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Park T, Woo H, Yang J, Kwon S, Won J, Seok C. Protein oligomer structure prediction using GALAXY in CASP14. Proteins 2021; 89:1844-1851. [PMID: 34363243 DOI: 10.1002/prot.26203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/17/2021] [Accepted: 07/29/2021] [Indexed: 11/10/2022]
Abstract
Proteins perform their functions by interacting with other biomolecules. For these interactions, proteins often form homo- or hetero-oligomers as well. Thus, oligomer protein structures provide important clues regarding the biological roles of proteins. To this end, computational prediction of oligomer structures may be a useful tool in the absence of experimentally resolved structures. Here, we describe our server and human-expert methods used to predict oligomer structures in the CASP14 experiment. Examples are provided for cases in which manual domain-splitting led to improved oligomeric domain structures by ab initio docking, automated oligomer structure refinement led to improved subunit orientation and terminal structure, and manual oligomer modeling utilizing literature information generated a reasonable oligomer model. We also discussed the results of post-prediction docking calculations with AlphaFold2 monomers as input in comparison to our blind prediction results. Overall, ab initio docking of AlphaFold2 models did not lead to better oligomer structure prediction, which may be attributed to the interfacial structural difference between the AlphaFold2 monomer structures and the crystal oligomer structures. This result poses a next-stage challenge in oligomer structure prediction after the success of AlphaFold2. For successful protein assembly structure prediction, a different approach that exploits further evolutionary information on the interface and/or flexible docking taking the interfacial conformational flexibilities of subunit structures into account is needed.
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Affiliation(s)
- Taeyong Park
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Hyeonuk Woo
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Jinsol Yang
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Sohee Kwon
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Jonghun Won
- Department of Chemistry, Seoul National University, Seoul, South Korea.,Galux Inc., Seoul, South Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, South Korea.,Galux Inc., Seoul, South Korea
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2
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Makbul C, Nassal M, Böttcher B. Slowly folding surface extension in the prototypic avian hepatitis B virus capsid governs stability. eLife 2020; 9:e57277. [PMID: 32795390 PMCID: PMC7455244 DOI: 10.7554/elife.57277] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022] Open
Abstract
Hepatitis B virus (HBV) is an important but difficult to study human pathogen. Most basics of the hepadnaviral life-cycle were unraveled using duck HBV (DHBV) as a model although DHBV has a capsid protein (CP) comprising ~260 rather than ~180 amino acids. Here we present high-resolution structures of several DHBV capsid-like particles (CLPs) determined by electron cryo-microscopy. As for HBV, DHBV CLPs consist of a dimeric α-helical frame-work with protruding spikes at the dimer interface. A fundamental new feature is a ~ 45 amino acid proline-rich extension in each monomer replacing the tip of the spikes in HBV CP. In vitro, folding of the extension takes months, implying a catalyzed process in vivo. DHBc variants lacking a folding-proficient extension produced regular CLPs in bacteria but failed to form stable nucleocapsids in hepatoma cells. We propose that the extension domain acts as a conformational switch with differential response options during viral infection.
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Affiliation(s)
- Cihan Makbul
- Julius Maximilian University of Würzburg, Department of Biochemistry and Rudolf Virchow CentreWürzburgGermany
| | - Michael Nassal
- University Hospital Freiburg, Internal Medicine 2/Molecular BiologyFreiburgGermany
| | - Bettina Böttcher
- Julius Maximilian University of Würzburg, Department of Biochemistry and Rudolf Virchow CentreWürzburgGermany
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Corcuera A, Stolle K, Hillmer S, Seitz S, Lee JY, Bartenschlager R, Birkmann A, Urban A. Novel non-heteroarylpyrimidine (HAP) capsid assembly modifiers have a different mode of action from HAPs in vitro. Antiviral Res 2018; 158:135-142. [PMID: 30031759 DOI: 10.1016/j.antiviral.2018.07.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/12/2018] [Accepted: 07/17/2018] [Indexed: 12/11/2022]
Abstract
One of the most promising viral targets in current hepatitis B virus (HBV) drug development is the core protein due to its multiple roles in the viral life cycle. Here we investigated the differences in the mode of action and antiviral activity of representatives of six different capsid assembly modifier (CAM) scaffolds: three from the well-characterized scaffolds heteroarylpyrimidine (HAP), sulfamoylbenzamide (SBA), and phenylpropenamide (PPA), and three from novel scaffolds glyoxamide-pyrrolamide (GPA), pyrazolyl-thiazole (PT), and dibenzo-thiazepin-2-one (DBT). The target activity and antiviral efficacy of the different CAMs were tested in biochemical and cellular assays. Analytical size exclusion chromatography and transmission electron microscopy showed that only the HAP compound induced formation of aberrant non-capsid structures (class II mode of action), while the remaining CAMs did not affect capsid gross morphology (class I mode of action). Intracellular lysates from the HepAD38 cell line, inducibly replicating HBV, showed no reduction in the quantities of intracellular core protein or capsid after treatment with SBA, PPA, GPA, PT, or DBT compounds; however HAP-treatment led to a profound decrease in both. Additionally, immunofluorescence staining of compound-treated HepAD38 cells showed that all non-HAP CAMs led to a shift in the equilibrium of HBV core antigen (HBcAg) towards complete cytoplasmic staining, while the HAP induced accumulation of HBcAg aggregates in the nucleus. Our study demonstrates that the novel scaffolds GPA, PT, and DBT exhibit class I modes of action, alike SBA and PPA, whereas HAP remains the only scaffold belonging to class II inhibitors.
