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Boyer JC, Véry AA, Fristot E, Guyot V, Sentenac H, Peltier JB. Cell-free expressed uniporter and symporter systems from the plant HKT transporter family display channel-like gating and unitary conductances. THE NEW PHYTOLOGIST 2024. [PMID: 38992953 DOI: 10.1111/nph.19958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/24/2024] [Indexed: 07/13/2024]
Affiliation(s)
- Jean-Christophe Boyer
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, CEDEX 2, Montpellier, 34060, France
| | - Anne-Aliénor Véry
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, CEDEX 2, Montpellier, 34060, France
| | - Elsa Fristot
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, CEDEX 2, Montpellier, 34060, France
| | - Valentin Guyot
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, CEDEX 2, Montpellier, 34060, France
| | - Hervé Sentenac
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, CEDEX 2, Montpellier, 34060, France
| | - Jean-Benoît Peltier
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, CEDEX 2, Montpellier, 34060, France
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2
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Babot M, Boulard Y, Agouda S, Pieri L, Fieulaine S, Bressanelli S, Gervais V. Oligomeric assembly of the C-terminal and transmembrane region of SARS-CoV-2 nsp3. J Virol 2024; 98:e0157523. [PMID: 38483167 PMCID: PMC11019948 DOI: 10.1128/jvi.01575-23] [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] [Received: 10/16/2023] [Accepted: 02/22/2024] [Indexed: 04/17/2024] Open
Abstract
As for all single-stranded, positive-sense RNA (+RNA) viruses, intracellular RNA synthesis relies on extensive remodeling of host cell membranes that leads to the formation of specialized structures. In the case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus causing COVID-19, endoplasmic reticulum membranes are modified, resulting in the formation of double-membrane vesicles (DMVs), which contain the viral dsRNA intermediate and constitute membrane-bound replication organelles. The non-structural and transmembrane protein nsp3 is a key player in the biogenesis of DMVs and, therefore, represents an interesting antiviral target. However, as an integral transmembrane protein, it is challenging to express for structural biology. The C-terminus of nsp3 encompasses all the membrane-spanning, -interacting, and -remodeling elements. By using a cell-free expression system, we successfully produced the C-terminal region of nsp3 (nsp3C) and reconstituted purified nsp3C into phospholipid nanodiscs, opening the way for structural studies. Negative-stain transmission electron microscopy revealed the presence of nsp3C oligomers very similar to the region abutting and spanning the membrane on the cytosolic side of DMVs in a recent subtomogram average of the SARS-CoV-2 nsp3-4 pore (1). AlphaFold-predicted structural models fit particularly well with our experimental data and support a pore-forming hexameric assembly. Altogether, our data give unprecedented clues to understand the structural organization of nsp3, the principal component that shapes the molecular pore that spans the DMVs and is required for the export of RNA in vivo. IMPORTANCE Membrane remodeling is at the heart of intracellular replication for single-stranded, positive-sense RNA viruses. In the case of coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), this leads to the formation of a network of double-membrane vesicles (DMVs). Targeting DMV biogenesis offers promising prospects for antiviral therapies. This requires a better understanding of the molecular mechanisms and proteins involved. Three non-structural proteins (nsp3, nsp4, and nsp6) direct the intracellular membrane rearrangements upon SARS-CoV-2 infection. All of them contain transmembrane helices. The nsp3 component, the largest and multi-functional protein of the virus, plays an essential role in this process. Aiming to understand its structural organization, we used a cell-free protein synthesis assay to produce and reconstitute the C-terminal part of nsp3 (nsp3C) including transmembrane domains into phospholipid nanodiscs. Our work reveals the oligomeric organization of one key player in the biogenesis of SARS-CoV-2 DMVs, providing basis for the design of future antiviral strategies.
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Affiliation(s)
- Marion Babot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Samira Agouda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Laura Pieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sonia Fieulaine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Virginie Gervais
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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3
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Maharjan A, Park JH. Cell-free protein synthesis system: A new frontier for sustainable biotechnology-based products. Biotechnol Appl Biochem 2023; 70:2136-2149. [PMID: 37735977 DOI: 10.1002/bab.2514] [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: 05/31/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Cell-free protein synthesis (CFPS) system is an innovative technology with a wide range of potential applications that could challenge current thinking and provide solutions to environmental and health issues. CFPS system has been demonstrated to be a successful way of producing biomolecules in a variety of applications, including the biomedical industry. Although there are still obstacles to overcome, its ease of use, versatility, and capacity for integration with other technologies open the door for it to continue serving as a vital instrument in synthetic biology research and industry. In this review, we mainly focus on the cell-free based platform for various product productions. Moreover, the challenges in the bio-therapeutic aspect using cell-free systems and their future prospective for the improvement and sustainability of the cell free systems.
