1
|
Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
Collapse
Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
| |
Collapse
|
2
|
Wu C, Wagner ND, Moyle AB, Feng A, Sharma N, Stubbs SH, Donahue C, Davey RA, Gross ML, Leung DW, Amarasinghe GK. Disruption of Ebola NP 0VP35 Inclusion Body-like Structures reduce Viral Infection. J Mol Biol 2023; 435:168241. [PMID: 37598728 PMCID: PMC11312838 DOI: 10.1016/j.jmb.2023.168241] [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: 01/04/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/22/2023]
Abstract
Viral inclusion bodies (IBs) are potential sites of viral replication and assembly. How viral IBs form remains poorly defined. Here we describe a combined biophysical and cellular approach to identify the components necessary for IB formation during Ebola virus (EBOV) infection. We find that the eNP0VP35 complex containing Ebola nucleoprotein (eNP) and viral protein 35 (eVP35), the functional equivalents of nucleoprotein (N) and phosphoprotein (P) in non-segmented negative strand viruses (NNSVs), phase separates to form inclusion bodies. Phase separation of eNP0VP35 is reversible and modulated by ionic strength. The multivalency of eVP35, and not eNP, is also critical for phase separation. Furthermore, overexpression of an eVP35 peptide disrupts eNP0VP35 complex formation, leading to reduced frequency of IB formation and limited viral infection. Together, our results show that upon EBOV infection, the eNP0VP35 complex forms the minimum unit to drive IB formation and viral replication.
Collapse
Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Austin B Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Annie Feng
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Nitin Sharma
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sarah H Stubbs
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Callie Donahue
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
3
|
Risso-Ballester J, Rameix-Welti MA. Spatial resolution of virus replication: RSV and cytoplasmic inclusion bodies. Adv Virus Res 2023; 116:1-43. [PMID: 37524479 DOI: 10.1016/bs.aivir.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Respiratory Syncytial Virus (RSV) is a major cause of respiratory illness in young children, elderly and immunocompromised individuals worldwide representing a severe burden for health systems. The urgent development of vaccines or specific antivirals against RSV is impaired by the lack of knowledge regarding its replication mechanisms. RSV is a negative-sense single-stranded RNA (ssRNA) virus belonging to the Mononegavirales order (MNV) which includes other viruses pathogenic to humans as Rabies (RabV), Ebola (EBOV), or measles (MeV) viruses. Transcription and replication of viral genomes occur within cytoplasmatic virus-induced spherical inclusions, commonly referred as inclusion bodies (IBs). Recently IBs were shown to exhibit properties of membrane-less organelles (MLO) arising by liquid-liquid phase separation (LLPS). Compartmentalization of viral RNA synthesis steps in viral-induced MLO is indeed a common feature of MNV. Strikingly these key compartments still remain mysterious. Most of our current knowledge on IBs relies on the use of fluorescence microscopy. The ability to fluorescently label IBs in cells has been key to uncover their dynamics and nature. The generation of recombinant viruses expressing a fluorescently-labeled viral protein and the immunolabeling or the expression of viral fusion proteins known to be recruited in IBs are some of the tools used to visualize IBs in infected cells. In this chapter, microscope techniques and the most relevant studies that have shed light on RSV IBs fundamental aspects, including biogenesis, organization and dynamics are being discussed and brought to light with the investigations carried out on other MNV.
Collapse
Affiliation(s)
| | - Marie-Anne Rameix-Welti
- Institut Pasteur, Université Paris-Saclay, Université de Versailles St. Quentin, UMR 1173 (2I), INSERM, Paris, France; Assistance Publique des Hôpitaux de Paris, Hôpital Ambroise Paré, Laboratoire de Microbiologie, DMU15, Paris, France.
| |
Collapse
|
4
|
Modrego A, Carlero D, Arranz R, Martín-Benito J. CryoEM of Viral Ribonucleoproteins and Nucleocapsids of Single-Stranded RNA Viruses. Viruses 2023; 15:v15030653. [PMID: 36992363 PMCID: PMC10053253 DOI: 10.3390/v15030653] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/05/2023] Open
Abstract
Single-stranded RNA viruses (ssRNAv) are characterized by their biological diversity and great adaptability to different hosts; traits which make them a major threat to human health due to their potential to cause zoonotic outbreaks. A detailed understanding of the mechanisms involved in viral proliferation is essential to address the challenges posed by these pathogens. Key to these processes are ribonucleoproteins (RNPs), the genome-containing RNA-protein complexes whose function is to carry out viral transcription and replication. Structural determination of RNPs can provide crucial information on the molecular mechanisms of these processes, paving the way for the development of new, more effective strategies to control and prevent the spread of ssRNAv diseases. In this scenario, cryogenic electron microscopy (cryoEM), relying on the technical and methodological revolution it has undergone in recent years, can provide invaluable help in elucidating how these macromolecular complexes are organized, packaged within the virion, or the functional implications of these structures. In this review, we summarize some of the most prominent achievements by cryoEM in the study of RNP and nucleocapsid structures in lipid-enveloped ssRNAv.
Collapse
Affiliation(s)
- Andrea Modrego
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Diego Carlero
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
| | - Rocío Arranz
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
- Correspondence: (R.A.); (J.M.-B.)
| | - Jaime Martín-Benito
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
- Correspondence: (R.A.); (J.M.-B.)
| |
Collapse
|
5
|
Wu C, Holehouse AS, Leung DW, Amarasinghe GK, Dutch RE. Liquid Phase Partitioning in Virus Replication: Observations and Opportunities. Annu Rev Virol 2022; 9:285-306. [PMID: 35709511 PMCID: PMC11331907 DOI: 10.1146/annurev-virology-093020-013659] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses frequently carry out replication in specialized compartments within cells. The effect of these structures on virus replication is poorly understood. Recent research supports phase separation as a foundational principle for organization of cellular components with the potential to influence viral replication. In this review, phase separation is described in the context of formation of viral replication centers, with an emphasis on the nonsegmented negative-strand RNA viruses. Consideration is given to the interplay between phase separation and the critical processes of viral transcription and genome replication, and the role of these regions in pathogen-host interactions is discussed. Finally, critical questions that must be addressed to fully understand how phase separation influences viral replication and the viral life cycle are presented, along with information about new approaches that could be used to make important breakthroughs in this emerging field.
Collapse
Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Science and Engineering Living Systems, Washington University, St. Louis, Missouri, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA;
| |
Collapse
|
6
|
Fang H, Tyukodi B, Rogers WB, Hagan MF. Polymorphic self-assembly of helical tubules is kinetically controlled. SOFT MATTER 2022; 18:6716-6728. [PMID: 36039801 PMCID: PMC9472595 DOI: 10.1039/d2sm00679k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger than the size scale of the individual monomers. In many such cases, the finite dimension is selected by a preferred curvature of the monomers, which leads to self-closure of the assembly. In this article, we study an example class of self-closing assemblies: cylindrical tubules that assemble from triangular monomers. By combining kinetic Monte Carlo simulations, free energy calculations, and simple theoretical models, we show that a range of programmable size scales can be targeted by controlling the intricate balance between the preferred curvature of the monomers and their interaction strengths. However, their assembly is kinetically controlled-the tubule morphology is essentially fixed shortly after closure, resulting in a distribution of tubule widths that is significantly broader than the equilibrium distribution. We develop a simple kinetic model based on this observation and the underlying free-energy landscape of assembling tubules that quantitatively describes the distributions. Our results are consistent with recent experimental observations of tubule assembly from triangular DNA origami monomers. The modeling framework elucidates design principles for assembling self-limited structures from synthetic components, such as artificial microtubules that have a desired width and chirality.
