1
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Ferrero DS, Tomás Gilabert O, Verdaguer N. Structural insights on the nucleoprotein C-terminal domain of Měnglà virus. Microbiol Spectr 2023; 11:e0237323. [PMID: 37888996 PMCID: PMC10714759 DOI: 10.1128/spectrum.02373-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Filoviruses are the causative agents of severe and often fatal hemorrhagic disease in humans. Měnglà virus (MLAV) is a recently reported filovirus, isolated from fruit bats that is capable to replicate in human cells, representing a potential risk for human health. An in-depth structural and functional knowledge of MLAV proteins is an essential step for antiviral research on this virus that can also be extended to other emerging filoviruses. In this study, we determined the first crystal structures of the C-terminal domain (CTD) of the MLAV nucleoprotein (NP), showing important similarities to the equivalent domain in MARV. The structural data also show that the NP CTD has the ability to form large helical oligomers that may participate in the control of cytoplasmic inclusion body formation during viral replication.
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Affiliation(s)
| | | | - Nuria Verdaguer
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
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2
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Abstract
Filovirus-infected cells are characterized by typical cytoplasmic inclusion bodies (IBs) located in the perinuclear region. The formation of these IBs is induced mainly by the accumulation of the filoviral nucleoprotein NP, which recruits the other nucleocapsid proteins, the polymerase co-factor VP35, the polymerase L, the transcription factor VP30 and VP24 via direct or indirect protein-protein interactions. Replication of the negative-strand RNA genomes by the viral polymerase L and VP35 occurs in the IBs, resulting in the synthesis of positive-strand genomes, which are encapsidated by NP, thus forming ribonucleoprotein complexes (antigenomic RNPs). These newly formed antigenomic RNPs in turn serve as templates for the synthesis of negative-strand RNA genomes that are also encapsidated by NP (genomic RNPs). Still in the IBs, genomic RNPs mature into tightly packed transport-competent nucleocapsids (NCs) by the recruitment of the viral protein VP24. NCs are tightly coiled left-handed helices whose structure is mainly determined by the multimerization of NP at its N-terminus, and these helices form the inner layer of the NCs. The RNA genome is fixed by 2 lobes of the NP N-terminus and is thus guided by individual NP molecules along the turns of the helix. Direct interaction of the NP C-terminus with the VP35 and VP24 molecules forms the outer layer of the NCs. Once formed, NCs that are located at the border of the IBs recruit actin polymerization machinery to one of their ends to drive their transport to budding sites for their envelopment and final release. Here, we review the current knowledge on the structure, assembly, and transport of filovirus NCs.
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Affiliation(s)
- Olga Dolnik
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Stephan Becker
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
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3
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Vanmechelen B, Stroobants J, Chiu W, Schepers J, Marchand A, Chaltin P, Vermeire K, Maes P. Identification of novel Ebola virus inhibitors using biologically contained virus. Antiviral Res 2022; 200:105294. [PMID: 35337896 DOI: 10.1016/j.antiviral.2022.105294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/09/2022] [Accepted: 03/20/2022] [Indexed: 12/13/2022]
Abstract
Despite recent advancements in the development of vaccines and monoclonal antibody therapies for Ebola virus disease, treatment options remain limited. Moreover, management and containment of Ebola virus outbreaks is often hindered by the remote nature of the locations in which the outbreaks originate. Small-molecule compounds offer the advantage of being relatively cheap and easy to produce, transport and store, making them an interesting modality for the development of novel therapeutics against Ebola virus disease. Furthermore, the repurposing of small-molecule compounds, previously developed for alternative applications, can aid in reducing the time needed to bring potential therapeutics from bench to bedside. For this purpose, the Medicines for Malaria Venture provides collections of previously developed small-molecule compounds for screening against other infectious diseases. In this study, we used biologically contained Ebola virus to screen over 4,200 small-molecule drugs and drug-like compounds provided by the Medicines for Malaria Venture (i.e., the Pandemic Response Box and the COVID Box) and the Centre for Drug Design and Discovery (CD3, KU Leuven, Belgium). In addition to confirming known Ebola virus inhibitors, illustrating the validity of our screening assays, we identified eight novel selective Ebola virus inhibitors. Although the inhibitory potential of these compounds remains to be validated in vivo, they represent interesting compounds for the study of potential interventions against Ebola virus disease and might serve as a basis for the development of new therapeutics.
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Affiliation(s)
- Bert Vanmechelen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Joren Stroobants
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Winston Chiu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Joost Schepers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Arnaud Marchand
- CISTIM Leuven vzw, Gaston Geenslaan 2, 3000, Leuven, Belgium
| | - Patrick Chaltin
- CISTIM Leuven vzw, Gaston Geenslaan 2, 3000, Leuven, Belgium; Centre for Drug Design and Discovery (CD3), KU Leuven, Gaston Geenslaan 2, 3000, Leuven, Belgium
| | - Kurt Vermeire
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium.
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4
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Wu L, Jin D, Wang D, Jing X, Gong P, Qin Y, Chen M. The two-stage interaction of Ebola virus VP40 with nucleoprotein results in a switch from viral RNA synthesis to virion assembly/budding. Protein Cell 2020; 13:120-140. [PMID: 33141416 PMCID: PMC8783937 DOI: 10.1007/s13238-020-00764-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/06/2020] [Indexed: 11/28/2022] Open
Abstract
Ebola virus (EBOV) is an enveloped negative-sense RNA virus and a member of the filovirus family. Nucleoprotein (NP) expression alone leads to the formation of inclusion bodies (IBs), which are critical for viral RNA synthesis. The matrix protein, VP40, not only plays a critical role in virus assembly/budding, but also can regulate transcription and replication of the viral genome. However, the molecular mechanism by which VP40 regulates viral RNA synthesis and virion assembly/budding is unknown. Here, we show that within IBs the N-terminus of NP recruits VP40 and is required for VLP-containing NP release. Furthermore, we find four point mutations (L692A, P697A, P698A and W699A) within the C-terminal hydrophobic core of NP result in a stronger VP40-NP interaction within IBs, sequestering VP40 within IBs, reducing VP40-VLP egress, abolishing the incorporation of NC-like structures into VP40-VLP, and inhibiting viral RNA synthesis, suggesting that the interaction of N-terminus of NP with VP40 induces a conformational change in the C-terminus of NP. Consequently, the C-terminal hydrophobic core of NP is exposed and binds VP40, thereby inhibiting RNA synthesis and initiating virion assembly/budding.