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Affiliation(s)
- Anoth Maharjan
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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4
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Manzer ZA, Selivanovitch E, Ostwalt AR, Daniel S. Membrane protein synthesis: no cells required. Trends Biochem Sci 2023; 48:642-654. [PMID: 37087310 DOI: 10.1016/j.tibs.2023.03.006] [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] [Received: 11/07/2022] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 04/24/2023]
Abstract
Despite advances in membrane protein (MP) structural biology and a growing interest in their applications, these proteins remain challenging to study. Progress has been hindered by the complex nature of MPs and innovative methods will be required to circumvent technical hurdles. Cell-free protein synthesis (CFPS) is a burgeoning technique for synthesizing MPs directly into a membrane environment using reconstituted components of the cellular transcription and translation machinery in vitro. We provide an overview of CFPS and how this technique can be applied to the synthesis and study of MPs. We highlight numerous strategies including synthesis methods and folding environments, each with advantages and limitations, to provide a survey of how CFPS techniques can advance the study of MPs.
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Affiliation(s)
- Zachary A Manzer
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Ekaterina Selivanovitch
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Alexis R Ostwalt
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Susan Daniel
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
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5
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Duchardt-Ferner E, Ferner J, Fürtig B, Hengesbach M, Richter C, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Schwalbe H. The COVID19-NMR Consortium: A Public Report on the Impact of this New Global Collaboration. Angew Chem Int Ed Engl 2023; 62:e202217171. [PMID: 36748955 DOI: 10.1002/anie.202217171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Indexed: 02/08/2023]
Abstract
The outbreak of COVID-19 in December 2019 required the formation of international consortia for a coordinated scientific effort to understand and combat the virus. In this Viewpoint Article, we discuss how the NMR community has gathered to investigate the genome and proteome of SARS-CoV-2 and tested them for binding to low-molecular-weight binders. External factors including extended lockdowns due to the global pandemic character of the viral infection triggered the transition from locally focused collaborative research conducted within individual research groups to digital exchange formats for immediate discussion of unpublished results and data analysis, sample sharing, and coordinated research between more than 50 groups from 18 countries simultaneously. We discuss key lessons that might pertain after the end of the pandemic and challenges that we need to address.
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Affiliation(s)
- Elke Duchardt-Ferner
- Institute for Biomolecular Sciences, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Andreas Schlundt
- Institute for Biomolecular Sciences, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Julia E Weigand
- Philipps-University Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35037, Marburg, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, OX4 2JY, UK
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6
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Duchardt‐Ferner E, Ferner J, Fürtig B, Hengesbach M, Richter C, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Schwalbe H. Das COVID19‐NMR‐Konsortium: Ein öffentlicher Bericht über den Einfluss dieser neuen globalen Kollaboration. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202217171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- Elke Duchardt‐Ferner
- Institute for Biomolecular Sciences Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt/M. Deutschland
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Andreas Schlundt
- Institute for Biomolecular Sciences Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt/M. Deutschland
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Julia E. Weigand
- Philipps-University Marburg Department of Pharmacy Institute of Pharmaceutical Chemistry Marbacher Weg 6 35037 Marburg Deutschland
| | - Julia Wirmer‐Bartoschek
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/M. Deutschland
- Instruct-ERIC Oxford House, Parkway Court John Smith Drive Oxford OX4 2JY Großbritannien
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7
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Molecular elucidation of drug-induced abnormal assemblies of the hepatitis B virus capsid protein by solid-state NMR. Nat Commun 2023; 14:471. [PMID: 36709212 PMCID: PMC9884277 DOI: 10.1038/s41467-023-36219-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
Hepatitis B virus (HBV) capsid assembly modulators (CAMs) represent a recent class of anti-HBV antivirals. CAMs disturb proper nucleocapsid assembly, by inducing formation of either aberrant assemblies (CAM-A) or of apparently normal but genome-less empty capsids (CAM-E). Classical structural approaches have revealed the CAM binding sites on the capsid protein (Cp), but conformational information on the CAM-induced off-path aberrant assemblies is lacking. Here we show that solid-state NMR can provide such information, including for wild-type full-length Cp183, and we find that in these assemblies, the asymmetric unit comprises a single Cp molecule rather than the four quasi-equivalent conformers typical for the icosahedral T = 4 symmetry of the normal HBV capsids. Furthermore, while in contrast to truncated Cp149, full-length Cp183 assemblies appear, on the mesoscopic level, unaffected by CAM-A, NMR reveals that on the molecular level, Cp183 assemblies are equally aberrant. Finally, we use a eukaryotic cell-free system to reveal how CAMs modulate capsid-RNA interactions and capsid phosphorylation. Our results establish a structural view on assembly modulation of the HBV capsid, and they provide a rationale for recently observed differences between in-cell versus in vitro capsid assembly modulation.
