1
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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research conducted within individual research groups to digital exchange formats for immediate discussion of unpublished results and data analysis, sample sharing, and coordinated research between more than 50 groups from 18 countries simultaneously.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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2
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Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
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3
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Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022; 61:e202205858. [PMID: 36115062 PMCID: PMC9539013 DOI: 10.1002/anie.202205858] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 11/17/2022]
Abstract
SARS‐CoV‐2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti‐virals. Within the international Covid19‐NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80% of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR‐detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure‐based drug design against the SCoV2 proteome.
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Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
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4
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Mertinkus KR, Grün JT, Altincekic N, Bains JK, Ceylan B, Ferner JP, Frydman L, Fürtig B, Hengesbach M, Hohmann KF, Hymon D, Kim J, Knezic B, Novakovic M, Oxenfarth A, Peter SA, Qureshi NS, Richter C, Scherf T, Schlundt A, Schnieders R, Schwalbe H, Stirnal E, Sudakov A, Vögele J, Wacker A, Weigand JE, Wirmer-Bartoschek J, Martin MAW, Wöhnert J. 1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5'-UTR of SARS-CoV-2. Biomol NMR Assign 2022; 16:17-25. [PMID: 35178672 PMCID: PMC8853908 DOI: 10.1007/s12104-021-10053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/16/2021] [Indexed: 06/14/2023]
Abstract
The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5'- and 3'-genomic ends that are highly conserved among Betacoronaviruses. These genomic ends contain structured cis-acting RNA elements, which are involved in the regulation of viral replication and translation. Structural information about these potential antiviral drug targets supports the development of novel classes of therapeutics against COVID-19. The highly conserved branched stem-loop 5 (SL5) found within the 5'-untranslated region (5'-UTR) consists of a basal stem and three stem-loops, namely SL5a, SL5b and SL5c. Both, SL5a and SL5b feature a 5'-UUUCGU-3' hexaloop that is also found among Alphacoronaviruses. Here, we report the extensive 1H, 13C and 15N resonance assignment of the 37 nucleotides (nts) long sequence spanning SL5b and SL5c (SL5b + c), as basis for further in-depth structural studies by solution NMR spectroscopy.
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Affiliation(s)
- Klara R Mertinkus
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jan-Peter Ferner
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jihyun Kim
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Božana Knezic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
- Institute for Biochemistry, ETH Zürich, Hönggerbergring 64, 8093, Zürich, Switzerland
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | | | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Tali Scherf
- Department of Chemical Research Support, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Deutero GmbH, Am Ring 29, 56288, Kastellaun, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
| | - Elke Stirnal
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jennifer Vögele
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Maria A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
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5
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Richter C, Hohmann KF, Toews S, Mathieu D, Altincekic N, Bains JK, Binas O, Ceylan B, Duchardt-Ferner E, Ferner J, Fürtig B, Grün JT, Hengesbach M, Hymon D, Jonker HRA, Knezic B, Korn SM, Landgraf T, Löhr F, Peter SA, Pyper DJ, Qureshi NS, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Vögele J, Weigand JE, Wirmer-Bartoschek J, Witt K, Wöhnert J, Schwalbe H, Wacker A. 1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2. Biomol NMR Assign 2021; 15:467-474. [PMID: 34453696 PMCID: PMC8401371 DOI: 10.1007/s12104-021-10047-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/19/2021] [Indexed: 05/27/2023]
Abstract
The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7-33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1H, 13C and 15N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.
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Affiliation(s)
- Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Sabrina Toews
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Daniel Mathieu
- Bruker BioSpin, Silberstreifen 4, 76287, Rheinstetten, Germany
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- BioNTech SE, An der Goldgrube 12, 55131, Mainz, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Faculty of Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Hendrik R A Jonker
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Sophie M Korn
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Frank Löhr
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Biophysical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Dennis J Pyper
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Nusrat S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Andreas Schlundt
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Deutero GmbH, Am Ring 29, 56288, Kastellaun, Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Jennifer Vögele
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Kerstin Witt
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany.
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue- Straße 7, 60438, Frankfurt, Germany.
