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Yoon J, Zhang YM, Her C, Grant RA, Ponomarenko AI, Ackermann BE, Hui T, Lin YS, Debelouchina GT, Shoulders MD. The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure. Sci Adv 2024; 10:eadl6144. [PMID: 38640233 PMCID: PMC11029814 DOI: 10.1126/sciadv.adl6144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/15/2024] [Indexed: 04/21/2024]
Abstract
Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. NP also determines the sensitivity of influenza to myxovirus resistance protein 1 (MxA), an innate immunity factor that restricts influenza replication. A few critical MxA-resistant mutations have been identified in NP, including the highly conserved proline-283 substitution. This essential proline-283 substitution impairs influenza growth, a fitness defect that becomes particularly prominent at febrile temperature (39°C) when host chaperones are depleted. Here, we biophysically characterize proline-283 NP and serine-283 NP to test whether the fitness defect is caused by the proline-283 substitution introducing folding defects. We show that the proline-283 substitution changes the folding pathway of NP, making NP more aggregation prone during folding, but does not alter the native structure of the protein. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape.
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Affiliation(s)
- Jimin Yoon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yu Meng Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cheenou Her
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Robert A. Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna I. Ponomarenko
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bryce E. Ackermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Tiffani Hui
- Department of Chemistry, Tufts University, Medford, MA, USA
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, MA, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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2
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Aoki K, Tsuda S, Ogata N, Kataoka M, Sasaki J, Inuki S, Ohno H, Watashi K, Yoshiya T, Oishi S. Synthesis of the full-length hepatitis B virus core protein and its capsid formation. Org Biomol Chem 2024; 22:2218-2225. [PMID: 38358380 DOI: 10.1039/d3ob02099a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Chronic infection with hepatitis B virus (HBV) is a major cause of cirrhosis and liver cancer. Capsid assembly modulators can induce error-prone assembly of HBV core proteins to prevent the formation of infectious virions, representing promising candidates for treating chronic HBV infections. To explore novel capsid assembly modulators from unexplored mirror-image libraries of natural products, we have investigated the synthetic process of the HBV core protein for preparing the mirror-image target protein. In this report, the chemical synthesis of full-length HBV core protein (Cp183) containing an arginine-rich nucleic acid-binding domain at the C-terminus is presented. Sequential ligations using four peptide segments enabled the synthesis of Cp183 via convergent and C-to-N direction approaches. After refolding under appropriate conditions, followed by the addition of nucleic acid, the synthetic Cp183 assembled into capsid-like particles.
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Affiliation(s)
- Keisuke Aoki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Shugo Tsuda
- Peptide Institute, Inc. Ibaraki, Osaka 567-0085, Japan
| | - Naoko Ogata
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Michiyo Kataoka
- Department of Pathology, National Institute of Infectious Disease, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Jumpei Sasaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Koichi Watashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Taku Yoshiya
- Peptide Institute, Inc. Ibaraki, Osaka 567-0085, Japan
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.
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3
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Wu Y, Thomas GM, Thomsen M, Bahri S, Lieberman RL. Lipid environment modulates processivity and kinetics of a presenilin homolog acting on multiple substrates in vitro. J Biol Chem 2023; 299:105401. [PMID: 38270390 PMCID: PMC10679502 DOI: 10.1016/j.jbc.2023.105401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/12/2023] [Accepted: 10/11/2023] [Indexed: 01/26/2024] Open
Abstract
Intramembrane proteases (IPs) hydrolyze peptides in the lipid membrane. IPs participate in a number of cellular pathways including immune response and surveillance, and cholesterol biosynthesis, and they are exploited by viruses for replication. Despite their broad importance across biology, how activity is regulated in the cell to control protein maturation and release of specific bioactive peptides at the right place and right time remains largely unanswered, particularly for the intramembrane aspartyl protease (IAP) subtype. At a molecular biochemical level, different IAP homologs can cleave non-biological substrates, and there is no sequence recognition motif among the nearly 150 substrates identified for just one IAP, presenilin-1, the catalytic component of γ-secretase known for its involvement in the production of amyloid-β plaques associated with Alzheimer disease. Here we used gel-based assays combined with quantitative mass spectrometry and FRET-based kinetics assays to probe the cleavage profile of the presenilin homolog from the methanogen Methanoculleus marisnigri JR1 as a function of the surrounding lipid-mimicking environment, either detergent micelles or bicelles. We selected four biological IAP substrates that have not undergone extensive cleavage profiling previously, namely, the viral core protein of Hepatitis C virus, the viral core protein of Classical Swine Fever virus, the transmembrane segment of Notch-1, and the tyrosine receptor kinase ErbB4. Our study demonstrates a proclivity toward cleavage of substrates at positions of low average hydrophobicity and a consistent role for the lipid environment in modulating kinetic properties.
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Affiliation(s)
- Yuqi Wu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Gwendell M Thomas
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Max Thomsen
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sara Bahri
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.
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4
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Wang J, Huang H, Zhao K, Teng Y, Zhao L, Xu Z, Zheng Y, Zhang L, Li C, Duan Y, Liang K, Zhou X, Cheng X, Xia Y. G-quadruplex in hepatitis B virus pregenomic RNA promotes its translation. J Biol Chem 2023; 299:105151. [PMID: 37567479 PMCID: PMC10485161 DOI: 10.1016/j.jbc.2023.105151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Hepatitis B virus (HBV) is a hepatotropic DNA virus that has a very compact genome. Due to this genomic density, several distinct mechanisms are used to facilitate the viral life cycle. Recently, accumulating evidence show that G-quadruplex (G4) in different viruses play essential regulatory roles in key steps of the viral life cycle. Although G4 structures in the HBV genome have been reported, their function in HBV replication remains elusive. In this study, we treated an HBV replication-competent cell line and HBV-infected cells with the G4 structure stabilizer pyridostatin (PDS) and evaluated different HBV replication markers to better understand the role played by the G4. In both models, we found PDS had no effect on viral precore RNA (pcRNA) or pre-genomic RNA (pgRNA), but treatment did increase HBeAg/HBc ELISA reads and intracellular levels of viral core/capsid protein (HBc) in a dose-dependent manner, suggesting post-transcriptional regulation. To further dissect the mechanism of G4 involvement, we used in vitro-synthesized HBV pcRNA and pgRNA. Interestingly, we found PDS treatment only enhanced HBc expression from pgRNA but not HBeAg expression from pcRNA. Our bioinformatic analysis and CD spectroscopy revealed that pgRNA harbors a conserved G4 structure. Finally, we introduced point mutations in pgRNA to disrupt its G4 structure and observed the resulting mutant failed to respond to PDS treatment and decreased HBc level in in vitro translation assay. Taken together, our data demonstrate that HBV pgRNA contains a G4 structure that plays a vital role in the regulation of viral mRNA translation.
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Affiliation(s)
- Jingjing Wang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Haiyan Huang
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yan Teng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Li Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Zaichao Xu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yingcheng Zheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Lu Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Conghui Li
- Department of Pathophysiology, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yurong Duan
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Kaiwei Liang
- Department of Pathophysiology, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China.
| | - Xiaoming Cheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China; Department of Pathology, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China; Hubei Jiangxia Laboratory, Wuhan, China.
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China; Hubei Jiangxia Laboratory, Wuhan, China.
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5
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Lubyova B, Tikalova E, Krulova K, Hodek J, Zabransky A, Hirsch I, Weber J. ATM-Dependent Phosphorylation of Hepatitis B Core Protein in Response to Genotoxic Stress. Viruses 2021; 13:v13122438. [PMID: 34960710 PMCID: PMC8705010 DOI: 10.3390/v13122438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 12/31/2022] Open
Abstract
Chronic hepatitis caused by infection with the Hepatitis B virus is a life-threatening condition. In fact, 1 million people die annually due to liver cirrhosis or hepatocellular carcinoma. Recently, several studies demonstrated a molecular connection between the host DNA damage response (DDR) pathway and HBV replication and reactivation. Here, we investigated the role of Ataxia-telangiectasia-mutated (ATM) and Ataxia telangiectasia and Rad3-related (ATR) PI3-kinases in phosphorylation of the HBV core protein (HBc). We determined that treatment of HBc-expressing hepatocytes with genotoxic agents, e.g., etoposide or hydrogen peroxide, activated the host ATM-Chk2 pathway, as determined by increased phosphorylation of ATM at Ser1981 and Chk2 at Thr68. The activation of ATM led, in turn, to increased phosphorylation of cytoplasmic HBc at serine-glutamine (SQ) motifs located in its C-terminal domain. Conversely, down-regulation of ATM using ATM-specific siRNAs or inhibitor effectively reduced etoposide-induced HBc phosphorylation. Detailed mutation analysis of S-to-A HBc mutants revealed that S170 (S168 in a 183-aa HBc variant) is the primary site targeted by ATM-regulated phosphorylation. Interestingly, mutation of two major phosphorylation sites involving serines at positions 157 and 164 (S155 and S162 in a 183-aa HBc variant) resulted in decreased etoposide-induced phosphorylation, suggesting that the priming phosphorylation at these serine-proline (SP) sites is vital for efficient phosphorylation of SQ motifs. Notably, the mutation of S172 (S170 in a 183-aa HBc variant) had the opposite effect and resulted in massively up-regulated phosphorylation of HBc, particularly at S170. Etoposide treatment of HBV infected HepG2-NTCP cells led to increased levels of secreted HBe antigen and intracellular HBc protein. Together, our studies identified HBc as a substrate for ATM-mediated phosphorylation and mapped the phosphorylation sites. The increased expression of HBc and HBe antigens in response to genotoxic stress supports the idea that the ATM pathway may provide growth advantage to the replicating virus.
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Affiliation(s)
- Barbora Lubyova
- IOCB Gilead Research Center, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic; (E.T.); (K.K.); (J.H.); (A.Z.); (I.H.)
- Correspondence: (B.L.); (J.W.)
| | - Eva Tikalova
- IOCB Gilead Research Center, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic; (E.T.); (K.K.); (J.H.); (A.Z.); (I.H.)
| | - Kristyna Krulova
- IOCB Gilead Research Center, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic; (E.T.); (K.K.); (J.H.); (A.Z.); (I.H.)
| | - Jan Hodek
- IOCB Gilead Research Center, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic; (E.T.); (K.K.); (J.H.); (A.Z.); (I.H.)
| | - Ales Zabransky
- IOCB Gilead Research Center, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic; (E.T.); (K.K.); (J.H.); (A.Z.); (I.H.)
| | - Ivan Hirsch
- IOCB Gilead Research Center, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic; (E.T.); (K.K.); (J.H.); (A.Z.); (I.H.)
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 252 50 Vestec, Czech Republic
| | - Jan Weber
- IOCB Gilead Research Center, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic; (E.T.); (K.K.); (J.H.); (A.Z.); (I.H.)
- Correspondence: (B.L.); (J.W.)
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6
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Liu H, Cheng J, Viswanathan U, Chang J, Lu F, Guo JT. Amino acid residues at core protein dimer-dimer interface modulate multiple steps of hepatitis B virus replication and HBeAg biogenesis. PLoS Pathog 2021; 17:e1010057. [PMID: 34752483 PMCID: PMC8604296 DOI: 10.1371/journal.ppat.1010057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/19/2021] [Accepted: 10/22/2021] [Indexed: 12/19/2022] Open
Abstract
The core protein (Cp) of hepatitis B virus (HBV) assembles pregenomic RNA (pgRNA) and viral DNA polymerase to form nucleocapsids where the reverse transcriptional viral DNA replication takes place. Core protein allosteric modulators (CpAMs) inhibit HBV replication by binding to a hydrophobic "HAP" pocket at Cp dimer-dimer interfaces to misdirect the assembly of Cp dimers into aberrant or morphologically "normal" capsids devoid of pgRNA. We report herein that a panel of CpAM-resistant Cp with single amino acid substitution of residues at the dimer-dimer interface not only disrupted pgRNA packaging, but also compromised nucleocapsid envelopment, virion infectivity and covalently closed circular (ccc) DNA biosynthesis. Interestingly, these mutations also significantly reduced the secretion of HBeAg. Biochemical analysis revealed that the CpAM-resistant mutations in the context of precore protein (p25) did not affect the levels of p22 produced by signal peptidase removal of N-terminal 19 amino acid residues, but significantly reduced p17, which is produced by furin cleavage of C-terminal arginine-rich domain of p22 and secreted as HBeAg. Interestingly, p22 existed as both unphosphorylated and phosphorylated forms. While the unphosphorylated p22 is in the membranous secretary organelles and the precursor of HBeAg, p22 in the cytosol and nuclei is hyperphosphorylated at the C-terminal arginine-rich domain and interacts with Cp to disrupt capsid assembly and viral DNA replication. The results thus indicate that in addition to nucleocapsid assembly, interaction of Cp at dimer-dimer interface also plays important roles in the production and infectivity of progeny virions through modulation of nucleocapsid envelopment and uncoating. Similar interaction at reduced p17 dimer-dimer interface appears to be important for its metabolic stability and sensitivity to CpAM suppression of HBeAg secretion.