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Affiliation(s)
- Linjuan Wu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Dongning Jin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Dan Wang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xuping Jing
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Peng Gong
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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5
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Fragment screening targeting Ebola virus nucleoprotein C-terminal domain identifies lead candidates. Antiviral Res 2020; 180:104822. [PMID: 32446802 PMCID: PMC7894038 DOI: 10.1016/j.antiviral.2020.104822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/08/2020] [Accepted: 05/15/2020] [Indexed: 01/24/2023]
Abstract
The Ebola Virus is a causative agent of viral hemorrhagic fever outbreaks and a potential global health risk. The outbreak in West Africa (2013-2016) led to 11,000+ deaths and 30,000+ Ebola infected individuals. The current outbreak in the Democratic Republic of Congo (DRC) with 3000+ confirmed cases and 2000+ deaths attributed to Ebola virus infections provides a reminder that innovative countermeasures are still needed. Ebola virus encodes 7 open reading frames (ORFs). Of these, the nucleocapsid protein (eNP) encoded by the first ORF plays many significant roles, including a role in viral RNA synthesis. Here we describe efforts to target the C-terminal domain of eNP (eNP-CTD) that contains highly conserved residues 641-739 as a pan-Ebola antiviral target. Interactions of eNP-CTD with Ebola Viral Protein 30 (eVP30) and Viral Protein 40 (eVP40) have been shown to be crucial for viral RNA synthesis, virion formation, and virion transport. We used nuclear magnetic response (NMR)-based methods to screened the eNP-CTD against a fragment library. Perturbations of 1D 1H NMR spectra identified of 48 of the 439 compounds screened as potential eNP CTD interactors. Subsequent analysis of these compounds to measure chemical shift perturbations in 2D 1H,15N NMR spectra of 15N-labeled protein identified six with low millimolar affinities. All six perturbed an area consisting mainly of residues at or near the extreme C-terminus that we named "Site 1" while three other sites were perturbed by other compounds. Our findings here demonstrate the potential utility of eNP as a target, several fragment hits, and provide an experimental pipeline to validate viral-viral interactions as potential panfiloviral inhibitor targets.
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6
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Miyake T, Farley CM, Neubauer BE, Beddow TP, Hoenen T, Engel DA. Ebola Virus Inclusion Body Formation and RNA Synthesis Are Controlled by a Novel Domain of Nucleoprotein Interacting with VP35. J Virol 2020; 94:e02100-19. [PMID: 32493824 PMCID: PMC7394894 DOI: 10.1128/jvi.02100-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/24/2020] [Indexed: 12/15/2022] Open
Abstract
Ebola virus (EBOV) inclusion bodies (IBs) are cytoplasmic sites of nucleocapsid formation and RNA replication, housing key steps in the virus life cycle that warrant further investigation. During infection, IBs display dynamic properties regarding their size and location. The contents of IBs also must transition prior to further viral maturation, assembly, and release, implying additional steps in IB function. Interestingly, the expression of the viral nucleoprotein (NP) alone is sufficient for the generation of IBs, indicating that it plays an important role in IB formation during infection. In addition to NP, other components of the nucleocapsid localize to IBs, including VP35, VP24, VP30, and the RNA polymerase L. We previously defined and solved the crystal structure of the C-terminal domain of NP (NP-Ct), but its role in virus replication remained unclear. Here, we show that NP-Ct is necessary for IB formation when NP is expressed alone. Interestingly, we find that NP-Ct is also required for the production of infectious virus-like particles (VLPs), and that defective VLPs with NP-Ct deletions are significantly reduced in viral RNA content. Furthermore, coexpression of the nucleocapsid component VP35 overcomes deletion of NP-Ct in triggering IB formation, demonstrating a functional interaction between the two proteins. Of all the EBOV proteins, only VP35 is able to overcome the defect in IB formation caused by the deletion of NP-Ct. This effect is mediated by a novel protein-protein interaction between VP35 and NP that controls both regulation of IB formation and RNA replication itself and that is mediated by a newly identified functional domain of NP, the central domain.IMPORTANCE Inclusion bodies (IBs) are cytoplasmic sites of RNA synthesis for a variety of negative-sense RNA viruses, including Ebola virus. In addition to housing important steps in the viral life cycle, IBs protect new viral RNA from innate immune attack and contain specific host proteins whose function is under study. A key viral factor in Ebola virus IB formation is the nucleoprotein, NP, which also is important in RNA encapsidation and synthesis. In this study, we have identified two domains of NP that control inclusion body formation. One of these, the central domain (CD), interacts with viral protein VP35 to control both inclusion body formation and RNA synthesis. The other is the NP C-terminal domain (NP-Ct), whose function has not previously been reported. These findings contribute to a model in which NP and its interactions with VP35 link the establishment of IBs to the synthesis of viral RNA.
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Affiliation(s)
- Tsuyoshi Miyake
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Charlotte M Farley
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Benjamin E Neubauer
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Thomas P Beddow
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Thomas Hoenen
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Daniel A Engel
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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7
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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] [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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8
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Lee W, Tonelli M, Wu C, Aceti DJ, Amarasinghe GK, Markley JL. Backbone resonance assignments and secondary structure of Ebola nucleoprotein 600-739 construct. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:315-319. [PMID: 31076990 PMCID: PMC6715526 DOI: 10.1007/s12104-019-09898-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
Ebola viral infections have resulted in several deadly epidemics in recent years in West and Central Africa. Because only one of the seven proteins encoded by the viral genome possesses enzymatic activity, disruption of protein-protein interactions is a promising route for antiviral drug development. We carried out a screening campaign to identify small, drug-like compounds that bind to the C-terminal region of the multifunctional Ebola nucleoprotein (eNP) with the objective of discovering ones that disrupt its binding to other Ebola proteins or to the single-stranded RNA genome. In the course of this effort we assigned the backbone 1H, 15N, and 13C resonances of residues 600‒739, the region that contains the critical eVP30 binding region 600‒615 targeted by host factors, and used the assigned chemical shifts to predict secondary structural features and peptide dynamics. This work supports and extends the previous X-ray crystal structures and NMR studies of residues 641‒739. We found that the 600‒739 domain consists of separate regions that are largely disordered and ordered.