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6
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Vögele J, Ferner JP, Altincekic N, Bains JK, Ceylan B, Fürtig B, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Löhr F, Peter SA, Pyper D, Qureshi NS, Richter C, Schlundt A, Schwalbe H, Stirnal E, Sudakov A, Wacker A, Weigand JE, Wirmer-Bartoschek J, Wöhnert J, Duchardt-Ferner E. 1H, 13C, 15N and 31P chemical shift assignment for stem-loop 4 from the 5'-UTR of SARS-CoV-2. Biomol NMR Assign 2021; 15:335-340. [PMID: 33928512 PMCID: PMC8083917 DOI: 10.1007/s12104-021-10026-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/16/2021] [Indexed: 06/01/2023]
Abstract
The SARS-CoV-2 virus is the cause of the respiratory disease COVID-19. As of today, therapeutic interventions in severe COVID-19 cases are still not available as no effective therapeutics have been developed so far. Despite the ongoing development of a number of effective vaccines, therapeutics to fight the disease once it has been contracted will still be required. Promising targets for the development of antiviral agents against SARS-CoV-2 can be found in the viral RNA genome. The 5'- and 3'-genomic ends of the 30 kb SCoV-2 genome are highly conserved among Betacoronaviruses and contain structured RNA elements involved in the translation and replication of the viral genome. The 40 nucleotides (nt) long highly conserved stem-loop 4 (5_SL4) is located within the 5'-untranslated region (5'-UTR) important for viral replication. 5_SL4 features an extended stem structure disrupted by several pyrimidine mismatches and is capped by a pentaloop. Here, we report extensive 1H, 13C, 15N and 31P resonance assignments of 5_SL4 as the basis for in-depth structural and ligand screening studies by solution NMR spectroscopy.
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Affiliation(s)
- Jennifer Vögele
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Jan-Peter Ferner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Nadide Altincekic
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Jasleen Kaur Bains
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Betül Ceylan
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Boris Fürtig
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - J Tassilo Grün
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Martin Hengesbach
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Katharina F Hohmann
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Daniel Hymon
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Bozana Knezic
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Frank Löhr
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Biophysical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Dennis Pyper
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | | | - Christian Richter
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Elke Stirnal
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Alexey Sudakov
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Anna Wacker
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Julia Wirmer-Bartoschek
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany.
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7
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Wacker A, Weigand JE, Akabayov SR, Altincekic N, Bains JK, Banijamali E, Binas O, Castillo-Martinez J, Cetiner E, Ceylan B, Chiu LY, Davila-Calderon J, Dhamotharan K, Duchardt-Ferner E, Ferner J, Frydman L, Fürtig B, Gallego J, Grün JT, Hacker C, Haddad C, Hähnke M, Hengesbach M, Hiller F, Hohmann KF, Hymon D, de Jesus V, Jonker H, Keller H, Knezic B, Landgraf T, Löhr F, Luo L, Mertinkus KR, Muhs C, Novakovic M, Oxenfarth A, Palomino-Schätzlein M, Petzold K, Peter SA, Pyper DJ, Qureshi NS, Riad M, Richter C, Saxena K, Schamber T, Scherf T, Schlagnitweit J, Schlundt A, Schnieders R, Schwalbe H, Simba-Lahuasi A, Sreeramulu S, Stirnal E, Sudakov A, Tants JN, Tolbert BS, Vögele J, Weiß L, Wirmer-Bartoschek J, Wirtz Martin MA, Wöhnert J, Zetzsche H. Correction to 'Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy'. Nucleic Acids Res 2021; 49:7204-7205. [PMID: 34161581 PMCID: PMC8266613 DOI: 10.1093/nar/gkab568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sabine R Akabayov
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Erhan Cetiner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | | | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Lucio Frydman
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - José Gallego
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Carolin Hacker
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Martin Hähnke
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Fabian Hiller
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Henry Jonker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Le Luo
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Klara R Mertinkus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Christina Muhs
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Mihajlo Novakovic
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Dennis J Pyper
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Nusrat S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Magdalena Riad
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tali Scherf
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | | | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alvaro Simba-Lahuasi
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Maria A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Heidi Zetzsche
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
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8
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Novakovic M, Kupče Ē, Scherf T, Oxenfarth A, Schnieders R, Grün JT, Wirmer-Bartoschek J, Richter C, Schwalbe H, Frydman L. Magnetization Transfer to Enhance NOE Cross-Peaks among Labile Protons: Applications to Imino-Imino Sequential Walks in SARS-CoV-2-Derived RNAs. Angew Chem Int Ed Engl 2021; 60:11884-11891. [PMID: 33683819 PMCID: PMC8251384 DOI: 10.1002/anie.202015948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/14/2021] [Indexed: 11/17/2022]
Abstract
2D NOESY plays a central role in structural NMR spectroscopy. We have recently discussed methods that rely on solvent‐driven exchanges to enhance NOE correlations between exchangeable and non‐exchangeable protons in nucleic acids. Such methods, however, fail when trying to establish connectivities within pools of labile protons. This study introduces an alternative that also enhances NOEs between such labile sites, based on encoding a priori selected peaks by selective saturations. The resulting selective magnetization transfer (SMT) experiment proves particularly useful for enhancing the imino–imino cross‐peaks in RNAs, which is a first step in the NMR resolution of these structures. The origins of these enhancements are discussed, and their potential is demonstrated on RNA fragments derived from the genome of SARS‐CoV‐2, recorded with better sensitivity and an order of magnitude faster than conventional 2D counterparts.