Collapse
Affiliation(s)
- Huang Fang
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Botond Tyukodi
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
- Department of Physics, Babes-Bolyai University, 400084 Cluj-Napoca, Romania
| | - W Benjamin Rogers
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| |
Collapse
|
7
|
Hopkins FR, Álvarez-Rodríguez B, Heath GR, Panayi K, Hover S, Edwards TA, Barr JN, Fontana J. The Native Orthobunyavirus Ribonucleoprotein Possesses a Helical Architecture. mBio 2022; 13:e0140522. [PMID: 35762594 PMCID: PMC9426602 DOI: 10.1128/mbio.01405-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Bunyavirales order is the largest group of negative-sense RNA viruses, containing many lethal human pathogens for which approved anti-infective measures are not available. The bunyavirus genome consists of multiple negative-sense RNA segments enwrapped by the virus-encoded nucleocapsid protein (NP), which together with the viral polymerase form ribonucleoproteins (RNPs). RNPs represent substrates for RNA synthesis and virion assembly, which require inherent flexibility, consistent with the appearance of RNPs spilled from virions. These observations have resulted in conflicting models describing the overall RNP architecture. Here, we purified RNPs from Bunyamwera virus (BUNV), the prototypical orthobunyavirus. The lengths of purified RNPs imaged by negative staining resulted in 3 populations of RNPs, suggesting that RNPs possess a consistent method of condensation. Employing microscopy approaches, we conclusively show that the NP portion of BUNV RNPs is helical. Furthermore, we present a pseudo-atomic model for this portion based on a cryo-electron microscopy average at 13 Å resolution, which allowed us to fit the BUNV NP crystal structure by molecular dynamics. This model was confirmed by NP mutagenesis using a mini-genome system. The model shows that adjacent NP monomers in the RNP chain interact laterally through flexible N- and C-terminal arms only, with no longitudinal helix-stabilizing interactions, thus providing a potential model for the molecular basis for RNP flexibility. Excessive RNase treatment disrupts native RNPs, suggesting that RNA was key in maintaining the RNP structure. Overall, this work will inform studies on bunyaviral RNP assembly, packaging, and RNA replication, and aid in future antiviral strategies. IMPORTANCE Bunyaviruses are emerging RNA viruses that cause significant disease and economic burden and for which vaccines or therapies approved for humans are not available. The bunyavirus genome is wrapped up by the nucleoprotein (NP) and interacts with the viral polymerase, forming a ribonucleoprotein (RNP). This is the only form of the genome active for viral replication and assembly. However, until now how NPs are organized within an RNP was not known for any orthobunyavirus. Here, we purified RNPs from the prototypical orthobunyavirus, Bunyamwera virus, and employed microscopy approaches to show that the NP portion of the RNP was helical. We then combined our helical average with the known structure of an NP monomer, generating a pseudo-atomic model of this region. This arrangement allowed the RNPs to be highly flexible, which was critical for several stages of the viral replication cycle, such as segment circularization.
Collapse
Affiliation(s)
- Francis R. Hopkins
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - Beatriz Álvarez-Rodríguez
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - George R. Heath
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - Kyriakoulla Panayi
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - Samantha Hover
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - Thomas A. Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - John N. Barr
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - Juan Fontana
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| |
Collapse
|
8
|
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.
Collapse
Affiliation(s)
- Olga Dolnik
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Stephan Becker
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| |
Collapse
|
9
|
Galão RP, Wilson H, Schierhorn KL, Debeljak F, Bodmer BS, Goldhill D, Hoenen T, Wilson SJ, Swanson CM, Neil SJD. TRIM25 and ZAP target the Ebola virus ribonucleoprotein complex to mediate interferon-induced restriction. PLoS Pathog 2022; 18:e1010530. [PMID: 35533151 PMCID: PMC9119685 DOI: 10.1371/journal.ppat.1010530] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 05/19/2022] [Accepted: 04/18/2022] [Indexed: 12/14/2022] Open
Abstract
Ebola virus (EBOV) causes highly pathogenic disease in primates. Through screening a library of human interferon-stimulated genes (ISGs), we identified TRIM25 as a potent inhibitor of EBOV transcription-and-replication-competent virus-like particle (trVLP) propagation. TRIM25 overexpression inhibited the accumulation of viral genomic and messenger RNAs independently of the RNA sensor RIG-I or secondary proinflammatory gene expression. Deletion of TRIM25 strongly attenuated the sensitivity of trVLPs to inhibition by type-I interferon. The antiviral activity of TRIM25 required ZAP and the effect of type-I interferon was modulated by the CpG dinucleotide content of the viral genome. We find that TRIM25 interacts with the EBOV vRNP, resulting in its autoubiquitination and ubiquitination of the viral nucleoprotein (NP). TRIM25 is recruited to incoming vRNPs shortly after cell entry and leads to dissociation of NP from the vRNA. We propose that TRIM25 targets the EBOV vRNP, exposing CpG-rich viral RNA species to restriction by ZAP.
Collapse
Affiliation(s)
- Rui Pedro Galão
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Harry Wilson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Kristina L. Schierhorn
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Franka Debeljak
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Bianca S. Bodmer
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Daniel Goldhill
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Thomas Hoenen
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Sam J. Wilson
- MRC Centre for Virus Research, University of Glasgow, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| |
Collapse
|
10
|
Wang Y, Binning JM, Pintilie GD, Chiu W, Amarasinghe GK, Leung DW, Su Z. Cryo-EM analysis of Ebola virus nucleocapsid-like assembly. STAR Protoc 2022; 3:101030. [PMID: 34977676 PMCID: PMC8689349 DOI: 10.1016/j.xpro.2021.101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
This protocol describes the reconstitution of the filamentous Ebola virus nucleocapsid-like assembly in vitro. This is followed by solving the cryo-EM structure using helical reconstruction, and flexible fitting of the existing model into the 5.8 Å cryo-EM map. The protocol can be applied to other filamentous viral protein assemblies, particularly those with high flexibility and moderate resolution maps, which present technical challenges to model building. For complete details on the use and execution of this profile, please refer to Su et al. (2018). Preparation of Ebola nucleocapsid-like assembly for cryo-EM Cryo-EM helical reconstruction of flexible filamentous protein assembly Flexible fitting of protein model into cryo-EM density at moderate resolution
Collapse
Affiliation(s)
- Yan Wang
- The State Key Laboratory of Biotherapy and Cancer Center, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610044, China
| | - Jennifer M. Binning
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Grigore D. Pintilie
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Corresponding author
| | - Daisy W. Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Corresponding author
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy and Cancer Center, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610044, China
- Corresponding author
| |
Collapse
|
11
|
Wu C, Qavi AJ, Moyle AB, Wagner ND, Hachim A, Kavian N, Cole AR, Sweeney-Gibbons J, Rohrs HW, Peiris JM, Basler CF, Gross ML, Valkenburg SA, Farnsworth CW, Amarasinghe GK, Leung DW. Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein. STAR Protoc 2021; 2:100906. [PMID: 34642671 PMCID: PMC8495048 DOI: 10.1016/j.xpro.2021.100906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Nucleocapsid proteins are essential for SARS-CoV-2 life cycle. Here, we describe protocols to gather domain-specific insights about essential properties of nucleocapsids. These assays include dynamic light scattering to characterize oligomerization, fluorescence polarization to quantify RNA binding, hydrogen-deuterium exchange mass spectrometry to map RNA binding regions, negative-stain electron microscopy to visualize oligomeric species, interferon reporter assay to evaluate interferon signaling modulation, and a serology assay to reveal insights for improved sensitivity and specificity. These assays are broadly applicable to RNA-encapsidated nucleocapsids. For complete details on the use and execution of this protocol, please refer to Wu et al. (2021).
