1
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Hilko DH, Fisher GM, Addison RS, Andrews KT, Poulsen SA. Thymidine Kinase-Independent Click Chemistry DNADetect Probes for DNA Proliferation Assessment in Malaria Parasites. ACS Chem Biol 2023; 18:2535-2543. [PMID: 38050717 DOI: 10.1021/acschembio.3c00530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Metabolic chemical probes are small-molecule reagents that utilize naturally occurring biosynthetic enzymes for in situ incorporation into biomolecules of interest. These reagents can be used to label, detect, and track important biological processes within living cells including protein synthesis, protein glycosylation, and nucleic acid proliferation. A limitation of current chemical probes, which have largely focused on mammalian cells, is that they often cannot be applied to other organisms due to metabolic differences. For example, the thymidine derivative 5-ethynyl-2'-deoxyuridine (EdU) is a gold standard metabolic chemical probe for assessing DNA proliferation in mammalian cells; however, it is unsuitable for the study of malaria parasites due to Plasmodium species lacking the thymidine kinase enzyme that is essential for metabolism of EdU. Herein, we report the design and synthesis of new thymidine-based probes that sidestep the requirement for a thymidine kinase enzyme in Plasmodium. Two of these DNADetect probes exhibit robust labeling of replicating asexual intraerythrocytic Plasmodium falciparum parasites, as determined by flow cytometry and fluorescence microscopy using copper-catalyzed azide-alkyne cycloaddition to a fluorescent azide. The DNADetect chemical probes are synthetically accessible and thus can be made widely available to researchers as tools to further understand the biology of different Plasmodium species, including laboratory lines and clinical isolates.
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Affiliation(s)
- David H Hilko
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Gillian M Fisher
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Russell S Addison
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Katherine T Andrews
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
- School of Environment and Science, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
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2
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Jungblut M, Backes S, Streit M, Gasteiger G, Doose S, Sauer M, Beliu G. Re-Engineered Pseudoviruses for Precise and Robust 3D Mapping of Viral Infection. ACS NANO 2023; 17:21822-21828. [PMID: 37913789 PMCID: PMC10655175 DOI: 10.1021/acsnano.3c07767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023]
Abstract
Engineered vesicular stomatitis virus (VSV) pseudotyping offers an essential method for exploring virus-cell interactions, particularly for viruses that require high biosafety levels. Although this approach has been employed effectively, the current methodologies for virus visualization and labeling can interfere with infectivity and lead to misinterpretation of results. In this study, we introduce an innovative approach combining genetic code expansion (GCE) and click chemistry with pseudotyped VSV to produce highly fluorescent and infectious pseudoviruses (clickVSVs). These clickVSVs enable robust and precise virus-cell interaction studies without compromising the biological function of the viral surface proteins. We evaluated this approach by generating VSVs bearing a unique chemical handle for click labeling and assessing the infectivity in relevant cell lines. Our results demonstrate that clickVSVs maintain their infectivity post-labeling and present an efficiency about two times higher in detecting surface proteins compared to classical immunolabeling. The utilization of clickVSVs further allowed us to visualize and track 3D virus binding and infection in living cells, offering enhanced observation of virus-host interactions. Thus, clickVSVs provide an efficient alternative for virus-associated research under the standard biosafety levels.
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Affiliation(s)
- Marvin Jungblut
- Department
of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Simone Backes
- Institute
for Virology and Immunbiology, University
of Würzburg, Versbacher
Str. 7, 97080 Würzburg, Germany
| | - Marcel Streit
- Rudolf
Virchow Center, Research Center for Integrative and Translational
Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Georg Gasteiger
- Institute
of Systems Immunology, Max Planck Research
Group University of Würzburg, Versbacher Str. 9, 97080 Würzburg, Germany
| | - Sören Doose
- Department
of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Sauer
- Department
of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Rudolf
Virchow Center, Research Center for Integrative and Translational
Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Gerti Beliu
- Rudolf
Virchow Center, Research Center for Integrative and Translational
Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
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3
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Petkidis A, Andriasyan V, Greber UF. Machine learning for cross-scale microscopy of viruses. CELL REPORTS METHODS 2023; 3:100557. [PMID: 37751685 PMCID: PMC10545915 DOI: 10.1016/j.crmeth.2023.100557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/05/2023] [Accepted: 07/20/2023] [Indexed: 09/28/2023]
Abstract
Despite advances in virological sciences and antiviral research, viruses continue to emerge, circulate, and threaten public health. We still lack a comprehensive understanding of how cells and individuals remain susceptible to infectious agents. This deficiency is in part due to the complexity of viruses, including the cell states controlling virus-host interactions. Microscopy samples distinct cellular infection stages in a multi-parametric, time-resolved manner at molecular resolution and is increasingly enhanced by machine learning and deep learning. Here we discuss how state-of-the-art artificial intelligence (AI) augments light and electron microscopy and advances virological research of cells. We describe current procedures for image denoising, object segmentation, tracking, classification, and super-resolution and showcase examples of how AI has improved the acquisition and analyses of microscopy data. The power of AI-enhanced microscopy will continue to help unravel virus infection mechanisms, develop antiviral agents, and improve viral vectors.
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Affiliation(s)
- Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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4
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Xie E, Ahmad S, Smyth RP, Sieben C. Advanced fluorescence microscopy in respiratory virus cell biology. Adv Virus Res 2023; 116:123-172. [PMID: 37524480 DOI: 10.1016/bs.aivir.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Respiratory viruses are a major public health burden across all age groups around the globe, and are associated with high morbidity and mortality rates. They can be transmitted by multiple routes, including physical contact or droplets and aerosols, resulting in efficient spreading within the human population. Investigations of the cell biology of virus replication are thus of utmost importance to gain a better understanding of virus-induced pathogenicity and the development of antiviral countermeasures. Light and fluorescence microscopy techniques have revolutionized investigations of the cell biology of virus infection by allowing the study of the localization and dynamics of viral or cellular components directly in infected cells. Advanced microscopy including high- and super-resolution microscopy techniques available today can visualize biological processes at the single-virus and even single-molecule level, thus opening a unique view on virus infection. We will highlight how fluorescence microscopy has supported investigations on virus cell biology by focusing on three major respiratory viruses: respiratory syncytial virus (RSV), Influenza A virus (IAV) and SARS-CoV-2. We will review our current knowledge of virus replication and highlight how fluorescence microscopy has helped to improve our state of understanding. We will start by introducing major imaging and labeling modalities and conclude the chapter with a perspective discussion on remaining challenges and potential opportunities.