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Affiliation(s)
- Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Tali Scherf
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, 60438, Frankfurt/Main, Germany
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 7610001, Rehovot, Israel
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9
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. Magn Reson (Gott) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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10
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Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, Bula A, Bütikofer M, Camacho-Zarco AR, Carlomagno T, Caruso IP, Ceylan B, Chaikuad A, Chu F, Cole L, Crosby MG, de Jesus V, Dhamotharan K, Felli IC, Ferner J, Fleischmann Y, Fogeron ML, Fourkiotis NK, Fuks C, Fürtig B, Gallo A, Gande SL, Gerez JA, Ghosh D, Gomes-Neto F, Gorbatyuk O, Guseva S, Hacker C, Häfner S, Hao B, Hargittay B, Henzler-Wildman K, Hoch JC, Hohmann KF, Hutchison MT, Jaudzems K, Jović K, Kaderli J, Kalniņš G, Kaņepe I, Kirchdoerfer RN, Kirkpatrick J, Knapp S, Krishnathas R, Kutz F, zur Lage S, Lambertz R, Lang A, Laurents D, Lecoq L, Linhard V, Löhr F, Malki A, Bessa LM, Martin RW, Matzel T, Maurin D, McNutt SW, Mebus-Antunes NC, Meier BH, Meiser N, Mompeán M, Monaca E, Montserret R, Mariño Perez L, Moser C, Muhle-Goll C, Neves-Martins TC, Ni X, Norton-Baker B, Pierattelli R, Pontoriero L, Pustovalova Y, Ohlenschläger O, Orts J, Da Poian AT, Pyper DJ, Richter C, Riek R, Rienstra CM, Robertson A, Pinheiro AS, Sabbatella R, Salvi N, Saxena K, Schulte L, Schiavina M, Schwalbe H, Silber M, Almeida MDS, Sprague-Piercy MA, Spyroulias GA, Sreeramulu S, Tants JN, Tārs K, Torres F, Töws S, Treviño MÁ, Trucks S, Tsika AC, Varga K, Wang Y, Weber ME, Weigand JE, Wiedemann C, Wirmer-Bartoschek J, Wirtz Martin MA, Zehnder J, Hengesbach M, Schlundt A. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications. Front Mol Biosci 2021; 8:653148. [PMID: 34041264 PMCID: PMC8141814 DOI: 10.3389/fmolb.2021.653148] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 01/18/2023] Open
Abstract
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
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Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sophie Marianne Korn
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Dujardin
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Martí Ninot-Pedrosa
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Jose Abi Saad
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Fabio C. L. Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Islam Alshamleh
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisele Cardoso de Amorim
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil
| | - Thomas K. Anderson
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cristiane D. Anobom
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chelsea Anorma
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriaan Bax
- LCP, NIDDK, NIH, Bethesda, MD, United States
| | | | - Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Louis Brigandat
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Anna Bula
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Matthias Bütikofer
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Teresa Carlomagno
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Icaro Putinhon Caruso
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Marquise G. Crosby
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karthikeyan Dhamotharan
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Isabella C. Felli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yanick Fleischmann
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Christin Fuks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Angelo Gallo
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Santosh L. Gande
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Juan Atilio Gerez
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Dhiman Ghosh
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Francisco Gomes-Neto
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Oksana Gorbatyuk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | | | - Sabine Häfner
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Bing Hao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Bruno Hargittay
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - K. Henzler-Wildman
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie T. Hutchison
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Katarina Jović
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Janina Kaderli
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Kaņepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Robert N. Kirchdoerfer
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - John Kirkpatrick
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Robin Krishnathas
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Felicitas Kutz
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne zur Lage
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Roderick Lambertz
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andras Lang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Douglas Laurents
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anas Malki
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Damien Maurin
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Nathane Cunha Mebus-Antunes
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Beat H. Meier
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nathalie Meiser
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Mompeán
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Elisa Monaca
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Celine Moser
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Thais Cristtina Neves-Martins
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Xiamonin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Brenna Norton-Baker
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Roberta Pierattelli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Letizia Pontoriero
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Yulia Pustovalova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | - Julien Orts
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Roland Riek
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Chad M. Rienstra
- Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anderson S. Pinheiro
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Linda Schulte
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marco Schiavina
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mara Silber
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcius da Silva Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | | | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jan-Niklas Tants
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Felix Torres
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sabrina Töws
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Á. Treviño
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Ying Wang
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Marco E. Weber
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Julia E. Weigand
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Zehnder
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Schlundt
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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11
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Grün JT, Blümler A, Burkhart I, Wirmer-Bartoschek J, Heckel A, Schwalbe H. Unraveling the Kinetics of Spare-Tire DNA G-Quadruplex Folding. J Am Chem Soc 2021; 143:6185-6193. [PMID: 33872503 DOI: 10.1021/jacs.1c01089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The folding of DNA G-quadruplexes (G4) is essential to regulate expression of oncogenes and involves polymorphic long-lived intermediate states. G4 formation requires four G-tracts, but human gene-promoters often contain multiple G-tracts that act as spare-tires. These additional G-tracts are highly conserved and add multiple layers of functional complexity, as they are crucial to maintain G4 function after oxidative damage. Herein, we unravel the folding dynamics of the G4 sequence containing five G-tracts from cMYC, the major proliferation-driving oncogene. We devise a general method to induce folding at constant experimental conditions using a photochemical trapping strategy. Our data dissect the individual kinetics and thermodynamics of the spare-tire mechanism of cMYC-G4.