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Affiliation(s)
- Woonghee Lee
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David J Aceti
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA.
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9
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Pleet ML, DeMarino C, Stonier SW, Dye JM, Jacobson S, Aman MJ, Kashanchi F. Extracellular Vesicles and Ebola Virus: A New Mechanism of Immune Evasion. Viruses 2019; 11:v11050410. [PMID: 31052499 PMCID: PMC6563240 DOI: 10.3390/v11050410] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 02/06/2023] Open
Abstract
Ebola virus (EBOV) disease can result in a range of symptoms anywhere from virtually asymptomatic to severe hemorrhagic fever during acute infection. Additionally, spans of asymptomatic persistence in recovering survivors is possible, during which transmission of the virus may occur. In acute infection, substantial cytokine storm and bystander lymphocyte apoptosis take place, resulting in uncontrolled, systemic inflammation in affected individuals. Recently, studies have demonstrated the presence of EBOV proteins VP40, glycoprotein (GP), and nucleoprotein (NP) packaged into extracellular vesicles (EVs) during infection. EVs containing EBOV proteins have been shown to induce apoptosis in recipient immune cells, as well as contain pro-inflammatory cytokines. In this manuscript, we review the current field of knowledge on EBOV EVs including the mechanisms of their biogenesis, their cargo and their effects in recipient cells. Furthermore, we discuss some of the effects that may be induced by EBOV EVs that have not yet been characterized and highlight the remaining questions and future directions.
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Affiliation(s)
- Michelle L Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
| | - Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
| | - Spencer W Stonier
- Department, Emergent BioSolutions, Gaithersburg, MD 20879, USA.
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - John M Dye
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Steven Jacobson
- Viral Immunology Section, Neuroimmunology Branch, National Institute for Neurological Disease and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - M Javad Aman
- Department. Integrated BioTherapeutics, Inc., Gaithersburg, MD 20850, USA.
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
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10
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Radwańska MJ, Jaskółowski M, Davydova E, Derewenda U, Miyake T, Engel DA, Kossiakoff AA, Derewenda ZS. The structure of the C-terminal domain of the nucleoprotein from the Bundibugyo strain of the Ebola virus in complex with a pan-specific synthetic Fab. Acta Crystallogr D Struct Biol 2018; 74:681-689. [PMID: 29968677 PMCID: PMC6038385 DOI: 10.1107/s2059798318007878] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/28/2018] [Indexed: 11/10/2022] Open
Abstract
The vast majority of platforms for the detection of viral or bacterial antigens rely on immunoassays, typically ELISA or sandwich ELISA, that are contingent on the availability of suitable monoclonal antibodies (mAbs). This is a major bottleneck, since the generation and production of mAbs is time-consuming and expensive. Synthetic antibody fragments (sFabs) generated by phage-display selection offer an alternative with many advantages over Fabs obtained from natural antibodies using hybridoma technology. Unlike mAbs, sFabs are generated using phage display, allowing selection for binding to specific strains or for pan-specificity, for identification of structural epitopes or unique protein conformations and even for complexes. Further, they can easily be produced in Escherichia coli in large quantities and engineered for purposes of detection technologies and other applications. Here, the use of phage-display selection to generate a pan-specific Fab (MJ20), based on a Herceptin Fab scaffold, with the ability to bind selectively and with high affinity to the C-terminal domains of the nucleoproteins (NPs) from all five known strains of the Ebola virus is reported. The high-resolution crystal structure of the complex of MJ20 with the antigen from the Bundibugyo strain of the Ebola virus reveals the basis for pan-specificity and illustrates how the phage-display technology can be used to manufacture suitable Fabs for use in diagnostic or therapeutic applications.
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Affiliation(s)
- Malwina J. Radwańska
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Mateusz Jaskółowski
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL 60637, USA
| | - Elena Davydova
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL 60637, USA
| | - Urszula Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Tsuyoshi Miyake
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Daniel A. Engel
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL 60637, USA
| | - Zygmunt S. Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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11
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Ding JN, Zhang YJ, Zhong H, Ao CC, Han JG. A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide. J Biomol Struct Dyn 2018; 36:1009-1028. [DOI: 10.1080/07391102.2017.1307143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jing-Na Ding
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
- Department of Clinical Medicine, Anqing Medical College, Anqing 246052, People’s Republic of China
| | - Yan-Jun Zhang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Hui Zhong
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Cheng-Cheng Ao
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Ju-Guang Han
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
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12
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Filovirus proteins for antiviral drug discovery: Structure/function of proteins involved in assembly and budding. Antiviral Res 2018; 150:183-192. [DOI: 10.1016/j.antiviral.2017.12.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/20/2017] [Accepted: 12/28/2017] [Indexed: 01/30/2023]
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13
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Wan W, Kolesnikova L, Clarke M, Koehler A, Noda T, Becker S, Briggs JAG. Structure and assembly of the Ebola virus nucleocapsid. Nature 2017; 551:394-397. [PMID: 29144446 PMCID: PMC5714281 DOI: 10.1038/nature24490] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/04/2017] [Indexed: 12/11/2022]
Abstract
Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein and other viral proteins to form a helical nucleocapsid. The nucleocapsid acts as a scaffold for virus assembly and as a template for genome transcription and replication. Insights into nucleoprotein-nucleoprotein interactions have been derived from structural studies of oligomerized, RNA-encapsidating nucleoprotein, and cryo-electron microscopy of nucleocapsid or nucleocapsid-like structures. There have been no high-resolution reconstructions of complete mononegavirus nucleocapsids. Here we apply cryo-electron tomography and subtomogram averaging to determine the structure of Ebola virus nucleocapsid within intact viruses and recombinant nucleocapsid-like assemblies. These structures reveal the identity and arrangement of the nucleocapsid components, and suggest that the formation of an extended α-helix from the disordered carboxy-terminal region of nucleoprotein-core links nucleoprotein oligomerization, nucleocapsid condensation, RNA encapsidation, and accessory protein recruitment.