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Affiliation(s)
- Angelica Corcuera
- AiCuris Anti-infective Cures GmbH, Friedrich-Ebert-Str.475, 42117, Wuppertal, Germany; Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Katharina Stolle
- AiCuris Anti-infective Cures GmbH, Friedrich-Ebert-Str.475, 42117, Wuppertal, Germany
| | - Stefan Hillmer
- Electron Microscopy Core Facility, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Stefan Seitz
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Ji-Young Lee
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Alexander Birkmann
- AiCuris Anti-infective Cures GmbH, Friedrich-Ebert-Str.475, 42117, Wuppertal, Germany
| | - Andreas Urban
- AiCuris Anti-infective Cures GmbH, Friedrich-Ebert-Str.475, 42117, Wuppertal, Germany.
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Chen JY, Gan CY, Cai XF, Zhang WL, Long QX, Wei XF, Hu Y, Tang N, Chen J, Guo H, Huang AL, Hu JL. Fluorescent protein tagged hepatitis B virus capsid protein with long glycine-serine linker that supports nucleocapsid formation. J Virol Methods 2018; 255:52-59. [PMID: 29447911 DOI: 10.1016/j.jviromet.2018.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/06/2018] [Accepted: 02/11/2018] [Indexed: 02/05/2023]
Abstract
Fusion core proteins of Hepatitis B virus can be used to study core protein functions or capsid trafficking. A problem in constructing fusion core proteins is functional impairment of the individual domains in these fusion proteins, might due to structural interference. We reported a method to construct fusion proteins of Hepatitis B virus core protein (HBc) in which the functions of fused domains were partially kept. This method follows two principles: (1) fuse heterogeneous proteins at the N terminus of HBc; (2) use long Glycine-serine linkers between the two domains. Using EGFP and RFP as examples, we showed that long flexible G4S linkers can effectively separate the two domains in function. Among these fusion proteins constructed, GFP-G4S186-HBc and RFP-G4S47-HBc showed the best efficiency in rescuing the replication of an HBV replicon deficient in the core protein expression, though both of the two fusion proteins failed to support the formation of the relaxed circular DNA. These fluorescent protein-tagged HBcs might help study related to HBc or capsids tracking in cells.
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Affiliation(s)
- Jiang-Yan Chen
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China; Department of Clinical Laboratory, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (CCID), Hangzhou, China
| | - Chun-Yang Gan
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xue-Fei Cai
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wen-Lu Zhang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Quan-Xin Long
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xia-Fei Wei
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ni Tang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Chen
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, United States
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (CCID), Hangzhou, China.
| | - Jie-Li Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (CCID), Hangzhou, China.