Collapse
Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Abraham J. Qavi
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Austin B. Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Nicole D. Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Asmaa Hachim
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Niloufar Kavian
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Paris Centre, Centre Hospitalier Universitaire Cochin, Service d’Immunologie Biologique, Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Aidan R. Cole
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Joyce Sweeney-Gibbons
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Henry W. Rohrs
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - J.S. Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Christopher F. Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Sophie A. Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Christopher W. Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Daisy W. Leung
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| |
Collapse
|
12
|
The Nucleocapsid of Paramyxoviruses: Structure and Function of an Encapsidated Template. Viruses 2021; 13:v13122465. [PMID: 34960734 PMCID: PMC8708338 DOI: 10.3390/v13122465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/28/2023] Open
Abstract
Viruses of the Paramyxoviridae family share a common and complex molecular machinery for transcribing and replicating their genomes. Their non-segmented, negative-strand RNA genome is encased in a tight homopolymer of viral nucleoproteins (N). This ribonucleoprotein complex, termed a nucleocapsid, is the template of the viral polymerase complex made of the large protein (L) and its co-factor, the phosphoprotein (P). This review summarizes the current knowledge on several aspects of paramyxovirus transcription and replication, including structural and functional data on (1) the architecture of the nucleocapsid (structure of the nucleoprotein, interprotomer contacts, interaction with RNA, and organization of the disordered C-terminal tail of N), (2) the encapsidation of the genomic RNAs (structure of the nucleoprotein in complex with its chaperon P and kinetics of RNA encapsidation in vitro), and (3) the use of the nucleocapsid as a template for the polymerase complex (release of the encased RNA and interaction network allowing the progress of the polymerase complex). Finally, this review presents models of paramyxovirus transcription and replication.
Collapse
|
13
|
Pyle JD, Whelan SPJ, Bloyet LM. Structure and function of negative-strand RNA virus polymerase complexes. Enzymes 2021; 50:21-78. [PMID: 34861938 DOI: 10.1016/bs.enz.2021.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Viruses with negative-strand RNA genomes (NSVs) include many highly pathogenic and economically devastating disease-causing agents of humans, livestock, and plants-highlighted by recent Ebola and measles virus epidemics, and continuously circulating influenza virus. Because of their protein-coding orientation, NSVs face unique challenges for efficient gene expression and genome replication. To overcome these barriers, NSVs deliver a large and multifunctional RNA-dependent RNA polymerase into infected host cells. NSV-encoded polymerases contain all the enzymatic activities required for transcription and replication of their genome-including RNA synthesis and mRNA capping. Here, we review the structures and functions of NSV polymerases with a focus on key domains responsible for viral replication and gene expression. We highlight shared and unique features among polymerases of NSVs from the Mononegavirales, Bunyavirales, and Articulavirales orders.
Collapse
Affiliation(s)
- Jesse D Pyle
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States; Ph.D. Program in Virology, Harvard Medical School, Boston, MA, United States
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States.
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States.
| |
Collapse
|
14
|
Structural and Functional Aspects of Ebola Virus Proteins. Pathogens 2021; 10:pathogens10101330. [PMID: 34684279 PMCID: PMC8538763 DOI: 10.3390/pathogens10101330] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 01/14/2023] Open
Abstract
Ebola virus (EBOV), member of genus Ebolavirus, family Filoviridae, have a non-segmented, single-stranded RNA that contains seven genes: (a) nucleoprotein (NP), (b) viral protein 35 (VP35), (c) VP40, (d) glycoprotein (GP), (e) VP30, (f) VP24, and (g) RNA polymerase (L). All genes encode for one protein each except GP, producing three pre-proteins due to the transcriptional editing. These pre-proteins are translated into four products, namely: (a) soluble secreted glycoprotein (sGP), (b) Δ-peptide, (c) full-length transmembrane spike glycoprotein (GP), and (d) soluble small secreted glycoprotein (ssGP). Further, shed GP is released from infected cells due to cleavage of GP by tumor necrosis factor α-converting enzyme (TACE). This review presents a detailed discussion on various functional aspects of all EBOV proteins and their residues. An introduction to ebolaviruses and their life cycle is also provided for clarity of the available analysis. We believe that this review will help understand the roles played by different EBOV proteins in the pathogenesis of the disease. It will help in targeting significant protein residues for therapeutic and multi-protein/peptide vaccine development.
Collapse
|
15
|
Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
Collapse
Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| |
Collapse
|
16
|
Ker DS, Jenkins HT, Greive SJ, Antson AA. CryoEM structure of the Nipah virus nucleocapsid assembly. PLoS Pathog 2021; 17:e1009740. [PMID: 34270629 PMCID: PMC8318291 DOI: 10.1371/journal.ppat.1009740] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/28/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022] Open
Abstract
Nipah and its close relative Hendra are highly pathogenic zoonotic viruses, storing their ssRNA genome in a helical nucleocapsid assembly formed by the N protein, a major viral immunogen. Here, we report the first cryoEM structure for a Henipavirus RNA-bound nucleocapsid assembly, at 3.5 Å resolution. The helical assembly is stabilised by previously undefined N- and C-terminal segments, contributing to subunit-subunit interactions. RNA is wrapped around the nucleocapsid protein assembly with a periodicity of six nucleotides per protomer, in the “3-bases-in, 3-bases-out” conformation, with protein plasticity enabling non-sequence specific interactions. The structure reveals commonalities in RNA binding pockets and in the conformation of bound RNA, not only with members of the Paramyxoviridae family, but also with the evolutionarily distant Filoviridae Ebola virus. Significant structural differences with other Paramyxoviridae members are also observed, particularly in the position and length of the exposed α-helix, residues 123–139, which may serve as a valuable epitope for surveillance and diagnostics. Nipah virus is a highly pathogenic RNA virus which, along with the closely related Hendra virus, emerged relatively recently. Due to ~40% mortality rate and evidence of animal-to-human as well as human-to-human transmission, development of antivirals against the Nipah and henipaviral disease is particularly urgent. In common with other single-stranded RNA viruses, including Ebola and coronaviruses, the nucleocapsid assembly of the Nipah virus safeguards the viral genome, protecting it from degradation and facilitating its encapsidation and storage inside the virion. Here, we used cryo-electron microscopy to determine accurate three-dimensional structure for several different assemblies of the Nipah virus nucleocapsid protein, in particular a detailed structure for the complex of this protein with RNA. This structural information is important for understanding detailed molecular interactions driving and stabilizing the nucleocapsid assembly formation that are of fundamental importance for understanding similar processes in a large group of ssRNA viruses. Apart from highlighting structural similarities and differences with nucleocapsid proteins of other viruses of the Paramyxoviridae family, these data will inform the development of new antiviral approaches for the henipaviruses.