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Affiliation(s)
- J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60323, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany
| | - Ines Burkhart
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60323, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60323, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60323, Germany
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12
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Kim J, Novakovic M, Jayanthi S, Lupulescu A, Kupce E, Grün JT, Mertinkus K, Oxenfarth A, Richter C, Schnieders R, Wirmer-Bartoschek J, Schwalbe H, Frydman L. 3D Heteronuclear Magnetization Transfers for the Establishment of Secondary Structures in SARS-CoV-2-Derived RNAs. J Am Chem Soc 2021; 143:4942-4948. [PMID: 33783202 PMCID: PMC8154514 DOI: 10.1021/jacs.1c01914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multidimensional NOESY experiments targeting correlations between exchangeable imino and amino protons provide valuable information about base pairing in nucleic acids. It has been recently shown that the sensitivity of homonuclear correlations involving RNA's labile imino protons can be significantly enhanced, by exploiting the repolarization brought about by solvent exchanges. Homonuclear correlations, however, are of limited spectral resolution, and usually incapable of tackling relatively large homopolymers with repeating structures like RNAs. This study presents a heteronuclear-resolved version of those NOESY experiments, in which magnetization transfers between the aqueous solvent and the nucleic acid protons are controlled by selecting specific chemical shift combinations of a coupled 1H-15N spin pair. This selective control effectively leads to a pseudo-3D version of HSQC-NOESY, but with cross-peaks enhanced by ∼2-5× as compared with conventional 2D NOESY counterparts. The enhanced signal sensitivity as well as access to both 15N-1H and 1H-1H NOESY dimensions can greatly facilitate RNA assignments and secondary structure determinations, as demonstrated here with the analysis of genome fragments derived from the SARS-CoV-2 virus.
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Affiliation(s)
- Jihyun Kim
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sundaresan Jayanthi
- Department of Physics, Indian Institute of Space Science and Technology, Valiamala, Thiruvananthapuram 695 547, Kerala, India
| | - Adonis Lupulescu
- Aleea Nicolae Titulescu nr. 8, Turda, 407405 Judeţul Cluj, Romania
| | - Eriks Kupce
- Bruker Ltd, Banner Lane, Coventry CV4 9GH, United Kingdom
| | - J Tassilo Grün
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, D-60438 Frankfurt/Main, Germany
| | - Klara Mertinkus
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, D-60438 Frankfurt/Main, Germany
| | - Andreas Oxenfarth
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, D-60438 Frankfurt/Main, Germany
| | - Christian Richter
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, D-60438 Frankfurt/Main, Germany
| | - Robbin Schnieders
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, D-60438 Frankfurt/Main, Germany
| | - Julia Wirmer-Bartoschek
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, D-60438 Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, D-60438 Frankfurt/Main, Germany
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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13
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Schnieders R, Peter SA, Banijamali E, Riad M, Altincekic N, Bains JK, Ceylan B, Fürtig B, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Oxenfarth A, Petzold K, Qureshi NS, Richter C, Schlagnitweit J, Schlundt A, Schwalbe H, Stirnal E, Sudakov A, Vögele J, Wacker A, Weigand JE, Wirmer-Bartoschek J, Wöhnert J. 1H, 13C and 15N chemical shift assignment of the stem-loop 5a from the 5'-UTR of SARS-CoV-2. Biomol NMR Assign 2021; 15:203-211. [PMID: 33484403 PMCID: PMC7822759 DOI: 10.1007/s12104-021-10007-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/08/2021] [Indexed: 05/27/2023]
Abstract
The SARS-CoV-2 (SCoV-2) virus is the causative agent of the ongoing COVID-19 pandemic. It contains a positive sense single-stranded RNA genome and belongs to the genus of Betacoronaviruses. The 5'- and 3'-genomic ends of the 30 kb SCoV-2 genome are potential antiviral drug targets. Major parts of these sequences are highly conserved among Betacoronaviruses and contain cis-acting RNA elements that affect RNA translation and replication. The 31 nucleotide (nt) long highly conserved stem-loop 5a (SL5a) is located within the 5'-untranslated region (5'-UTR) important for viral replication. SL5a features a U-rich asymmetric bulge and is capped with a 5'-UUUCGU-3' hexaloop, which is also found in stem-loop 5b (SL5b). We herein report the extensive 1H, 13C and 15N resonance assignment of SL5a as basis for in-depth structural studies by solution NMR spectroscopy.