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Affiliation(s)
- Hui Liu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Junjun Cheng
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Usha Viswanathan
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Jinhong Chang
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Fengmin Lu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- * E-mail: (FL); (J-TG)
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
- * E-mail: (FL); (J-TG)
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Chen R, Huang S, Lin T, Ma H, Shan W, Duan F, Lv J, Zhang J, Ren L, Nie L. Photoacoustic molecular imaging-escorted adipose photodynamic-browning synergy for fighting obesity with virus-like complexes. Nat Nanotechnol 2021; 16:455-465. [PMID: 33526836 DOI: 10.1038/s41565-020-00844-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
Photodynamic therapy and adipose browning induction are two promising approaches to reverse obesity. The former strategy acts rapidly and locally, whereas the latter has a more gradual and widespread effect. Despite their complementarity, they have rarely been combined and imaged non-invasively in vivo. Here we introduce an adipose-targeting hepatitis B core protein complex that contains a traceable photosensitizer (ZnPcS4 (zinc phthalocyanine tetrasulfonate)) and a browning agent (rosiglitazone) that allows simultaneous photodynamic and browning treatments, with photoacoustic molecular imaging. After intravenous injection in obese mice, the complex binds specifically to white adipose tissues, especially those rich in blood supply, and drives adipose reduction thanks to the synergy of ZnPcS4 photodynamics and rosiglitazone browning. Using photoacoustic molecular imaging, we could monitor the changes induced by the treatment, which included complex activity, lipid catabolism and angiogenesis. Our findings demonstrate the anti-obesity potential of our feedback-based synergic regimen orchestrated by the targeted hepatitis B core complex.
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Affiliation(s)
- Ronghe Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnosis & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Shanshan Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnosis & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Tongtong Lin
- Department of Biomaterials, Key Laboratory of Biomedical Engineering of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surface, College of Materials, Xiamen University, Xiamen, China
| | - Haosong Ma
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnosis & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Wenjun Shan
- Department of Pharmacology, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing, China
| | - Fei Duan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnosis & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Jing Lv
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnosis & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Jinde Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnosis & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Lei Ren
- Department of Biomaterials, Key Laboratory of Biomedical Engineering of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surface, College of Materials, Xiamen University, Xiamen, China
| | - Liming Nie
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnosis & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China.
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8
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Khan S, Fakhar Z, Ahmad A. Targeting ebola virus VP40 protein through novel inhibitors: exploring the structural and dynamic perspectives on molecular landscapes. J Mol Model 2021; 27:49. [PMID: 33495861 DOI: 10.1007/s00894-021-04682-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 01/17/2021] [Indexed: 11/27/2022]
Abstract
Ebola filovirus (EBOV) is one of the deadliest known infectious agents, and a cause of Western African epidemics from 2013 to 2016. The virus has infected nearly 3000 humans and almost 1900 have died. In the past few years, various small molecules have been discovered to display efficiency against EBOV and some of them have progressed towards clinical trials. Even though continuous attempts have been made to find antiEBOV therapeutics, no potential drugs are yet approved against this viral infection. The development of small antiviral inhibitors has gained tremendous attention in the attempt to overcome EVD. With this background, we seek to offer molecular insights into EBOV VP40 protein inhibition, using all atom molecular mechanics methodology and binding free energy calculations. We have selected five novel reported inhibitors against VP40 protein, namely Comp1, Comp2, Comp3, Comp4, and Comp5, and explored their binding against the same target. It was evident from the analysis that all the inhibitors displayed stability in complex with VP40 protein; however, Comp1 exhibited enhanced stability and compactness. Comp1 unveiled favorable binding, which accounted for positive correlation motions in the active site residues. Likewise, Comp1 revealed the most promising binding (ΔGbind - 40.3504 kcal/mol) as compared to the other four inhibitors, which disclosed relatively less favorable ΔGbind. The highest binding energy of Comp1 to VP40 protein can be primarily endorsed to the upsurge in van der Waals energy by ΔEvdW - 37.1609 kcal/mol and Coulomb energy by ΔEele - 52.7332 kcal/mol. Also, the hydrogen bond network is robust in Comp1-VP40 complex, with four hydrogen bonds, whilst it is less in other inhibitors. The outcomes from this report may assist in the advancement of novel VP40 inhibitors with high selectivity and potency for EVD therapeutics.
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Affiliation(s)
- Shama Khan
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Zeynab Fakhar
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Aijaz Ahmad
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg, 2193, South Africa.
- Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, 2193, South Africa.
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9
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Xi J, Luckenbaugh L, Hu J. Multiple roles of PP2A binding motif in hepatitis B virus core linker and PP2A in regulating core phosphorylation state and viral replication. PLoS Pathog 2021; 17:e1009230. [PMID: 33493210 PMCID: PMC7861550 DOI: 10.1371/journal.ppat.1009230] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 02/04/2021] [Accepted: 12/08/2020] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) capsid or core protein (HBc) contains an N-terminal domain (NTD) and a C-terminal domain (CTD) connected by a short linker peptide. HBc plays a critical role in virtually every step of viral replication, which is further modulated by dynamic phosphorylation and dephosphorylation of its CTD. While several cellular kinases have been identified that mediate HBc CTD phosphorylation, there is little information on the cellular phosphatases that mediate CTD dephosphorylation. Herein, a consensus binding motif for the protein phosphatase 2A (PP2A) regulatory subunit B56 was recognized within the HBc linker peptide. Mutations within this motif designed to block or enhance B56 binding showed pleiotropic effects on CTD phosphorylation state as well as on viral RNA packaging, reverse transcription, and virion secretion. Furthermore, linker mutations affected the HBV nuclear episome (the covalently closed circular or CCC DNA) differentially during intracellular amplification vs. infection. The effects of linker mutations on CTD phosphorylation state varied with different phosphorylation sites and were only partially consistent with the linker motif serving to recruit PP2A-B56, specifically, to dephosphorylate CTD, suggesting that multiple phosphatases and/or kinases may be recruited to modulate CTD (de)phosphorylation. Furthermore, pharmacological inhibition of PP2A could decrease HBc CTD dephosphorylation and increase the nuclear HBV episome. These results thus strongly implicate the HBc linker in recruiting PP2A and other host factors to regulate multiple stages of HBV replication. Hepatitis B virus (HBV) causes acute and chronic viral hepatitis, liver fibrosis, cirrhosis and cancer. The dynamic phosphorylation and dephosphorylation of the viral capsid protein (HBc), which are controlled by host cell protein kinases and phosphatases, play a critical role in regulating multiple stages of HBV replication. While a number of cellular kinases have been identified that mediate HBc phosphorylation, there is little information on cellular phosphatases that mediate its dephosphorylation. Herein we have identified a consensus binding motif in HBc for one of the major cellular phosphatases, the protein phosphatase 2A (PP2A). Genetic analysis of this motif revealed that it played multiple roles in regulating CTD phosphorylation state, as well as viral RNA packaging, reverse transcription, virion secretion, and formation of the nuclear HBV episome responsible for viral persistence. Furthermore, pharmacological inhibition of PP2A decreased HBc dephosphorylation and increased the nuclear episome, further supporting a role of PP2A in HBc dephosphorylation and HBV persistence. These results thus suggest that HBc recruits PP2A, among other host factors, to regulate HBc phosphorylation and dephosphorylation dynamics and HBV replication and persistence.
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Affiliation(s)
- Ji Xi
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Laura Luckenbaugh
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Jianming Hu
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail:
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10
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Ivanov A, Ramanathan P, Parry C, Ilinykh PA, Lin X, Petukhov M, Obukhov Y, Ammosova T, Amarasinghe GK, Bukreyev A, Nekhai S. Global phosphoproteomic analysis of Ebola virions reveals a novel role for VP35 phosphorylation-dependent regulation of genome transcription. Cell Mol Life Sci 2020; 77:2579-2603. [PMID: 31562565 PMCID: PMC7101265 DOI: 10.1007/s00018-019-03303-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/26/2019] [Accepted: 09/16/2019] [Indexed: 12/27/2022]
Abstract
Ebola virus (EBOV) causes severe human disease with a high case fatality rate. The balance of evidence implies that the virus circulates in bats. The molecular basis for host-viral interactions, including the role for phosphorylation during infections, is largely undescribed. To address this, and to better understand the biology of EBOV, the phosphorylation of EBOV proteins was analyzed in virions purified from infected monkey Vero-E6 cells and bat EpoNi/22.1 cells using high-resolution mass spectrometry. All EBOV structural proteins were detected with high coverage, along with phosphopeptides. Phosphorylation sites were identified in all viral structural proteins. Comparison of EBOV protein phosphorylation in monkey and bat cells showed only partial overlap of phosphorylation sites, with shared sites found in NP, VP35, and VP24 proteins, and no common sites in the other proteins. Three-dimensional structural models were built for NP, VP35, VP40, GP, VP30 and VP24 proteins using available crystal structures or by de novo structure prediction to elucidate the potential role of the phosphorylation sites. Phosphorylation of one of the identified sites in VP35, Thr-210, was demonstrated to govern the transcriptional activity of the EBOV polymerase complex. Thr-210 phosphorylation was also shown to be important for VP35 interaction with NP. This is the first study to compare phosphorylation of all EBOV virion proteins produced in primate versus bat cells, and to demonstrate the role of VP35 phosphorylation in the viral life cycle. The results uncover a novel mechanism of EBOV transcription and identify novel targets for antiviral drug development.
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Affiliation(s)
- Andrey Ivanov
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
| | - Palaniappan Ramanathan
- Department of Pathology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA
| | - Christian Parry
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
- Department of Microbiology, Howard University, Washington, D.C., 20059, USA
| | - Philipp A Ilinykh
- Department of Pathology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA
| | - Xionghao Lin
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
- College of Dentistry, Howard University, Washington, D.C., 20059, USA
| | - Michael Petukhov
- Division of Molecular and Radiation Biophysics, Russian Nuclear Physics Institute Named After B. P. Konstantinov, National Research Center "Kurchatov Institute", Gatchina, 188300, Russia
- Russian Scientific Center of Radiology and Surgical Technologies Named After A. M. Granov, St. Petersburg, 197758, Russia
| | - Yuri Obukhov
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
| | - Tatiana Ammosova
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
- Department of Medicine, Howard University, Washington, D.C., 20059, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA.
- Department of Microbiology and Immunology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA.
- Galveston National Laboratory, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA.
| | - Sergei Nekhai
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA.
- Department of Microbiology, Howard University, Washington, D.C., 20059, USA.
- Department of Medicine, Howard University, Washington, D.C., 20059, USA.
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11
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Zhang P, Yang S, Pineda-Gómez R, Ibarlucea B, Ma J, Lohe MR, Akbar TF, Baraban L, Cuniberti G, Feng X. Electrochemically Exfoliated High-Quality 2H-MoS 2 for Multiflake Thin Film Flexible Biosensors. Small 2019; 15:e1901265. [PMID: 31034144 DOI: 10.1002/smll.201901265] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/13/2019] [Indexed: 06/09/2023]
Abstract
2D molybdenum disulfide (MoS2 ) gives a new inspiration for the field of nanoelectronics, photovoltaics, and sensorics. However, the most common processing technology, e.g., liquid-phase based scalable exfoliation used for device fabrication, leads to the number of shortcomings that impede their large area production and integration. Major challenges are associated with the small size and low concentration of MoS2 flakes, as well as insufficient control over their physical properties, e.g., internal heterogeneity of the metallic and semiconducting phases. Here it is demonstrated that large semiconducting MoS2 sheets (with dimensions up to 50 µm) can be obtained by a facile cathodic exfoliation approach in nonaqueous electrolyte. The synthetic process avoids surface oxidation thus preserving the MoS2 sheets with intact crystalline structure. It is further demonstrated at the proof-of-concept level, a solution-processed large area (60 × 60 µm) flexible Ebola biosensor, based on a MoS2 thin film (6 µm thickness) fabricated via restacking of the multiple flakes on the polyimide substrate. The experimental results reveal a low detection limit (in femtomolar-picomolar range) of the fabricated sensor devices. The presented exfoliation method opens up new opportunities for fabrication of large arrays of multifunctional biomedical devices based on novel 2D materials.
