- Institute of Molecular Genetics of National Research Center, Kurchatov Institute, 123182, Moscow, Russia
| | - Alexey A Komissarov
- Institute of Molecular Genetics of National Research Center, Kurchatov Institute, 123182, Moscow, Russia
| | - Dina R Safina
- Institute of Molecular Genetics of National Research Center, Kurchatov Institute, 123182, Moscow, Russia
| | - Nataliya A Lunina
- Institute of Molecular Genetics of National Research Center, Kurchatov Institute, 123182, Moscow, Russia
| | - Marina P Roschina
- Institute of Molecular Genetics of National Research Center, Kurchatov Institute, 123182, Moscow, Russia
| | - Eugene D Sverdlov
- Institute of Molecular Genetics of National Research Center, Kurchatov Institute, 123182, Moscow, Russia
| | - Ilya V Demidyuk
- Institute of Molecular Genetics of National Research Center, Kurchatov Institute, 123182, Moscow, Russia
| | - Sergey V Kostrov
- Institute of Molecular Genetics of National Research Center, Kurchatov Institute, 123182, Moscow, Russia
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3
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Theoretical studies on the electronic and optoelectronic properties of DNA/RNA hybrid-metal complexes. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.115015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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GII.4 Norovirus Protease Shows pH-Sensitive Proteolysis with a Unique Arg-His Pairing in the Catalytic Site. J Virol 2019; 93:JVI.01479-18. [PMID: 30626675 DOI: 10.1128/jvi.01479-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/17/2018] [Indexed: 11/20/2022] Open
Abstract
Human noroviruses (NoVs) are the main cause of epidemic and sporadic gastroenteritis. Phylogenetically, noroviruses are divided into seven genogroups, with each divided into multiple genotypes. NoVs belonging to genogroup II and genotype 4 (GII.4) are globally most prevalent. Genetic diversity among the NoVs and the periodic emergence of novel strains present a challenge for the development of vaccines and antivirals to treat NoV infection. NoV protease is essential for viral replication and is an attractive target for the development of antivirals. The available structure of GI.1 protease provided a basis for the design of inhibitors targeting the active site of the protease. These inhibitors, although potent against the GI proteases, poorly inhibit the GII proteases, for which structural information is lacking. To elucidate the structural basis for this difference in the inhibitor efficiency, we determined the crystal structure of a GII.4 protease. The structure revealed significant changes in the S2 substrate-binding pocket, making it noticeably smaller, and in the active site, with the catalytic triad residues showing conformational changes. Furthermore, a conserved arginine is found inserted into the active site, interacting with the catalytic histidine and restricting substrate/inhibitor access to the S2 pocket. This interaction alters the relationships between the catalytic residues and may allow for a pH-dependent regulation of protease activity. The changes we observed in the GII.4 protease structure may explain the reduced potency of the GI-specific inhibitors against the GII protease and therefore must be taken into account when designing broadly cross-reactive antivirals against NoVs.IMPORTANCE Human noroviruses (NoVs) cause sporadic and epidemic gastroenteritis worldwide. They are divided into seven genogroups (GI to GVII), with each genogroup further divided into several genotypes. Human NoVs belonging to genogroup II and genotype 4 (GII.4) are the most prevalent. Currently, there are no vaccines or antiviral drugs available for NoV infection. The protease encoded by NoV is considered a valuable target because of its essential role in replication. NoV protease structures have only been determined for the GI genogroup. We show here that the structure of the GII.4 protease exhibits several significant changes from GI proteases, including a unique pairing of an arginine with the catalytic histidine that makes the proteolytic activity of GII.4 protease pH sensitive. A comparative analysis of NoV protease structures may provide a rational framework for structure-based drug design of broadly cross-reactive inhibitors targeting NoVs.