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Affiliation(s)
- Enyu Xie
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Shazeb Ahmad
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany; Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Christian Sieben
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany.
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5
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Grazing on Marine Viruses and Its Biogeochemical Implications. mBio 2023; 14:e0192121. [PMID: 36715508 PMCID: PMC9973340 DOI: 10.1128/mbio.01921-21] [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] [Indexed: 01/31/2023] Open
Abstract
Viruses are the most abundant biological entities in the ocean and show great diversity in terms of size, host specificity, and infection cycle. Lytic viruses induce host cell lysis to release their progeny and thereby redirect nutrients from higher to lower trophic levels. Studies continue to show that marine viruses can be ingested by nonhost organisms. However, not much is known about the role of viral particles as a nutrient source and whether they possess a nutritional value to the grazing organisms. This review seeks to assess the elemental composition and biogeochemical relevance of marine viruses, including roseophages, which are a highly abundant group of bacteriophages in the marine environment. We place a particular emphasis on the phylum Nucleocytoviricota (NCV) (formerly known as nucleocytoplasmic large DNA viruses [NCLDVs]), which comprises some of the largest viral particles in the marine plankton that are well in the size range of prey for marine grazers. Many NCVs contain lipid membranes in their capsid that are rich carbon and energy sources, which further increases their nutritional value. Marine viruses may thus be an important nutritional component of the marine plankton, which can be reintegrated into the classical food web by nonhost organism grazing, a process that we coin the "viral sweep." Possibilities for future research to resolve this process are highlighted and discussed in light of current technological advancements.
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6
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Zheng M, Lin Y, Wang W, Zhao Y, Bao X. Application of nucleoside or nucleotide analogues in RNA dynamics and RNA-binding protein analysis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1722. [PMID: 35218164 DOI: 10.1002/wrna.1722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/07/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Cellular RNAs undergo dynamic changes during RNA biological processes, which are tightly orchestrated by RNA-binding proteins (RBPs). Yet, the investigation of RNA dynamics is hurdled by highly abundant steady-state RNAs, which make the signals of dynamic RNAs less detectable. Notably, the exert of nucleoside or nucleotide analogue-based RNA technologies has provided a remarkable platform for RNA dynamics research, revealing diverse unnoticed features in RNA metabolism. In this review, we focus on the application of two types of analogue-based RNA sequencing, antigen-/antibody- and click chemistry-based methodologies, and summarize the RNA dynamics features revealed. Moreover, we discuss emerging single-cell newly transcribed RNA sequencing methodologies based on nucleoside analogue labeling, which provides novel insights into RNA dynamics regulation at single-cell resolution. On the other hand, we also emphasize the identification of RBPs that interact with polyA, non-polyA RNAs, or newly transcribed RNAs and also their associated RNA-binding domains at genomewide level through ultraviolet crosslinking and mass spectrometry in different contexts. We anticipated that further modification and development of these analogue-based RNA and RBP capture technologies will aid in obtaining an unprecedented understanding of RNA biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Meifeng Zheng
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingying Lin
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- The Center for Infection and Immunity Study, School of Medicine, Sun Yat-sen University, Guangming Science City, Shenzhen, China
| | - Wei Wang
- Center for Biosafety, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xichen Bao
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
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7
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Zhang F, Wang Z, Vijver MG, Peijnenburg WJGM. Theoretical investigation on the interactions of microplastics with a SARS-CoV-2 RNA fragment and their potential impacts on viral transport and exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156812. [PMID: 35738381 PMCID: PMC9212631 DOI: 10.1016/j.scitotenv.2022.156812] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/08/2022] [Accepted: 06/15/2022] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease-19 (COVID-19) pandemic spread across the world and remains difficult to control. Environmental pollution and habitat conditions do facilitate SARS-CoV-2 transmission as well as increase the risk of exposure to SARS-CoV-2. The coexistence of microplastics (MPs) with SARS-CoV-2 affects the viral behavior in the indoor and outdoor environment, and it is essential to study the interactions between MPs and SARS-CoV-2 because they both are ubiquitously present in our environment. To determine the mechanisms underlying the impact of MPs on SARS-CoV-2, we used molecular dynamic simulations to investigate the molecular interactions between five MPs and a SARS-CoV-2 RNA fragment at temperatures ranging from 223 to 310 K in vacuum and in water. We furthermore compared the interactions of MPs and SARS-CoV-2 RNA fragment to the performance of SARS-CoV-1 and Hepatitis B virus (HBV) RNA fragments in interacting with the MPs. The interaction affinity between the MPs and the SARS-CoV-2 RNA fragment was found to be greater than the affinity between the MPs and the SARS-CoV-1 or HBV RNA fragments, independent of the environmental media, temperature, and type of MPs. The mechanisms of the interaction between the MPs and the SARS-CoV-2 RNA fragment involved electrostatic and hydrophobic processes, and the interaction affinity was associated with the inherent structural parameters (i.e., molecular volume, polar surface area, and molecular topological index) of the MPs monomers. Although the evidence on the infectious potential of SARS-CoV-2 RNA is not fully understood, humans are exposed to MPs via their lungs, and the strong interaction with the gene materials of SARS-CoV-2 likely affects the exposure of humans to SARS-CoV-2.
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Affiliation(s)
- Fan Zhang
- Institute of Environmental Sciences (CML), Leiden University, Leiden 2300 RA, the Netherlands
| | - Zhuang Wang
- School of Environmental Science and Engineering, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Nanjing University of Information Science and Technology, Nanjing 210044, PR China
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, Leiden 2300 RA, the Netherlands
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, Leiden 2300 RA, the Netherlands; Centre for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), Bilthoven 3720 BA, the Netherlands.