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8
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Fieulaine S, Tubiana T, Bressanelli S. De novo modelling of HEV replication polyprotein: Five-domain breakdown and involvement of flexibility in functional regulation. Virology 2023; 578:128-140. [PMID: 36527931 DOI: 10.1016/j.virol.2022.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
Hepatitis E virus (HEV), a major cause of acute viral hepatitis, is a single-stranded, positive-sense RNA virus. As such, it encodes a 1700-residue replication polyprotein pORF1 that directs synthesis of new viral RNA in infected cells. Here we report extensive modeling with AlphaFold2 of the full-length pORF1, and its production by in vitro translation. From this, we give a detailed update on the breakdown into domains of HEV pORF1. We also provide evidence that pORF1's N-terminal domain is likely to oligomerize to form a dodecameric pore, homologously to what has been described for Chikungunya virus. Beyond providing accurate folds for its five domains, our work highlights that there is no canonical protease encoded in pORF1 and that flexibility in several functionally important regions rather than proteolytic processing may serve to regulate HEV RNA synthesis.
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Affiliation(s)
- Sonia Fieulaine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Thibault Tubiana
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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9
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Pandey Y, Dondapati SK, Wüstenhagen D, Kubick S. Cell-Free Synthesis and Electrophysiological Analysis of Multipass Voltage-Gated Ion Channels Tethered in Microsomal Membranes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:103-120. [PMID: 37640910 DOI: 10.1007/10_2023_228] [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] [Indexed: 08/31/2023]
Abstract
Cell-free protein synthesis (CFPS) has emerged as a powerful tool for the rapid synthesis and analysis of various structurally and functionally distinct proteins. These include 'difficult-to-express' membrane proteins such as large multipass ion channel receptors. Owing to their membrane localization, eukaryotic CFPS supplemented with endoplasmic reticulum (ER)-derived microsomal vesicles has proven to be an efficient system for the synthesis of functional membrane proteins. Here we demonstrate the applicability of the eukaryotic cell-free systems based on lysates from the mammalian Chinese Hamster Ovary (CHO) and insect Spodoptera frugiperda (Sf21) cells. We demonstrate the efficiency of the systems in the de novo cell-free synthesis of the human cardiac ion channels: ether-a-go-go potassium channel (hERG) KV11.1 and the voltage-gated sodium channel hNaV1.5.
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Affiliation(s)
- Yogesh Pandey
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institut für Biochemie und Biologie, University of Potsdam, Potsdam, OT Golm, Germany
| | - Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.
| | - Doreen Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Institute of Chemistry and Biochemistry-Biochemistry, Freie Universität Berlin, Berlin, Germany
- Faculty of Health Science, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
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10
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Cell-free protein crystallization for nanocrystal structure determination. Sci Rep 2022; 12:16031. [PMID: 36192567 PMCID: PMC9530169 DOI: 10.1038/s41598-022-19681-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022] Open
Abstract
In-cell protein crystallization (ICPC) has been investigated as a technique to support the advancement of structural biology because it does not require protein purification and a complicated crystallization process. However, only a few protein structures have been reported because these crystals formed incidentally in living cells and are insufficient in size and quality for structure analysis. Here, we have developed a cell-free protein crystallization (CFPC) method, which involves direct protein crystallization using cell-free protein synthesis. We have succeeded in crystallization and structure determination of nano-sized polyhedra crystal (PhC) at a high resolution of 1.80 Å. Furthermore, nanocrystals were synthesized at a reaction scale of only 20 μL using the dialysis method, enabling structural analysis at a resolution of 1.95 Å. To further demonstrate the potential of CFPC, we attempted to determine the structure of crystalline inclusion protein A (CipA), whose structure had not yet been determined. We added chemical reagents as a twinning inhibitor to the CFPC solution, which enabled us to determine the structure of CipA at 2.11 Å resolution. This technology greatly expands the high-throughput structure determination method of unstable, low-yield, fusion, and substrate-biding proteins that have been difficult to analyze with conventional methods.