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Affiliation(s)
- Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum, Solnavägen 9, 17177, Stockholm, Sweden
| | - Magdalena Riad
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum, Solnavägen 9, 17177, Stockholm, Sweden
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum, Solnavägen 9, 17177, Stockholm, Sweden
| | | | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum, Solnavägen 9, 17177, Stockholm, Sweden
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany.
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Jennifer Vögele
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
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14
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Kubatova N, Qureshi NS, Altincekic N, Abele R, Bains JK, Ceylan B, Ferner J, Fuks C, Hargittay B, Hutchison MT, de Jesus V, Kutz F, Wirtz Martin MA, Meiser N, Linhard V, Pyper DJ, Trucks S, Fürtig B, Hengesbach M, Löhr F, Richter C, Saxena K, Schlundt A, Schwalbe H, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Wöhnert J. 1H, 13C, and 15N backbone chemical shift assignments of coronavirus-2 non-structural protein Nsp10. Biomol NMR Assign 2021; 15:65-71. [PMID: 33159807 PMCID: PMC7648550 DOI: 10.1007/s12104-020-09984-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
The international Covid19-NMR consortium aims at the comprehensive spectroscopic characterization of SARS-CoV-2 RNA elements and proteins and will provide NMR chemical shift assignments of the molecular components of this virus. The SARS-CoV-2 genome encodes approximately 30 different proteins. Four of these proteins are involved in forming the viral envelope or in the packaging of the RNA genome and are therefore called structural proteins. The other proteins fulfill a variety of functions during the viral life cycle and comprise the so-called non-structural proteins (nsps). Here, we report the near-complete NMR resonance assignment for the backbone chemical shifts of the non-structural protein 10 (nsp10). Nsp10 is part of the viral replication-transcription complex (RTC). It aids in synthesizing and modifying the genomic and subgenomic RNAs. Via its interaction with nsp14, it ensures transcriptional fidelity of the RNA-dependent RNA polymerase, and through its stimulation of the methyltransferase activity of nsp16, it aids in synthesizing the RNA cap structures which protect the viral RNAs from being recognized by the innate immune system. Both of these functions can be potentially targeted by drugs. Our data will aid in performing additional NMR-based characterizations, and provide a basis for the identification of possible small molecule ligands interfering with nsp10 exerting its essential role in viral replication.
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Affiliation(s)
- N Kubatova
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - N S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - N Altincekic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - R Abele
- Institute for Biochemistry, Biocentre, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J K Bains
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - B Ceylan
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J Ferner
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - C Fuks
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - B Hargittay
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - M T Hutchison
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - V de Jesus
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - F Kutz
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - M A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - N Meiser
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - V Linhard
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - D J Pyper
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - S Trucks
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - B Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - M Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany.
| | - F Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - C Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - K Saxena
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - A Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - H Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany.
| | - S Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - A Wacker
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr 10, 64287, Darmstadt, Germany
| | - J Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
| | - J Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt/M, Germany
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15
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Wacker A, Weigand JE, Akabayov SR, Altincekic N, Bains JK, Banijamali E, Binas O, Castillo-Martinez J, Cetiner E, Ceylan B, Chiu LY, Davila-Calderon J, Dhamotharan K, Duchardt-Ferner E, Ferner J, Frydman L, Fürtig B, Gallego J, Grün JT, Hacker C, Haddad C, Hähnke M, Hengesbach M, Hiller F, Hohmann KF, Hymon D, de Jesus V, Jonker H, Keller H, Knezic B, Landgraf T, Löhr F, Luo L, Mertinkus KR, Muhs C, Novakovic M, Oxenfarth A, Palomino-Schätzlein M, Petzold K, Peter SA, Pyper DJ, Qureshi NS, Riad M, Richter C, Saxena K, Schamber T, Scherf T, Schlagnitweit J, Schlundt A, Schnieders R, Schwalbe H, Simba-Lahuasi A, Sreeramulu S, Stirnal E, Sudakov A, Tants JN, Tolbert BS, Vögele J, Weiß L, Wirmer-Bartoschek J, Wirtz Martin MA, Wöhnert J, Zetzsche H. Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy. Nucleic Acids Res 2020; 48:12415-12435. [PMID: 33167030 PMCID: PMC7736788 DOI: 10.1093/nar/gkaa1013] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/08/2020] [Accepted: 10/14/2020] [Indexed: 12/24/2022] Open
Abstract
The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-untranslated region (3'-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.