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8
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González-Gamboa I, Caparco AA, McCaskill JM, Steinmetz NF. Bioconjugation Strategies for Tobacco Mild Green Mosaic Virus. Chembiochem 2022; 23:e202200323. [PMID: 35835718 PMCID: PMC9624232 DOI: 10.1002/cbic.202200323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/03/2022] [Indexed: 11/06/2022]
Abstract
Tobacco mild green mosaic virus (TMGMV) is a plant virus closely related to Tobacco mosaic virus (TMV), sharing many of its structural and chemical features. These rod-shaped viruses, comprised of 2130 identical coat protein subunits, have been utilized as nanotechnological platforms for a myriad of applications, ranging from drug delivery to precision agriculture. This versatility for functionalization is due to their chemically active external and internal surfaces. While both viruses are similar, they do exhibit some key differences in their surface chemistry, suggesting the reactive residue distribution on TMGMV should not overlap with TMV. In this work, we focused on the establishment and refinement of chemical bioconjugation strategies to load molecules into or onto TMGMV for targeted delivery. A combination of NHS, EDC, and diazo coupling reactions in combination with click chemistry were used to modify the N-terminus, glutamic/aspartic acid residues, and tyrosines in TMGMV. We report loading with over 600 moieties per TMGMV via diazo-coupling, which is a >3-fold increase compared to previous studies. We also report that cargo can be loaded to the solvent-exposed N-terminus and carboxylates on the exterior/interior surfaces. Mass spectrometry revealed the most reactive sites to be Y12 and Y72, both tyrosine side chains are located on the exterior surface. For the carboxylates, interior E106 (66.53 %) was the most reactive for EDC-propargylamine coupled reactions, with the exterior E145 accounting for >15 % reactivity, overturning previous assumptions that only interior glutamic acid residues are accessible. A deeper understanding of the chemical properties of TMGMV further enables its functionalization and use as a multifunctional nanocarrier platform for applications in medicine and precision farming.
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Affiliation(s)
- Ivonne González-Gamboa
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Adam A Caparco
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Justin M McCaskill
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Institute for Materials Discovery and Design, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Moores Cancer Center, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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9
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Kasza P, Pociecha K, Wójcik-Pszczoła K, Canale V, Wyska E, Zajdel P, Szafrański PW, Cegła M. Ligand assisted CuAAC labelling and RP-HPLC analysis of zidovudine and Retrovir using propargyl-Fmoc probe. Eur J Pharm Sci 2022; 178:106293. [PMID: 36116697 DOI: 10.1016/j.ejps.2022.106293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/24/2022] [Accepted: 09/14/2022] [Indexed: 11/30/2022]
Abstract
The extensive application of zidovudine (ZDV) as a stand-alone anti-HIV drug and a component in antiviral combination therapies, has made its analysis important both in the pharmaceutical and environmental context. The azide group in ZDV structure makes it a ready-to-use substrate for copper-catalyzed azide-alkyne cycloaddition (CuAAC), which is an efficient method for "click chemistry" labeling. In this paper, we describe a ligand-assisted CuAAC procedure for the precolumn derivatization of ZDV. We used propargyl-Fmoc fluorescent label and trans-2-(4-((dimethylamino)methyl)-1H-1,2,3-triazol-1-yl)cyclohexan-1-ol (AMTC) as a copper-binding ligand. We tested the applicability of AMTC for precolumn derivatization and developed chromatographic analytical procedures for ZDV and its formulation (50 mg/5 ml oral solution, Retrovir™ syrup). Our research aimed to improve labeling efficiency with a Cu-chelating ligand, using an accessible and affordable fluorescent probe. We also developed a sustainable mechanochemical synthesis procedure for obtaining propargyl-Fmoc in a gram scale and thus boosted the accessibility of this probe. The advantages of the developed derivatization procedure are its simplicity and easy availability of the propargyl-Fmoc probe. Moreover, the high lipophilicity of the propargyl-Fmoc probe enables efficient separation of the analyte from polar matrix components. In addition, the derivatization procedure can be performed directly on a sample solution. We tested its usability for samples in environmental and biological matrices, including tap water, river water, urine, and human serum.
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Affiliation(s)
- Patryk Kasza
- Department of Organic Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Krakow 30-688, Poland
| | - Krzysztof Pociecha
- Department of Pharmacokinetics and Physical Pharmacy, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Krakow 30-688, Poland
| | - Katarzyna Wójcik-Pszczoła
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Vittorio Canale
- Department of Organic Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Krakow 30-688, Poland
| | - Elżbieta Wyska
- Department of Pharmacokinetics and Physical Pharmacy, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Krakow 30-688, Poland
| | - Paweł Zajdel
- Department of Organic Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Krakow 30-688, Poland
| | - Przemysław W Szafrański
- Department of Organic Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Krakow 30-688, Poland.
| | - Marek Cegła
- Department of Organic Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Krakow 30-688, Poland
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10
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Direct Capsid Labeling of Infectious HIV-1 by Genetic Code Expansion Allows Detection of Largely Complete Nuclear Capsids and Suggests Nuclear Entry of HIV-1 Complexes via Common Routes. mBio 2022; 13:e0195922. [PMID: 35972146 PMCID: PMC9600849 DOI: 10.1128/mbio.01959-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The cone-shaped mature HIV-1 capsid is the main orchestrator of early viral replication. After cytosolic entry, it transports the viral replication complex along microtubules toward the nucleus. While it was initially believed that the reverse transcribed genome is released from the capsid in the cytosol, recent observations indicate that a high amount of capsid protein (CA) remains associated with subviral complexes during import through the nuclear pore complex (NPC). Observation of postentry events via microscopic detection of HIV-1 CA is challenging, since epitope shielding limits immunodetection and the genetic fragility of CA hampers direct labeling approaches. Here, we present a minimally invasive strategy based on genetic code expansion and click chemistry that allows for site-directed fluorescent labeling of HIV-1 CA, while retaining virus morphology and infectivity. Thereby, we could directly visualize virions and subviral complexes using advanced microscopy, including nanoscopy and correlative imaging. Quantification of signal intensities of subviral complexes revealed an amount of CA associated with nuclear complexes in HeLa-derived cells and primary T cells consistent with a complete capsid and showed that treatment with the small molecule inhibitor PF74 did not result in capsid dissociation from nuclear complexes. Cone-shaped objects detected in the nucleus by electron tomography were clearly identified as capsid-derived structures by correlative microscopy. High-resolution imaging revealed dose-dependent clustering of nuclear capsids, suggesting that incoming particles may follow common entry routes.