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Shubin AV, Demidyuk IV, Lunina NA, Komissarov AA, Roschina MP, Leonova OG, Kostrov SV. Protease 3C of hepatitis A virus induces vacuolization of lysosomal/endosomal organelles and caspase-independent cell death. BMC Cell Biol 2015; 16:4. [PMID: 25886889 PMCID: PMC4355371 DOI: 10.1186/s12860-015-0050-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 01/26/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND 3C proteases, the main proteases of picornaviruses, play the key role in viral life cycle by processing polyproteins. In addition, 3C proteases digest certain host cell proteins to suppress antiviral defense, transcription, and translation. The activity of 3C proteases per se induces host cell death, which makes them critical factors of viral cytotoxicity. To date, cytotoxic effects have been studied for several 3C proteases, all of which induce apoptosis. This study for the first time describes the cytotoxic effect of 3C protease of human hepatitis A virus (3Cpro), the only proteolytic enzyme of the virus. RESULTS Individual expression of 3Cpro induced catalytic activity-dependent cell death, which was not abrogated by the pan-caspase inhibitor (z-VAD-fmk) and was not accompanied by phosphatidylserine externalization in contrast to other picornaviral 3C proteases. The cell survival was also not affected by the inhibitors of cysteine proteases (z-FA-fmk) and RIP1 kinase (necrostatin-1), critical enzymes involved in non-apoptotic cell death. A substantial fraction of dying cells demonstrated numerous non-acidic cytoplasmic vacuoles with not previously described features and originating from several types of endosomal/lysosomal organelles. The lysosomal protein Lamp1 and GTPases Rab5, Rab7, Rab9, and Rab11 were associated with the vacuolar membranes. The vacuolization was completely blocked by the vacuolar ATPase inhibitor (bafilomycin A1) and did not depend on the activity of the principal factors of endosomal transport, GTPases Rab5 and Rab7, as well as on autophagy and macropinocytosis. CONCLUSIONS 3Cpro, apart from other picornaviral 3C proteases, induces caspase-independent cell death, accompanying by cytoplasmic vacuolization. 3Cpro-induced vacuoles have unique properties and are formed from several organelle types of the endosomal/lysosomal compartment. The data obtained demonstrate previously undocumented morphological characters of the 3Cpro-induced cell death, which can reflect unknown aspects of the human hepatitis A virus-host cell interaction.
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Affiliation(s)
- Andrey V Shubin
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
| | - Ilya V Demidyuk
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
| | - Nataliya A Lunina
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
| | - Alexey A Komissarov
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
| | - Marina P Roschina
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
| | - Olga G Leonova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119992, Russia.
| | - Sergey V Kostrov
- Laboratory of Protein Engineering, Institute of Molecular Genetics, Russian Academy of Science, Moscow, 123182, Russia.
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
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Boyaci IH, Temiz HT, Geniş HE, Acar Soykut E, Yazgan NN, Güven B, Uysal RS, Bozkurt AG, İlaslan K, Torun O, Dudak Şeker FC. Dispersive and FT-Raman spectroscopic methods in food analysis. RSC Adv 2015. [DOI: 10.1039/c4ra12463d] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Raman spectroscopy is a powerful technique for molecular analysis of food samples.
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Affiliation(s)
- Ismail Hakki Boyaci
- Department of Food Engineering
- Faculty of Engineering
- Hacettepe University
- 06800 Ankara
- Turkey
| | - Havva Tümay Temiz
- Department of Food Engineering
- Faculty of Engineering
- Hacettepe University
- 06800 Ankara
- Turkey
| | - Hüseyin Efe Geniş
- Department of Food Engineering
- Faculty of Engineering
- Hacettepe University
- 06800 Ankara
- Turkey
| | | | - Nazife Nur Yazgan
- Department of Food Engineering
- Faculty of Engineering
- Hacettepe University
- 06800 Ankara
- Turkey
| | - Burcu Güven
- Department of Food Engineering
- Faculty of Engineering
- Hacettepe University
- 06800 Ankara
- Turkey
| | - Reyhan Selin Uysal
- Department of Food Engineering
- Faculty of Engineering
- Hacettepe University
- 06800 Ankara
- Turkey
| | - Akif Göktuğ Bozkurt
- Department of Food Engineering
- Faculty of Engineering
- Hacettepe University
- 06800 Ankara
- Turkey
| | - Kerem İlaslan
- Department of Food Engineering
- Faculty of Engineering
- Hacettepe University
- 06800 Ankara
- Turkey
| | - Ozlem Torun
- Department of Food Engineering
- Faculty of Engineering
- Hacettepe University
- 06800 Ankara
- Turkey
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Rusnati M, Chiodelli P, Bugatti A, Urbinati C. Bridging the past and the future of virology: surface plasmon resonance as a powerful tool to investigate virus/host interactions. Crit Rev Microbiol 2013; 41:238-60. [PMID: 24059853 DOI: 10.3109/1040841x.2013.826177] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Despite decades of antiviral drug research and development, viruses still remain a top global healthcare problem. Compared to eukaryotic cells, viruses are composed by a limited numbers of proteins that, nevertheless, set up multiple interactions with cellular components, allowing the virus to take control of the infected cell. Each virus/host interaction can be considered as a therapeutical target for new antiviral drugs but, unfortunately, the systematic study of a so huge number of interactions is time-consuming and expensive, calling for models overcoming these drawbacks. Surface plasmon resonance (SPR) is a label-free optical technique to study biomolecular interactions in real time by detecting reflected light from a prism-gold film interface. Launched 20 years ago, SPR has become a nearly irreplaceable technology for the study of biomolecular interactions. Accordingly, SPR is increasingly used in the field of virology, spanning from the study of biological interactions to the identification of putative antiviral drugs. From the literature available, SPR emerges as an ideal link between conventional biological experimentation and system biology studies functional to the identification of highly connected viral or host proteins that act as nodal points in virus life cycle and thus considerable as therapeutical targets for the development of innovative antiviral strategies.