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Affiliation(s)
- Panpan Zhang
- Chair for Molecular Functional Materials, Department of Chemistry and Food Chemistry, School of Science, Technische Universität Dresden, Mommsenstr. 4, 01069, Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany
| | - Sheng Yang
- Chair for Molecular Functional Materials, Department of Chemistry and Food Chemistry, School of Science, Technische Universität Dresden, Mommsenstr. 4, 01069, Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany
| | - Roberto Pineda-Gómez
- Max Bergman Center of Biomaterials Dresden and Institute for Materials Science, Technische Universität Dresden, 01062, Dresden, Germany
| | - Bergoi Ibarlucea
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany
- Max Bergman Center of Biomaterials Dresden and Institute for Materials Science, Technische Universität Dresden, 01062, Dresden, Germany
| | - Ji Ma
- Chair for Molecular Functional Materials, Department of Chemistry and Food Chemistry, School of Science, Technische Universität Dresden, Mommsenstr. 4, 01069, Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany
| | - Martin R Lohe
- Chair for Molecular Functional Materials, Department of Chemistry and Food Chemistry, School of Science, Technische Universität Dresden, Mommsenstr. 4, 01069, Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany
| | - Teuku Fawzul Akbar
- Max Bergman Center of Biomaterials Dresden and Institute for Materials Science, Technische Universität Dresden, 01062, Dresden, Germany
| | - Larysa Baraban
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany
- Max Bergman Center of Biomaterials Dresden and Institute for Materials Science, Technische Universität Dresden, 01062, Dresden, Germany
| | - Gianaurelio Cuniberti
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany
- Max Bergman Center of Biomaterials Dresden and Institute for Materials Science, Technische Universität Dresden, 01062, Dresden, Germany
| | - Xinliang Feng
- Chair for Molecular Functional Materials, Department of Chemistry and Food Chemistry, School of Science, Technische Universität Dresden, Mommsenstr. 4, 01069, Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany
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12
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Wang Z, Liang H, Cao H, Zhang B, Li J, Wang W, Qin S, Wang Y, Xuan L, Lai L, Shui W. Efficient ligand discovery from natural herbs by integrating virtual screening, affinity mass spectrometry and targeted metabolomics. Analyst 2019; 144:2881-2890. [PMID: 30788466 DOI: 10.1039/c8an02482k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although natural herbs have been a rich source of compounds for drug discovery, identification of bioactive components from natural herbs suffers from low efficiency and prohibitive cost of the conventional bioassay-based screening platforms. Here we develop a new strategy that integrates virtual screening, affinity mass spectrometry (MS) and targeted metabolomics for efficient discovery of herb-derived ligands towards a specific protein target site. Herb-based virtual screening conveniently selects herbs of potential bioactivity whereas affinity MS combined with targeted metabolomics readily screens candidate compounds in a high-throughput manner. This new integrated approach was benchmarked on screening chemical ligands that target the hydrophobic pocket of the nucleoprotein (NP) of Ebola viruses for which no small molecule ligands have been reported. Seven compounds identified by this approach from the crude extracts of three natural herbs were all validated to bind to the NP target in pure ligand binding assays. Among them, three compounds isolated from Piper nigrum (HJ-1, HJ-4 and HJ-6) strongly promoted the formation of large NP oligomers and reduced the protein thermal stability. In addition, cooperative binding between these chemical ligands and an endogenous peptide ligand was observed, and molecular docking was employed to propose a possible mechanism. Taken together, we established a platform integrating in silico and experimental screening approaches for efficient discovery of herb-derived bioactive ligands especially towards non-enzyme protein targets.
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Affiliation(s)
- Zhihua Wang
- College of Pharmacy, Nankai University, Tianjin 300071, China
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Hao Liang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Haijie Cao
- College of Pharmacy, Nankai University, Tianjin 300071, China
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| | - Bingjie Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| | - Jun Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China.
| | - Wenqiong Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China.
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| | - Yuefei Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Lijiang Xuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China.
| | - Luhua Lai
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
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13
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Jansons J, Sominskaya I, Petrakova N, Starodubova ES, Smirnova OA, Alekseeva E, Bruvere R, Eliseeva O, Skrastina D, Kashuba E, Mihailova M, Kochetkov SN, Ivanov AV, Isaguliants MG. The Immunogenicity in Mice of HCV Core Delivered as DNA Is Modulated by Its Capacity to Induce Oxidative Stress and Oxidative Stress Response. Cells 2019; 8:cells8030208. [PMID: 30823485 PMCID: PMC6468923 DOI: 10.3390/cells8030208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/06/2019] [Accepted: 02/20/2019] [Indexed: 12/16/2022] Open
Abstract
HCV core is an attractive HCV vaccine target, however, clinical or preclinical trials of core-based vaccines showed little success. We aimed to delineate what restricts its immunogenicity and improve immunogenic performance in mice. We designed plasmids encoding full-length HCV 1b core and its variants truncated after amino acids (aa) 60, 98, 152, 173, or up to aa 36 using virus-derived or synthetic polynucleotides (core191/60/98/152/173/36_191v or core152s DNA, respectively). We assessed their level of expression, route of degradation, ability to trigger the production of reactive oxygen species/ROS, and to activate the components of the Nrf2/ARE antioxidant defense pathway heme oxygenase 1/HO-1 and NAD(P)H: quinone oxidoreductase/Nqo-1. All core variants with the intact N-terminus induced production of ROS, and up-regulated expression of HO-1 and Nqo-1. The capacity of core variants to induce ROS and up-regulate HO-1 and Nqo-1 expression predetermined their immunogenicity in DNA-immunized BALB/c and C57BL/6 mice. The most immunogenic was core 152s, expressed at a modest level and inducing moderate oxidative stress and oxidative stress response. Thus, immunogenicity of HCV core is shaped by its ability to induce ROS and oxidative stress response. These considerations are important in understanding the mechanisms of viral suppression of cellular immune response and in HCV vaccine design.
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Affiliation(s)
- Juris Jansons
- Department of Pathology, Riga Stradins University, LV-1007 Riga, Latvia.
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
| | - Irina Sominskaya
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
| | - Natalia Petrakova
- N.F. Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
| | - Elizaveta S Starodubova
- N.F. Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Olga A Smirnova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Ekaterina Alekseeva
- Department of Pathology, Riga Stradins University, LV-1007 Riga, Latvia.
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
| | - Ruta Bruvere
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
| | - Olesja Eliseeva
- N.F. Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
| | - Dace Skrastina
- Department of Pathology, Riga Stradins University, LV-1007 Riga, Latvia.
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
| | - Elena Kashuba
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
- RE Kavetsky Institite of Experimental Pathology, Oncology and Radiobiology, The National Academy of Sciences of Ukraine, 03022 Kyiv, Ukraine.
| | - Marija Mihailova
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Alexander V Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Maria G Isaguliants
- Department of Pathology, Riga Stradins University, LV-1007 Riga, Latvia.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
- N.F. Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
- MP Chumakov Center for Research and Development of Immune and Biological Preparations of RAS, 108819 Moscow, Russia.
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14
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Bian WX, Xie Y, Wang XN, Xu GH, Fu BS, Li S, Long G, Zhou X, Zhang XL. Binding of cellular nucleolin with the viral core RNA G-quadruplex structure suppresses HCV replication. Nucleic Acids Res 2019; 47:56-68. [PMID: 30462330 PMCID: PMC6326805 DOI: 10.1093/nar/gky1177] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/22/2018] [Accepted: 11/16/2018] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a major cause of human chronic liver disease and hepatocellular carcinoma. G-quadruplex (G4) is an important four-stranded secondary structure of nucleic acids. Recently, we discovered that the core gene of HCV contains a G4 RNA structure; however, the interaction between the HCV core RNA G4 and host cellular proteins, and the roles of the HCV core RNA G4 in HCV infection and pathogenesis remain elusive. Here, we identified a cellular protein, nucleolin (NCL), which bound and stabilized the HCV core RNA G4 structure. We demonstrated the direct interaction and colocalization between NCL and wild-type core RNA G4 at both in vitro and in cell physiological conditions of the alive virus; however no significant interaction was found between NCL and G4-modified core RNA. NCL is also associated with HCV particles. HCV infection induced NCL mRNA and protein expression, while NCL suppressed wild-type viral replication and expression, but not G4-modified virus. Silencing of NCL greatly enhanced viral RNA replication. Our findings provide new insights that NCL may act as a host factor for anti-viral innate immunity, and binding of cellular NCL with the viral core RNA G4 structure is involved in suppressing HCV replication.
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Affiliation(s)
- Wen-Xiu Bian
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Yan Xie
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Xiao-Ning Wang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guo-Hua Xu
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Bo-Shi Fu
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei Province, Wuhan 430072, China
| | - Shu Li
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
| | - Gang Long
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei Province, Wuhan 430072, China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Medical Research Institute and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, PR China
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15
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Di Palma F, Daino GL, Ramaswamy VK, Corona A, Frau A, Fanunza E, Vargiu AV, Tramontano E, Ruggerone P. Relevance of Ebola virus VP35 homo-dimerization on the type I interferon cascade inhibition. Antivir Chem Chemother 2019; 27:2040206619889220. [PMID: 31744306 PMCID: PMC6883671 DOI: 10.1177/2040206619889220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/13/2019] [Indexed: 01/10/2023] Open
Abstract
Ebola virus high lethality relies on its ability to efficiently bypass the host innate antiviral response, which senses the viral dsRNA through the RIG-I receptor and induces type I interferon α/β production. In the bypassing action, the Ebola virus protein VP35 plays a pivotal role at multiple levels of the RIG-I cascade, masking the viral 5′-triphosphorylated dsRNA from RIG-I, and interacting with other cascade components. The VP35 type I interferon inhibition is exerted by the C-terminal domain, while the N-terminal domain, containing a coiled-coil region, is primarily required for oligomerization. However, mutations at key VP35 residues L90/93/107A (VP35-3m) in the coiled-coil region were reported to affect oligomerization and reduce type I interferon antagonism, indicating a possible but unclear role of homo-oligomerization on VP35 interaction with the RIG-I pathway components. In this work, we investigated the VP35 dimerization thermodynamics and its contribution to type I interferon antagonism by computational and biological methods. Focusing on the coiled-coil region, we combined coarse-grained and all-atom simulations on wild type VP35 and VP35-3m homo-dimerization. According to our results, wild type VP35 coiled-coil is able to self-assemble into dimers, while VP35-3m coiled-coil shows poor propensity to even dimerize. Free-energy calculations confirmed the key role of L90, L93 and L107 in stabilizing the coiled-coil homo-dimeric structure. In vitro type I interferon antagonism studies, using full-length wild type VP35 and VP35-3m, revealed that VP35 homo-dimerization is an essential preliminary step for dsRNA binding, which appears to be the main factor of the VP35 RIG-I cascade inhibition, while it is not essential to block the other steps.
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Affiliation(s)
- Francesco Di Palma
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
| | - Gian Luca Daino
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | | | - Angela Corona
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Aldo Frau
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Elisa Fanunza
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale
delle Ricerche (CNR), Monserrato, Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
- Istituto Officina dei Materiali (CNR-IOM), UOS Cagliari SLACS,
Monserrato, Italy
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16
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Li Y, Sun L, Zheng W, Madina Mahesutihan, Li J, Bi Y, Wang H, Liu W, Luo TR. Phosphorylation and dephosphorylation of threonine 188 in nucleoprotein is crucial for the replication of influenza A virus. Virology 2018; 520:30-38. [PMID: 29775781 DOI: 10.1016/j.virol.2018.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
Abstract
Nucleoprotein (NP) is a major component of the viral ribonucleoprotein (vRNP) complex that is responsible for viral replication, transcription and packaging of influenza A virus. Phosphorylation of NP plays an important role during viral infection. In the present study, we identified threonine 188 (T188) as a novel phosphorylated residue in the NP of influenza A virus by using mass spectrometry. T188 is located within nuclear export signal 2 (NES2) which is chromosome region maintenance 1 (CRM1)-independent. We observed that the phosphorylation and dephosphorylation of residue T188 regulated viral replication by controlling NES2-dependent NP nuclear export and the polymerase activity of the vRNP complex. Our findings provide further insights for understanding the replication of influenza A virus.