Collapse
Affiliation(s)
- De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Sandra J. Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
- * E-mail:
| |
Collapse
|
17
|
Structural plasticity of mumps virus nucleocapsids with cryo-EM structures. Commun Biol 2021; 4:833. [PMID: 34215847 PMCID: PMC8253768 DOI: 10.1038/s42003-021-02362-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 06/11/2021] [Indexed: 11/08/2022] Open
Abstract
Mumps virus (MuV) is a highly contagious human pathogen and frequently causes worldwide outbreaks despite available vaccines. Similar to other mononegaviruses such as Ebola and rabies, MuV uses a single-stranded negative-sense RNA as its genome, which is enwrapped by viral nucleoproteins into the helical nucleocapsid. The nucleocapsid acts as a scaffold for genome condensation and as a template for RNA replication and transcription. Conformational changes in the MuV nucleocapsid are required to switch between different activities, but the underlying mechanism remains elusive due to the absence of high-resolution structures. Here, we report two MuV nucleoprotein-RNA rings with 13 and 14 protomers, one stacked-ring filament and two nucleocapsids with distinct helical pitches, in dense and hyperdense states, at near-atomic resolutions using cryo-electron microscopy. Structural analysis of these in vitro assemblies indicates that the C-terminal tail of MuV nucleoprotein likely regulates the assembly of helical nucleocapsids, and the C-terminal arm may be relevant for the transition between the dense and hyperdense states of helical nucleocapsids. Our results provide the molecular mechanism for structural plasticity among different MuV nucleocapsids and create a possible link between structural plasticity and genome condensation. Shan et al. describes the high-resolution structures of Nucleoprotein in two different oligomeric states and four different higher-order helical structures. They further describe the structural rearrangements required to transition between the different helical assemblies obtained, highlighting the basis for structural plasticity among different MuV nucleocapsids.
Collapse
|
18
|
Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR. SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Nat Chem 2021; 13:651-659. [PMID: 34031561 PMCID: PMC8249329 DOI: 10.1038/s41557-021-00707-0] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/14/2021] [Indexed: 01/20/2023]
Abstract
SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression and replication that depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate 0.1 seconds of the viral proteome. Our adaptive sampling simulations predict dramatic opening of the apo spike complex, far beyond that seen experimentally, explaining and predicting the existence of 'cryptic' epitopes. Different spike variants modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also discover dramatic conformational changes across the proteome, which reveal over 50 'cryptic' pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas.
Collapse
Affiliation(s)
- Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Justin R Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Michael D Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Artur Meller
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Upasana L Mallimadugula
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Catherine E Kuhn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Jonathan H Borowsky
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Rafal P Wiewiora
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, NY, New York, USA
| | | | - Aoife M Harbison
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | | | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, PA, USA
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, NY, New York, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA.
| |
Collapse
|
19
|
Wu C, Qavi AJ, Hachim A, Kavian N, Cole AR, Moyle AB, Wagner ND, Sweeney-Gibbons J, Rohrs HW, Gross ML, Peiris JSM, Basler CF, Farnsworth CW, Valkenburg SA, Amarasinghe GK, Leung DW. Characterization of SARS-CoV-2 nucleocapsid protein reveals multiple functional consequences of the C-terminal domain. iScience 2021; 24:102681. [PMID: 34095780 PMCID: PMC8168301 DOI: 10.1016/j.isci.2021.102681] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/13/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Nucleocapsid (N) encoded by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays key roles in the replication cycle and is a critical serological marker. Here, we characterize essential biochemical properties of N and describe the utility of these insights in serological studies. We define N domains important for oligomerization and RNA binding and show that N oligomerization provides a high-affinity RNA-binding platform. We also map the RNA-binding interface, showing protection in the N-terminal domain and linker region. In addition, phosphorylation causes reduction of RNA binding and redistribution of N from liquid droplets to loose coils, showing how N-RNA accessibility and assembly may be regulated by phosphorylation. Finally, we find that the C-terminal domain of N is the most immunogenic, based on antibody binding to patient samples. Together, we provide a biochemical description of SARS-CoV-2 N and highlight the value of using N domains as highly specific and sensitive diagnostic markers.
Collapse
Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Abraham J. Qavi
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Asmaa Hachim
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Niloufar Kavian
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Paris Centre, Centre Hospitalier Universitaire Cochin, Service d’Immunologie Biologique, Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Aidan R. Cole
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Austin B. Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicole D. Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Joyce Sweeney-Gibbons
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Henry W. Rohrs
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - J. S. Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Christopher F. Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Christopher W. Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sophie A. Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Daisy W. Leung
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| |
Collapse
|
20
|
Xu C, Katyal N, Nesterova T, Perilla JR. Molecular determinants of Ebola nucleocapsid stability from molecular dynamics simulations. J Chem Phys 2021; 153:155102. [PMID: 33092380 DOI: 10.1063/5.0021491] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ebola virus (EBOV) is a human pathogen with the ability to cause hemorrhagic fever and bleeding diathesis in hosts. The life cycle of EBOV depends on its nucleocapsid. The Ebola nucleocapsid consists of a helical assembly of nucleoproteins (NPs) encapsidating single-stranded viral RNA (ssRNA). Knowledge of the molecular determinants of Ebola nucleocapsid stability is essential for the development of therapeutics against EBOV. However, large degrees of freedom associated with the Ebola nucleocapsid helical assembly pose a computational challenge, thereby limiting the previous simulation studies to the level of monomers. In the present work, we have performed all atom molecular dynamics (MD) simulations of the helical assembly of EBOV nucleoproteins in the absence and presence of ssRNA. We found that ssRNA is essential for maintaining structural integrity of the nucleocapsid. Other molecular determinants observed to stabilize the nucleocapsid include NP-RNA and NP-NP interactions and ion distributions. Additionally, the structural and dynamical behavior of the nucleocapsid monomer depends on its position in the helical assembly. NP monomers present on the longitudinal edges of the helical tube are more exposed, flexible, and have weaker NP-NP interactions than those residing in the center. This work provides key structural features stabilizing the nucleocapsid that may serve as therapeutic targets.