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Affiliation(s)
- Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia , Brescia , Italy
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Yin J, Bergmann EM. Hepatitis A Virus Picornain 3C. HANDBOOK OF PROTEOLYTIC ENZYMES 2013. [PMCID: PMC7149673 DOI: 10.1016/b978-0-12-382219-2.00540-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The third edition of the Handbook of Proteolytic Enzymes aims to be a comprehensive reference work for the enzymes that cleave proteins and peptides, and contains over 800 chapters. Each chapter is organized into sections describing the name and history, activity and specificity, structural chemistry, preparation, biological aspects, and distinguishing features for a specific peptidase. The subject of Chapter 540 is Hepatitis A Virus Picornain 3C. Keywords: β-barrel, β-ribbon, catalytic triad, cleavage site, hepatitis A virus, polyprotein processing, substrate specificity pocket, picornain 3C, picornavirus, viral cysteine proteinase.
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Blaum BS, Wünsche W, Benie AJ, Kusov Y, Peters H, Gauss-Müller V, Peters T, Sczakiel G. Functional binding of hexanucleotides to 3C protease of hepatitis A virus. Nucleic Acids Res 2012; 40:3042-55. [PMID: 22156376 PMCID: PMC3326307 DOI: 10.1093/nar/gkr1152] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 12/01/2022] Open
Abstract
Oligonucleotides as short as 6 nt in length have been shown to bind specifically and tightly to proteins and affect their biological function. Yet, sparse structural data are available for corresponding complexes. Employing a recently developed hexanucleotide array, we identified hexadeoxyribonucleotides that bind specifically to the 3C protease of hepatitis A virus (HAV 3C(pro)). Inhibition assays in vitro identified the hexanucleotide 5'-GGGGGT-3' (G(5)T) as a 3C(pro) protease inhibitor. Using (1)H NMR spectroscopy, G(5)T was found to form a G-quadruplex, which might be considered as a minimal aptamer. With the help of (1)H, (15)N-HSQC experiments the binding site for G(5)T was located to the C-terminal β-barrel of HAV 3C(pro). Importantly, the highly conserved KFRDI motif, which has previously been identified as putative viral RNA binding site, is not part of the G(5)T-binding site, nor does G(5)T interfere with the binding of viral RNA. Our findings demonstrate that sequence-specific nucleic acid-protein interactions occur with oligonucleotides as small as hexanucleotides and suggest that these compounds may be of pharmaceutical relevance.
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Affiliation(s)
- Bärbel S. Blaum
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Winfried Wünsche
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Andrew J. Benie
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Yuri Kusov
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Hannelore Peters
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Verena Gauss-Müller
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Thomas Peters
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Georg Sczakiel
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
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Cui S, Wang J, Fan T, Qin B, Guo L, Lei X, Wang J, Wang M, Jin Q. Crystal structure of human enterovirus 71 3C protease. J Mol Biol 2011; 408:449-61. [PMID: 21396941 PMCID: PMC7094522 DOI: 10.1016/j.jmb.2011.03.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 03/03/2011] [Accepted: 03/03/2011] [Indexed: 12/03/2022]
Abstract
Human enterovirus 71 (EV71) is the major pathogen that causes hand, foot and mouth disease that particularly affects young children. Growing hand, foot and mouth disease outbreaks were observed worldwide in recent years and caused devastating losses both economically and politically. However, vaccines or effective drugs are unavailable to date. The genome of EV71 consists of a positive sense, single-stranded RNA of ∼7400 bp, encoding a large precursor polyprotein that requires proteolytic processing to generate mature viral proteins. The proteolytic processing mainly depends on EV71 3C protease (3C(pro)) that possesses both proteolysis and RNA binding activities, which enable the protease to perform multiple tasks in viral replication and pathogen-host interactions. The central roles played by EV71 3C(pro) make it an appealing target for antiviral drug development. We determined the first crystal structure of EV71 3C(pro) and analyzed its enzymatic activity. The crystal structure shows that EV71 3C(pro) has a typical chymotrypsin-like fold that is common in picornaviral 3C(pro). Strikingly, we found an important surface loop, also denoted as β-ribbon, which adopts a novel open conformation in EV71 3C(pro). We identified two important residues located at the base of the β-ribbon, Gly123 and His133, which form hinges that govern the intrinsic flexibility of the ribbon. Structure-guided mutagenesis studies revealed that the hinge residues are important to EV71 3C(pro) proteolytic activities. In summary, our work provides the first structural insight into EV71 3C(pro), including a mobile β-ribbon, which is relevant to the proteolytic mechanism. Our data also provides a framework for structure-guided inhibitor design against EV71 3C(pro).