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11
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Müller TG, Zila V, Müller B, Kräusslich HG. Nuclear Capsid Uncoating and Reverse Transcription of HIV-1. Annu Rev Virol 2022; 9:261-284. [PMID: 35704745 DOI: 10.1146/annurev-virology-020922-110929] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
After cell entry, human immunodeficiency virus type 1 (HIV-1) replication involves reverse transcription of the RNA genome, nuclear import of the subviral complex without nuclear envelope breakdown, and integration of the viral complementary DNA into the host genome. Here, we discuss recent evidence indicating that completion of reverse transcription and viral genome uncoating occur in the nucleus rather than in the cytoplasm, as previously thought, and suggest a testable model for nuclear import and uncoating. Multiple recent studies indicated that the cone-shaped capsid, which encases the genome and replication proteins, not only serves as a reaction container for reverse transcription and as a shield from innate immune sensors but also may constitute the elusive HIV-1 nuclear import factor. Rupture of the capsid may be triggered in the nucleus by completion of reverse transcription, by yet-unknown nuclear factors, or by physical damage, and it appears to occur in close temporal and spatial association with the integration process. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany;
| | - Vojtech Zila
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany;
| | - Barbara Müller
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany;
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany; .,German Center for Infection Research, Heidelberg, Germany
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12
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Liu D, Shu X, Xiang S, Li T, Huang C, Cheng M, Cao J, Hua Y, Liu J. N4 -allyldeoxycytidine: A New DNA Tag with Chemical Sequencing Power for Pinpointing Labelling Sites, Mapping Epigenetic Mark, and in situ Imaging. Chembiochem 2022; 23:e202200143. [PMID: 35438823 DOI: 10.1002/cbic.202200143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Indexed: 11/08/2022]
Abstract
DNA tagging with base analogs has found numerous applications. To precisely record the DNA labelling information, it will be highly beneficial to develop chemical sequencing tags that can be encoded into DNA as regular bases and decoded as mutant bases upon a mild, efficient and bioorthognal chemical treatment. Here we reported such a DNA tag, N4-allyldeoxycytidine (a4dC), to label and identify DNA by in vitro assays. The iodination of a4dC led to fast and complete formation of 3, N4-cyclized deoxycytidine, which induced base misincorporation during DNA replication and thus could be located at single base resolution. We explored the applications of a4dC in pinpointing DNA labelling sites at single base resolution, mapping epigenetic mark N4-methyldeoxycytidine, and imaging nucleic acids in situ. In addition, mammalian cellular DNA could be metabolically labelled with a4dC. Together,our study sheds light on the design of next generation DNA tags with chemical sequencing power.
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Affiliation(s)
- Donghong Liu
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Xiao Shu
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Siying Xiang
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Tengwei Li
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Chenyang Huang
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Mohan Cheng
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Jie Cao
- Zhejiang University, Life Sciences Institute; Department of Polymer Science and Engineering, CHINA
| | - Yuejin Hua
- Zhejiang University, he MOE Key Laboratory of Biosystems Homeostasis & Protection; Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, CHINA
| | - Jianzhao Liu
- Zhejiang University, Department of Polymer Science and Engineering, Zheda road 38, 310007, hangzhou, CHINA
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13
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High accumulation of Mx2 renders limited multiplication of oncolytic herpes simplex virus-1 in human tumor cells. Sci Rep 2021; 11:21227. [PMID: 34707174 PMCID: PMC8551283 DOI: 10.1038/s41598-021-00691-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/14/2021] [Indexed: 11/08/2022] Open
Abstract
Increasing studies demonstrated that oncolytic activities of oHSV-1 are limited to the capacity of virus replicating in tumors. In order to potentiate the oHSV-1 oncolytic activity and expand the application of oHSV-1 treatment in multiple types of tumors, it is critical to explore the potential factors or mechanisms mediating tumor resistance to oHSV-1 infection. Here we evaluated the levels of oHSV-1 multiplication in various tumor cell lines and showed that glioblastoma cell line A172 had the lowest virus yields but intrinsically accumulated the highest levels of Mx2 protein. Subsequently we demonstrated that genetic depletion of Mx2 specifically enhanced oHSV-1 productive replication in A172 cells through promoting the nuclear translocation of uncoated viral genomic DNA and down-regulating innate antiviral response. In the further investigation, we found that Mx2 knockdown could alter the intrinsic mRNA accumulation of diverse sets innate immune genes in A172 cells, in particular DHX36 and MyD88. Mx2 depletion led to a decrease in mRNA levels of MyD88 and DHX36 in A172 cells and MyD88/DHX36 knockdown increased virus yield in A172 cells and decreased the production of IFNα, activation of IRF3 activity and NF-κB signaling in A172 cells. This shed new lights on understanding the roles of some intrinsic antiviral genes in oHSV-1 resistance, facilitating to offer potential targets to improve oHSV-1 oncolytic efficacy and develop candidates of biomarkers to predict the efficiency of oHSV-1 multiplication in tumors.
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14
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Turzynski V, Monsees I, Moraru C, Probst AJ. Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples. Viruses 2021; 13:2126. [PMID: 34834933 PMCID: PMC8622608 DOI: 10.3390/v13112126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.