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Affiliation(s)
- Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sabine R Akabayov
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Erhan Cetiner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | | | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Lucio Frydman
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - José Gallego
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Carolin Hacker
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Martin Hähnke
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Fabian Hiller
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Henry Jonker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Le Luo
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Klara R Mertinkus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Christina Muhs
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Mihajlo Novakovic
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Dennis J Pyper
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Nusrat S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Magdalena Riad
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tali Scherf
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | | | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alvaro Simba-Lahuasi
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Maria A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Heidi Zetzsche
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
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16
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Binas O, de Jesus V, Landgraf T, Völklein AE, Martins J, Hymon D, Kaur Bains J, Berg H, Biedenbänder T, Fürtig B, Lakshmi Gande S, Niesteruk A, Oxenfarth A, Shahin Qureshi N, Schamber T, Schnieders R, Tröster A, Wacker A, Wirmer-Bartoschek J, Wirtz Martin MA, Stirnal E, Azzaoui K, Richter C, Sreeramulu S, José Blommers MJ, Schwalbe H. 19 F NMR-Based Fragment Screening for 14 Different Biologically Active RNAs and 10 DNA and Protein Counter-Screens. Chembiochem 2020; 22:423-433. [PMID: 32794266 PMCID: PMC7436455 DOI: 10.1002/cbic.202000476] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/11/2020] [Indexed: 11/17/2022]
Abstract
We report here the nuclear magnetic resonance 19F screening of 14 RNA targets with different secondary and tertiary structure to systematically assess the druggability of RNAs. Our RNA targets include representative bacterial riboswitches that naturally bind with nanomolar affinity and high specificity to cellular metabolites of low molecular weight. Based on counter‐screens against five DNAs and five proteins, we can show that RNA can be specifically targeted. To demonstrate the quality of the initial fragment library that has been designed for easy follow‐up chemistry, we further show how to increase binding affinity from an initial fragment hit by chemistry that links the identified fragment to the intercalator acridine. Thus, we achieve low‐micromolar binding affinity without losing binding specificity between two different terminator structures.
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Affiliation(s)
- Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Albrecht Eduard Völklein
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jason Martins
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Hannes Berg
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Thomas Biedenbänder
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Santosh Lakshmi Gande
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Anna Niesteruk
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Alix Tröster
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Kamal Azzaoui
- Saverna Therapeutics, Gewerbestrasse 24, 4123, Allschwil, Switzerland
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | | | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
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17
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Schlundt A, Wirtz MA, Knezic B, Hengesbach M, Fürtig B, Weigand JE, Wöhnert J, Ferner J, Saxena K, Wacker A, Richter C, Sreeramulu S, Wirmer-Bartoschek J, Schwalbe H. Gemeinschaftlich in Krisenzeiten: NMR-Strukturbiologie gegen COVID-19. Biospektrum 2020; 26:440-441. [PMID: 32834541 PMCID: PMC7318729 DOI: 10.1007/s12268-020-1396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Universität Frankfurt a. M., Max-von-Laue-Straße 7, D-60438 Frankfurt a. M., Deutschland
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18
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Wirmer-Bartoschek J, Bendel LE, Jonker HRA, Grün JT, Papi F, Bazzicalupi C, Messori L, Gratteri P, Schwalbe H. Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding. Angew Chem Int Ed Engl 2017; 56:7102-7106. [DOI: 10.1002/anie.201702135] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 03/31/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Lars Erik Bendel
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Francesco Papi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Carla Bazzicalupi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Luigi Messori
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Paola Gratteri
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco; Salute del Bambino (NEUROFARBA); Università degli Studi di Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
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19
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Wirmer-Bartoschek J, Bendel LE, Jonker HRA, Grün JT, Papi F, Bazzicalupi C, Messori L, Gratteri P, Schwalbe H. Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702135] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Lars Erik Bendel
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
| | - Francesco Papi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Carla Bazzicalupi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Luigi Messori
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI) Italy
| | - Paola Gratteri
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco; Salute del Bambino (NEUROFARBA); Università degli Studi di Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue-Strasse 7 60439 Frankfurt Germany
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20
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Henker J, Wirmer-Bartoschek J, Bendel LE, Xiang Y, Fu C, Harms K, Schwalbe H, Meggers E. Progress in the Synthesis and Bioactivity of Hexacoordinate Silicon(IV) Complexes. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600953] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jens Henker
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35043 Marburg Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue Strasse 7 60438 Frankfurt Germany
| | - Lars Erik Bendel
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue Strasse 7 60438 Frankfurt Germany
| | - Yonggang Xiang
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35043 Marburg Germany
| | - Chen Fu
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35043 Marburg Germany
| | - Klaus Harms
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35043 Marburg Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Center of Biomolecular Magnetic Resonance (BMRZ); Goethe University Frankfurt/Main; Max-von-Laue Strasse 7 60438 Frankfurt Germany
| | - Eric Meggers
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35043 Marburg Germany
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Abstract
Tied up in knots: The crystal structure of a DNA enzyme in its post-catalytic state was solved. The results provide insight into the structural possibilities for DNA and the mechanism of DNA catalysis.