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Key Words
- ev71, human enterovirus 71
- hfmd, hand, foot and mouth disease
- 3cpro, 3c protease
- fmdv, foot-and-mouth disease virus
- hav, hepatitis a virus
- pv, poliovirus
- hrv, human rhinovirus
- cvb, coxsackievirus b
- asu, asymmetric unit
- sars-cov, severe acute respiratory syndrome-coronavirus
- wt, wild-type
- pdb, protein data bank
- sls, swiss light source
- chymotrypsin-like fold
- β-ribbon
- picornaviral 3c
- hfmd
- crystallography
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Affiliation(s)
- Sheng Cui
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Jing Wang
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Tingting Fan
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Bo Qin
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Li Guo
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Xiaobo Lei
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Jianwei Wang
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Meitian Wang
- Swiss Light Source at Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Qi Jin
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
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11
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Xia Y, Zhu Q, Jun KY, Wang J, Gao X. Clean STD-NMR spectrum for improved detection of ligand-protein interactions at low concentration of protein. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:918-924. [PMID: 20957656 DOI: 10.1002/mrc.2687] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Saturation transfer difference (STD)-NMR has been widely used to screen ligand compound libraries for their binding activities to proteins and to determine the binding epitopes of the ligands. We report herein, a Clean STD-NMR method developed to overcome false positives (artifacts) observed in the STD-NMR spectrum due to the power spillover of RF irradiation. The method achieved higher degree of resonance saturation through digital editing of two STD-NMR spectra to generate a concatenated difference spectrum and three times of sensitivity enhancement for a loose binding complex involving DNA oligonucleotide and an RNA-binding protein, CUGBP-1ab (25.2 kDa). The interesting binding characteristics of the complex dCTGTCT-CUGBP1ab were obtained. The method was applied to a mixture of small ligand and bovine serum albumin protein (BSA, 66.3 kDa), and detected the intermolecular contacts at a BSA concentration as low as 0.1 µM, a working concentration useful for the detection of proteins of low solubility at biologically relevant conditions.
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Affiliation(s)
- Youlin Xia
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA.
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12
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Claridge JK, Headey SJ, Chow JYH, Schwalbe M, Edwards PJ, Jeffries CM, Venugopal H, Trewhella J, Pascal SM. A picornaviral loop-to-loop replication complex. J Struct Biol 2009; 166:251-62. [PMID: 19268541 PMCID: PMC7172786 DOI: 10.1016/j.jsb.2009.02.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 01/30/2009] [Accepted: 02/21/2009] [Indexed: 11/28/2022]
Abstract
Picornaviruses replicate their RNA genomes through a highly conserved mechanism that involves an interaction between the principal viral protease (3C(pro)) and the 5'-UTR region of the viral genome. The 3C(pro) catalytic site is the target of numerous replication inhibitors. This paper describes the first structural model of a complex between a picornaviral 3C(pro) and a region of the 5'-UTR, stem-loop D (SLD). Using human rhinovirus as a model system, we have combined NMR contact information, small-angle X-ray scattering (SAXS) data, and previous mutagenesis results to determine the shape, position and relative orientation of the 3C(pro) and SLD components. The results clearly identify a 1:1 binding stoichiometry, with pronounced loops from each molecule providing the key binding determinants for the interaction. Binding between SLD and 3C(pro) induces structural changes in the proteolytic active site that is positioned on the opposite side of the protease relative to the RNA/protein interface, suggesting that subtle conformational changes affecting catalytic activity are relayed through the protein.