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Affiliation(s)
- Victoria Turzynski
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Indra Monsees
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany;
| | - Alexander J. Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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15
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Avota E, Bodem J, Chithelen J, Mandasari P, Beyersdorf N, Schneider-Schaulies J. The Manifold Roles of Sphingolipids in Viral Infections. Front Physiol 2021; 12:715527. [PMID: 34658908 PMCID: PMC8511394 DOI: 10.3389/fphys.2021.715527] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
Sphingolipids are essential components of eukaryotic cells. In this review, we want to exemplarily illustrate what is known about the interactions of sphingolipids with various viruses at different steps of their replication cycles. This includes structural interactions during entry at the plasma membrane or endosomal membranes, early interactions leading to sphingolipid-mediated signal transduction, interactions with internal membranes and lipids during replication, and interactions during virus assembly and budding. Targeted interventions in sphingolipid metabolism - as far as they can be tolerated by cells and organisms - may open novel possibilities to support antiviral therapies. Human immunodeficiency virus type 1 (HIV-1) infections have intensively been studied, but for other viral infections, such as influenza A virus (IAV), measles virus (MV), hepatitis C virus (HCV), dengue virus, Ebola virus, and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), investigations are still in their beginnings. As many inhibitors of sphingolipid metabolism are already in clinical use against other diseases, repurposing studies for applications in some viral infections appear to be a promising approach.
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Affiliation(s)
- Elita Avota
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Jochen Bodem
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Janice Chithelen
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Putri Mandasari
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Niklas Beyersdorf
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
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16
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Takahashi JA, Barbosa BVR, Lima MTNS, Cardoso PG, Contigli C, Pimenta LPS. Antiviral fungal metabolites and some insights into their contribution to the current COVID-19 pandemic. Bioorg Med Chem 2021; 46:116366. [PMID: 34438338 PMCID: PMC8363177 DOI: 10.1016/j.bmc.2021.116366] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/23/2021] [Accepted: 08/03/2021] [Indexed: 12/11/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak, which started in late 2019, drove the scientific community to conduct innovative research to contain the spread of the pandemic and to care for those already affected. Since then, the search for new drugs that are effective against the virus has been strengthened. Featuring a relatively low cost of production under well-defined methods of cultivation, fungi have been providing a diversity of antiviral metabolites with unprecedented chemical structures. In this review, we present viral RNA infections highlighting SARS-CoV-2 morphogenesis and the infectious cycle, the targets of known antiviral drugs, and current developments in this area such as drug repurposing. We also explored the metabolic adaptability of fungi during fermentation to produce metabolites active against RNA viruses, along with their chemical structures, and mechanisms of action. Finally, the state of the art of research on SARS-CoV-2 inhibitors of fungal origin is reported, highlighting the metabolites selected by docking studies.
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Affiliation(s)
- Jacqueline Aparecida Takahashi
- Department of Chemistry, Exact Sciences Institute, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, CEP 31270-901 Belo Horizonte, MG, Brazil.
| | - Bianca Vianna Rodrigues Barbosa
- Department of Chemistry, Exact Sciences Institute, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, CEP 31270-901 Belo Horizonte, MG, Brazil
| | - Matheus Thomaz Nogueira Silva Lima
- Department of Food Science, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, CEP 31270-901 Belo Horizonte, MG, Brazil.
| | - Patrícia Gomes Cardoso
- Department of Biology, Universidade Federal de Lavras, Av. Dr. Sylvio Menicucci, 1001, CEP 37200-900 Lavras, MG, Brazil.
| | - Christiane Contigli
- Cell Biology Service, Research and Development Department, Fundação Ezequiel Dias, R. Conde Pereira Carneiro, 80, CEP 30510-010 Belo Horizonte, MG, Brazil
| | - Lúcia Pinheiro Santos Pimenta
- Department of Chemistry, Exact Sciences Institute, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, CEP 31270-901 Belo Horizonte, MG, Brazil
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17
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Schneider-Schaulies S, Schumacher F, Wigger D, Schöl M, Waghmare T, Schlegel J, Seibel J, Kleuser B. Sphingolipids: Effectors and Achilles Heals in Viral Infections? Cells 2021; 10:cells10092175. [PMID: 34571822 PMCID: PMC8466362 DOI: 10.3390/cells10092175] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022] Open
Abstract
As viruses are obligatory intracellular parasites, any step during their life cycle strictly depends on successful interaction with their particular host cells. In particular, their interaction with cellular membranes is of crucial importance for most steps in the viral replication cycle. Such interactions are initiated by uptake of viral particles and subsequent trafficking to intracellular compartments to access their replication compartments which provide a spatially confined environment concentrating viral and cellular components, and subsequently, employ cellular membranes for assembly and exit of viral progeny. The ability of viruses to actively modulate lipid composition such as sphingolipids (SLs) is essential for successful completion of the viral life cycle. In addition to their structural and biophysical properties of cellular membranes, some sphingolipid (SL) species are bioactive and as such, take part in cellular signaling processes involved in regulating viral replication. It is especially due to the progress made in tools to study accumulation and dynamics of SLs, which visualize their compartmentalization and identify interaction partners at a cellular level, as well as the availability of genetic knockout systems, that the role of particular SL species in the viral replication process can be analyzed and, most importantly, be explored as targets for therapeutic intervention.
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Affiliation(s)
- Sibylle Schneider-Schaulies
- Institute for Virology and Immunobiology, University of Wuerzburg, 97078 Würzburg, Germany; (S.S.-S.); (M.S.); (T.W.)
| | - Fabian Schumacher
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany; (F.S.); (D.W.)
| | - Dominik Wigger
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany; (F.S.); (D.W.)
| | - Marie Schöl
- Institute for Virology and Immunobiology, University of Wuerzburg, 97078 Würzburg, Germany; (S.S.-S.); (M.S.); (T.W.)
| | - Trushnal Waghmare
- Institute for Virology and Immunobiology, University of Wuerzburg, 97078 Würzburg, Germany; (S.S.-S.); (M.S.); (T.W.)
| | - Jan Schlegel
- Department for Biotechnology and Biophysics, University of Wuerzburg, 97074 Würzburg, Germany;
| | - Jürgen Seibel
- Department for Organic Chemistry, University of Wuerzburg, 97074 Würzburg, Germany;
| | - Burkhard Kleuser
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany; (F.S.); (D.W.)