Collapse
Affiliation(s)
- Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Nidhi Katyal
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Tanya Nesterova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| |
Collapse
|
21
|
Zhang N, Shan H, Liu M, Li T, Luo R, Yang L, Qi L, Chu X, Su X, Wang R, Liu Y, Sun W, Shen QT. Structure and assembly of double-headed Sendai virus nucleocapsids. Commun Biol 2021; 4:494. [PMID: 33888861 PMCID: PMC8062630 DOI: 10.1038/s42003-021-02027-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 03/23/2021] [Indexed: 01/17/2023] Open
Abstract
Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids. Here, we reported a double-headed SeV nucleocapsid assembled in a tail-to-tail manner, and resolved its helical stems and clam-shaped joint at the respective resolutions of 2.9 and 3.9 Å, via cryo-electron microscopy. Our structures offer important insights into the mechanism of the helical polymerization, in particular via an unnoticed exchange of a N-terminal hole formed by three loops of nucleoproteins, and unveil the clam-shaped joint in a hyper-closed state for nucleocapsid dimerization. Direct visualization of the loop from the disordered C-terminal tail provides structural evidence that C-terminal tail is correlated to the curvature of nucleocapsid and links nucleocapsid condensation and genome replication and transcription with different assembly forms.
Collapse
Affiliation(s)
- Na Zhang
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Shan
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mingdong Liu
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianhao Li
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Liuyan Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lei Qi
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaofeng Chu
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Su
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Wang
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yunhui Liu
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wenzhi Sun
- Chinese Institute for Brain Research, Beijing, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Qing-Tao Shen
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| |
Collapse
|
22
|
Affiliation(s)
- Tobias
P. Wörner
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Tatiana M. Shamorkina
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
23
|
Seychell BC, Beck T. Molecular basis for protein-protein interactions. Beilstein J Org Chem 2021; 17:1-10. [PMID: 33488826 PMCID: PMC7801801 DOI: 10.3762/bjoc.17.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/07/2020] [Indexed: 01/11/2023] Open
Abstract
This minireview provides an overview on the current knowledge of protein-protein interactions, common characterisation methods to characterise them, and their role in protein complex formation with some examples. A deep understanding of protein-protein interactions and their molecular interactions is important for a number of applications, including drug design. Protein-protein interactions and their discovery are thus an interesting avenue for understanding how protein complexes, which make up the majority of proteins, work.
Collapse
Affiliation(s)
- Brandon Charles Seychell
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Tobias Beck
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
| |
Collapse
|
24
|
Abstract
RNA viruses include many important human and animal pathogens, such as the influenza viruses, respiratory syncytial virus, Ebola virus, measles virus and rabies virus. The genomes of these viruses consist of single or multiple RNA segments that assemble with oligomeric viral nucleoprotein into ribonucleoprotein complexes. Replication and transcription of the viral genome is performed by ~250-450 kDa viral RNA-dependent RNA polymerases that also contain capping or cap-snatching activity. In this Review, we compare recent high-resolution X-ray and cryoelectron microscopy structures of RNA polymerases of negative-sense RNA viruses with segmented and non-segmented genomes, including orthomyxoviruses, peribunyaviruses, phenuiviruses, arenaviruses, rhabdoviruses, pneumoviruses and paramyxoviruses. In addition, we discuss how structural insights into these enzymes contribute to our understanding of the molecular mechanisms of viral transcription and replication, and how we can use these insights to identify targets for antiviral drug design.
Collapse
|
25
|
Wu C, Qavi AJ, Hachim A, Kavian N, Cole AR, Moyle AB, Wagner ND, Sweeney-Gibbons J, Rohrs HW, Gross ML, Peiris JSM, Basler CF, Farnsworth CW, Valkenburg SA, Amarasinghe GK, Leung DW. Characterization of SARS-CoV-2 N protein reveals multiple functional consequences of the C-terminal domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.30.404905. [PMID: 33269347 PMCID: PMC7709165 DOI: 10.1101/2020.11.30.404905] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nucleocapsid protein (N) is the most abundant viral protein encoded by SARS-CoV-2, the causative agent of COVID-19. N plays key roles at different steps in the replication cycle and is used as a serological marker of infection. Here we characterize the biochemical properties of SARS-CoV-2 N. We define the N domains important for oligomerization and RNA binding that are associated with spherical droplet formation and suggest that N accessibility and assembly may be regulated by phosphorylation. We also map the RNA binding interface using hydrogen-deuterium exchange mass spectrometry. Finally, we find that the N protein C-terminal domain is the most immunogenic by sensitivity, based upon antibody binding to COVID-19 patient samples from the US and Hong Kong. Together, these findings uncover domain-specific insights into the significance of SARS-CoV-2 N and highlight the diagnostic value of using N domains as highly specific and sensitive markers of COVID-19.
Collapse
Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Abraham J Qavi
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Asmaa Hachim
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Niloufar Kavian
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Paris Centre, Centre Hospitalier Universitaire Cochin, Service d'Immunologie Biologique, Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, Sorbonne Paris Cité, Paris
| | - Aidan R Cole
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Austin B Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Joyce Sweeney-Gibbons
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Henry W Rohrs
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - J S Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Christopher W Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| |
Collapse
|
26
|
Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR. SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.27.175430. [PMID: 32637963 PMCID: PMC7337393 DOI: 10.1101/2020.06.27.175430] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate an unprecedented 0.1 seconds of the viral proteome. Our simulations capture dramatic opening of the apo Spike complex, far beyond that seen experimentally, which explains and successfully predicts the existence of 'cryptic' epitopes. Different Spike homologues modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also observe dramatic conformational changes across the proteome, which reveal over 50 'cryptic' pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas.
Collapse
Affiliation(s)
- Maxwell I. Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Justin R. Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Michael D. Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Artur Meller
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Upasana L. Mallimadugula
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Catherine E. Kuhn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jonathan H. Borowsky
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Rafal P. Wiewiora
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York 10065, United States
| | - Matthew F. D. Hurley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Aoife M Harbison
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland
| | | | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland
| | - Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York 10065, United States
| | - Gregory R. Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| |
Collapse
|
27
|
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.
Collapse
|
28
|
Porter JR, Meller A, Zimmerman MI, Greenberg MJ, Bowman GR. Conformational distributions of isolated myosin motor domains encode their mechanochemical properties. eLife 2020; 9:e55132. [PMID: 32479265 PMCID: PMC7259954 DOI: 10.7554/elife.55132] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/04/2020] [Indexed: 01/25/2023] Open
Abstract
Myosin motor domains perform an extraordinary diversity of biological functions despite sharing a common mechanochemical cycle. Motors are adapted to their function, in part, by tuning the thermodynamics and kinetics of steps in this cycle. However, it remains unclear how sequence encodes these differences, since biochemically distinct motors often have nearly indistinguishable crystal structures. We hypothesized that sequences produce distinct biochemical phenotypes by modulating the relative probabilities of an ensemble of conformations primed for different functional roles. To test this hypothesis, we modeled the distribution of conformations for 12 myosin motor domains by building Markov state models (MSMs) from an unprecedented two milliseconds of all-atom, explicit-solvent molecular dynamics simulations. Comparing motors reveals shifts in the balance between nucleotide-favorable and nucleotide-unfavorable P-loop conformations that predict experimentally measured duty ratios and ADP release rates better than sequence or individual structures. This result demonstrates the power of an ensemble perspective for interrogating sequence-function relationships.