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Affiliation(s)
- Jolyon K Claridge
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
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Martínez-Cruz LA, Encinar JA, Kortazar D, Prieto J, Gómez J, Fernández-Millán P, Lucas M, Arribas EA, Fernández JA, Martínez-Chantar ML, Mato JM, Neira JL. The CBS Domain Protein MJ0729 of Methanocaldococcus jannaschii Is a Thermostable Protein with a pH-Dependent Self-Oligomerization. Biochemistry 2009; 48:2760-76. [DOI: 10.1021/bi801920r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Luis Alfonso Martínez-Cruz
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - José A. Encinar
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - Danel Kortazar
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - Jesús Prieto
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - Javier Gómez
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - Pablo Fernández-Millán
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - María Lucas
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - Egoitz Astigarraga Arribas
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - José Andrés Fernández
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - María Luz Martínez-Chantar
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - José M. Mato
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
| | - José Luis Neira
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Vizcaya, Ed. 800, 48160 Derio, Bizkaia, Spain, Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain, Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), 28007 Madrid, Spain, Departamento de Química-Física, Universidad del País Vasco UPV-EHU, Lejona, Bizkaia, Spain, Unidad de Metabolómica, CIC bioGUNE, Parque
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14
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Severe acute respiratory syndrome coronavirus nsp9 dimerization is essential for efficient viral growth. J Virol 2009; 83:3007-18. [PMID: 19153232 DOI: 10.1128/jvi.01505-08] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) devotes a significant portion of its genome to producing nonstructural proteins required for viral replication. SARS-CoV nonstructural protein 9 (nsp9) was identified as an essential protein with RNA/DNA-binding activity, and yet its biological function within the replication complex remains unknown. Nsp9 forms a dimer through the interaction of parallel alpha-helices containing the protein-protein interaction motif GXXXG. In order to study the role of the nsp9 dimer in viral reproduction, residues G100 and G104 at the helix interface were targeted for mutation. Multi-angle light scattering measurements indicated that G100E, G104E, and G104V mutants are monomeric in solution, thereby disrupting the dimer. However, electrophoretic mobility assays revealed that the mutants bound RNA with similar affinity. Further experiments using fluorescence anisotropy showed a 10-fold reduction in RNA binding in the G100E and G104E mutants, whereas the G104V mutant had only a 4-fold reduction. The structure of G104E nsp9 was determined to 2.6-A resolution, revealing significant changes at the dimer interface. The nsp9 mutations were introduced into SARS-CoV using a reverse genetics approach, and the G100E and G104E mutations were found to be lethal to the virus. The G104V mutant produced highly debilitated virus and eventually reverted back to the wild-type protein sequence through a codon transversion. Together, these data indicate that dimerization of SARS-CoV nsp9 at the GXXXG motif is not critical for RNA binding but is necessary for viral replication.
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15
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Picornaviruses. VIRAL PROTEASES AND ANTIVIRAL PROTEASE INHIBITOR THERAPY 2009. [PMCID: PMC7122559 DOI: 10.1007/978-90-481-2348-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Amero CD, Arnold JJ, Moustafa IM, Cameron CE, Foster MP. Identification of the oriI-binding site of poliovirus 3C protein by nuclear magnetic resonance spectroscopy. J Virol 2008; 82:4363-70. [PMID: 18305026 PMCID: PMC2293054 DOI: 10.1128/jvi.02087-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 02/21/2008] [Indexed: 12/17/2022] Open
Abstract
Replication of picornaviral genomes requires recognition of at least three cis-acting replication elements: oriL, oriI, and oriR. Although these elements lack an obvious consensus sequence or structure, they are all recognized by the virus-encoded 3C protein. We have studied the poliovirus 3C-oriI interaction in order to begin to decipher the code of RNA recognition by picornaviral 3C proteins. oriI is a stem-loop structure that serves as the template for uridylylation of the peptide primer VPg by the viral RNA-dependent RNA polymerase. In this report, we have used nuclear magnetic resonance (NMR) techniques to study 3C alone and in complex with two single-stranded RNA oligonucleotides derived from the oriI stem. The (1)H-(15)N spectra of 3C recorded in the presence of these RNAs revealed site-specific chemical shift perturbations. Residues that exhibit significant perturbations are primarily localized in the amino terminus and in a highly conserved loop between residues 81 and 89. In general, the RNA-binding site defined in this study is consistent with predictions based on biochemical and mutagenesis studies. Although some residues implicated in RNA binding by previous studies are perturbed in the 3C-RNA complex reported here, many are unique. These studies provide unique site-specific insight into residues of 3C that interact with RNA and set the stage for detailed structural investigation of the 3C-RNA complex by NMR. Interpretation of our results in the context of an intact oriI provides insight into the architecture of the picornavirus VPg uridylylation complex.