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Affiliation(s)
- Julia Wirmer-Bartoschek
- Institut für Organische Chemie und Chemische Biologie, Biomolekulares Magnetresonanz-Zentrum (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Biomolekulares Magnetresonanz-Zentrum (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany.
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Sziegat F, Silvers R, Hähnke M, Jensen MR, Blackledge M, Wirmer-Bartoschek J, Schwalbe H. Disentangling the Coil: Modulation of Conformational and Dynamic Properties by Site-Directed Mutation in the Non-Native State of Hen Egg White Lysozyme. Biochemistry 2012; 51:3361-72. [DOI: 10.1021/bi300222f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Friederike Sziegat
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt a. M., Max-von-Laue-Straße
7, D-60438 Frankfurt, Germany
| | - Robert Silvers
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt a. M., Max-von-Laue-Straße
7, D-60438 Frankfurt, Germany
| | - Martin Hähnke
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt a. M., Max-von-Laue-Straße
7, D-60438 Frankfurt, Germany
| | - Malene Ringkjøbing Jensen
- Protein Dynamics and Flexibility by NMR, Institut de Biologie Structurale
Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075, 41 Rue Jules Horowitz, Grenoble 38027, France
| | - Martin Blackledge
- Protein Dynamics and Flexibility by NMR, Institut de Biologie Structurale
Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075, 41 Rue Jules Horowitz, Grenoble 38027, France
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt a. M., Max-von-Laue-Straße
7, D-60438 Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt a. M., Max-von-Laue-Straße
7, D-60438 Frankfurt, Germany
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23
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Silvers R, Sziegat F, Tachibana H, Segawa SI, Whittaker S, Günther UL, Gabel F, Huang JR, Blackledge M, Wirmer-Bartoschek J, Schwalbe H. Modulation of structure and dynamics by disulfide bond formation in unfolded states. J Am Chem Soc 2012; 134:6846-54. [PMID: 22414027 DOI: 10.1021/ja3009506] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During oxidative folding, the formation of disulfide bonds has profound effects on guiding the protein folding pathway. Until now, comparatively little is known about the changes in the conformational dynamics in folding intermediates of proteins that contain only a subset of their native disulfide bonds. In this comprehensive study, we probe the conformational landscape of non-native states of lysozyme containing a single native disulfide bond utilizing nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), circular dichroism (CD) data, and modeling approaches. The impact on conformational dynamics varies widely depending on the loop size of the single disulfide variants and deviates significantly from random coil predictions for both NMR and SAXS data. From these experiments, we conclude that the introduction of single disulfides spanning a large portion of the polypeptide chain shifts the structure and dynamics of hydrophobic core residues of the protein so that these regions exhibit levels of order comparable to the native state on the nanosecond time scale.