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Affiliation(s)
- Yun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresourses & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning 530004, Guangxi, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Weinan Zheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Madina Mahesutihan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Heran Wang
- International Department, Beijing National Day School, Beijing 100039, China
| | - Wenjun Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresourses & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning 530004, Guangxi, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ting Rong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresourses & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning 530004, Guangxi, China.
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17
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Lecoq L, Wang S, Wiegand T, Bressanelli S, Nassal M, Meier BH, Böckmann A. Solid-state [ 13C- 15N] NMR resonance assignment of hepatitis B virus core protein. Biomol NMR Assign 2018; 12:205-214. [PMID: 29450824 DOI: 10.1007/s12104-018-9810-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/08/2018] [Indexed: 06/08/2023]
Abstract
Each year, nearly 900,000 deaths are due to serious liver diseases caused by chronic hepatitis B virus infection. The viral particle is composed of an outer envelope and an inner icosahedral nucleocapsid formed by multiple dimers of a ~ 20 kDa self-assembling core protein (Cp). Here we report the solid-state 13C and 15N resonance assignments of the assembly domain, Cp149, of the core protein in its capsid form. A secondary chemical shift analysis of the 140 visible residues suggests an overall alpha-helical three-dimensional fold matching that derived for Cp149 from the X-ray crystallography of the capsid, and from solution-state NMR of the Cp149 dimer. Interestingly, however, at three distinct regions the chemical shifts in solution differ significantly between core proteins in the capsid state versus in the dimer state, strongly suggesting the respective residues to be involved in capsid assembly.
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Affiliation(s)
- Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Shishan Wang
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198, Gif sur Yvette Cedex, France
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
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18
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Hsia HP, Yang YH, Szeto WC, Nilsson BE, Lo CY, Ng AKL, Fodor E, Shaw PC. Amino acid substitutions affecting aspartic acid 605 and valine 606 decrease the interaction strength between the influenza virus RNA polymerase PB2 '627' domain and the viral nucleoprotein. PLoS One 2018; 13:e0191226. [PMID: 29338047 PMCID: PMC5770049 DOI: 10.1371/journal.pone.0191226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/29/2017] [Indexed: 11/19/2022] Open
Abstract
The influenza virus RNA genome is transcribed and replicated in the context of the viral ribonucleoprotein (vRNP) complex by the viral RNA polymerase. The nucleoprotein (NP) is the structural component of the vRNP providing a scaffold for the viral RNA. In the vRNP as well as during transcription and replication the viral polymerase interacts with NP but it is unclear which parts of the polymerase and NP mediate these interactions. Previously the C-terminal ‘627’ domain (amino acids 538–693) of PB2 was shown to interact with NP. Here we report that a fragment encompassing amino acids 146–185 of NP is sufficient to mediate this interaction. Using NMR chemical shift perturbation assays we show that amino acid region 601 to 607 of the PB2 ‘627’ domain interacts with this fragment of NP. Substitutions of these PB2 amino acids resulted in diminished RNP activity and surface plasmon resonance assays showed that amino acids D605 was essential for the interaction with NP and V606 may also play a partial role in the interaction. Collectively these results reveal a possible interaction surface between NP and the PB2 subunit of the RNA polymerase complex.
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Affiliation(s)
- Ho-Pan Hsia
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Yin-Hua Yang
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Wun-Chung Szeto
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Benjamin E. Nilsson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Chun-Yeung Lo
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Andy Ka-Leung Ng
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Pang-Chui Shaw
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- * E-mail:
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19
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Thuenemann EC, Lomonossoff GP. Delivering Cargo: Plant-Based Production of Bluetongue Virus Core-Like and Virus-Like Particles Containing Fluorescent Proteins. Methods Mol Biol 2018; 1776:319-334. [PMID: 29869252 DOI: 10.1007/978-1-4939-7808-3_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This chapter provides a practical guide to the in planta transient production of bluetongue virus-like particles containing a fluorescent cargo protein. Bluetongue virus (BTV) particles are icosahedral, multishelled entities of a relatively large size. Heterologous expression of the four main structural proteins of BTV results in the assembly of empty virus-like particles which resemble the native virus externally, but are devoid of nucleic acid. The space within the particles is sufficient to allow incorporation of relatively large cargo proteins, such as green fluorescent protein (GFP), by genetic fusion to the structural protein VP3. The method described utilizes the pEAQ vectors for high-level transient expression of such particles in Nicotiana benthamiana.
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Affiliation(s)
- Eva C Thuenemann
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK.
| | - George P Lomonossoff
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
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20
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Lee LS, Brunk N, Haywood DG, Keifer D, Pierson E, Kondylis P, Wang JC, Jacobson SC, Jarrold MF, Zlotnick A. A molecular breadboard: Removal and replacement of subunits in a hepatitis B virus capsid. Protein Sci 2017; 26:2170-2180. [PMID: 28795465 PMCID: PMC5654856 DOI: 10.1002/pro.3265] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/29/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022]
Abstract
Hepatitis B virus (HBV) core protein is a model system for studying assembly and disassembly of icosahedral structures. Controlling disassembly will allow re-engineering the 120 subunit HBV capsid, making it a molecular breadboard. We examined removal of subunits from partially crosslinked capsids to form stable incomplete particles. To characterize incomplete capsids, we used two single molecule techniques, resistive-pulse sensing and charge detection mass spectrometry. We expected to find a binomial distribution of capsid fragments. Instead, we found a preponderance of 3 MDa complexes (90 subunits) and no fragments smaller than 3 MDa. We also found 90-mers in the disassembly of uncrosslinked HBV capsids. 90-mers seem to be a common pause point in disassembly reactions. Partly explaining this result, graph theory simulations have showed a threshold for capsid stability between 80 and 90 subunits. To test a molecular breadboard concept, we showed that missing subunits could be refilled resulting in chimeric, 120 subunit particles. This result may be a means of assembling unique capsids with functional decorations.
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Affiliation(s)
- Lye Siang Lee
- Molecular and Cellular Biochemistry DepartmentIndiana UniversityBloomingtonIndiana47405
| | - Nicholas Brunk
- Molecular and Cellular Biochemistry DepartmentIndiana UniversityBloomingtonIndiana47405
- Intelligent Systems Engineering DepartmentBloomingtonIndiana47405
| | | | - David Keifer
- Department of ChemistryIndiana UniversityBloomingtonIndiana47405
- Present address:
Department of Analytical Sciences, Pharmaceutical Sciences and Clinical SuppliesMerck Research Laboratories, Merck & Co., Inc., RahwayNew Jersey07065.
| | - Elizabeth Pierson
- Department of ChemistryIndiana UniversityBloomingtonIndiana47405
- Present address:
Department of ChemistrySalisbury University, 1101 Camden AveSalisburyMD 21801.
| | | | - Joseph Che‐Yen Wang
- Molecular and Cellular Biochemistry DepartmentIndiana UniversityBloomingtonIndiana47405
| | | | | | - Adam Zlotnick
- Molecular and Cellular Biochemistry DepartmentIndiana UniversityBloomingtonIndiana47405
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21
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Hassan AO, Amen O, Sayedahmed EE, Vemula SV, Amoah S, York I, Gangappa S, Sambhara S, Mittal SK. Adenovirus vector-based multi-epitope vaccine provides partial protection against H5, H7, and H9 avian influenza viruses. PLoS One 2017; 12:e0186244. [PMID: 29023601 PMCID: PMC5638338 DOI: 10.1371/journal.pone.0186244] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/27/2017] [Indexed: 11/18/2022] Open
Abstract
The emergence of H5, H7, and H9 avian influenza virus subtypes in humans reveals their pandemic potential. Although human-to-human transmission has been limited, the genetic reassortment of the avian and human/porcine influenza viruses or mutations in some of the genes resulting in virus replication in the upper respiratory tract of humans could generate novel pandemic influenza viruses. Current vaccines do not provide cross protection against antigenically distinct strains of the H5, H7, and H9 influenza viruses. Therefore, newer vaccine approaches are needed to overcome these potential threats. We developed an egg-independent, adenovirus vector-based, multi-epitope (ME) vaccine approach using the relatively conserved immunogenic domains of the H5N1 influenza virus [M2 ectodomain (M2e), hemagglutinin (HA) fusion domain (HFD), T-cell epitope of nucleoprotein (TNP). and HA α-helix domain (HαD)]. Our ME vaccine induced humoral and cell-mediated immune responses and caused a significant reduction in the viral loads in the lungs of vaccinated mice that were challenged with antigenically distinct H5, H7, or H9 avian influenza viruses. These results suggest that our ME vaccine approach provided broad protection against the avian influenza viruses. Further improvement of this vaccine will lead to a pre-pandemic vaccine that may lower morbidity, hinder transmission, and prevent mortality in a pandemic situation before a strain-matched vaccine becomes available.
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Affiliation(s)
- Ahmed O. Hassan
- Department of Comparative Pathobiology and Purdue Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, United States of America
| | - Omar Amen
- Department of Comparative Pathobiology and Purdue Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, United States of America
- Poultry Diseases Department, Faculty of Veterinary Medicine, Assiut University, Assiut, Egypt
| | - Ekramy E. Sayedahmed
- Department of Comparative Pathobiology and Purdue Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, United States of America
| | - Sai V. Vemula
- Department of Comparative Pathobiology and Purdue Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, United States of America
| | - Samuel Amoah
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Ian York
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Shivaprakash Gangappa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Suryaprakash Sambhara
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- * E-mail: (SKM); (SS)
| | - Suresh K. Mittal
- Department of Comparative Pathobiology and Purdue Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, United States of America
- * E-mail: (SKM); (SS)
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22
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Gc JB, Pokhrel R, Bhattarai N, Johnson KA, Gerstman BS, Stahelin RV, Chapagain PP. Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filaments. Biochem Biophys Res Commun 2017; 493:176-181. [PMID: 28917841 DOI: 10.1016/j.bbrc.2017.09.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/11/2017] [Indexed: 02/02/2023]
Abstract
Ebola virus infections cause hemorrhagic fever that often results in very high fatality rates. In addition to exploring vaccines, development of drugs is also essential for treating the disease and preventing the spread of the infection. The Ebola virus matrix protein VP40 exists in various conformational and oligomeric forms and is a potential pharmacological target for disrupting the virus life-cycle. Here we explored graphene-VP40 interactions using molecular dynamics simulations and graphene pelleting assays. We found that graphene sheets associate strongly with VP40 at various interfaces. We also found that the graphene is able to disrupt the C-terminal domain (CTD-CTD) interface of VP40 hexamers. This VP40 hexamer-hexamer interface is crucial in forming the Ebola viral matrix and disruption of this interface may provide a method to use graphene or similar nanoparticle based solutions as a disinfectant that can significantly reduce the spread of the disease and prevent an Ebola epidemic.
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Affiliation(s)
- Jeevan B Gc
- Department of Physics, Florida International University, Miami, FL 33199, United States
| | - Rudramani Pokhrel
- Department of Physics, Florida International University, Miami, FL 33199, United States
| | - Nisha Bhattarai
- Department of Physics, Florida International University, Miami, FL 33199, United States
| | - Kristen A Johnson
- Department of Chemistry and Biochemistry, The Eck Institute for Global Health, The Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, United States; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
| | - Robert V Stahelin
- Department of Chemistry and Biochemistry, The Eck Institute for Global Health, The Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617, United States
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, United States; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States.
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23
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Karamichali E, Serti E, Gianneli A, Papaefthymiou A, Kakkanas A, Foka P, Seremetakis A, Katsarou K, Trougakos IP, Georgopoulou U. The unexpected function of a highly conserved YXXΦ motif in HCV core protein. Infect Genet Evol 2017; 54:251-262. [PMID: 28687362 DOI: 10.1016/j.meegid.2017.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/27/2017] [Accepted: 07/02/2017] [Indexed: 01/09/2023]
Abstract
Hepatitis C virus (HCV) is an RNA positive strand virus, member of the Flaviviridae family. The HCV viral particle is composed of a capsid containing the genome, surrounded by an endoplasmic reticulum (ER)-derived lipid bilayer where E1 and E2 are assembled as heterodimers. However, different forms of viral particles have been identified in the serum of HCV-infected patients, including non-enveloped particles. Previous reports have demonstrated that HCV non-enveloped capsid-like particles (HCVne) can be generated by HCV core protein sequence. This sequence possesses a highly conserved ΥΧΧΦ motif and distal di-leucine motifs that confer primary endocytosis signals, enabling HCVne to enter hepatic cells via clathrin-mediated endocytosis. Although HCV core's primary function is to encapsidate the viral genome, it also interacts with a variety of cellular proteins in order to regulate host cell functions such as gene transcription, lipid metabolism, apoptosis and several signaling pathways. In this report, we demonstrate that the YXXΦ motif of HCV core protein is crucial for the architectural integrity of the particulate form of HCVne. Moreover, we show that the YXXΦ motif in the HCV core sequence plays a pivotal role in the signaling events following HCVne clathrin-mediated endocytosis by inducing the AP-2 clathrin adaptor protein, which in turn redirect HCVne trafficking to the lipid droplets (LDs) via the endosomal-lysosomal pathway. HCVne and LDs co-localization affects the HCV life cycle by enhancing viral replication.