- Correspondence: ; Tel.: +49-30-8386-9823
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18
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Agrahari AK, Bose P, Jaiswal MK, Rajkhowa S, Singh AS, Hotha S, Mishra N, Tiwari VK. Cu(I)-Catalyzed Click Chemistry in Glycoscience and Their Diverse Applications. Chem Rev 2021; 121:7638-7956. [PMID: 34165284 DOI: 10.1021/acs.chemrev.0c00920] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Copper(I)-catalyzed 1,3-dipolar cycloaddition between organic azides and terminal alkynes, commonly known as CuAAC or click chemistry, has been identified as one of the most successful, versatile, reliable, and modular strategies for the rapid and regioselective construction of 1,4-disubstituted 1,2,3-triazoles as diversely functionalized molecules. Carbohydrates, an integral part of living cells, have several fascinating features, including their structural diversity, biocompatibility, bioavailability, hydrophilicity, and superior ADME properties with minimal toxicity, which support increased demand to explore them as versatile scaffolds for easy access to diverse glycohybrids and well-defined glycoconjugates for complete chemical, biochemical, and pharmacological investigations. This review highlights the successful development of CuAAC or click chemistry in emerging areas of glycoscience, including the synthesis of triazole appended carbohydrate-containing molecular architectures (mainly glycohybrids, glycoconjugates, glycopolymers, glycopeptides, glycoproteins, glycolipids, glycoclusters, and glycodendrimers through regioselective triazole forming modular and bio-orthogonal coupling protocols). It discusses the widespread applications of these glycoproducts as enzyme inhibitors in drug discovery and development, sensing, gelation, chelation, glycosylation, and catalysis. This review also covers the impact of click chemistry and provides future perspectives on its role in various emerging disciplines of science and technology.
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Affiliation(s)
- Anand K Agrahari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Priyanka Bose
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Manoj K Jaiswal
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Sanchayita Rajkhowa
- Department of Chemistry, Jorhat Institute of Science and Technology (JIST), Jorhat, Assam 785010, India
| | - Anoop S Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Srinivas Hotha
- Department of Chemistry, Indian Institute of Science and Engineering Research (IISER), Pune, Maharashtra 411021, India
| | - Nidhi Mishra
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Vinod K Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
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19
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Sommers P, Chatterjee A, Varsani A, Trubl G. Integrating Viral Metagenomics into an Ecological Framework. Annu Rev Virol 2021; 8:133-158. [PMID: 34033501 DOI: 10.1146/annurev-virology-010421-053015] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viral metagenomics has expanded our knowledge of the ecology of uncultured viruses, within both environmental (e.g., terrestrial and aquatic) and host-associated (e.g., plants and animals, including humans) contexts. Here, we emphasize the implementation of an ecological framework in viral metagenomic studies to address questions in virology rarely considered ecological, which can change our perception of viruses and how they interact with their surroundings. An ecological framework explicitly considers diverse variants of viruses in populations that make up communities of interacting viruses, with ecosystem-level effects. It provides a structure for the study of the diversity, distributions, dynamics, and interactions of viruses with one another, hosts, and the ecosystem, including interactions with abiotic factors. An ecological framework in viral metagenomics stands poised to broadly expand our knowledge in basic and applied virology. We highlight specific fundamental research needs to capitalize on its potential and advance the field. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA.,These authors contributed equally to this article
| | - Anushila Chatterjee
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA.,These authors contributed equally to this article
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA; .,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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20
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Müller TG, Zila V, Peters K, Schifferdecker S, Stanic M, Lucic B, Laketa V, Lusic M, Müller B, Kräusslich HG. HIV-1 uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells. eLife 2021; 10:64776. [PMID: 33904396 PMCID: PMC8169111 DOI: 10.7554/elife.64776] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
HIV-1 replication commences inside the cone-shaped viral capsid, but timing, localization, and mechanism of uncoating are under debate. We adapted a strategy to visualize individual reverse-transcribed HIV-1 cDNA molecules and their association with viral and cellular proteins using fluorescence and correlative-light-and-electron-microscopy (CLEM). We specifically detected HIV-1 cDNA inside nuclei, but not in the cytoplasm. Nuclear cDNA initially co-localized with a fluorescent integrase fusion (IN-FP) and the viral CA (capsid) protein, but cDNA-punctae separated from IN-FP/CA over time. This phenotype was conserved in primary HIV-1 target cells, with nuclear HIV-1 complexes exhibiting strong CA-signals in all cell types. CLEM revealed cone-shaped HIV-1 capsid-like structures and apparently broken capsid-remnants at the position of IN-FP signals and elongated chromatin-like structures in the position of viral cDNA punctae lacking IN-FP. Our data argue for nuclear uncoating by physical disruption rather than cooperative disassembly of the CA-lattice, followed by physical separation from the pre-integration complex.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vojtech Zila
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Kyra Peters
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sandra Schifferdecker
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mia Stanic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Bojana Lucic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
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21
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Nkanga CI, Steinmetz NF. The pharmacology of plant virus nanoparticles. Virology 2021; 556:39-61. [PMID: 33545555 PMCID: PMC7974633 DOI: 10.1016/j.virol.2021.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/14/2022]
Abstract
The application of nanoparticles for medical purposes has made enormous strides in providing new solutions to health problems. The observation that plant virus-based nanoparticles (VNPs) can be repurposed and engineered as smart bio-vehicles for targeted drug delivery and imaging has launched extensive research for improving the therapeutic and diagnostic management of various diseases. There is evidence that VNPs are promising high value nanocarriers with potential for translational development. This is mainly due to their unique features, encompassing structural uniformity, ease of manufacture and functionalization by means of expression, chemical biology and self-assembly. While the development pipeline is moving rapidly, with many reports focusing on engineering and manufacturing aspects to tailor the properties and efficacy of VNPs, fewer studies have focused on gaining insights into the nanotoxicity of this novel platform nanotechnology. Herein, we discuss the pharmacology of VNPs as a function of formulation and route of administration. VNPs are reviewed in the context of their application as therapeutic adjuvants or nanocarrier excipients to initiate, enhance, attenuate or impede the formulation's toxicity. The summary of the data however also underlines the need for meticulous VNP structure-nanotoxicity studies to improve our understanding of their in vivo fates and pharmacological profiles to pave the way for translation of VNP-based formulations into the clinical setting.
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Affiliation(s)
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California-San Diego, La Jolla, CA, 92039, United States; Department of Bioengineering, Department of Radiology, Center for NanoImmunoEngineering, Moores Cancer Center, Institute for Materials Discovery and Design, University of California-San Diego, La Jolla, CA, 92039, United States.