Collapse
Affiliation(s)
- Justin R Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. LouisSt. LouisUnited States
| | - Artur Meller
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. LouisSt. LouisUnited States
| | - Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. LouisSt. LouisUnited States
| | - Michael J Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. LouisSt. LouisUnited States
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. LouisSt. LouisUnited States
- Center for the Science and Engineering of Living Systems, Washington University in St. LouisSt. LouisUnited States
| |
Collapse
|
29
|
Lin AE, Diehl WE, Cai Y, Finch CL, Akusobi C, Kirchdoerfer RN, Bollinger L, Schaffner SF, Brown EA, Saphire EO, Andersen KG, Kuhn JH, Luban J, Sabeti PC. Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111. Viruses 2020; 12:E105. [PMID: 31952352 PMCID: PMC7019320 DOI: 10.3390/v12010105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 01/17/2023] Open
Abstract
For highly pathogenic viruses, reporter assays that can be rapidly performed are critically needed to identify potentially functional mutations for further study under maximal containment (e.g., biosafety level 4 [BSL-4]). The Ebola virus nucleoprotein (NP) plays multiple essential roles during the viral life cycle, yet few tools exist to study the protein under BSL-2 or equivalent containment. Therefore, we adapted reporter assays to measure NP oligomerization and virion-like particle (VLP) production in live cells and further measured transcription and replication using established minigenome assays. As a proof-of-concept, we examined the NP-R111C substitution, which emerged during the 2013‒2016 Western African Ebola virus disease epidemic and rose to high frequency. NP-R111C slightly increased NP oligomerization and VLP budding but slightly decreased transcription and replication. By contrast, a synthetic charge-reversal mutant, NP-R111E, greatly increased oligomerization but abrogated transcription and replication. These results are intriguing in light of recent structures of NP oligomers, which reveal that the neighboring residue, K110, forms a salt bridge with E349 on adjacent NP molecules. By developing and utilizing multiple reporter assays, we find that the NP-111 position mediates a complex interplay between NP's roles in protein structure, virion budding, and transcription and replication.
Collapse
Affiliation(s)
- Aaron E. Lin
- Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William E. Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; (W.E.D.); (J.L.)
| | - Yingyun Cai
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Courtney L. Finch
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Chidiebere Akusobi
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02120, USA;
| | | | - Laura Bollinger
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Stephen F. Schaffner
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elizabeth A. Brown
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Kristian G. Andersen
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA;
- Scripps Translational Science Institute, La Jolla, CA 92037, USA
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; (W.E.D.); (J.L.)
| | - Pardis C. Sabeti
- Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| |
Collapse
|
30
|
Hume AJ, Mühlberger E. Distinct Genome Replication and Transcription Strategies within the Growing Filovirus Family. J Mol Biol 2019; 431:4290-4320. [PMID: 31260690 PMCID: PMC6879820 DOI: 10.1016/j.jmb.2019.06.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/31/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022]
Abstract
Research on filoviruses has historically focused on the highly pathogenic ebola- and marburgviruses. Indeed, until recently, these were the only two genera in the filovirus family. Recent advances in sequencing technologies have facilitated the discovery of not only a new ebolavirus, but also three new filovirus genera and a sixth proposed genus. While two of these new genera are similar to the ebola- and marburgviruses, the other two, discovered in saltwater fishes, are considerably more diverse. Nonetheless, these viruses retain a number of key features of the other filoviruses. Here, we review the key characteristics of filovirus replication and transcription, highlighting similarities and differences between the viruses. In particular, we focus on key regulatory elements in the genomes, replication and transcription strategies, and the conservation of protein domains and functions among the viruses. In addition, using computational analyses, we were able to identify potential homology and functions for some of the genes of the novel filoviruses with previously unknown functions. Although none of the newly discovered filoviruses have yet been isolated, initial studies of some of these viruses using minigenome systems have yielded insights into their mechanisms of replication and transcription. In general, the Cuevavirus and proposed Dianlovirus genera appear to follow the transcription and replication strategies employed by the ebola- and marburgviruses, respectively. While our knowledge of the fish filoviruses is currently limited to sequence analysis, the lack of certain conserved motifs and even entire genes necessitates that they have evolved distinct mechanisms of replication and transcription.
Collapse
Affiliation(s)
- Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA.
| |
Collapse
|
31
|
Malhotra S, Träger S, Dal Peraro M, Topf M. Modelling structures in cryo-EM maps. Curr Opin Struct Biol 2019; 58:105-114. [PMID: 31394387 DOI: 10.1016/j.sbi.2019.05.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 12/20/2022]
Abstract
Recent advances in structure determination of sub-cellular structures using cryo-electron microscopy and tomography have enabled us to understand their architecture in a more detailed manner and gain insight into their function. The choice of approach to use for atomic model building, fitting, refinement and validation in the 3D map resulting from these experiments depends primarily on the resolution of the map and the prior information on the corresponding model. Here, we survey some of such methods and approaches and highlight their uses in specific recent examples.
Collapse
Affiliation(s)
- Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Sylvain Träger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom.
| |
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Guseva S, Milles S, Blackledge M, Ruigrok RWH. The Nucleoprotein and Phosphoprotein of Measles Virus. Front Microbiol 2019; 10:1832. [PMID: 31496998 PMCID: PMC6713020 DOI: 10.3389/fmicb.2019.01832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/25/2019] [Indexed: 01/04/2023] Open
Abstract
Measles virus is a negative strand virus and the genomic and antigenomic RNA binds to the nucleoprotein (N), assembling into a helical nucleocapsid. The polymerase complex comprises two proteins, the Large protein (L), that both polymerizes RNA and caps the mRNA, and the phosphoprotein (P) that co-localizes with L on the nucleocapsid. This review presents recent results about N and P, in particular concerning their intrinsically disordered domains. N is a protein of 525 residues with a 120 amino acid disordered C-terminal domain, Ntail. The first 50 residues of Ntail extricate the disordered chain from the nucleocapsid, thereby loosening the otherwise rigid structure, and the C-terminus contains a linear motif that binds P. Recent results show how the 5′ end of the viral RNA binds to N within the nucleocapsid and also show that the bases at the 3′ end of the RNA are rather accessible to the viral polymerase. P is a tetramer and most of the protein is disordered; comprising 507 residues of which around 380 are disordered. The first 37 residues of P bind N, chaperoning against non-specific interaction with cellular RNA, while a second interaction site, around residue 200 also binds N. In addition, there is another interaction between C-terminal domain of P (XD) and Ntail. These results allow us to propose a new model of how the polymerase binds to the nucleocapsid and suggests a mechanism for initiation of transcription.