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Affiliation(s)
| | - Elisavet Serti
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Greece
| | | | | | | | - Pelagia Foka
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Greece
| | | | | | - Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15784, Greece
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24
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Purpura LJ, Rogers E, Baller A, White S, Soka M, Choi MJ, Mahmoud N, Wasunna C, Massaquoi M, Kollie J, Dweh S, Bemah P, Ladele V, Kpaka J, Jawara M, Mugisha M, Subah O, Faikai M, Bailey JA, Rollin P, Marston B, Nyenswah T, Gasasira A, Knust B, Nichol S, Williams D. Ebola Virus RNA in Semen from an HIV-Positive Survivor of Ebola. Emerg Infect Dis 2017; 23:714-715. [PMID: 28287374 PMCID: PMC5367423 DOI: 10.3201/eid2304.161743] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Ebola virus is known to persist in semen of male survivors of Ebola virus disease (EVD). However, maximum duration of, or risk factors for, virus persistence are unknown. We report an EVD survivor with preexisting HIV infection, whose semen was positive for Ebola virus RNA 565 days after recovery from EVD.
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25
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Makau JN, Watanabe K, Ishikawa T, Mizuta S, Hamada T, Kobayashi N, Nishida N. Identification of small molecule inhibitors for influenza a virus using in silico and in vitro approaches. PLoS One 2017; 12:e0173582. [PMID: 28273150 PMCID: PMC5342234 DOI: 10.1371/journal.pone.0173582] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/22/2017] [Indexed: 01/23/2023] Open
Abstract
Influenza viruses have acquired resistance to approved neuraminidase-targeting drugs, increasing the need for new drug targets for the development of novel anti-influenza drugs. Nucleoprotein (NP) is an attractive target since it has an indispensable role in virus replication and its amino acid sequence is well conserved. In this study, we aimed to identify new inhibitors of the NP using a structure-based drug discovery algorithm, named Nagasaki University Docking Engine (NUDE), which has been established especially for the Destination for GPU Intensive Machine (DEGIMA) supercomputer. The hit compounds that showed high binding scores during in silico screening were subsequently evaluated for anti-influenza virus effects using a cell-based assay. A 4-hydroxyquinolinone compound, designated as NUD-1, was found to inhibit the replication of influenza virus in cultured cells. Analysis of binding between NUD-1 and NP using surface plasmon resonance assay and fragment molecular orbital calculations confirmed that NUD-1 binds to NP and could interfere with NP-NP interactions essential for virus replication. Time-of-addition experiments showed that the compound inhibited the mid-stage of infection, corresponding to assembly of the NP and other viral proteins. Moreover, NUD-1 was also effective against various types of influenza A viruses including a clinical isolate of A(H1N1)pdm09 influenza with a 50% inhibitory concentration range of 1.8-2.1 μM. Our data demonstrate that the combined use of NUDE system followed by the cell-based assay is useful to obtain lead compounds for the development of novel anti-influenza drugs.
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Affiliation(s)
- Juliann Nzembi Makau
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
- Leading Program, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Ken Watanabe
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Takeshi Ishikawa
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Satoshi Mizuta
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Tsuyoshi Hamada
- Nagasaki Advanced Computing Center, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
| | - Nobuyuki Kobayashi
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
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26
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Wall GV, Rutkowska DA, Mizrachi E, Huismans H, van Staden V. A Dual Laser Scanning Confocal and Transmission Electron Microscopy Analysis of the Intracellular Localization, Aggregation and Particle Formation of African Horse Sickness Virus Major Core Protein VP7. Microsc Microanal 2017; 23:56-68. [PMID: 28112080 DOI: 10.1017/s143192761601268x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The bulk of the major core protein VP7 in African horse sickness virus (AHSV) self-assembles into flat, hexagonal crystalline particles in a process appearing unrelated to viral replication. Why this unique characteristic of AHSV VP7 is genetically conserved, and whether VP7 aggregation and particle formation have an effect on cellular biology or the viral life cycle, is unknown. Here we investigated how different small peptide and enhanced green fluorescent protein (eGFP) insertions into the VP7 top domain affected VP7 localization, aggregation, and particle formation. This was done using a dual laser scanning confocal and transmission electron microscopy approach in conjunction with analyses of the solubility, aggregation, and fluorescence profiles of the proteins. VP7 top domain modifications did not prevent trimerization, or intracellular trafficking, to one or two discrete sites in the cell. However, modifications that resulted in a misfolded and insoluble VP7-eGFP component blocked trafficking, and precluded protein accumulation at a single cellular site, perhaps by interfering with normal trimer-trimer interactions. Furthermore, the modifications disrupted the stable layering of the trimers into characteristic AHSV VP7 crystalline particles. It was concluded that VP7 trafficking is driven by a balance between VP7 solubility, trimer forming ability, and trimer-trimer interactions.
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Affiliation(s)
- Gayle V Wall
- Department of Genetics,University of Pretoria,Pretoria,0002,South Africa
| | - Daria A Rutkowska
- Department of Genetics,University of Pretoria,Pretoria,0002,South Africa
| | - Eshchar Mizrachi
- Department of Genetics,University of Pretoria,Pretoria,0002,South Africa
| | - Henk Huismans
- Department of Genetics,University of Pretoria,Pretoria,0002,South Africa
| | - Vida van Staden
- Department of Genetics,University of Pretoria,Pretoria,0002,South Africa
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27
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Gc JB, Gerstman BS, Stahelin RV, Chapagain PP. The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P 2 lipids in the plasma membrane. Phys Chem Chem Phys 2016; 18:28409-28417. [PMID: 27757455 PMCID: PMC5084917 DOI: 10.1039/c6cp03776c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The Ebola virus is a lipid-enveloped virus that obtains its lipid coat from the plasma membrane of the host cell it infects during the budding process. The Ebola virus protein VP40 localizes to the inner leaflet of the plasma membrane and forms the viral matrix, which provides the major structure for the Ebola virus particles. VP40 is initially a dimer that rearranges to a hexameric structure that mediates budding. VP40 hexamers and larger filaments have been shown to be stabilized by PI(4,5)P2 in the plasma membrane inner leaflet. Reduction in the plasma membrane levels of PI(4,5)P2 significantly reduce formation of VP40 oligomers and virus-like particles. We investigated the lipid-protein interactions in VP40 hexamers at the plasma membrane. We quantified lipid-lipid self-clustering by calculating the fractional interaction matrix and found that the VP40 hexamer significantly enhances the PI(4,5)P2 clustering. The radial pair distribution functions suggest a strong interaction between PI(4,5)P2 and the VP40 hexamer. The cationic Lys side chains are found to mediate the PIP2 clustering around the protein, with cholesterol filling the space between the interacting PIP2 molecules. These computational studies support recent experimental data and provide new insights into the mechanisms by which VP40 assembles at the plasma membrane inner leaflet, alters membrane curvature, and forms new virus-like particles.
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Affiliation(s)
- Jeevan B Gc
- Department of Physics, Florida International University, Miami, FL 33199, USA.
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA. and Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
| | - Robert V Stahelin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617, USA and Department of Chemistry and Biochemistry, The Eck Institute for Global Health, and the Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA. and Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
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28
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Avgousti DC, Herrmann C, Kulej K, Pancholi NJ, Sekulic N, Petrescu J, Molden RC, Blumenthal D, Paris AJ, Reyes ED, Ostapchuk P, Hearing P, Seeholzer SH, Worthen GS, Black BE, Garcia BA, Weitzman MD. A core viral protein binds host nucleosomes to sequester immune danger signals. Nature 2016; 535:173-7. [PMID: 27362237 PMCID: PMC4950998 DOI: 10.1038/nature18317] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/11/2016] [Indexed: 01/06/2023]
Abstract
Viral proteins mimic host protein structure and function to redirect cellular processes and subvert innate defenses. Small basic proteins compact and regulate both viral and cellular DNA genomes. Nucleosomes are the repeating units of cellular chromatin and play an important part in innate immune responses. Viral-encoded core basic proteins compact viral genomes, but their impact on host chromatin structure and function remains unexplored. Adenoviruses encode a highly basic protein called protein VII that resembles cellular histones. Although protein VII binds viral DNA and is incorporated with viral genomes into virus particles, it is unknown whether protein VII affects cellular chromatin. Here we show that protein VII alters cellular chromatin, leading us to hypothesize that this has an impact on antiviral responses during adenovirus infection in human cells. We find that protein VII forms complexes with nucleosomes and limits DNA accessibility. We identified post-translational modifications on protein VII that are responsible for chromatin localization. Furthermore, proteomic analysis demonstrated that protein VII is sufficient to alter the protein composition of host chromatin. We found that protein VII is necessary and sufficient for retention in the chromatin of members of the high-mobility-group protein B family (HMGB1, HMGB2 and HMGB3). HMGB1 is actively released in response to inflammatory stimuli and functions as a danger signal to activate immune responses. We showed that protein VII can directly bind HMGB1 in vitro and further demonstrated that protein VII expression in mouse lungs is sufficient to decrease inflammation-induced HMGB1 content and neutrophil recruitment in the bronchoalveolar lavage fluid. Together, our in vitro and in vivo results show that protein VII sequesters HMGB1 and can prevent its release. This study uncovers a viral strategy in which nucleosome binding is exploited to control extracellular immune signaling.
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Affiliation(s)
- Daphne C. Avgousti
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA USA
| | - Christin Herrmann
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Katarzyna Kulej
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA USA
| | - Neha J. Pancholi
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Nikolina Sekulic
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
- Epigenetics Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
- Currently: Biotechnology Centre of Oslo and Department of Chemistry, University of Oslo, Oslo, Norway
| | - Joana Petrescu
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA USA
- Villanova University, Villanova, PA USA
| | - Rosalynn C. Molden
- Epigenetics Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Daniel Blumenthal
- Division of Cell Pathology, Children's Hospital of Philadelphia, Philadelphia, PA USA
| | - Andrew J. Paris
- Division of Pulmonary, Allergy, and Critical Care Medicine, Hospital of the University of Pennsylvania, and the Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Emigdio D. Reyes
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA USA
| | - Philomena Ostapchuk
- Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, New York USA
| | - Patrick Hearing
- Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, New York USA
| | - Steven H. Seeholzer
- Protein and Proteomics Core, Children's Hospital of Philadelphia, Philadelphia, PA USA
| | - G. Scott Worthen
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ben E. Black
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
- Epigenetics Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
- Epigenetics Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Matthew D. Weitzman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA USA
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29
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Wang SR, Min YQ, Wang JQ, Liu CX, Fu BS, Wu F, Wu LY, Qiao ZX, Song YY, Xu GH, Wu ZG, Huang G, Peng NF, Huang R, Mao WX, Peng S, Chen YQ, Zhu Y, Tian T, Zhang XL, Zhou X. A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target. Sci Adv 2016; 2:e1501535. [PMID: 27051880 PMCID: PMC4820367 DOI: 10.1126/sciadv.1501535] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/18/2016] [Indexed: 05/24/2023]
Abstract
G-quadruplex (G4) is one of the most important secondary structures in nucleic acids. Until recently, G4 RNAs have not been reported in any ribovirus, such as the hepatitis C virus. Our bioinformatics analysis reveals highly conserved guanine-rich consensus sequences within the core gene of hepatitis C despite the high genetic variability of this ribovirus; we further show using various methods that such consensus sequences can fold into unimolecular G4 RNA structures, both in vitro and under physiological conditions. Furthermore, we provide direct evidences that small molecules specifically targeting G4 can stabilize this structure to reduce RNA replication and inhibit protein translation of intracellular hepatitis C. Ultimately, the stabilization of G4 RNA in the genome of hepatitis C represents a promising new strategy for anti-hepatitis C drug development.