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22
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Avota E, Bodem J, Chithelen J, Mandasari P, Beyersdorf N, Schneider-Schaulies J. The Manifold Roles of Sphingolipids in Viral Infections. Front Physiol 2021. [PMID: 34658908 DOI: 10.3389/fphys.2021.71552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Sphingolipids are essential components of eukaryotic cells. In this review, we want to exemplarily illustrate what is known about the interactions of sphingolipids with various viruses at different steps of their replication cycles. This includes structural interactions during entry at the plasma membrane or endosomal membranes, early interactions leading to sphingolipid-mediated signal transduction, interactions with internal membranes and lipids during replication, and interactions during virus assembly and budding. Targeted interventions in sphingolipid metabolism - as far as they can be tolerated by cells and organisms - may open novel possibilities to support antiviral therapies. Human immunodeficiency virus type 1 (HIV-1) infections have intensively been studied, but for other viral infections, such as influenza A virus (IAV), measles virus (MV), hepatitis C virus (HCV), dengue virus, Ebola virus, and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), investigations are still in their beginnings. As many inhibitors of sphingolipid metabolism are already in clinical use against other diseases, repurposing studies for applications in some viral infections appear to be a promising approach.
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Affiliation(s)
- Elita Avota
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Jochen Bodem
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Janice Chithelen
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Putri Mandasari
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Niklas Beyersdorf
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
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23
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Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
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Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
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24
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Abstract
Mass spectrometry imaging (MSI) is a label-free molecular imaging technique allowing an untargeted detection of a broad range of biomolecules and xenobiotics. MSI enables imaging of the spatial distribution of proteins, peptides, lipids and metabolites from a wide range of samples. To date, this technique is commonly applied to tissue sections in cancer diagnostics and biomarker development, but also molecular histology in general. Advances in the methodology and bioinformatics improved the resolution of MS images below the single cell level and increased the flexibility of the workflow. However, MSI-based research in virology is just starting to gain momentum and its full potential has not been exploited yet. In this review, we discuss the main applications of MSI in virology. We review important aspects of matrix-assisted laser desorption/ionization (MALDI) MSI, the most widely used MSI technique in virology. In addition, we summarize relevant literature on MSI studies that aim to unravel virus-host interactions and virus pathogenesis, to elucidate antiviral drug kinetics and to improve current viral disease diagnostics. Collectively, these studies strongly improve our general understanding of virus-induced changes in the proteome, metabolome and metabolite distribution in host tissues of humans, animals and plants upon infection. Furthermore, latest MSI research provided important insights into the drug distribution and distribution kinetics, especially in antiretroviral research. Finally, MSI-based investigations of oncogenic viruses greatly increased our knowledge on tumor mass signatures and facilitated the identification of cancer biomarkers.
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Affiliation(s)
- Luca D Bertzbach
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | | | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
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25
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Liu CG, Wang Y, Liu P, Yao QL, Zhou YY, Li CF, Zhao Q, Liu GH, Zhang XL. Aptamer-T Cell Targeted Therapy for Tumor Treatment Using Sugar Metabolism and Click Chemistry. ACS Chem Biol 2020; 15:1554-1565. [PMID: 32401486 DOI: 10.1021/acschembio.0c00164] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The development of a tumor-targeted immunotherapy is highly required. The most advanced application is the use of CD19 chimeric antigen receptor (CAR)T (CAR-T) cells to B cell malignancies, but there are still side effects including potential carcinogenicity of lentiviral or retroviral insertion into the host cell genome. Here, we developed a nonviral aptamer-T cell targeted strategy for tumor therapy. Tumor cells surface-specific ssDNA aptamers were conjugated to CD3+T cells (aptamer-T cells) using N-azidomannosamine (ManNAz) sugar metabolic cell labeling and click chemistry. We found that the aptamer-T cells could specifically target and bind to tumor cells (such as SGC-7901 gastric cancer cell and CT26 colon carcinoma cell) in vitro and in mice after adoptively transfer in. Aptamer-T cells led to significant regression in tumor volume due to being enriched at tumor microenvironment and producing strong cytotoxicity activities of CD3+T cells with enhanced perforin, granzyme B, CD107a, CD69, and FasL expression. Moreover, aptamer-T displayed even stronger antitumor effects than an anti-PD1 immune-checkpoint monoclonal antibody (mAb) treatment in mice and combination with anti-PD1 yielded synergic antitumor effects. This study uncovers the strong potential of the adoptive nonviral aptamer-T cell strategy as a feasible and efficacious approach for tumor-targeted immunotherapy application.