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Affiliation(s)
- C D Amero
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 201 Althouse Laboratory, University Park, PA 16802, USA
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17
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Interaction between polypeptide 3ABC and the 5'-terminal structural elements of the genome of Aichi virus: implication for negative-strand RNA synthesis. J Virol 2008; 82:6161-71. [PMID: 18448525 DOI: 10.1128/jvi.02151-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Secondary structural elements at the 5' end of picornavirus genomic RNA function as cis-acting replication elements and are known to interact specifically with viral P3 proteins in several picornaviruses. In poliovirus, ribonucleoprotein complex formation at the 5' end of the genome is required for negative-strand synthesis. We have previously shown that the 5'-end 115 nucleotides of the Aichi virus genome, which are predicted to fold into two stem-loops (SL-A and SL-C) and one pseudoknot (PK-B), act as a cis-acting replication element and that correct folding of these structures is required for negative-strand synthesis. In this study, we investigated the interaction between the 5'-terminal 120 nucleotides of the genome and the P3 proteins, 3AB, 3ABC, 3C, and 3CD, by gel shift assay and Northwestern analysis. The results showed that 3ABC and 3CD bound to the 5'-terminal region specifically. The binding of 3ABC was observed on both assays, while that of 3CD was detected only on Northwestern analysis. No binding of 3AB or 3C was observed. Binding assays using mutant RNAs demonstrated that disruption of the base pairings of the stem of SL-A and one of the two stem segments of PK-B (stem-B1) abolished the 3ABC binding. In addition, the specific nucleotide sequence of stem-B1 was responsible for the efficient 3ABC binding. These results suggest that the interaction of 3ABC with the 5'-terminal region of the genome is involved in negative-strand synthesis. On the other hand, the ability of 3CD to interact with the 5'-terminal region did not correlate with the RNA replication ability.
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18
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An RNA microchip containing immobilized oligoribonucleotides with protective groups at 2'-O-positions. Biotechniques 2008; 44:77-83. [PMID: 18254383 DOI: 10.2144/000112677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To analyze RNA interactions with RNA binding molecules an RNA microchip containing immobilized oligoribonucleotides with protective groups [t-butyldimethylsilyl (tBDMS)] at 2'-O- positions was developed. The oligonucleotides were immobilized within three-dimensional (3-D) hydrogel pads fixed on a glass support. The protective groups preserved the oligoribonucleodes from degradation and were suitable to be removed directly on the microchip when needed, right before its use. These immobilized, deprotected oligoribonucleotides were tested for their interaction with afluorescently labeled oligodeoxyribonucleotide and analyzed for their availability to be cleaved enzymatically by the RNase binase. Stability of tBDMS-protected immobilized oligoribonucleotides after 2.5 years of storage as well as after direct RNase action was also tested. Melting curves of short RNA/DNA hybrids that had formed into gel pads of the microchip were found to exhibit clearly defined S-like shapes, with the melting temperatures in full accordance with those theoretically predicted for the same ionic strength. This approach, based on keeping the protective groups attached to oligoribonucleotides, can be applied for manufacturing any RNA microchips containing immobilized oligoribonucleotides, including microchips with two-dimensional (2-D) features. These RNA microchips can be used to measure thermodynamic parameters of RNA/RNA or RNA/DNA duplexes as well as to study ligand- or protein-RNA interactions.
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19
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Shen M, Reitman ZJ, Zhao Y, Moustafa I, Wang Q, Arnold JJ, Pathak HB, Cameron CE. Picornavirus genome replication. Identification of the surface of the poliovirus (PV) 3C dimer that interacts with PV 3Dpol during VPg uridylylation and construction of a structural model for the PV 3C2-3Dpol complex. J Biol Chem 2008; 283:875-88. [PMID: 17993457 PMCID: PMC2186065 DOI: 10.1074/jbc.m707907200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Picornaviruses have a peptide termed VPg covalently linked to the 5'-end of the genome. Attachment of VPg to the genome occurs in at least two steps. First, Tyr-3 of VPg, or some precursor thereof, is used as a primer by the viral RNA-dependent RNA polymerase, 3Dpol, to produce VPg-pUpU. Second, VPg-pUpU is used as a primer to produce full-length genomic RNA. Production of VPg-pUpU is templated by a single adenylate residue located in the loop of an RNA stem-loop structure termed oriI by using a slide-back mechanism. Recruitment of 3Dpol to and its stability on oriI have been suggested to require an interaction between the back of the thumb subdomain of 3Dpol and an undefined region of the 3C domain of viral protein 3CD. We have performed surface acidic-to-alanine-scanning mutagenesis of 3C to identify the surface of 3C with which 3Dpol interacts. This analysis identified numerous viable poliovirus mutants with reduced growth kinetics that correlated to reduced kinetics of RNA synthesis that was attributable to a change in VPg-pUpU production. Importantly, these 3C derivatives were all capable of binding to oriI as well as wild-type 3C. Synthetic lethality was observed for these mutants when placed in the context of a poliovirus mutant containing 3Dpol-R455A, a residue on the back of the thumb required for VPg uridylylation. These data were used to guide molecular docking of the structures for a poliovirus 3C dimer and 3Dpol, leading to a structural model for the 3C(2)-3Dpol complex that extrapolates well to all picornaviruses.