Collapse
Affiliation(s)
- Serafima Guseva
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
| | - Sigrid Milles
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
| | - Martin Blackledge
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
| | - Rob W H Ruigrok
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
| |
Collapse
|
34
|
Conserved peptide vaccine candidates containing multiple Ebola nucleoprotein epitopes display interactions with diverse HLA molecules. Med Microbiol Immunol 2019; 208:227-238. [DOI: 10.1007/s00430-019-00584-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
|
35
|
Assembly and cryo-EM structures of RNA-specific measles virus nucleocapsids provide mechanistic insight into paramyxoviral replication. Proc Natl Acad Sci U S A 2019; 116:4256-4264. [PMID: 30787192 DOI: 10.1073/pnas.1816417116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Assembly of paramyxoviral nucleocapsids on the RNA genome is an essential step in the viral cycle. The structural basis of this process has remained obscure due to the inability to control encapsidation. We used a recently developed approach to assemble measles virus nucleocapsid-like particles on specific sequences of RNA hexamers (poly-Adenine and viral genomic 5') in vitro, and determined their cryoelectron microscopy maps to 3.3-Å resolution. The structures unambiguously determine 5' and 3' binding sites and thereby the binding-register of viral genomic RNA within nucleocapsids. This observation reveals that the 3' end of the genome is largely exposed in fully assembled measles nucleocapsids. In particular, the final three nucleotides of the genome are rendered accessible to the RNA-dependent RNA polymerase complex, possibly enabling efficient RNA processing. The structures also reveal local and global conformational changes in the nucleoprotein upon assembly, in particular involving helix α6 and helix α13 that form edges of the RNA binding groove. Disorder is observed in the bound RNA, localized at one of the two backbone conformational switch sites. The high-resolution structure allowed us to identify putative nucleobase interaction sites in the RNA-binding groove, whose impact on assembly kinetics was measured using real-time NMR. Mutation of one of these sites, R195, whose sidechain stabilizes both backbone and base of a bound nucleic acid, is thereby shown to be essential for nucleocapsid-like particle assembly.
Collapse
|
36
|
Porter JR, Moeder KE, Sibbald CA, Zimmerman MI, Hart KM, Greenberg MJ, Bowman GR. Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling. Biophys J 2019; 116:818-830. [PMID: 30744991 DOI: 10.1016/j.bpj.2018.11.3144] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 01/19/2023] Open
Abstract
Proteins are dynamic molecules that undergo conformational changes to a broad spectrum of different excited states. Unfortunately, the small populations of these states make it difficult to determine their structures or functional implications. Computer simulations are an increasingly powerful means to identify and characterize functionally relevant excited states. However, this advance has uncovered a further challenge: it can be extremely difficult to identify the most salient features of large simulation data sets. We reasoned that many functionally relevant conformational changes are likely to involve large, cooperative changes to the surfaces that are available to interact with potential binding partners. To examine this hypothesis, we introduce a method that returns a prioritized list of potentially functional conformational changes by segmenting protein structures into clusters of residues that undergo cooperative changes in their solvent exposure, along with the hierarchy of interactions between these groups. We term these groups exposons to distinguish them from other types of clusters that arise in this analysis and others. We demonstrate, using three different model systems, that this method identifies experimentally validated and functionally relevant conformational changes, including conformational switches, allosteric coupling, and cryptic pockets. Our results suggest that key functional sites are hubs in the network of exposons. As a further test of the predictive power of this approach, we apply it to discover cryptic allosteric sites in two different β-lactamase enzymes that are widespread sources of antibiotic resistance. Experimental tests confirm our predictions for both systems. Importantly, we provide the first evidence, to our knowledge, for a cryptic allosteric site in CTX-M-9 β-lactamase. Experimentally testing this prediction did not require any mutations and revealed that this site exerts the most potent allosteric control over activity of any pockets found in β-lactamases to date. Discovery of a similar pocket that was previously overlooked in the well-studied TEM-1 β-lactamase demonstrates the utility of exposons.
Collapse
Affiliation(s)
- Justin R Porter
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Katelyn E Moeder
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Carrie A Sibbald
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Maxwell I Zimmerman
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Kathryn M Hart
- Department of Chemistry, Williams College, Williamstown, Massachusetts
| | - Michael J Greenberg
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Gregory R Bowman
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri; Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri.
| |
Collapse
|
37
|
Chanthamontri CK, Jordan DS, Wang W, Wu C, Lin Y, Brett TJ, Gross ML, Leung DW. The Ebola Viral Protein 35 N-Terminus Is a Parallel Tetramer. Biochemistry 2019; 58:657-664. [PMID: 30592210 DOI: 10.1021/acs.biochem.8b01154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Members of Mononegavirales, the order that includes nonsegmented negative sense RNA viruses (NNSVs), encode a small number of multifunctional proteins. In members of the Filoviridae family, virus protein 35 (VP35) facilitates immune evasion and functions as an obligatory cofactor for viral RNA synthesis. VP35 functions in a manner orthologous to that of phosphoproteins from other NNSVs. Although the critical roles of Ebola viral VP35 (eVP35) in immune evasion and RNA synthesis are well-appreciated, a complete understanding of its organization and its role in carrying out its many functions has yet to be fully realized. In particular, we currently lack information about the role of the oligomerization domain within eVP35. To address this limitation, we report here an investigation of the oligomer structure of eVP35 using hybrid methods that include multiangle light scattering, small-angle X-ray scattering, and cross-linking coupled with mass spectrometry to determine the shape and orientation of the eVP35 oligomer. Our integrative results are consistent with a parallel tetramer in which the N-terminal regions that are required for RNA synthesis are all oriented in the same direction. Furthermore, these results define a framework for targeting the symmetric tetramer for structure-based antiviral discovery.
Collapse
Affiliation(s)
- Chamnongsak Ken Chanthamontri
- Department of Chemistry , Washington University in St. Louis , Box 1134, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - David S Jordan
- Department of Pathology and Immunology , Washington University School of Medicine in St. Louis , St. Louis , Missouri 63110 , United States
| | - Wenjie Wang
- Department of Pathology and Immunology , Washington University School of Medicine in St. Louis , St. Louis , Missouri 63110 , United States
| | - Chao Wu
- Department of Pathology and Immunology , Washington University School of Medicine in St. Louis , St. Louis , Missouri 63110 , United States
| | - Yanchun Lin
- Department of Chemistry , Washington University in St. Louis , Box 1134, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Tom J Brett
- Department of Medicine , Washington University School of Medicine in St. Louis , St. Louis , Missouri 63110 , United States
| | - Michael L Gross
- Department of Chemistry , Washington University in St. Louis , Box 1134, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Daisy W Leung
- Department of Pathology and Immunology , Washington University School of Medicine in St. Louis , St. Louis , Missouri 63110 , United States
| |
Collapse
|
38
|
Knoverek CR, Amarasinghe GK, Bowman GR. Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities. Trends Biochem Sci 2018; 44:351-364. [PMID: 30555007 DOI: 10.1016/j.tibs.2018.11.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/11/2018] [Accepted: 11/20/2018] [Indexed: 12/18/2022]
Abstract
A protein is a dynamic shape-shifter whose function is determined by the set of structures it adopts. Unfortunately, atomically detailed structures are only available for a few conformations of any given protein, and these structures have limited explanatory and predictive power. Here, we provide a brief historical perspective on protein dynamics and introduce recent advances in computational and experimental methods that are providing unprecedented access to protein shape-shifting. Next, we focus on how these tools are revealing the mechanism of allosteric communication and features like cryptic pockets; both of which present new therapeutic opportunities. A major theme is the importance of considering the relative probabilities of different structures and the control one can exert over protein function by modulating this balance.