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Affiliation(s)
- William Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Larissa Kolesnikova
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Mairi Clarke
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Alexander Koehler
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - Takeshi Noda
- Laboratory of Ultrastructural virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
| | - John A. G. Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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14
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Garza JA, Taylor AB, Sherwood LJ, Hart PJ, Hayhurst A. Unveiling a Drift Resistant Cryptotope within Marburgvirus Nucleoprotein Recognized by Llama Single-Domain Antibodies. Front Immunol 2017; 8:1234. [PMID: 29038656 PMCID: PMC5630700 DOI: 10.3389/fimmu.2017.01234] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022] Open
Abstract
Marburg virus (MARV) is a highly lethal hemorrhagic fever virus that is increasingly re-emerging in Africa, has been imported to both Europe and the US, and is also a Tier 1 bioterror threat. As a negative sense RNA virus, MARV has error prone replication which can yield progeny capable of evading countermeasures. To evaluate this vulnerability, we sought to determine the epitopes of 4 llama single-domain antibodies (sdAbs or VHH) specific for nucleoprotein (NP), each capable of forming MARV monoclonal affinity reagent sandwich assays. Here, we show that all sdAb bound the C-terminal region of NP, which was produced recombinantly to derive X-ray crystal structures of the three best performing antibody-antigen complexes. The common epitope is a trio of alpha helices that form a novel asymmetric basin-like depression that accommodates each sdAb paratope via substantial complementarity-determining region (CDR) restructuring. Shared core contacts were complemented by unique accessory contacts on the sides and overlooks of the basin yielding very different approach routes for each sdAb to bind the antigen. The C-terminal region of MARV NP was unable to be crystallized alone and required engagement with sdAb to form crystals suggesting the antibodies acted as crystallization chaperones. While gross structural homology is apparent between the two most conserved helices of MARV and Ebolavirus, the positions and morphologies of the resulting basins were markedly different. Naturally occurring amino acid variations occurring in bat and human Marburgvirus strains all mapped to surfaces distant from the predicted sdAb contacts suggesting a vital role for the NP interface in virus replication. As an essential internal structural component potentially interfacing with a partner protein it is likely the C-terminal epitope remains hidden or “cryptic” until virion disruption occurs. Conservation of this epitope over 50 years of Marburgvirus evolution should make these sdAb useful foundations for diagnostics and therapeutics resistant to drift.
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Affiliation(s)
- John Anthony Garza
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Alexander Bryan Taylor
- X-Ray Crystallography Core Laboratory, Department of Biochemistry and Structural Biology, Institutional Research Cores, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Laura Jo Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Peter John Hart
- X-Ray Crystallography Core Laboratory, Department of Biochemistry and Structural Biology, Institutional Research Cores, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX, United States
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
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15
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Crystal Structure of the Marburg Virus Nucleoprotein Core Domain Chaperoned by a VP35 Peptide Reveals a Conserved Drug Target for Filovirus. J Virol 2017; 91:JVI.00996-17. [PMID: 28659479 DOI: 10.1128/jvi.00996-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 02/03/2023] Open
Abstract
Filovirus nucleoprotein (NP), viral protein 35 (VP35), and polymerase L are essential for viral replication and nucleocapsid formation. Here, we identify a 28-residue peptide (NP binding peptide [NPBP]) from Marburg virus (MARV) VP35 through sequence alignment with previously identified Ebola virus (EBOV) NPBP, which bound to the core region (residues 18 to 344) of the N-terminal portion of MARV NP with high affinity. The crystal structure of the MARV NP core/NPBP complex at a resolution of 2.6 Å revealed that NPBP binds to the C-terminal region of the NP core via electrostatic and nonpolar interactions. Further structural analysis revealed that the MARV and EBOV NP cores hold a conserved binding pocket for NPBP, and this pocket could serve as a promising target for the design of universal drugs against filovirus infection. In addition, cross-binding assays confirmed that the NP core of MARV or EBOV can bind the NPBP from the other virus, although with moderately reduced binding affinities that result from termini that are distinct between the MARV and EBOV NPBPs.IMPORTANCE Historically, Marburg virus (MARV) has caused severe disease with up to 90% lethality. Among the viral proteins produced by MARV, NP and VP35 are both multifunctional proteins that are essential for viral replication. In its relative, Ebola virus (EBOV), an N-terminal peptide from VP35 binds to the NP N-terminal region with high affinity. Whether this is a common mechanism among filoviruses is an unsolved question. Here, we present the crystal structure of a complex that consists of the core domain of MARV NP and the NPBP peptide from VP35. As we compared MARV NPBP with EBOV NPBP, several different features at the termini were identified. Although these differences reduce the affinity of the NP core for NPBPs across genera, a conserved pocket in the C-terminal region of the NP core makes cross-species binding possible. Our results expand our knowledge of filovirus NP-VP35 interactions and provide more details for therapeutic intervention.
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16
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Yu DS, Weng TH, Wu XX, Wang FXC, Lu XY, Wu HB, Wu NP, Li LJ, Yao HP. The lifecycle of the Ebola virus in host cells. Oncotarget 2017; 8:55750-55759. [PMID: 28903457 PMCID: PMC5589696 DOI: 10.18632/oncotarget.18498] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/29/2017] [Indexed: 01/01/2023] Open
Abstract
Ebola haemorrhagic fever causes deadly disease in humans and non-human primates resulting from infection with the Ebola virus (EBOV) genus of the family Filoviridae. However, the mechanisms of EBOV lifecycle in host cells, including viral entry, membrane fusion, RNP formation, GP-tetherin interaction, and VP40-inner leaflet association remain poorly understood. This review describes the biological functions of EBOV proteins and their roles in the lifecycle, summarizes the factors related to EBOV proteins or RNA expression throughout the different phases, and reviews advances with regards to the molecular events and mechanisms of the EBOV lifecycle. Furthermore, the review outlines the aspects remain unclear that urgently need to be solved in future research.