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Affiliation(s)
- Miaoqing Shen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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20
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Czypionka A, de los Paños OR, Mateu MG, Barrera FN, Hurtado-Gómez E, Gómez J, Vidal M, Neira JL. The isolated C-terminal domain of Ring1B is a dimer made of stable, well-structured monomers. Biochemistry 2007; 46:12764-76. [PMID: 17935356 DOI: 10.1021/bi701343q] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Ring1B is a core subunit protein of the PRC1 (polycomb repressive complex 1), which plays key roles in the regulation of the Homeobox gene expression, X-chromosome inactivation, stem cell self-renewal, and tumorigenesis. The C-terminal region of Ring1B interacts with RYBP, a transcriptional repressor in transiently transfected cells, and also with M33, another transcriptional repressor involved in mesoderm patterning. In this work, we show that the C-terminal domain of Ring1B, C-Ring1B, is a dimer in solution, with a dissociation constant of 200 microM, as shown by NMR, ITC, and analytical gel filtration. Each monomer is stable at physiological conditions in a wide pH range ( approximately 5 kcal mol-1 at 298 K), with a well-formed core and a spherical shape. The dimer has a high content of alpha-helix and beta-sheet, as indicated by FTIR spectra, and it is formed by the mutual docking of the preformed folded monomers. Since the C-terminal region is important for interaction with other proteins of the PRC1, the dimerization and the presence of those well-structured monomers might be a form of regulation.
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Affiliation(s)
- Anna Czypionka
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
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21
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Endo K, Takahashi M, Masuko K, Inoue K, Akahane Y, Okamoto H. Full-length sequences of subgenotype IIIA and IIIB hepatitis A virus isolates: Characterization of genotype III HAV genomes. Virus Res 2007; 126:116-27. [PMID: 17376556 DOI: 10.1016/j.virusres.2007.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 02/03/2007] [Accepted: 02/08/2007] [Indexed: 01/08/2023]
Abstract
To elucidate the extent of genomic heterogeneity of human hepatitis A virus (HAV) strains and to characterize genotype III HAV strains over the entire genome, the full-length sequence of three subgenotype IIIA isolates (HA-JNG04-90F, HA-JNG08-92F, and HAJ95-8F) and one IIIB isolate (HAJ85-1F) was determined. The HA-JNG04-90F, HA-JNG08-92F, and HAJ95-8F genomes which comprised 7463 or 7464 nt excluding the poly(A) tail, were closest to a reported nearly entire sequence of a IIIA isolate (NOR-21) with identities of 94.4-97.8% over the entire ORF sequence, and the HAJ85-1 genome (7462 nt) to HA-JNG06-90F of IIIB with an identity of 98.6%. The phylogenetic trees constructed based on the complete ORF sequence or the 168-nt VP1/2A junction sequence and comparative analysis with reported HAV isolates suggested the presence of three distinct clusters within IIIA represented by HA-JNG04-90F, HA-JNG08-92F, and HAJ95-8F. The extreme 5' end sequences of IIIA and IIIB were well-conserved, beginning with the sequence UUCAAGAGGG. A single base deletion of G at nt 20, which is involved in the formation of a small loop in domain I, was characteristic of both IIIA and IIIB. Conserved and divergent amino acid sequences as well as amino acids unique to genotype III, IIIA or IIIB were recognized.