Collapse
Affiliation(s)
- Catherine R Knoverek
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Gaya K Amarasinghe
- Department of Pathology & Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Gregory R Bowman
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
| |
Collapse
|
39
|
Batra J, Hultquist JF, Liu D, Shtanko O, Von Dollen J, Satkamp L, Jang GM, Luthra P, Schwarz TM, Small GI, Arnett E, Anantpadma M, Reyes A, Leung DW, Kaake R, Haas P, Schmidt CB, Schlesinger LS, LaCount DJ, Davey RA, Amarasinghe GK, Basler CF, Krogan NJ. Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication. Cell 2018; 175:1917-1930.e13. [PMID: 30550789 PMCID: PMC6366944 DOI: 10.1016/j.cell.2018.08.044] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/17/2018] [Accepted: 08/17/2018] [Indexed: 01/21/2023]
Abstract
Ebola virus (EBOV) infection often results in fatal illness in humans, yet little is known about how EBOV usurps host pathways during infection. To address this, we used affinity tag-purification mass spectrometry (AP-MS) to generate an EBOV-host protein-protein interaction (PPI) map. We uncovered 194 high-confidence EBOV-human PPIs, including one between the viral transcription regulator VP30 and the host ubiquitin ligase RBBP6. Domain mapping identified a 23 amino acid region within RBBP6 that binds to VP30. A crystal structure of the VP30-RBBP6 peptide complex revealed that RBBP6 mimics the viral nucleoprotein (NP) binding to the same interface of VP30. Knockdown of endogenous RBBP6 stimulated viral transcription and increased EBOV replication, whereas overexpression of either RBBP6 or the peptide strongly inhibited both. These results demonstrate the therapeutic potential of biologics that target this interface and identify additional PPIs that may be leveraged for novel therapeutic strategies.
Collapse
Affiliation(s)
- Jyoti Batra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Dandan Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Olena Shtanko
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - John Von Dollen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Laura Satkamp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Gwendolyn M Jang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Priya Luthra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Toni M Schwarz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriel I Small
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Eusondia Arnett
- Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Ann Reyes
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Robyn Kaake
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Paige Haas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Carson B Schmidt
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Douglas J LaCount
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA.
| |
Collapse
|
40
|
Basler CF, Krogan NJ, Leung DW, Amarasinghe GK. Virus and host interactions critical for filoviral RNA synthesis as therapeutic targets. Antiviral Res 2018; 162:90-100. [PMID: 30550800 DOI: 10.1016/j.antiviral.2018.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 01/24/2023]
Abstract
Filoviruses, which include Ebola virus (EBOV) and Marburg virus, are negative-sense RNA viruses associated with sporadic outbreaks of severe viral hemorrhagic fever characterized by uncontrolled virus replication. The extreme virulence and emerging nature of these zoonotic pathogens make them a significant threat to human health. Replication of the filovirus genome and production of viral RNAs require the function of a complex of four viral proteins, the nucleoprotein (NP), viral protein 35 (VP35), viral protein 30 (VP30) and large protein (L). The latter performs the enzymatic activities required for production of viral RNAs and capping of viral mRNAs. Although it has been recognized that interactions between the virus-encoded components of the EBOV RNA polymerase complex are required for viral RNA synthesis reactions, specific molecular details have, until recently, been lacking. New efforts have combined structural biology and molecular virology to reveal in great detail the molecular basis for critical protein-protein interactions (PPIs) necessary for viral RNA synthesis. These efforts include recent studies that have identified a range of interacting host factors and in some instances demonstrated unique mechanisms by which they act. For a select number of these interactions, combined use of mutagenesis, over-expressing of peptides corresponding to PPI interfaces and identification of small molecules that disrupt PPIs have demonstrated the functional significance of virus-virus and virus-host PPIs and suggest several as potential targets for therapeutic intervention.
Collapse
Affiliation(s)
- Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), UCSF, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
41
|
Sugita Y, Matsunami H, Kawaoka Y, Noda T, Wolf M. Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 Å resolution. Nature 2018; 563:137-140. [PMID: 30333622 DOI: 10.1038/s41586-018-0630-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/21/2018] [Indexed: 11/09/2022]
Abstract
Ebola virus causes haemorrhagic fever with a high fatality rate in humans and non-human primates. It belongs to the family Filoviridae in the order Mononegavirales, which are viruses that contain linear, non-segmented, negative-sense, single-stranded genomic RNA1,2. The enveloped, filamentous virion contains the nucleocapsid, consisting of the helical nucleoprotein-RNA complex, VP24, VP30, VP35 and viral polymerase1,3. The nucleoprotein-RNA complex acts as a scaffold for nucleocapsid formation and as a template for RNA replication and transcription by condensing RNA into the virion4,5. RNA binding and nucleoprotein oligomerization are synergistic and do not readily occur independently6. Although recent cryo-electron tomography studies have revealed the overall architecture of the nucleocapsid core4,5, there has been no high-resolution reconstruction of the nucleocapsid. Here we report the structure of a recombinant Ebola virus nucleoprotein-RNA complex expressed in mammalian cells without chemical fixation, at near-atomic resolution using single-particle cryo-electron microscopy. Our structure reveals how the Ebola virus nucleocapsid core encapsidates its viral genome, its sequence-independent coordination with RNA by nucleoprotein, and the dynamic transition between the RNA-free and RNA-bound states. It provides direct structural evidence for the role of the N terminus of nucleoprotein in subunit oligomerization, and for the hydrophobic and electrostatic interactions that lead to the formation of the helical assembly. The structure is validated as representative of the native biological assembly of the nucleocapsid core by consistent dimensions and symmetry with the full virion5. The atomic model provides a detailed mechanistic basis for understanding nucleocapsid assembly and highlights key structural features that may serve as targets for anti-viral drug development.
Collapse
Affiliation(s)
- Yukihiko Sugita
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Laboratory of Advanced Protein Characterization, Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hideyuki Matsunami
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - 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
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| |
Collapse
|
42
|
Oluwagbemi O, Awe O. A comparative computational genomics of Ebola Virus Disease strains: In-silico Insight for Ebola control. INFORMATICS IN MEDICINE UNLOCKED 2018. [DOI: 10.1016/j.imu.2018.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
|