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Affiliation(s)
- Dong-Shan Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Tian-Hao Weng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiao-Xin Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Frederick X C Wang
- Department of Bioengineering, Erik Jonsson School of Engineering and Computer Science, The University of Texas at Dallas, Dallas, TX, USA
| | - Xiang-Yun Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hai-Bo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Nan-Ping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Lan-Juan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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17
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Xu W, Luthra P, Wu C, Batra J, Leung DW, Basler CF, Amarasinghe GK. Ebola virus VP30 and nucleoprotein interactions modulate viral RNA synthesis. Nat Commun 2017; 8:15576. [PMID: 28593988 PMCID: PMC5472179 DOI: 10.1038/ncomms15576] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/11/2017] [Indexed: 12/20/2022] Open
Abstract
Ebola virus (EBOV) is an enveloped negative-sense RNA virus that causes sporadic outbreaks with high case fatality rates. Ebola viral protein 30 (eVP30) plays a critical role in EBOV transcription initiation at the nucleoprotein (eNP) gene, with additional roles in the replication cycle such as viral assembly. However, the mechanistic basis for how eVP30 functions during the virus replication cycle is currently unclear. Here we define a key interaction between eVP30 and a peptide derived from eNP that is important to facilitate interactions leading to the recognition of the RNA template. We present crystal structures of the eVP30 C-terminus in complex with this eNP peptide. Functional analyses of the eVP30–eNP interface identify residues that are critical for viral RNA synthesis. Altogether, these results support a model where the eVP30–eNP interaction plays a critical role in transcription initiation and provides a novel target for the development of antiviral therapy. Ebola virus (EBOV) VP30 is a multifunctional protein that plays a role in transcription, but molecular details remain unknown. Here, using X-ray crystallography and minigenome assays, Xu et al. define the interaction between VP30 and a portion of NP that is critical for optimal EBOV RNA synthesis.
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Affiliation(s)
- Wei Xu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63105, USA
| | - Priya Luthra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303, USA
| | - Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63105, USA
| | - Jyoti Batra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63105, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63105, USA
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18
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Pacheco DADMRA, Rodrigues AAG, Silva CMLD. Ebola virus - from neglected threat to global emergency state. Rev Assoc Med Bras (1992) 2017; 62:458-67. [PMID: 27656857 DOI: 10.1590/1806-9282.62.05.458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/11/2015] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE This review aims to update knowledge about Ebola virus disease (EVD) and recent advances in its diagnosis, treatment and prevention. METHOD A literature review was performed using the following databases: ISI Web of Knowledge, PubMed, IRIS, Scopus and the websites of the CDC and the WHO. Additionally, we have included articles and reports referenced in the basic literature search, and news that were considered relevant. RESULTS The Ebola virus, endemic in some parts of Africa, is responsible for a severe form of hemorrhagic fever in humans; bats are probably its natural reservoir. It is an extremely virulent virus and easily transmitted by bodily fluids. EVD's complex pathophysiology, characterized by immunosuppression as well as stimulation of an intense inflammatory response, results in a syndrome similar to septic shock. The diagnosis is difficult due to the initial symptoms that mimic other diseases. Despite the high mortality rates that can amount to 90%, a prophylaxis (chemical or vaccine) or effective treatment does not exist. Two vaccines and experimental therapies are being developed for the prevention and treatment of EVD. CONCLUSION Although the virus is known for about 40 years, the lack of knowledge obtained and the disinterest of government authorities in the countries involved justify the state of emergency currently exists regarding this infectious agent. Only the coordination of multiple entities and the effective commitment of the international community will facilitate the control and effective prevention of EVD.
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Affiliation(s)
| | - Acácio Agostinho Gonçalves Rodrigues
- PhD - Director of the Department and Laboratory of Microbiology, Faculdade de Medicina, Universidade do Porto. MD, Department of Anesthesiology and Intensive Care, Burns Unit, Hospital de São João, Porto, Portugal
| | - Carmen Maria Lisboa da Silva
- PhD - Professor of the Department and Laboratory of Microbiology, Faculdade de Medicina, Universidade do Porto. MD, Department of Dermatovenereology, Hospital São João, Porto, Portugal
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19
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Filovirus proteins for antiviral drug discovery: Structure/function bases of the replication cycle. Antiviral Res 2017; 141:48-61. [PMID: 28192094 DOI: 10.1016/j.antiviral.2017.02.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/12/2017] [Accepted: 02/07/2017] [Indexed: 12/26/2022]
Abstract
Filoviruses are important pathogens that cause severe and often fatal hemorrhagic fever in humans, for which no approved vaccines and antiviral treatments are yet available. In an earlier article (Martin et al., Antiviral Research, 2016), we reviewed the role of the filovirus surface glycoprotein in replication and as a target for drugs and vaccines. In this review, we focus on recent findings on the filovirus replication machinery and how they could be used for the identification of new therapeutic targets and the development of new antiviral compounds. First, we summarize the recent structural and functional advances on the molecules involved in filovirus replication/transcription cycle, particularly the NP, VP30, VP35 proteins, and the "large" protein L, which harbors the RNA-dependent RNA polymerase (RdRp) and mRNA capping activities. These proteins are essential for viral mRNA synthesis and genome replication, and consequently they constitute attractive targets for drug design. We then describe how these insights into filovirus replication mechanisms and the structure/function characterization of the involved proteins have led to the development of new and innovative antiviral strategies that may help reduce the filovirus disease case fatality rate through post-exposure or prophylactic treatments.