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Affiliation(s)
- Shao-Ru Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Yuan-Qin Min
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine, Wuhan University, Wuhan 430071, Hubei, China
| | - Jia-Qi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Chao-Xing Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Bo-Shi Fu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Fan Wu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Ling-Yu Wu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Zhi-Xian Qiao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Yan-Yan Song
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Guo-Hua Xu
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Zhi-Guo Wu
- College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Gai Huang
- College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Nan-Fang Peng
- College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Rong Huang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Wu-Xiang Mao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Shuang Peng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Yu-Qi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Ying Zhu
- College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Tian Tian
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine, Wuhan University, Wuhan 430071, Hubei, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China
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30
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Liu M, Lam MKH, Zhang Q, Elderfield R, Barclay WS, Shaw PC. The Functional Study of the N-Terminal Region of Influenza B Virus Nucleoprotein. PLoS One 2015; 10:e0137802. [PMID: 26368391 PMCID: PMC4569402 DOI: 10.1371/journal.pone.0137802] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/21/2015] [Indexed: 11/18/2022] Open
Abstract
Influenza nucleoprotein (NP) is a major component of the ribonucleoprotein (vRNP) in influenza virus, which functions for the transcription and replication of viral genome. Compared to the nucleoprotein of influenza A (ANP), the N-terminal region of influenza B nucleoprotein (BNP) is much extended. By virus reconstitution, we found that the first 38 residues are essential for viral growth. We further illustrated the function of BNP by mini-genome reconstitution, fluorescence microscopy, electron microscopy, light scattering and gel shift. Results show that the N terminus is involved in the formation of both higher homo-oligomers of BNP and BNP-RNA complex.
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Affiliation(s)
- Ming Liu
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Mandy Ka-Han Lam
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Qinfen Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ruth Elderfield
- Section of Virology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Wendy S. Barclay
- Section of Virology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pang-Chui Shaw
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- * E-mail:
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31
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Hou Y, Zhao D, Liu G, He F, Liu B, Fu S, Hao Y, Zhang W. [Research Progress in the Core Proteins of the Classical Swine Fever Virus]. Bing Du Xue Bao 2015; 31:579-584. [PMID: 26738299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The core protein (CP) of the classical swine fever virus (CSFV) is one of its structural proteins. Apart from forming the nucleocapsid to protect internal viral genomic RNA, this protein is involved in transcriptional regulation. Also, during viral infection, the CP is involved in interactions with many host proteins. In this review, we combine study of this protein with its disorders, structural/functional characteristics, as well as its interactions with the non-structural proteins NS3, NS5B and host proteins such as SUMO-1, UBC9, OS9 and IQGAP1. We also summarize the important part played by the CP in CSFV pathogenicity, virulence and replication of genomic RNA. We also provide guidelines for further studies in the CP of the CSFV.
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32
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Narkpuk J, Jaru-Ampornpan P, Subali T, Bertulfo FCT, Wongthida P, Jongkaewwattana A. Mechanistic study of intertypic nucleoprotein complex formation and its inhibitory effect toward influenza A virus. Virology 2015. [PMID: 26218215 DOI: 10.1016/j.virol.2015.06.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Co-infection of influenza A and B viruses (IAV and IBV) results in marked decreases in IAV replication. Multiple mechanisms have been proposed for this phenomenon. Recently, we reported that IBV nucleoprotein (BNP) alone can suppress IAV replication and proposed an inhibition model in which BNP binds IAV nucleoprotein (ANP) and disrupts IAV polymerase complexes. Here, using mutagenesis and co-immunoprecipitation, we determined the protein motifs mediating the intertypic ANP-BNP complex and showed that it specifically interferes with ANP׳s interaction with the PB2 subunit of the IAV polymerase but not with the other subunit PB1. We further demonstrated that BNP only suppresses growth of IAVs but not other RNA viruses. However, different IAV strains display varied sensitivity toward the BNP׳s inhibitory effect. Together, our data provide mechanistic insights into intertypic nucleoprotein complex formation and highlight the role of BNP as a potential broad-spectrum anti-IAV agent.
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Affiliation(s)
- Jaraspim Narkpuk
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Peera Jaru-Ampornpan
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand.
| | - Theressa Subali
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Fatima Carla T Bertulfo
- Department of Molecular Biology and Biotechnology, University of the Phillipines Los Banos, Laguna, Phillipines
| | - Phonphimon Wongthida
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Anan Jongkaewwattana
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand.
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33
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Kirchdoerfer RN, Abelson DM, Li S, Wood MR, Saphire EO. Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex. Cell Rep 2015; 12:140-149. [PMID: 26119732 PMCID: PMC4500542 DOI: 10.1016/j.celrep.2015.06.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/01/2015] [Accepted: 05/29/2015] [Indexed: 12/25/2022] Open
Abstract
Ebolavirus NP oligomerizes into helical filaments found at the core of the virion, encapsidates the viral RNA genome, and serves as a scaffold for additional viral proteins within the viral nucleocapsid. We identified a portion of the phosphoprotein homolog VP35 that binds with high affinity to nascent NP and regulates NP assembly and viral genome binding. Removal of the VP35 peptide leads to NP self-assembly via its N-terminal oligomerization arm. NP oligomerization likely causes a conformational change between the NP N- and C-terminal domains, facilitating RNA binding. These functional data are complemented by crystal structures of the NP°-VP35 complex at 2.4 Å resolution. The interactions between NP and VP35 illuminated by these structures are conserved among filoviruses and provide key targets for therapeutic intervention.
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Affiliation(s)
- Robert N Kirchdoerfer
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dafna M Abelson
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Malcolm R Wood
- Core Microscopy Facility, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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34
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Awuni Y, Mu Y. Reduction of false positives in structure-based virtual screening when receptor plasticity is considered. Molecules 2015; 20:5152-64. [PMID: 25808156 PMCID: PMC6272817 DOI: 10.3390/molecules20035152] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 12/04/2022] Open
Abstract
Structure-based virtual screening for selecting potential drug candidates is usually challenged by how numerous false positives in a molecule library are excluded when receptor plasticity is considered. In this study, based on the binding energy landscape theory, a hypothesis that a true inhibitor can bind to different conformations of the binding site favorably was put forth, and related strategies to defeat this challenge were devised; reducing false positives when receptor plasticity is considered. The receptor in the study is the influenza A nucleoprotein, whose oligomerization is a requirement for RNA binding. The structural flexibility of influenza A nucleoprotein was explored by molecular dynamics simulations. The resultant distinctive structures and the crystal structure were used as receptor models in docking exercises in which two binding sites, the tail-loop binding pocket and the RNA binding site, were targeted with the Otava PrimScreen1 diversity-molecule library using the GOLD software. The intersection ligands that were listed in the top-ranked molecules from all receptor models were selected. Such selection strategy successfully distinguished high-affinity and low-affinity control molecules added to the molecule library. This work provides an applicable approach for reducing false positives and selecting true ligands from molecule libraries.
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Affiliation(s)
- Yaw Awuni
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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Abstract
Integrating nanotechnology into useable devices requires a combination of bottom up and top down methodology. Often the techniques to measure and control these different components are entirely different, so methods that can analyse the nanoscale component in situ are of increasing importance. Here we describe a strategy that employs a self-assembling monolayer of engineered protein chimeras to display an array of oriented antibodies (IgG) on a microelectronic device for the label free detection of influenza nucleoprotein. The structural and functional properties of the bio-interface were characterised by a range of physical techniques including surface plasmon resonance, quartz-crystal microbalance and neutron reflectometry. This combination of methods reveals a 13.5 nm thick engineered-monolayer that (i) self-assembles on gold surfaces, (ii) captures IgG with high affinity in a defined orientation and (iii) specifically recognises the influenza A nucleoprotein. Furthermore we also show that this non-covalent self-assembled structure can render the dissociation of bound IgG irreversible by chemical crosslinking in situ without affecting the IgG function. The methods can thus describe in detail the transition from soluble engineered molecules with nanometre dimensions to an array that demonstrates the principles of a working influenza sensor.
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Affiliation(s)
- Anton P. Le Brun
- />Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232 Australia
| | - Andrei Soliakov
- />Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH UK
- />Fujifilm Diosynth, Belasis Avenue, Billingham, Cleveland TS23 1LH UK
| | - Deepan S. H. Shah
- />Orla Protein Technologies Ltd, Biosciences Centre, International Centre for Life, Times Square, Newcastle upon Tyne, NE1 4EP UK
| | - Stephen A. Holt
- />Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232 Australia
| | - Alison McGill
- />Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH UK
- />Fujifilm Diosynth, Belasis Avenue, Billingham, Cleveland TS23 1LH UK
| | - Jeremy H. Lakey
- />Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH UK
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36
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Crescenzo-Chaigne B, Barbezange C, Frigard V, Poulain D, van der Werf S. Chimeric NP non coding regions between type A and C influenza viruses reveal their role in translation regulation. PLoS One 2014; 9:e109046. [PMID: 25268971 PMCID: PMC4182659 DOI: 10.1371/journal.pone.0109046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 09/01/2014] [Indexed: 12/14/2022] Open
Abstract
Exchange of the non coding regions of the NP segment between type A and C influenza viruses was used to demonstrate the importance not only of the proximal panhandle, but also of the initial distal panhandle strength in type specificity. Both elements were found to be compulsory to rescue infectious virus by reverse genetics systems. Interestingly, in type A influenza virus infectious context, the length of the NP segment 5' NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication.
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Affiliation(s)
- Bernadette Crescenzo-Chaigne
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Cyril Barbezange
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Vianney Frigard
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Damien Poulain
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
- Université Paris Diderot Sorbonne Paris Cité, Paris, France
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37
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Selzer L, Katen S, Zlotnick A. The hepatitis B virus core protein intradimer interface modulates capsid assembly and stability. Biochemistry 2014; 53:5496-504. [PMID: 25102363 PMCID: PMC4151697 DOI: 10.1021/bi500732b] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/05/2014] [Indexed: 12/19/2022]
Abstract
During the hepatitis B virus (HBV) life cycle, capsid assembly and disassembly must ensure correct packaging and release of the viral genome. Here we show that changes in the dynamics of the core protein play an important role in regulating these processes. The HBV capsid assembles from 120 copies of the core protein homodimer. Each monomer contains a conserved cysteine at position 61 that can form an intradimer disulfide that we use as a marker for dimer conformational states. We show that dimers in the context of capsids form intradimer disulfides relatively rapidly. Surprisingly, compared to reduced dimers, fully oxidized dimers assembled slower and into capsids that were morphologically similar but less stable. We hypothesize that oxidized protein adopts a geometry (or constellation of geometries) that is unfavorable for capsid assembly, resulting in weaker dimer-dimer interactions as well as slower assembly kinetics. Our results suggest that structural flexibility at the core protein intradimer interface is essential for regulating capsid assembly and stability. We further suggest that capsid destabilization by the C61-C61 disulfide has a regulatory function to support capsid disassembly and release of the viral genome.
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Affiliation(s)
- Lisa Selzer
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Sarah
P. Katen
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
- Department
of Biology and Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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38
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Bianchini P, Cardarelli F, Luca MD, Diaspro A, Bizzarri R. Nanoscale protein diffusion by STED-based pair correlation analysis. PLoS One 2014; 9:e99619. [PMID: 24967681 PMCID: PMC4072630 DOI: 10.1371/journal.pone.0099619] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 05/17/2014] [Indexed: 11/18/2022] Open
Abstract
We describe for the first time the combination between cross-pair correlation function analysis (pair correlation analysis or pCF) and stimulated emission depletion (STED) to obtain diffusion maps at spatial resolution below the optical diffraction limit (super-resolution). Our approach was tested in systems characterized by high and low signal to noise ratio, i.e. Capsid Like Particles (CLPs) bearing several (>100) active fluorescent proteins and monomeric fluorescent proteins transiently expressed in living Chinese Hamster Ovary cells, respectively. The latter system represents the usual condition encountered in living cell studies on fluorescent protein chimeras. Spatial resolution of STED-pCF was found to be about 110 nm, with a more than twofold improvement over conventional confocal acquisition. We successfully applied our method to highlight how the proximity to nuclear envelope affects the mobility features of proteins actively imported into the nucleus in living cells. Remarkably, STED-pCF unveiled the existence of local barriers to diffusion as well as the presence of a slow component at distances up to 500-700 nm from either sides of nuclear envelope. The mobility of this component is similar to that previously described for transport complexes. Remarkably, all these features were invisible in conventional confocal mode.