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11
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Zyrina NV, Agalarov SC. 16S rRNA from E. coli Significantly Stimulates Translation of Reporter mRNA in a Eucaryotic Cell-Free System. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922050232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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12
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Characterization and Utilization of Disulfide-Bonded SARS-CoV-2 Receptor Binding Domain of Spike Protein Synthesized by Wheat Germ Cell-Free Production System. Viruses 2022; 14:v14071461. [PMID: 35891441 PMCID: PMC9321213 DOI: 10.3390/v14071461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 02/05/2023] Open
Abstract
The spike protein (SP) of SARS-CoV-2 is an important target for COVID-19 therapeutics and vaccines as it binds to the ACE2 receptor and enables viral infection. Rapid production and functional characterization of properly folded SP is of the utmost importance for studying the immunogenicity and receptor-binding activity of this protein considering the emergence of highly infectious viral variants. In this study, we attempted to express the receptor-binding region (RBD) of SARS-CoV-2 SP containing disulfide bonds using the wheat germ cell-free protein synthesis system. By adding protein disulfide isomerase (PDI) and endoplasmic reticulum oxidase (ERO1α) to the translational reaction mixture, we succeeded in synthesizing a functionally intact RBD protein that can interact with ACE2. Using this RBD protein, we have developed a high-throughput AlphaScreen assay to evaluate the RBD–ACE2 interaction, which can be applied for drug screening and mutation analysis. Thus, our method sheds new light on the structural and functional properties of SARS-CoV-2 SP and has the potential to contribute to the development of new COVID-19 therapeutics.
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Clark ET, Sievers EE, Debelouchina GT. A Chemical Biology Primer for NMR Spectroscopists. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100044. [PMID: 35494416 PMCID: PMC9053072 DOI: 10.1016/j.jmro.2022.100044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Among structural biology techniques, NMR spectroscopy offers unique capabilities that enable the atomic resolution studies of dynamic and heterogeneous biological systems under physiological and native conditions. Complex biological systems, however, often challenge NMR spectroscopists with their low sensitivity, crowded spectra or large linewidths that reflect their intricate interaction patterns and dynamics. While some of these challenges can be overcome with the development of new spectroscopic approaches, chemical biology can also offer elegant and efficient solutions at the sample preparation stage. In this tutorial, we aim to present several chemical biology tools that enable the preparation of selectively and segmentally labeled protein samples, as well as the introduction of site-specific spectroscopic probes and post-translational modifications. The four tools covered here, namely cysteine chemistry, inteins, native chemical ligation, and unnatural amino acid incorporation, have been developed and optimized in recent years to be more efficient and applicable to a wider range of proteins than ever before. We briefly introduce each tool, describe its advantages and disadvantages in the context of NMR experiments, and offer practical advice for sample preparation and analysis. We hope that this tutorial will introduce beginning researchers in the field to the possibilities chemical biology can offer to NMR spectroscopists, and that it will inspire new and exciting applications in the quest to understand protein function in health and disease.