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20
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The Ebola Virus VP30-NP Interaction Is a Regulator of Viral RNA Synthesis. PLoS Pathog 2016; 12:e1005937. [PMID: 27755595 PMCID: PMC5068707 DOI: 10.1371/journal.ppat.1005937] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/14/2016] [Indexed: 12/20/2022] Open
Abstract
Filoviruses are capable of causing deadly hemorrhagic fevers. All nonsegmented negative-sense RNA-virus nucleocapsids are composed of a nucleoprotein (NP), a phosphoprotein (VP35) and a polymerase (L). However, the VP30 RNA-synthesis co-factor is unique to the filoviruses. The assembly, structure, and function of the filovirus RNA replication complex remain unclear. Here, we have characterized the interactions of Ebola, Sudan and Marburg virus VP30 with NP using in vitro biochemistry, structural biology and cell-based mini-replicon assays. We have found that the VP30 C-terminal domain interacts with a short peptide in the C-terminal region of NP. Further, we have solved crystal structures of the VP30-NP complex for both Ebola and Marburg viruses. These structures reveal that a conserved, proline-rich NP peptide binds a shallow hydrophobic cleft on the VP30 C-terminal domain. Structure-guided Ebola virus VP30 mutants have altered affinities for the NP peptide. Correlation of these VP30-NP affinities with the activity for each of these mutants in a cell-based mini-replicon assay suggests that the VP30-NP interaction plays both essential and inhibitory roles in Ebola virus RNA synthesis. Filoviruses use a system of proteins and RNA to regulate viral RNA genome transcription and replication. Here, we have determined crystal structures and the biological functions of the protein complex formed by the filovirus transcriptional activator, VP30, and the core component of the nucleocapsid machinery, NP. The complex of these two essential players represses Ebola virus RNA synthesis and may have played a role in the evolution of filoviruses to tune viral RNA synthesis activity to a level ideal for infection. This interaction is conserved across the filoviruses and may provide an opportunity for therapeutic development.
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21
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Jamin M, Yabukarski F. Nonsegmented Negative-Sense RNA Viruses-Structural Data Bring New Insights Into Nucleocapsid Assembly. Adv Virus Res 2016; 97:143-185. [PMID: 28057258 DOI: 10.1016/bs.aivir.2016.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Viruses with a nonsegmented negative-sense RNA genome (NNVs) include important human pathogens as well as life-threatening zoonotic viruses. These viruses share a common RNA replication complex, including the genomic RNA and three proteins, the nucleoprotein (N), the phosphoprotein (P), and the RNA-dependent RNA polymerase (L). During genome replication, the RNA polymerase complex first synthesizes positive-sense antigenomes, which in turn serve as template for the production of negative-sense progeny genomes. These newly synthesized antigenomic and genomic RNAs must be encapsidated by N, and the source of soluble, RNA-free N, competent for the encapsidation is a complex between N and P, named the N0-P complex. In this review, we summarize recent progress made in the structural characterization of the different components of this peculiar RNA polymerase machinery. We discuss common features and replication strategies and highlight idiosyncrasies encountered in different viruses, along with the key role of the dual ordered/disordered architecture of protein components and the dynamics of the viral polymerase machinery. In particular, we focus on the N0-P complex and its role in the nucleocapsid assembly process. These new results provide evidence that the mechanism of NC assembly is conserved between the different families and thus support a divergent evolution from a common ancestor. In addition, the successful inhibition of infection due to different NNVs by peptides derived from P suggests that the mechanism of NC assembly is a potential target for antiviral development.
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Affiliation(s)
- M Jamin
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France.
| | - F Yabukarski
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
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22
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In vitro assembly of Ebola virus nucleocapsid-like complex expressed in E. coli. Protein Cell 2016; 7:888-898. [PMID: 27650953 PMCID: PMC5205660 DOI: 10.1007/s13238-016-0314-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/12/2016] [Indexed: 11/02/2022] Open
Abstract
Ebola virus (EBOV) harbors an RNA genome encapsidated by nucleoprotein (NP) along with other viral proteins to form a nucleocapsid complex. Previous Cryo-eletron tomography and biochemical studies have shown the helical structure of EBOV nucleocapsid at nanometer resolution and the first 450 amino-acid of NP (NPΔ451-739) alone is capable of forming a helical nucleocapsid-like complex (NLC). However, the structural basis for NP-NP interaction and the dynamic procedure of the nucleocapsid assembly is yet poorly understood. In this work, we, by using an E. coli expression system, captured a series of images of NPΔ451-739 conformers at different stages of NLC assembly by negative-stain electron microscopy, which allowed us to picture the dynamic procedure of EBOV nucleocapsid assembly. Along with further biochemical studies, we showed the assembly of NLC is salt-sensitive, and also established an indispensible role of RNA in this process. We propose the diverse modes of NLC elongation might be the key determinants shaping the plasticity of EBOV virions. Our findings provide a new model for characterizing the self-oligomerization of viral nucleoproteins and studying the dynamic assembly process of viral nucleocapsid in vitro.
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23
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Binding of RNA by the Nucleoproteins of Influenza Viruses A and B. Viruses 2016; 8:v8090247. [PMID: 27649229 PMCID: PMC5035961 DOI: 10.3390/v8090247] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/26/2016] [Accepted: 08/29/2016] [Indexed: 11/16/2022] Open
Abstract
This paper describes a biochemical study for making complexes between the nucleoprotein of influenza viruses A and B (A/NP and B/NP) and small RNAs (polyUC RNAs from 5 to 24 nucleotides (nt)), starting from monomeric proteins. We used negative stain electron microscopy, size exclusion chromatography-multi-angle laser light scattering (SEC-MALLS) analysis, and fluorescence anisotropy measurements to show how the NP-RNA complexes evolve. Both proteins make small oligomers with 24-nt RNAs, trimers for A/NP, and dimers, tetramers, and larger complexes for B/NP. With shorter RNAs, the affinities of NP are all in the same range at 50 mM NaCl, showing that the RNAs bind on the same site. The affinity of B/NP for a 24-nt RNA does not change with salt. However, the affinity of A/NP for a 24-nt RNA is lower at 150 and 300 mM NaCl, suggesting that the RNA binds to another site, either on the same protomer or on a neighbour protomer. For our fluorescence anisotropy experiments, we used 6-fluorescein amidite (FAM)-labelled RNAs. By using a (UC)6-FAM3′ RNA with 150 mM NaCl, we observed an interesting phenomenon that gives macromolecular complexes similar to the ribonucleoprotein particles purified from the viruses.
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24
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Goh GKM, Dunker AK, Uversky VN. Detection of links between Ebola nucleocapsid and virulence using disorder analysis. MOLECULAR BIOSYSTEMS 2016; 11:2337-44. [PMID: 26086270 DOI: 10.1039/c5mb00240k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The underlying reasons for the differences in the virulence of various types of Ebola virus (EBOV) remain unknown. Comparison of the percentage of disorder (PID) in nucleocapsid proteins VP30 and NP reveals high correlation between nucleocapsid PIDs and the case-fatality rates of EBOV. The higher disorder of these proteins is likely to be needed for more efficient multiplication of virus copies via more efficient viral RNA transcription and more promiscuous protein binding potential. This is important for the more efficient assistance of nucleocapsid in viral particle budding and of the assembly and mobility of viral proteins across the host membrane and within the cytoplasm. A more comprehensive knowledge of the molecular mechanisms of EBOV virulence would also lead to new and more effective strategies in vaccine development.