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Affiliation(s)
- Paolo Bianchini
- Nanophysics, IIT—Italian Institute of Technology, Genoa, Italy
| | - Francesco Cardarelli
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Pisa, Italy
| | | | - Alberto Diaspro
- Nanophysics, IIT—Italian Institute of Technology, Genoa, Italy
| | - Ranieri Bizzarri
- Nanophysics, IIT—Italian Institute of Technology, Genoa, Italy
- NEST, Scuola Normale Superiore and Istituto Nanoscienze - CNR, Pisa, Italy
- Istituto di Biofisica – CNR, Pisa, Italy
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39
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Weber ND, Stone D, Sedlak RH, De Silva Feelixge HS, Roychoudhury P, Schiffer JT, Aubert M, Jerome KR. AAV-mediated delivery of zinc finger nucleases targeting hepatitis B virus inhibits active replication. PLoS One 2014. [PMID: 24827459 DOI: 10.1371/journal.pone.009757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite an existing effective vaccine, hepatitis B virus (HBV) remains a major public health concern. There are effective suppressive therapies for HBV, but they remain expensive and inaccessible to many, and not all patients respond well. Furthermore, HBV can persist as genomic covalently closed circular DNA (cccDNA) that remains in hepatocytes even during otherwise effective therapy and facilitates rebound in patients after treatment has stopped. Therefore, the need for an effective treatment that targets active and persistent HBV infections remains. As a novel approach to treat HBV, we have targeted the HBV genome for disruption to prevent viral reactivation and replication. We generated 3 zinc finger nucleases (ZFNs) that target sequences within the HBV polymerase, core and X genes. Upon the formation of ZFN-induced DNA double strand breaks (DSB), imprecise repair by non-homologous end joining leads to mutations that inactivate HBV genes. We delivered HBV-specific ZFNs using self-complementary adeno-associated virus (scAAV) vectors and tested their anti-HBV activity in HepAD38 cells. HBV-ZFNs efficiently disrupted HBV target sites by inducing site-specific mutations. Cytotoxicity was seen with one of the ZFNs. scAAV-mediated delivery of a ZFN targeting HBV polymerase resulted in complete inhibition of HBV DNA replication and production of infectious HBV virions in HepAD38 cells. This effect was sustained for at least 2 weeks following only a single treatment. Furthermore, high specificity was observed for all ZFNs, as negligible off-target cleavage was seen via high-throughput sequencing of 7 closely matched potential off-target sites. These results show that HBV-targeted ZFNs can efficiently inhibit active HBV replication and suppress the cellular template for HBV persistence, making them promising candidates for eradication therapy.
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Affiliation(s)
- Nicholas D Weber
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America; Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ruth Hall Sedlak
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Harshana S De Silva Feelixge
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America; Division of Allergy and Infectious Disease, Department of Medicine, University of Washington, Seattle, Washington, United States of America; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Martine Aubert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America; Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America; Department of Microbiology, University of Washington, Seattle, Washington, United States of America
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40
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Weber ND, Stone D, Sedlak RH, De Silva Feelixge HS, Roychoudhury P, Schiffer JT, Aubert M, Jerome KR. AAV-mediated delivery of zinc finger nucleases targeting hepatitis B virus inhibits active replication. PLoS One 2014; 9:e97579. [PMID: 24827459 PMCID: PMC4020843 DOI: 10.1371/journal.pone.0097579] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 04/21/2014] [Indexed: 02/07/2023] Open
Abstract
Despite an existing effective vaccine, hepatitis B virus (HBV) remains a major public health concern. There are effective suppressive therapies for HBV, but they remain expensive and inaccessible to many, and not all patients respond well. Furthermore, HBV can persist as genomic covalently closed circular DNA (cccDNA) that remains in hepatocytes even during otherwise effective therapy and facilitates rebound in patients after treatment has stopped. Therefore, the need for an effective treatment that targets active and persistent HBV infections remains. As a novel approach to treat HBV, we have targeted the HBV genome for disruption to prevent viral reactivation and replication. We generated 3 zinc finger nucleases (ZFNs) that target sequences within the HBV polymerase, core and X genes. Upon the formation of ZFN-induced DNA double strand breaks (DSB), imprecise repair by non-homologous end joining leads to mutations that inactivate HBV genes. We delivered HBV-specific ZFNs using self-complementary adeno-associated virus (scAAV) vectors and tested their anti-HBV activity in HepAD38 cells. HBV-ZFNs efficiently disrupted HBV target sites by inducing site-specific mutations. Cytotoxicity was seen with one of the ZFNs. scAAV-mediated delivery of a ZFN targeting HBV polymerase resulted in complete inhibition of HBV DNA replication and production of infectious HBV virions in HepAD38 cells. This effect was sustained for at least 2 weeks following only a single treatment. Furthermore, high specificity was observed for all ZFNs, as negligible off-target cleavage was seen via high-throughput sequencing of 7 closely matched potential off-target sites. These results show that HBV-targeted ZFNs can efficiently inhibit active HBV replication and suppress the cellular template for HBV persistence, making them promising candidates for eradication therapy.
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Affiliation(s)
- Nicholas D. Weber
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ruth Hall Sedlak
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Harshana S. De Silva Feelixge
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Division of Allergy and Infectious Disease, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Martine Aubert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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41
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Yousif M, Bell TG, Mudawi H, Glebe D, Kramvis A. Analysis of ultra-deep pyrosequencing and cloning based sequencing of the basic core promoter/precore/core region of hepatitis B virus using newly developed bioinformatics tools. PLoS One 2014; 9:e95377. [PMID: 24740330 PMCID: PMC3989311 DOI: 10.1371/journal.pone.0095377] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 03/26/2014] [Indexed: 12/18/2022] Open
Abstract
Aims The aims of this study were to develop bioinformatics tools to explore ultra-deep pyrosequencing (UDPS) data, to test these tools, and to use them to determine the optimum error threshold, and to compare results from UDPS and cloning based sequencing (CBS). Methods Four serum samples, infected with either genotype D or E, from HBeAg-positive and HBeAg-negative patients were randomly selected. UDPS and CBS were used to sequence the basic core promoter/precore region of HBV. Two online bioinformatics tools, the “Deep Threshold Tool” and the “Rosetta Tool” (http://hvdr.bioinf.wits.ac.za/tools/), were built to test and analyze the generated data. Results A total of 10952 reads were generated by UDPS on the 454 GS Junior platform. In the four samples, substitutions, detected at 0.5% threshold or above, were identified at 39 unique positions, 25 of which were non-synonymous mutations. Sample #2 (HBeAg-negative, genotype D) had substitutions in 26 positions, followed by sample #1 (HBeAg-negative, genotype E) in 12 positions, sample #3 (HBeAg-positive, genotype D) in 7 positions and sample #4 (HBeAg-positive, genotype E) in only four positions. The ratio of nucleotide substitutions between isolates from HBeAg-negative and HBeAg-positive patients was 3.5∶1. Compared to genotype E isolates, genotype D isolates showed greater variation in the X, basic core promoter/precore and core regions. Only 18 of the 39 positions identified by UDPS were detected by CBS, which detected 14 of the 25 non-synonymous mutations detected by UDPS. Conclusion UDPS data should be approached with caution. Appropriate curation of read data is required prior to analysis, in order to clean the data and eliminate artefacts. CBS detected fewer than 50% of the substitutions detected by UDPS. Furthermore it is important that the appropriate consensus (reference) sequence is used in order to identify variants correctly.
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Affiliation(s)
- Mukhlid Yousif
- Hepatitis Virus Diversity Research Programme, Department of Internal Medicine, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Trevor G. Bell
- Hepatitis Virus Diversity Research Programme, Department of Internal Medicine, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Hatim Mudawi
- Department of Medicine, Faculty of Medicine, University of Khartoum, Khartoum, Khartoum State, Sudan
| | - Dieter Glebe
- Institute of Medical Virology, National Reference Centre of Hepatitis B and D, Justus, Liebig-University of Giessen, Giessen, Hesse, Germany
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Programme, Department of Internal Medicine, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
- * E-mail:
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42
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Abstract
Adenovirus encodes for the pVII protein, which interacts and modulates virus DNA structure in the infected cells. The pVII protein is synthesized as the precursor protein and undergoes proteolytic processing by viral proteinase Avp, leading to release of a propeptide sequence and accumulation of the mature VII protein. Here we elucidate the molecular functions of the propeptide sequence present in the precursor pVII protein. The results show that the propeptide is the destabilizing element targeting the precursor pVII protein for proteasomal degradation. Our data further indicate that the propeptide sequence and the lysine residues K26 and K27 regulate the precursor pVII protein stability in a co-dependent manner. We also provide evidence that the Cullin-3 E3 ubiquitin ligase complex alters the precursor pVII protein stability by association with the propeptide sequence. In addition, we show that inactivation of the Cullin-3 protein activity reduces adenovirus E1A gene expression during early phase of virus infection. Collectively, our results indicate a novel function of the adenovirus propeptide sequence and involvement of Cullin-3 in adenovirus gene expression.
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Affiliation(s)
- Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Srinivas Thaduri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail:
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Tsuda Y, Mori Y, Abe T, Yamashita T, Okamoto T, Ichimura T, Moriishi K, Matsuura Y. Nucleolar Protein B23 Interacts with Japanese Encephalitis Virus Core Protein and Participates in Viral Replication. Microbiol Immunol 2013; 50:225-34. [PMID: 16547420 DOI: 10.1111/j.1348-0421.2006.tb03789.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Japanese encephalitis virus (JEV) core protein is detected not only in the cytoplasm but also in the nucleoli of infected cells. We previously showed that a mutant JEV lacking the nucleolar localization of the core protein impaired viral replication in mammalian cells. In this study, we identified a nucleolar phosphoprotein B23 as a protein binding with the core protein of JEV but not with that of dengue virus. The region binding with JEV core protein was mapped to amino acid residues 38 to 77 of B23. Upon JEV infection, some fraction of B23 was translocated from the nucleoli to the cytoplasm, and cytoplasmic B23 was colocalized with the core protein of wild-type JEV but not with that of the mutant JEV. Furthermore, overexpression of dominant negatives of B23 reduced JEV replication. These results suggest that B23 plays an important role in the intracellular localization of the core protein and replication of JEV.
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Affiliation(s)
- Yoshimi Tsuda
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
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44
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Takao Y, Yamada A, Yutani S, Sata M, Itoh K. Antibody Reactive to a Hepatitis C Virus (HCV)-Derived Peptide Capable of Inducing HLA-A2 Restricted Cytotoxic T Lymphocytes Is Detectable in a Majority of HCV-Infected Individuals without HLA-A2 Restriction. Microbiol Immunol 2013; 48:507-17. [PMID: 15272196 DOI: 10.1111/j.1348-0421.2004.tb03546.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hepatitis C virus (HCV) is a single-strand RNA virus. Approximately 170 million people around the world are persistently infected and are at risk of liver cirrhosis or cancer. There is an urgent need to develop both therapeutic and diagnostic modalities of HCV. One approach to achieve these goals would be to determine highly immunodominant HCV peptides which are recognized by both cellular and humoral immunities. This study reports one such peptide, HCV-core protein at positions 35-44, having HLA-A2 binding motifs. IgG specific to this CTL-epitope peptide is consistently detectable in a majority of the patients with HCV infection regardless of the different HLA types, different disease conditions, and different HCV-genotypes tested. The sequence LPRR at positions 37-40 is considered to be the fine epitope recognized by the IgG. These results may provide new insights for the development of both therapeutic and diagnostic modalities of HCV at lower costs.