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Affiliation(s)
- Kazunori Endo
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-Shi, Tochigi-Ken 329-0498, Japan
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22
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Zeitler CE, Estes MK, Venkataram Prasad BV. X-ray crystallographic structure of the Norwalk virus protease at 1.5-A resolution. J Virol 2006; 80:5050-8. [PMID: 16641296 PMCID: PMC1472067 DOI: 10.1128/jvi.80.10.5050-5058.2006] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Norwalk virus (NV), a member of the Caliciviridae family, is the major cause of acute, epidemic, viral gastroenteritis. The NV genome is a positive sense, single-stranded RNA that encodes three open reading frames (ORFs). The first ORF produces a polyprotein that is processed by the viral cysteine protease into six nonstructural proteins. We have determined the structure of the NV protease to 1.5 and 2.2 A from crystals grown in the absence or presence, respectively, of the protease inhibitor AEBSF [4-(2-aminoethyl)-benzenesulfonyl fluoride]. The protease, which crystallizes as a stable dimer, exhibits a two-domain structure similar to those of other viral cysteine proteases with a catalytic triad composed of His 30, Glu 54, and Cys 139. The native structure of the protease reveals strong hydrogen bond interactions between His 30 and Glu 54, in the favorable syn configuration, indicating a role of Glu 54 during proteolysis. Mutation of this residue to Ala abolished the protease activity, in a fluorogenic peptide substrate assay, further substantiating the role of Glu 54 during proteolysis. These observations contrast with the suggestion, from a previous study of another norovirus protease, that this residue may not have a prominent role in proteolysis (K. Nakamura, Y. Someya, T. Kumasaka, G. Ueno, M. Yamamoto, T. Sato, N. Takeda, T. Miyamura, and N. Tanaka, J. Virol. 79:13685-13693, 2005). In the structure from crystals grown in the presence of AEBSF, Glu 54 undergoes a conformational change leading to disruption of the hydrogen bond interactions with His 30. Since AEBSF was not apparent in the electron density map, it is possible that these conformational changes are due to subtle changes in pH caused by its addition during crystallization.
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Affiliation(s)
- Corinne E Zeitler
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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23
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Abstract
We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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24
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Yin J, Bergmann EM, Cherney MM, Lall MS, Jain RP, Vederas JC, James MN. Dual modes of modification of hepatitis A virus 3C protease by a serine-derived beta-lactone: selective crystallization and formation of a functional catalytic triad in the active site. J Mol Biol 2005; 354:854-71. [PMID: 16288920 PMCID: PMC7118759 DOI: 10.1016/j.jmb.2005.09.074] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 09/22/2005] [Accepted: 09/23/2005] [Indexed: 12/30/2022]
Abstract
Hepatitis A virus (HAV) 3C proteinase is a member of the picornain cysteine proteases responsible for the processing of the viral polyprotein, a function essential for viral maturation and infectivity. This and its structural similarity to other 3C and 3C-like proteases make it an attractive target for the development of antiviral drugs. Previous solution NMR studies have shown that a Cys24Ser (C24S) variant of HAV 3C protein, which displays catalytic properties indistinguishable from the native enzyme, is irreversibly inactivated by N-benzyloxycarbonyl-l-serine-beta-lactone (1a) through alkylation of the sulfur atom at the active site Cys172. However, crystallization of an enzyme-inhibitor adduct from the reaction mixture followed by X-ray structural analysis shows only covalent modification of the epsilon2-nitrogen of the surface His102 by the beta-lactone with no reaction at Cys172. Re-examination of the heteronuclear multiple quantum coherence (HMQC) NMR spectra of the enzyme-inhibitor mixture indicates that dual modes of single covalent modification occur with a >/=3:1 ratio of S-alkylation of Cys172 to N-alkylation of His102. The latter product crystallizes readily, probably due to the interaction between the phenyl ring of the N-benzyloxycarbonyl (N-Cbz) moiety and a hydrophobic pocket of a neighboring protein molecule in the crystal. Furthermore, significant structural changes are observed in the active site of the 3C protease, which lead to the formation of a functional catalytic triad with Asp84 accepting one hydrogen bond from His44. Although the 3C protease modified at Cys172 is catalytically inactive, the singly modified His102 N(epsilon2)-alkylated protein displays a significant level of enzymatic activity, which can be further modified/inhibited by N-iodoacetyl-valine-phenylalanine-amide (IVF) (in solution and in crystal) or excessive amount of the same beta-lactone inhibitor (in solution). The success of soaking IVF into HAV 3C-1a crystals demonstrates the usefulness of this new crystal form in the study of enzyme-inhibitor interactions in the proteolytic active site.
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Affiliation(s)
- Jiang Yin
- CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7
| | - Ernst M. Bergmann
- CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7
- Alberta Synchrotron Institute, University of Alberta, Edmonton, Alta., Canada T6G 2E1
| | - Maia M. Cherney
- CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7
| | - Manjinder S. Lall
- Department of Chemistry, University of Alberta, Edmonton, Alta., Canada T6G 2G2
| | - Rajendra P. Jain
- Department of Chemistry, University of Alberta, Edmonton, Alta., Canada T6G 2G2
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alta., Canada T6G 2G2
| | - Michael N.G. James
- CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7
- Alberta Synchrotron Institute, University of Alberta, Edmonton, Alta., Canada T6G 2E1
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