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25
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Grifoni A, Lo Presti A, Giovanetti M, Montesano C, Amicosante M, Colizzi V, Lai A, Zehender G, Cella E, Angeletti S, Ciccozzi M. Genetic diversity in Ebola virus: Phylogenetic and in silico structural studies of Ebola viral proteins. ASIAN PAC J TROP MED 2016; 9:337-343. [PMID: 27086151 DOI: 10.1016/j.apjtm.2016.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/20/2016] [Accepted: 03/01/2016] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVE To explore the genetic diversity and the modification of antibody response in the recent outbreak of Ebola Virus. METHODS Sequences retrieved from public databases, the selective pressure analysis and the homology modeling based on the all protein (nucleoprotein, VP35, VP40, soluble glycoprotein, small soluble glycoprotein, VP30, VP24 and polymerase) were used. RESULTS Structural proteins VP24, VP30, VP35 and VP40 showed relative conserved sequences making them suitable target candidates for antiviral treatment. On the contrary, nucleoprotein, polymerase and soluble glycoprotein have high mutation frequency. CONCLUSIONS Data from this study point out important aspects of Ebola virus sequence variability that for epitope and vaccine design should be considered for appropriate targeting of conserved protein regions.
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Affiliation(s)
| | - Alessandra Lo Presti
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy
| | - Marta Giovanetti
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Carla Montesano
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Massimo Amicosante
- ProxAgen Ltd, Sofia, Bulgaria; Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Rome, Italy
| | - Vittorio Colizzi
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Alessia Lai
- Laboratory of Infectious Diseases and Tropical Medicine, University of Milan, Italy
| | | | - Eleonora Cella
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Silvia Angeletti
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; University Campus Bio-Medico, Rome, Italy.
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26
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Baker LE, Ellena JF, Handing KB, Derewenda U, Utepbergenov D, Engel DA, Derewenda ZS. Molecular architecture of the nucleoprotein C-terminal domain from the Ebola and Marburg viruses. Acta Crystallogr D Struct Biol 2016; 72:49-58. [PMID: 26894534 PMCID: PMC4905509 DOI: 10.1107/s2059798315021439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/11/2015] [Indexed: 11/10/2022] Open
Abstract
The Filoviridae family of negative-sense, single-stranded RNA (ssRNA) viruses is comprised of two species of Marburgvirus (MARV and RAVV) and five species of Ebolavirus, i.e. Zaire (EBOV), Reston (RESTV), Sudan (SUDV), Taï Forest (TAFV) and Bundibugyo (BDBV). In each of these viruses the ssRNA encodes seven distinct proteins. One of them, the nucleoprotein (NP), is the most abundant viral protein in the infected cell and within the viral nucleocapsid. It is tightly associated with the viral RNA in the nucleocapsid, and during the lifecycle of the virus is essential for transcription, RNA replication, genome packaging and nucleocapsid assembly prior to membrane encapsulation. The structure of the unique C-terminal globular domain of the NP from EBOV has recently been determined and shown to be structurally unrelated to any other known protein [Dziubańska et al. (2014), Acta Cryst. D70, 2420-2429]. In this paper, a study of the C-terminal domains from the NP from the remaining four species of Ebolavirus, as well as from the MARV strain of Marburgvirus, is reported. As expected, the crystal structures of the BDBV and TAFV proteins show high structural similarity to that from EBOV, while the MARV protein behaves like a molten globule with a core residual structure that is significantly different from that of the EBOV protein.
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Affiliation(s)
- Laura E. Baker
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA
| | - Jeffrey F. Ellena
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904-4319, USA
| | - Katarzyna B. Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA
| | - Urszula Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA
| | - Darkhan Utepbergenov
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA
| | - Daniel A. Engel
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA
| | - Zygmunt S. Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA
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27
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Olabode AS, Jiang X, Robertson DL, Lovell SC. Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak. Virology 2015; 482:202-7. [PMID: 25880111 PMCID: PMC4503884 DOI: 10.1016/j.virol.2015.03.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/11/2015] [Accepted: 03/15/2015] [Indexed: 01/05/2023]
Abstract
The 2014 epidemic of Ebola virus disease (EVD) has had a devastating impact in West Africa. Sequencing of ebolavirus (EBOV) from infected individuals has revealed extensive genetic variation, leading to speculation that the virus may be adapting to humans, accounting for the scale of the 2014 outbreak. We computationally analyze the variation associated with all EVD outbreaks, and find none of the amino acid replacements lead to identifiable functional changes. These changes have minimal effect on protein structure, being neither stabilizing nor destabilizing, are not found in regions of the proteins associated with known functions and tend to cluster in poorly constrained regions of proteins, specifically intrinsically disordered regions. We find no evidence that the difference between the current and previous outbreaks is due to evolutionary changes associated with transmission to humans. Instead, epidemiological factors are likely to be responsible for the unprecedented spread of EVD.
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Affiliation(s)
- Abayomi S Olabode
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Xiaowei Jiang
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK; Department of Genetics, University of Cambridge, Cambridge, UK
| | - David L Robertson
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
| | - Simon C Lovell
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
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28
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Abstract
Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus.