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Affiliation(s)
- Evan T. Clark
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Elanor E. Sievers
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Corresponding author: Galia Debelouchina, University of California, San Diego, Natural Sciences Building 4322, 9500 Gilman Dr., La Jolla, CA 92093, 858-534-3038,
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14
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Fogeron ML, Lecoq L, Cole L, Montserret R, David G, Page A, Delolme F, Nassal M, Böckmann A. Phosphorylation of the Hepatitis B Virus Large Envelope Protein. Front Mol Biosci 2022; 8:821755. [PMID: 35282608 PMCID: PMC8904964 DOI: 10.3389/fmolb.2021.821755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 01/05/2023] Open
Abstract
We here establish the phosphorylation sites in the human hepatitis B virus (HBV) large envelope protein (L). L is involved in several functionally important interactions in the viral life cycle, including with the HBV cellular receptor, HBV capsid, Hsc70 chaperone, and cellular membranes during fusion. We have recently shown that cell-free synthesis of the homologous L protein of duck HBV in wheat germ extract results in very similar phosphorylation events to those previously observed in animal cells. Here, we used mass spectrometry and NMR to establish the phosphorylation patterns of human HBV L protein produced by both in vitro cell-free synthesis and in E. coli with the co-expression of the human MAPK14 kinase. While in the avian virus the phosphorylation of L has been shown to be dispensable for infectivity, the identified locations in the human virus protein, both in the PreS1 and PreS2 domains, raise the intriguing possibility that they might play a functional role, since they are found at strategic sites predicted to be involved in L interactions. This would warrant the further investigation of a possible function in virion formation or cell entry.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Guillaume David
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences CNRS UAR 3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Frédéric Delolme
- Protein Science Facility, SFR BioSciences CNRS UAR 3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Michael Nassal
- Department of Medicine II / Molecular Biology, Medical Center, University Hospital Freiburg, University of Freiburg, Freiburg im Breisgau, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
- *Correspondence: Anja Böckmann,
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15
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Frelet-Barrand A. Lactococcus lactis, an Attractive Cell Factory for the Expression of Functional Membrane Proteins. Biomolecules 2022; 12:biom12020180. [PMID: 35204681 PMCID: PMC8961550 DOI: 10.3390/biom12020180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 01/27/2023] Open
Abstract
Membrane proteins play key roles in most crucial cellular processes, ranging from cell-to-cell communication to signaling processes. Despite recent improvements, the expression of functionally folded membrane proteins in sufficient amounts for functional and structural characterization remains a challenge. Indeed, it is still difficult to predict whether a protein can be overproduced in a functional state in some expression system(s), though studies of high-throughput screens have been published in recent years. Prokaryotic expression systems present several advantages over eukaryotic ones. Among them, Lactococcus lactis (L. lactis) has emerged in the last two decades as a good alternative expression system to E. coli. The purpose of this chapter is to describe L. lactis and its tightly inducible system, NICE, for the effective expression of membrane proteins from both prokaryotic and eukaryotic origins.
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Affiliation(s)
- Annie Frelet-Barrand
- FEMTO-ST Institute, UMR 6174, CNRS, Université Bourgogne Franche-Comté, 15B Avenue des Montboucons, CEDEX, 25030 Besançon, France
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16
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Monck C, Elani Y, Ceroni F. Cell-free protein synthesis: biomedical applications and future perspectives. Chem Eng Res Des 2022. [DOI: 10.1016/j.cherd.2021.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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Callon M, Malär AA, Pfister S, Římal V, Weber ME, Wiegand T, Zehnder J, Chávez M, Cadalbert R, Deb R, Däpp A, Fogeron ML, Hunkeler A, Lecoq L, Torosyan A, Zyla D, Glockshuber R, Jonas S, Nassal M, Ernst M, Böckmann A, Meier BH. Biomolecular solid-state NMR spectroscopy at 1200 MHz: the gain in resolution. JOURNAL OF BIOMOLECULAR NMR 2021; 75:255-272. [PMID: 34170475 PMCID: PMC8275511 DOI: 10.1007/s10858-021-00373-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/11/2021] [Indexed: 05/12/2023]
Abstract
Progress in NMR in general and in biomolecular applications in particular is driven by increasing magnetic-field strengths leading to improved resolution and sensitivity of the NMR spectra. Recently, persistent superconducting magnets at a magnetic field strength (magnetic induction) of 28.2 T corresponding to 1200 MHz proton resonance frequency became commercially available. We present here a collection of high-field NMR spectra of a variety of proteins, including molecular machines, membrane proteins, viral capsids, fibrils and large molecular assemblies. We show this large panel in order to provide an overview over a range of representative systems under study, rather than a single best performing model system. We discuss both carbon-13 and proton-detected experiments, and show that in 13C spectra substantially higher numbers of peaks can be resolved compared to 850 MHz while for 1H spectra the most impressive increase in resolution is observed for aliphatic side-chain resonances.
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Affiliation(s)
- Morgane Callon
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Sara Pfister
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Václav Římal
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Marco E Weber
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Matías Chávez
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Rajdeep Deb
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Alexander Däpp
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon, 69367, Lyon, France
| | | | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon, 69367, Lyon, France
| | | | - Dawid Zyla
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - Rudolf Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - Michael Nassal
- Department of Medicine II / Molecular Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon, 69367, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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