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Affiliation(s)
- Robert Silvers
- Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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Buck J, Wacker A, Warkentin E, Wöhnert J, Wirmer-Bartoschek J, Schwalbe H. Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain. Nucleic Acids Res 2011; 39:9768-78. [PMID: 21890900 PMCID: PMC3239184 DOI: 10.1093/nar/gkr664] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket. In addition, it often crucially depends on the stability of peripheral structural elements. The ligand-bound complex of the guanine-sensing riboswitch from Bacillus subtilis, for example, is stabilized by extensive interactions between apical loop regions of the aptamer domain. Previously, we have shown that destabilization of this tertiary loop–loop interaction abrogates ligand binding of the G37A/C61U-mutant aptamer domain (Gswloop) in the absence of Mg2+. However, if Mg2+ is available, ligand-binding capability is restored by a population shift of the ground-state RNA ensemble toward RNA conformations with pre-formed loop–loop interactions. Here, we characterize the striking influence of long-range tertiary structure on RNA folding kinetics and on ligand-bound complex structure, both by X-ray crystallography and time-resolved NMR. The X-ray structure of the ligand-bound complex reveals that the global architecture is almost identical to the wild-type aptamer domain. The population of ligand-binding competent conformations in the ground-state ensemble of Gswloop is tunable through variation of the Mg2+ concentration. We quantitatively describe the influence of distinct Mg2+ concentrations on ligand-induced folding trajectories both by equilibrium and time-resolved NMR spectroscopy at single-residue resolution.
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Affiliation(s)
- Janina Buck
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7 & 9, 60438 Frankfurt am Main, Germany
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Sziegat F, Wirmer-Bartoschek J, Schwalbe H. Characteristics of Human Lysozyme and Its Disease-Related Mutants in their Unfolded States. Angew Chem Int Ed Engl 2011; 50:5514-8. [DOI: 10.1002/anie.201008040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 04/06/2011] [Indexed: 11/10/2022]
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26
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Sziegat F, Wirmer-Bartoschek J, Schwalbe H. Characteristics of Human Lysozyme and Its Disease-Related Mutants in their Unfolded States. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Gerum C, Silvers R, Wirmer-Bartoschek J, Schwalbe H. Unfolded-state structure and dynamics influence the fibril formation of human prion protein. Angew Chem Int Ed Engl 2010; 48:9452-6. [PMID: 19882604 DOI: 10.1002/anie.200903771] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christian Gerum
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-Universität, 60438 Frankfurt, Germany
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28
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Gerum C, Silvers R, Wirmer-Bartoschek J, Schwalbe H. Unfolded-State Structure and Dynamics Influence the Fibril Formation of Human Prion Protein. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903771] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Hanessian S, Szychowski J, Adhikari SS, Vasquez G, Kandasamy P, Swayze EE, Migawa MT, Ranken R, François B, Wirmer-Bartoschek J, Kondo J, Westhof E. Structure-based design, synthesis, and A-site rRNA cocrystal complexes of functionally novel aminoglycoside antibiotics: C2" ether analogues of paromomycin. J Med Chem 2007. [PMID: 17458946 DOI: 10.1021/jm061200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of 2"-O-substituted ether analogues of paromomycin were prepared based on new site-selective functionalizations. X-ray cocrystal complexes of several such analogues revealed a new mode of binding in the A-site rRNA, whereby rings I and II adopted the familiar orientation and position previously observed with paromomycin, but rings III and IV were oriented differently. With few exceptions, all of the new analogues showed potent inhibitory activity equal or better than paromomycin against a sensitive strain of S. aureus. Single digit microM MIC values were obtained against E. coli, with some of the ether appendages containing polar or basic end groups. Two analogues showed excellent survival rate in a mouse septicemia protection assay. Preliminary histopathological analysis of the kidney showed no overt signs of toxicity, while controls with neomycin and kanamycin were toxic at lower doses.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, C. P. 6128, Succ. Centre-Ville, Montréal, P. Q., Canada.
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Hanessian S, Szychowski J, Adhikari SS, Vasquez G, Kandasamy P, Swayze EE, Migawa MT, Ranken R, François B, Wirmer-Bartoschek J, Kondo J, Westhof E. Structure-based design, synthesis, and A-site rRNA cocrystal complexes of functionally novel aminoglycoside antibiotics: C2" ether analogues of paromomycin. J Med Chem 2007; 50:2352-69. [PMID: 17458946 DOI: 10.1021/jm061200+] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of 2"-O-substituted ether analogues of paromomycin were prepared based on new site-selective functionalizations. X-ray cocrystal complexes of several such analogues revealed a new mode of binding in the A-site rRNA, whereby rings I and II adopted the familiar orientation and position previously observed with paromomycin, but rings III and IV were oriented differently. With few exceptions, all of the new analogues showed potent inhibitory activity equal or better than paromomycin against a sensitive strain of S. aureus. Single digit microM MIC values were obtained against E. coli, with some of the ether appendages containing polar or basic end groups. Two analogues showed excellent survival rate in a mouse septicemia protection assay. Preliminary histopathological analysis of the kidney showed no overt signs of toxicity, while controls with neomycin and kanamycin were toxic at lower doses.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, C. P. 6128, Succ. Centre-Ville, Montréal, P. Q., Canada.
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