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Affiliation(s)
- Chuan-Gang Liu
- State Key Laboratory of Virology, Department of Immunology Wuhan University School of Basic Medical Sciences, Medical Research Institute, Wuhan University School of Medicine, Wuhan 430071, China
| | - Yong Wang
- State Key Laboratory of Virology, Department of Immunology Wuhan University School of Basic Medical Sciences, Medical Research Institute, Wuhan University School of Medicine, Wuhan 430071, China
| | - Peng Liu
- State Key Laboratory of Virology, Department of Immunology Wuhan University School of Basic Medical Sciences, Medical Research Institute, Wuhan University School of Medicine, Wuhan 430071, China
| | - Qi-Li Yao
- State Key Laboratory of Virology, Department of Immunology Wuhan University School of Basic Medical Sciences, Medical Research Institute, Wuhan University School of Medicine, Wuhan 430071, China
| | - Yuan-Yuan Zhou
- State Key Laboratory of Virology, Department of Immunology Wuhan University School of Basic Medical Sciences, Medical Research Institute, Wuhan University School of Medicine, Wuhan 430071, China
| | - Chao-Fan Li
- State Key Laboratory of Virology, Department of Immunology Wuhan University School of Basic Medical Sciences, Medical Research Institute, Wuhan University School of Medicine, Wuhan 430071, China
| | - Qiu Zhao
- Department of Gastroenterology and Clinical Research Center for Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan 430071, China
| | - Guang-Hui Liu
- Hubei Province Key Laboratory of Allergy and Immune-related Diseases, Allergy Department of Zhongnan Hospital Wuhan University, Wuhan 430071, China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology, Department of Immunology Wuhan University School of Basic Medical Sciences, Medical Research Institute, Wuhan University School of Medicine, Wuhan 430071, China
- Hubei Province Key Laboratory of Allergy and Immune-related Diseases, Allergy Department of Zhongnan Hospital Wuhan University, Wuhan 430071, China
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Cardoen B, Yedder HB, Sharma A, Chou KC, Nabi IR, Hamarneh G. ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:1942-1956. [PMID: 31880546 DOI: 10.1109/tmi.2019.2962361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single molecule localization microscopy (SMLM) allows unprecedented insight into the three-dimensional organization of proteins at the nanometer scale. The combination of minimal invasive cell imaging with high resolution positions SMLM at the forefront of scientific discovery in cancer, infectious, and degenerative diseases. By stochastic temporal and spatial separation of light emissions from fluorescent labelled proteins, SMLM is capable of nanometer scale reconstruction of cellular structures. Precise localization of proteins in 3D astigmatic SMLM is dependent on parameter sensitive preprocessing steps to select regions of interest. With SMLM acquisition highly variable over time, it is non-trivial to find an optimal static parameter configuration. The high emitter density required for reconstruction of complex protein structures can compromise accuracy and introduce artifacts. To address these problems, we introduce two modular auto-tuning pre-processing methods: adaptive signal detection and learned recurrent signal density estimation that can leverage the information stored in the sequence of frames that compose the SMLM acquisition process. We show empirically that our contributions improve accuracy, precision and recall with respect to the state of the art. Both modules auto-tune their hyper-parameters to reduce the parameter space for practitioners, improve robustness and reproducibility, and are validated on a reference in silico dataset. Adaptive signal detection and density prediction can offer a practitioner, in addition to informed localization, a tool to tune acquisition parameters ensuring improved reconstruction of the underlying protein complex. We illustrate the challenges faced by practitioners in applying SMLM algorithms on real world data markedly different from the data used in development and show how ERGO can be run on new datasets without retraining while motivating the need for robust transfer learning in SMLM.
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Koehler M, Delguste M, Sieben C, Gillet L, Alsteens D. Initial Step of Virus Entry: Virion Binding to Cell-Surface Glycans. Annu Rev Virol 2020; 7:143-165. [PMID: 32396772 DOI: 10.1146/annurev-virology-122019-070025] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virus infection is an intricate process that requires the concerted action of both viral and host cell components. Entry of viruses into cells is initiated by interactions between viral proteins and cell-surface receptors. Various cell-surface glycans function as initial, usually low-affinity attachment factors, providing a first anchor of the virus to the cell surface, and further facilitate high-affinity binding to virus-specific cell-surface receptors, while other glycans function as specific entry receptors themselves. It is now possible to rapidly identify specific glycan receptors using different techniques, define atomic-level structures of virus-glycan complexes, and study these interactions at the single-virion level. This review provides a detailed overview of the role of glycans in viral infection and highlights experimental approaches to study virus-glycan binding along with specific examples. In particular, we highlight the development of the atomic force microscope to investigate interactions with glycans at the single-virion level directly on living mammalian cells, which offers new perspectives to better understand virus-glycan interactions in physiologically relevant conditions.
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Affiliation(s)
- Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium;
| | - Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium;
| | - Christian Sieben
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Laurent Gillet
- Immunology-Vaccinology Laboratory, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals and Health center (FARAH), University of Liège, 4000 Liège, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium; .,Walloon Excellence in Life sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
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Pied N, Wodrich H. Imaging the adenovirus infection cycle. FEBS Lett 2019; 593:3419-3448. [PMID: 31758703 DOI: 10.1002/1873-3468.13690] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022]
Abstract
Incoming adenoviruses seize control of cytosolic transport mechanisms to relocate their genome from the cell periphery to specialized sites in the nucleoplasm. The nucleus is the site for viral gene expression, genome replication, and the production of progeny for the next round of infection. By taking control of the cell, adenoviruses also suppress cell-autonomous immunity responses. To succeed in their production cycle, adenoviruses rely on well-coordinated steps, facilitated by interactions between viral proteins and cellular factors. Interactions between virus and host can impose remarkable morphological changes in the infected cell. Imaging adenoviruses has tremendously influenced how we delineate individual steps in the viral life cycle, because it allowed the development of specific optical markers to label these morphological changes in space and time. As technology advances, innovative imaging techniques and novel tools for specimen labeling keep uncovering previously unseen facets of adenovirus biology emphasizing why imaging adenoviruses is as attractive today as it was in the past. This review will summarize past achievements and present developments in adenovirus imaging centered on fluorescence microscopy approaches.
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Affiliation(s)
- Noémie Pied
- CNRS UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, France
| | - Harald Wodrich
- CNRS UMR 5234, Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, France
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Nussinov R, Tsai CJ, Shehu A, Jang H. Computational Structural Biology: Successes, Future Directions, and Challenges. Molecules 2019; 24:molecules24030637. [PMID: 30759724 PMCID: PMC6384756 DOI: 10.3390/molecules24030637] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/05/2019] [Accepted: 02/10/2019] [Indexed: 02/06/2023] Open
Abstract
Computational biology has made powerful advances. Among these, trends in human health have been uncovered through heterogeneous 'big data' integration, and disease-associated genes were identified and classified. Along a different front, the dynamic organization of chromatin is being elucidated to gain insight into the fundamental question of genome regulation. Powerful conformational sampling methods have also been developed to yield a detailed molecular view of cellular processes. when combining these methods with the advancements in the modeling of supramolecular assemblies, including those at the membrane, we are finally able to get a glimpse into how cells' actions are regulated. Perhaps most intriguingly, a major thrust is on to decipher the mystery of how the brain is coded. Here, we aim to provide a broad, yet concise, sketch of modern aspects of computational biology, with a special focus on computational structural biology. We attempt to forecast the areas that computational structural biology will embrace in the future and the challenges that it may face. We skirt details, highlight successes, note failures, and map directions.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Amarda Shehu
- Departments of Computer Science, Department of Bioengineering, and School of Systems Biology, George Mason University, Fairfax, VA 22030, USA.
| | - Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
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