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Affiliation(s)
- Qian Cong
- a Departments of Biophysics and Biochemistry ; University of Texas Southwestern Medical Center at Dallas ; Dallas , TX USA
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29
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Insight into the Ebola virus nucleocapsid assembly mechanism: crystal structure of Ebola virus nucleoprotein core domain at 1.8 Å resolution. Protein Cell 2015; 6:351-62. [PMID: 25910597 PMCID: PMC4417675 DOI: 10.1007/s13238-015-0163-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/14/2015] [Indexed: 02/03/2023] Open
Abstract
Ebola virus (EBOV) is a key member of Filoviridae family and causes severe human infectious diseases with high morbidity and mortality. As a typical negative-sense single-stranded RNA (-ssRNA) viruses, EBOV possess a nucleocapsid protein (NP) to facilitate genomic RNA encapsidation to form viral ribonucleoprotein complex (RNP) together with genome RNA and polymerase, which plays the most essential role in virus proliferation cycle. However, the mechanism of EBOV RNP formation remains unclear. In this work, we solved the high resolution structure of core domain of EBOV NP. The polypeptide of EBOV NP core domain (NP(core)) possesses an N-lobe and C-lobe to clamp a RNA binding groove, presenting similarities with the structures of the other reported viral NPs encoded by the members from Mononegavirales order. Most strikingly, a hydrophobic pocket at the surface of the C-lobe is occupied by an α-helix of EBOV NP(core) itself, which is highly conserved among filoviridae family. Combined with other biochemical and biophysical evidences, our results provides great potential for understanding the mechanism underlying EBOV RNP formation via the mobility of EBOV NP element and enables the development of antiviral therapies targeting EBOV RNP formation.
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30
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Leung DW, Borek D, Luthra P, Binning JM, Anantpadma M, Liu G, Harvey IB, Su Z, Endlich-Frazier A, Pan J, Shabman RS, Chiu W, Davey RA, Otwinowski Z, Basler CF, Amarasinghe GK. An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions. Cell Rep 2015; 11:376-89. [PMID: 25865894 DOI: 10.1016/j.celrep.2015.03.034] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/18/2015] [Accepted: 03/12/2015] [Indexed: 01/19/2023] Open
Abstract
During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.
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Affiliation(s)
- Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Dominika Borek
- Departments of Biophysics and Biochemistry and Center for Structural Genomics of Infectious Diseases, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Priya Luthra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jennifer M Binning
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Gai Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Ian B Harvey
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Zhaoming Su
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ariel Endlich-Frazier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juanli Pan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Reed S Shabman
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Zbyszek Otwinowski
- Departments of Biophysics and Biochemistry and Center for Structural Genomics of Infectious Diseases, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA.
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31
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Del Rio C, Guarner J. Ebola: Implications and Perspectives. TRANSACTIONS OF THE AMERICAN CLINICAL AND CLIMATOLOGICAL ASSOCIATION 2015; 126:93-112. [PMID: 26330663 PMCID: PMC4530678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The 2014 Ebola virus disease outbreak in West Africa has been the largest in recorded history. During this Ebola epidemic, the media has focused much attention to the magnitude of the problem in West Africa but has also overplayed the potential for an Ebola virus pandemic as patients have been transported for treatment to the United States and Europe causing panic and paranoia in the population. Knowledge of the epidemiology, pathogenesis, clinical presentation, treatment, and prevention of this infection will allow a better understanding of the disease and decrease irrational fear of spread.
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32
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Chakraborty S, Rao BJ, Asgeirsson B, Dandekar A. Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions. F1000Res 2014; 3:251. [PMID: 25717367 PMCID: PMC4329671 DOI: 10.12688/f1000research.5573.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/26/2015] [Indexed: 01/28/2023] Open
Abstract
Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into a potentially global humanitarian crisis. The genome of Ebola, a member of the Filoviridae family, encodes seven proteins. Based on the recently implemented software (PAGAL) for analyzing the hydrophobicity and amphipathicity properties of alpha helices (AH) in proteins, we characterize the helices in the Ebola proteome. We demonstrate that AHs with characteristically unique features are involved in critical interactions with the host proteins. For example, the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain has an AH with a large hydrophobic moment. The neutralizing antibody (KZ52) derived from a human survivor of the 1995 Kikwit outbreak recognizes a protein epitope on this AH, emphasizing the critical nature of this secondary structure in the virulence of the Ebola virus. Our method ensures a comprehensive list of such `hotspots'. These helices probably are or can be the target of molecules designed to inhibit AH mediated protein-protein interactions. Further, by comparing the AHs in proteins of the related Marburg viruses, we are able to elicit subtle changes in the proteins that might render them ineffective to previously successful drugs. Such differences are difficult to identify by a simple sequence or structural alignment. Thus, analyzing AHs in the small Ebola proteome can aid rational design aimed at countering the `largest Ebola epidemic, affecting multiple countries in West Africa' (
http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/index.html).
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Affiliation(s)
- Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, 95616, USA ; Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Bjarni Asgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, Dunhaga 3, IS-107 Reykjavik, Iceland
| | - Abhaya Dandekar
- Plant Sciences Department, University of California, Davis, 95616, USA
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33
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Chakraborty S, Rao BJ, Asgeirsson B, Dandekar A. Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions. F1000Res 2014; 3:251. [PMID: 25717367 PMCID: PMC4329671 DOI: 10.12688/f1000research.5573.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/26/2015] [Indexed: 08/06/2023] Open
Abstract
Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into a potentially global humanitarian crisis. The genome of Ebola, a member of the Filoviridae family, encodes seven proteins. Based on the recently implemented software (PAGAL) for analyzing the hydrophobicity and amphipathicity properties of alpha helices (AH) in proteins, we characterize the helices in the Ebola proteome. We demonstrate that AHs with characteristically unique features are involved in critical interactions with the host proteins. For example, the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain has an AH with a large hydrophobic moment. The neutralizing antibody (KZ52) derived from a human survivor of the 1995 Kikwit outbreak recognizes a protein epitope on this AH, emphasizing the critical nature of this secondary structure in the virulence of the Ebola virus. Our method ensures a comprehensive list of such `hotspots'. These helices probably are or can be the target of molecules designed to inhibit AH mediated protein-protein interactions. Further, by comparing the AHs in proteins of the related Marburg viruses, we are able to elicit subtle changes in the proteins that might render them ineffective to previously successful drugs. Such differences are difficult to identify by a simple sequence or structural alignment. Thus, analyzing AHs in the small Ebola proteome can aid rational design aimed at countering the `largest Ebola epidemic, affecting multiple countries in West Africa' ( http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/index.html).
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Affiliation(s)
- Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, 95616, USA
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Basuthkar J. Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Bjarni Asgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, Dunhaga 3, IS-107 Reykjavik, Iceland
| | - Abhaya Dandekar
- Plant Sciences Department, University of California, Davis, 95616, USA
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