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Affiliation(s)
- Yukari Takao
- Departments of Immunology, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
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45
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Yu X, Jin L, Jih J, Shih C, Hong Zhou Z. 3.5Å cryoEM structure of hepatitis B virus core assembled from full-length core protein. PLoS One 2013; 8:e69729. [PMID: 24039702 PMCID: PMC3765168 DOI: 10.1371/journal.pone.0069729] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 06/12/2013] [Indexed: 12/14/2022] Open
Abstract
The capsid shell of infectious hepatitis B virus (HBV) is composed of 240 copies of a single protein called HBV core antigen (HBc). An atomic model of a core assembled from truncated HBc was determined previously by X-ray crystallography. In an attempt to obtain atomic structural information of HBV core in a near native, non-crystalline environment, we reconstructed a 3.5Å-resolution structure of a recombinant core assembled from full-length HBc by cryo electron microscopy (cryoEM) and derived an atomic model. The structure shows that the 240 molecules of full-length HBc form a core with two layers. The outer layer, composed of the N-terminal assembly domain, is similar to the crystal structure of the truncated HBc, but has three differences. First, unlike the crystal structure, our cryoEM structure shows no disulfide bond between the Cys61 residues of the two subunits within the dimer building block, indicating such bond is not required for core formation. Second, our cryoEM structure reveals up to four more residues in the linker region (amino acids 140-149). Third, the loops in the cryoEM structures containing this linker region in subunits B and C are oriented differently (~30° and ~90°) from their counterparts in the crystal structure. The inner layer, composed of the C-terminal arginine-rich domain (ARD) and the ARD-bound RNAs, is partially-ordered and connected with the outer layer through linkers positioned around the two-fold axes. Weak densities emanate from the rims of positively charged channels through the icosahedral three-fold and local three-fold axes. We attribute these densities to the exposed portions of some ARDs, thus explaining ARD's accessibility by proteases and antibodies. Our data supports a role of ARD in mediating communication between inside and outside of the core during HBV maturation and envelopment.
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Affiliation(s)
- Xuekui Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lei Jin
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jonathan Jih
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Chiaho Shih
- Institute of Biomedical Sciences (IBMS), Academia Sinica, Taipei, Taiwan
| | - Z. Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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46
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Garcia ML, Reynolds TD, Mothes W, Robek MD. Functional characterization of the putative hepatitis B virus core protein late domain using retrovirus chimeras. PLoS One 2013; 8:e72845. [PMID: 24009707 PMCID: PMC3756966 DOI: 10.1371/journal.pone.0072845] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022] Open
Abstract
The hepatitis B virus (HBV) Core protein encodes a late (L)-domain like motif (129PPAYRPPNAP138) that has been purported to serve as a docking site for recruitment of host factors such as Nedd4 that can mediate viral particle release from infected cells. However, mutation of this region of Core typically disrupts nucleocapsid formation in the cytoplasm, making it difficult to ascertain if the Core PPAY motif constitutes a functional L-domain that mediates HBV release in the context of replicating virus. Since many viral L-domains are functionally interchangeable between different virus families, and such swapping experiments have been used as a tool to identify other viral sequences with L-domain activity, we generated chimeric constructs between murine leukemia virus (MLV) Gag and HBV Core to determine if the potential HBV L-domain motif is sufficient to stimulate virus release. We found that the HBV Core PPAY motif, but not the PNAP motif, demonstrates L-domain activity in the context of MLV replication to direct virus release and infectious virion production. Additionally, we found that overexpression of the cellular Nedd4 or WWP1 ubiquitin ligases stimulates release of a partially defective PPAY domain mutant, providing further evidence supporting a role for the Nedd4 ubiquitin ligase in promoting HBV release. These studies lend further insight into the mechanisms used by HBV to mediate its release from infected cells.
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Affiliation(s)
- Mayra L. Garcia
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Tracy D. Reynolds
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Michael D. Robek
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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Kikuchi M, Iwabuchi S, Kikkou T, Noguchi K, Odaka M, Yohda M, Kawata M, Sato C, Matsumoto O. Expression, purification, crystallization and preliminary crystallographic analysis of hepatitis B virus core protein dimerized via a peptide linker containing an EGFP insertion. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:942-5. [PMID: 23908049 PMCID: PMC3729180 DOI: 10.1107/s1744309113019957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/19/2013] [Indexed: 11/11/2022]
Abstract
Virus-like particles (VLPs) have many potentially useful applications. The core proteins of human hepatitis B virus self-assemble into icosahedral VLPs. As previously reported, core protein dimers (CPDs), produced by connecting two core proteins via a peptide linker, can also assemble into VLPs. CPDs in which heterologous proteins were connected to the C-terminus (CPD1) were found to rearrange into symmetrical octahedra during crystallization. In this study, a heterologous protein was inserted into the peptide linker of the CPD (CPD2). CPD2 was expressed in Escherichia coli, assembled into VLPs, purified and crystallized. A single crystal diffracted to 2.8 Å resolution and belonged to the cubic space group F432, with unit-cell parameters a = b = c = 218.6 Å. Single-crystal analysis showed that CPD1 and CPD2 rearranged into the same octahedral organization in a crystallization solution.
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Affiliation(s)
- Masaki Kikuchi
- Faculty of Pharmaceutical Sciences, Chiba Institute of Science, 15-8 Shiomi-cho, Chosi, Chiba 288-0025, Japan
| | - Shinichiro Iwabuchi
- Faculty of Pharmaceutical Sciences, Chiba Institute of Science, 15-8 Shiomi-cho, Chosi, Chiba 288-0025, Japan
| | - Tatsuhiko Kikkou
- Faculty of Pharmaceutical Sciences, Chiba Institute of Science, 15-8 Shiomi-cho, Chosi, Chiba 288-0025, Japan
| | - Keiichi Noguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masafumi Odaka
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masaaki Kawata
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 2, Tsukuba 305-8568, Japan
| | - Chikara Sato
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 2, Tsukuba 305-8568, Japan
| | - Osamu Matsumoto
- Faculty of Pharmaceutical Sciences, Chiba Institute of Science, 15-8 Shiomi-cho, Chosi, Chiba 288-0025, Japan
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48
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Anjum S, Afzal MS, Ahmad T, Aslam B, Waheed Y, Shafi T, Qadri I. Mutations in the STAT1‑interacting domain of the hepatitis C virus core protein modulate the response to antiviral therapy. Mol Med Rep 2013; 8:487-92. [PMID: 23799612 DOI: 10.3892/mmr.2013.1541] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/31/2013] [Indexed: 02/07/2023] Open
Abstract
RNA viruses, such as hepatitis C virus (HCV), have markedly error-prone replication, resulting in high rates of mutagenesis. In addition, the standard treatment includes ribavirin, a base analog that is likely to cause mutations in different regions of the HCV genome, resulting in deleterious effects on HCV itself. The N-terminal region of the core protein is reported to block interferon (IFN) signaling by interaction with the STAT1‑SH2 domain, resulting in HCV resistance to IFN therapy. In this study, mutations in the HCV core protein from IFN/ribavirin‑treated patients were analyzed, with particular focus on the N‑terminal domain of the HCV core which is reported to interact with STAT1. HCV PCR positive patients enrolled in this study were either undergoing pegylated IFN/ribavirin bitherapy and had completed 12 weeks of initial treatment or were treatment‑naïve patients. The HCV core protein was cloned and sequenced from these patients and mutations observed in the STAT1‑interacting domain of the core protein from treated patients were characterized using in silico interaction to depict the role of these mutations in disease outcomes. Our results suggest that the amino acids at positions 2, 3, 8, 16 and 23 of the HCV core protein are critical for core-STAT1 interaction and ribavirin-induced mutations at these positions interfere with the interaction, resulting in a better response of the treated patients. In conclusion, this study anticipates that HCV core residues 2, 3, 8, 16 and 23 directly interact with STAT1. We propose that IFN/ribavirin bitherapy‑induced mutations in the STAT1‑interacting domain of the HCV core protein may be responsible for the improved therapeutic response and viral clearance, thus amino acids 1-23 of the N-terminus of the core protein are an ideal antiviral target. However, this treatment may give rise to resistant variants that are able to escape the current therapy. We propose similar studies in responsive and non-responsive genotypes in order to gain a broader picture of this proposed mechanism of viral clearance.
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Affiliation(s)
- Sadia Anjum
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan.
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49
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Vitelli A, Quirion MR, Lo CY, Misplon JA, Grabowska AK, Pierantoni A, Ammendola V, Price GE, Soboleski MR, Cortese R, Colloca S, Nicosia A, Epstein SL. Vaccination to conserved influenza antigens in mice using a novel Simian adenovirus vector, PanAd3, derived from the bonobo Pan paniscus. PLoS One 2013; 8:e55435. [PMID: 23536756 PMCID: PMC3594242 DOI: 10.1371/journal.pone.0055435] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 12/23/2012] [Indexed: 12/11/2022] Open
Abstract
Among approximately 1000 adenoviruses from chimpanzees and bonobos studied recently, the Pan Adenovirus type 3 (PanAd3, isolated from a bonobo, Pan paniscus) has one of the best profiles for a vaccine vector, combining potent transgene immunogenicity with minimal pre-existing immunity in the human population. In this study, we inserted into a replication defective PanAd3 a transgene expressing a fusion protein of conserved influenza antigens nucleoprotein (NP) and matrix 1 (M1). We then studied antibody and T cell responses as well as protection from challenge infection in a mouse model. A single intranasal administration of PanAd3-NPM1 vaccine induced strong antibody and T cell responses, and protected against high dose lethal influenza virus challenge. Thus PanAd3 is a promising candidate vector for vaccines, including universal influenza vaccines.
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MESH Headings
- Adenoviruses, Human/immunology
- Adenoviruses, Simian/genetics
- Adenoviruses, Simian/immunology
- Amino Acid Sequence
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Cross Reactions/immunology
- Female
- Gene Expression
- Genetic Vectors/administration & dosage
- Genetic Vectors/genetics
- Genetic Vectors/immunology
- Humans
- Immunity, Mucosal
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/immunology
- Mice
- Molecular Sequence Data
- Nucleocapsid Proteins
- Nucleophosmin
- Orthomyxoviridae Infections/prevention & control
- Pan paniscus
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/immunology
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/immunology
- T-Lymphocytes/immunology
- Viral Core Proteins/chemistry
- Viral Core Proteins/genetics
- Viral Core Proteins/immunology
- Viral Matrix Proteins/chemistry
- Viral Matrix Proteins/genetics
- Viral Matrix Proteins/immunology
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Affiliation(s)
| | - Mary R. Quirion
- Gene Therapy and Immunogenicity Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Chia-Yun Lo
- Gene Therapy and Immunogenicity Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Julia A. Misplon
- Gene Therapy and Immunogenicity Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
| | | | | | | | - Graeme E. Price
- Gene Therapy and Immunogenicity Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Mark R. Soboleski
- Gene Therapy and Immunogenicity Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
| | | | | | - Alfredo Nicosia
- Okairòs, Rome, Italy
- Centro di Ingegneria Genetica e Biotecnologia Avanzate (CEINGE), Naples, Italy
- Department of Biochemistry and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Suzanne L. Epstein
- Gene Therapy and Immunogenicity Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
- * E-mail:
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50
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Ueda Y, Kaido T, Ogura Y, Ogawa K, Yoshizawa A, Hata K, Fujimoto Y, Miyagawa-Hayashino A, Haga H, Marusawa H, Teramukai S, Uemoto S, Chiba T. Pretransplant serum hepatitis C virus RNA levels predict response to antiviral treatment after living donor liver transplantation. PLoS One 2013; 8:e58380. [PMID: 23505497 PMCID: PMC3591322 DOI: 10.1371/journal.pone.0058380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 02/04/2013] [Indexed: 12/24/2022] Open
Abstract
Background Given the limited efficacy and high adverse event rate associated with treatment of recurrent hepatitis C after liver transplantation, an individualized treatment strategy should be considered. The aim of this study was to identify predictors of response to antiviral therapy for hepatitis C after living donor liver transplantation (LDLT) and to study the associated adverse events. Methods A retrospective chart review was performed on 125 hepatitis C virus (HCV)-positive LDLT recipients who received interferon plus ribavirin and/or peginterferon plus ribavirin therapy at Kyoto University between January 2001 and June 2011. Results Serum HCV RNA reached undetectable levels within 48 weeks in 77 (62%) of 125 patients, and these patients were defined as showing virological response (VR). Of 117 patients, 50 (43%) achieved sustained VR (SVR). Predictive factors associated with both VR and SVR by univariate analysis included low pretransplant serum HCV RNA levels, a non-1 HCV genotype, and low pretreatment serum HCV RNA levels. In addition, LDLT from ABO-mismatched donors was significantly associated with VR, and white cell and neutrophil counts before interferon therapy were associated with SVR. Multivariate analysis showed that 2 variables–pretransplant serum HCV RNA level less than 500 kIU/mL and a non-1 HCV genotype–remained in models of both VR and SVR and that an ABO mismatch was associated with VR. No variables with a significant effect on treatment withdrawal were found. Conclusions Virological response to antiviral therapy in patients with hepatitis C recurring after LDLT can be predicted prior to transplant, based on pretransplant serum HCV-RNA levels and HCV genotype. LDLT from ABO-mismatched donors may contribute to more efficacious interferon therapy. Trial Registration UMIN-CTR
UMIN000003286
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Affiliation(s)
- Yoshihide Ueda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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