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Functional association of cellular microtubules with viral capsid assembly supports efficient hepatitis B virus replication. Sci Rep 2017; 7:10620. [PMID: 28878350 PMCID: PMC5587681 DOI: 10.1038/s41598-017-11015-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/18/2017] [Indexed: 12/23/2022] Open
Abstract
Viruses exploit host factors and environment for their efficient replication. The virus-host interaction mechanisms for achieving an optimal hepatitis B virus (HBV) replication have been largely unknown. Here, a single cell cloning revealed that HepAD38 cells, a widely-used HBV-inducible cell line, contain cell clones with diverse permissiveness to HBV replication. The HBV permissiveness was impaired upon treatment with microtubule inhibitor nocodazole, which was identified as an HBV replication inhibitor from a pharmacological screening. In the microtubule-disrupted cells, the efficiency of HBV capsid assembly was remarkably decreased without significant change in pre-assembly process. We further found that HBV core interacted with tubulin and co-localized with microtubule-like fibriforms, but this association was abrogated upon microtubule-disassembly agents, resulting in attenuation of capsid formation. Our data thus suggest a significant role of microtubules in the efficient capsid formation during HBV replication. In line with this, a highly HBV permissive cell clone of HepAD38 cells showed a prominent association of core-microtubule and thus a high capacity to support the capsid formation. These findings provide a new aspect of virus-cell interaction for rendering efficient HBV replication.
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Ogura N, Watashi K, Noguchi T, Wakita T. Formation of covalently closed circular DNA in Hep38.7-Tet cells, a tetracycline inducible hepatitis B virus expression cell line. Biochem Biophys Res Commun 2014; 452:315-21. [PMID: 25150444 DOI: 10.1016/j.bbrc.2014.08.029] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/06/2014] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) plays a central role in chronic HBV infection. However, analysis of the molecular mechanism of cccDNA formation is difficult because of the low efficiency in tissue cultured cells. In this study, we developed a more efficient cccDNA expression cell, Hep38.7-Tet, by subcloning from a tetracycline inducible HBV expression cell, HepAD38. Higher levels of cccDNA were produced in Hep38.7-Tet cells compared to HepAD38 cells. In Hep38.7-Tet cells, the cccDNA was detectable at six days after HBV induction. HBV e antigen (HBeAg) secretion was dependent upon cccDNA production. We screened chemical compounds using Hep38.7-Tet cells and HBeAg secretion as a marker. Most of the hit compounds have already been reported as anti-HBV compounds. These data suggested that Hep38.7-Tet cells will be powerful tools for analysis of the molecular mechanism of cccDNA formation/maintenance and development of novel therapeutic agents to control HBV infection.
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Affiliation(s)
- Naoki Ogura
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan.
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Toru Noguchi
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan.
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
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Identification of disubstituted sulfonamide compounds as specific inhibitors of hepatitis B virus covalently closed circular DNA formation. Antimicrob Agents Chemother 2012; 56:4277-88. [PMID: 22644022 DOI: 10.1128/aac.00473-12] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) plays a central role in viral infection and persistence and is the basis for viral rebound after the cessation of therapy, as well as the elusiveness of a cure even after extended treatment. Therefore, there is an urgent need for the development of novel therapeutic agents that directly target cccDNA formation and maintenance. By employing an innovative cell-based cccDNA assay in which secreted HBV e antigen is a cccDNA-dependent surrogate, we screened an in-house small-molecule library consisting of 85,000 drug-like compounds. Two structurally related disubstituted sulfonamides (DSS), termed CCC-0975 and CCC-0346, emerged and were confirmed as inhibitors of cccDNA production, with low micromolar 50% effective concentrations (EC(50)s) in cell culture. Further mechanistic studies demonstrated that DSS compound treatment neither directly inhibited HBV DNA replication in cell culture nor reduced viral polymerase activity in the in vitro endogenous polymerase assay but synchronously reduced the levels of HBV cccDNA and its putative precursor, deproteinized relaxed circular DNA (DP-rcDNA). However, DSS compounds did not promote the intracellular decay of HBV DP-rcDNA and cccDNA, suggesting that the compounds interfere primarily with rcDNA conversion into cccDNA. In addition, we demonstrated that CCC-0975 was able to reduce cccDNA biosynthesis in duck HBV-infected primary duck hepatocytes. This is the first attempt, to our knowledge, to identify small molecules that target cccDNA formation, and DSS compounds thus potentially serve as proof-of-concept drug candidates for development into therapeutics to eliminate cccDNA from chronic HBV infection.
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Alkylated porphyrins have broad antiviral activity against hepadnaviruses, flaviviruses, filoviruses, and arenaviruses. Antimicrob Agents Chemother 2010; 55:478-86. [PMID: 21135183 DOI: 10.1128/aac.00989-10] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We screened ∼2,200 compounds known to be safe in people for the ability to reduce the amount of virion-associated hepatitis B virus (HBV) DNA in the culture medium of producer cells. These efforts led to the discovery of an alkylated porphyrin, chlorophyllide, as the compound that achieved the greatest reduction in signal. Here we report that chlorophyllide directly and quantitatively disrupted HBV virions at micromolar concentrations, resulting in the loss of all detectable virion DNA, without detectably affecting cell viability or intracellular viral gene products. Chemophores of chlorophyllide were also tested. Chlorin e6, a metal-free chlorophyllide-like molecule, showed the strongest antiviral activity against HBV as well as profound antiviral effects on other enveloped viruses, such as hepatitis C virus (HCV), human immunodeficiency virus (HIV), dengue virus (DENV), Marburg virus (MARV), Tacaribe virus (TCRV), and Junin viruses (JUNV). Remarkably, chlorin e6 inactivated DENV at subnanomolar-level concentrations. However, the compound had no antiviral effect against encephalomyocarditis virus and adenovirus, suggesting that chlorin e6 may be less active or inactive against nonenveloped viruses. Although other porphyrin derivatives have been previously reported to possess antiviral activity, this is the first analysis of the biochemical impact of chlorophyllide and chlorin e6 against HBV and of the dramatic anti-infectivity impact upon DENV. The possible application of this family of compounds as antiviral agents, as microbicides and systemic virus neutralizing agents, is discussed.
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Interferons accelerate decay of replication-competent nucleocapsids of hepatitis B virus. J Virol 2010; 84:9332-40. [PMID: 20610715 DOI: 10.1128/jvi.00918-10] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Alpha interferon (IFN-alpha) is an approved medication for chronic hepatitis B. Gamma interferon (IFN-gamma) is a key mediator of host antiviral immunity against hepatitis B virus (HBV) infection in vivo. However, the molecular mechanism by which these antiviral cytokines suppress HBV replication remains elusive. Using an immortalized murine hepatocyte (AML12)-derived cell line supporting tetracycline-inducible HBV replication, we show in this report that both IFN-alpha and IFN-gamma efficiently reduce the amount of intracellular HBV nucleocapsids. Furthermore, we provide evidence suggesting that the IFN-induced cellular antiviral response is able to distinguish and selectively accelerate the decay of HBV replication-competent nucleocapsids but not empty capsids in a proteasome-dependent manner. Our findings thus reveal a novel antiviral mechanism of IFNs and provide a basis for a better understanding of HBV pathobiology.
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Nassal M, Leifer I, Wingert I, Dallmeier K, Prinz S, Vorreiter J. A structural model for duck hepatitis B virus core protein derived by extensive mutagenesis. J Virol 2007; 81:13218-29. [PMID: 17881438 PMCID: PMC2169103 DOI: 10.1128/jvi.00846-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Duck hepatitis B virus (DHBV) shares many fundamental features with human HBV. However, the DHBV core protein (DHBc), forming the nucleocapsid shell, is much larger than that of HBV (HBc) and, in contrast to HBc, there is little direct information on its structure. Here we applied an efficient expression system for recombinant DHBc particles to the biochemical analysis of a large panel of mutant DHBc proteins. By combining these data with primary sequence alignments, secondary structure prediction, and three-dimensional modeling, we propose a model for the fold of DHBc. Its major features are a HBc-like two-domain structure with an assembly domain comprising the first about 185 amino acids and a C-terminal nucleic acid binding domain (CTD), connected by a morphogenic linker region that is longer than in HBc and extends into the CTD. The assembly domain shares with HBc a framework of four major alpha-helices but is decorated at its tip with an extra element that contains at least one helix and that is made up only in part by the previously predicted insertion sequence. All subelements are interconnected, such that structural changes at one site are transmitted to others, resulting in an unexpected variability of particle morphologies. Key features of the model are independently supported by the accompanying epitope mapping study. These data should be valuable for functional studies on the impact of core protein structure on virus replication, and some of the mutant proteins may be particularly suitable for higher-resolution structural investigations.
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Affiliation(s)
- Michael Nassal
- University Hospital Freiburg, Internal Medicine 2/Molecular Biology, Hugstetter Str. 55, D-79106 Freiburg, Germany.
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