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Hutchison MT, Bellomo G, Cherepanov A, Stirnal E, Fürtig B, Richter C, Linhard V, Gurewitsch E, Lelli M, Morgner N, Schrader T, Schwalbe H. Modulation of Aβ42 Aggregation Kinetics and Pathway by Low-Molecular-Weight Inhibitors. Chembiochem 2023; 24:e202200760. [PMID: 36652672 DOI: 10.1002/cbic.202200760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
The aggregation of amyloid-β 42 (Aβ42) is directly related to the pathogenesis of Alzheimer's disease. Here, we have investigated the early stages of the aggregation process, during which most of the cytotoxic species are formed. Aβ42 aggregation kinetics, characterized by the quantification of Aβ42 monomer consumption, were tracked by real-time solution NMR spectroscopy (RT-NMR) allowing the impact that low-molecular-weight (LMW) inhibitors and modulators exert on the aggregation process to be analysed. Distinct differences in the Aβ42 kinetic profiles were apparent and were further investigated kinetically and structurally by using thioflavin T (ThT) and transmission electron microscopy (TEM), respectively. LMW inhibitors were shown to have a differential impact on early-state aggregation. Insight provided here could direct future therapeutic design based on kinetic profiling of the process of fibril formation.
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Affiliation(s)
- Marie-Theres Hutchison
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Giovanni Bellomo
- Laboratory of Clinical Neurochemistry Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, Italy
| | - Alexey Cherepanov
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, 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/Main, 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/Main, Germany
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Elina Gurewitsch
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Moreno Lelli
- Chemistry Department, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.,Magnetic Resonance Center (CERM/CIRMMP), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Nina Morgner
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Thomas Schrader
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, 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/Main, Germany
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2
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Sudakov A, Knezic B, Hengesbach M, Fürtig B, Stirnal E, Schwalbe H. Site-Specific Labeling of RNAs with Modified and 19 F-Labeled Nucleotides by Chemo-Enzymatic Synthesis. Chemistry 2023; 29:e202203368. [PMID: 36594705 DOI: 10.1002/chem.202203368] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/04/2023]
Abstract
More than 170 post-transcriptional modifications of RNAs have currently been identified. Detailed biophysical investigations of these modifications have been limited since large RNAs containing these post-transcriptional modifications are difficult to produce. Further, adequate readout of spectroscopic fingerprints are important, necessitating additional labeling procedures beyond the naturally occurring RNA modifications. Here, we report the chemo-enzymatic synthesis of RNA modifications and several structurally similar fluorine-modified analogs further optimizing a recently developed methodology.[1] This chemo-enzymatic method allows synthesis of also large RNAs. We were able to incorporate 16 modified nucleotides and 6 19 F-labeled nucleotides. To showcase the applicability of such modified large RNAs, we incorporated a 19 F-labeled cytidine into the aptamer domain of the 2'dG sensing riboswitch (2'dG-sw) from Mesoplasma florum, enabling characterizing RNA fold, ligand binding and kinetics. Thanks to the large chemical shift dispersion of 19 F, we can detect conformational heterogeneity in the apo state of the riboswitch.
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Affiliation(s)
- Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
| | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7+9, 60438, Frankfurt, Germany
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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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4
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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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5
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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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6
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Sreeramulu S, Richter C, Berg H, Wirtz Martin MA, Ceylan B, Matzel T, Adam J, Altincekic N, Azzaoui K, Bains JK, Blommers MJJ, Ferner J, Fürtig B, Göbel M, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Martins JN, Mertinkus KR, Niesteruk A, Peter SA, Pyper DJ, Qureshi NS, Scheffer U, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Tröster A, Vögele J, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Wöhnert J, Schwalbe H. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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7
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Sreeramulu S, Richter C, Berg H, Wirtz Martin MA, Ceylan B, Matzel T, Adam J, Altincekic N, Azzaoui K, Bains JK, Blommers MJJ, Ferner J, Fürtig B, Göbel M, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Martins JN, Mertinkus KR, Niesteruk A, Peter SA, Pyper DJ, Qureshi NS, Scheffer U, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Tröster A, Vögele J, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Wöhnert J, Schwalbe H. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS-CoV-2 Genome. Angew Chem Int Ed Engl 2021; 60:19191-19200. [PMID: 34161644 PMCID: PMC8426693 DOI: 10.1002/anie.202103693] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/03/2021] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 contains a positive single-stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS-CoV and SARS-CoV-2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex-vivo structural probing experiments. These elements contain non-base-paired regions that potentially harbor ligand-binding pockets. Here, we performed an NMR-based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1 H-based 1D NMR binding assays. The screening identified common as well as RNA-element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS-CoV-2.
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8
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Elamri I, Abdellaoui C, Bains JK, Hohmann KF, Gande SL, Stirnal E, Wachtveitl J, Schwalbe H. Wavelength-Selective Uncaging of Two Different Photoresponsive Groups on One Effector Molecule for Light-Controlled Activation and Deactivation. J Am Chem Soc 2021; 143:10596-10603. [PMID: 34236854 DOI: 10.1021/jacs.1c02817] [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: 01/28/2023]
Abstract
Photocleavable protecting groups (PPGs) play a pivotal role in numerous studies. They enable controlled release of small effector molecules to induce biochemical function. The number of PPGs attached to a variety of effector molecules has grown rapidly in recent years satisfying the high demand for new applications. However, until now molecules carrying PPGs have been designed to activate function only in a single direction, namely the release of the effector molecule. Herein, we present the new approach Two-PPGs-One-Molecule (TPOM) that exploits the orthogonal photolysis of two photoprotecting groups to first release the effector molecule and then to modify it to suppress its induced effect. The moiety resembling the tyrosyl side chain of the translation inhibitor puromycin was synthetically modified to the photosensitive ortho-nitrophenylalanine that cyclizes upon near UV-irradiation to an inactive puromycin cinnoline derivative. Additionally, the modified puromycin analog was protected by the thio-coumarylmethyl group as the second PPG. This TPOM strategy allows an initial wavelength-selective activation followed by a second light-induced deactivation. Both photolysis processes were spectroscopically studied in the UV/vis- and IR-region. In combination with quantum-chemical calculations and time-resolved NMR spectroscopy, the photoproducts of both activation and deactivation steps upon illumination were characterized. We further probed the translation inhibition effect of the new synthesized puromycin analog upon light activation/deactivation in a cell-free GFP translation assay. TPOM as a new method for precise triggering activation/deactivation of effector molecules represents a valuable addition for the control of biological processes with light.
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Affiliation(s)
- Isam Elamri
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Chahinez Abdellaoui
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Jasleen Kaur Bains
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Katharina Felicitas Hohmann
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Santosh Lakshmi Gande
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Elke Stirnal
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany
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9
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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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10
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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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11
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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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12
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Lieblein T, Zangl R, Martin J, Hoffmann J, Hutchison MJ, Stark T, Stirnal E, Schrader T, Schwalbe H, Morgner N. Structural rearrangement of amyloid-β upon inhibitor binding suppresses formation of Alzheimer's disease related oligomers. eLife 2020; 9:59306. [PMID: 33095161 PMCID: PMC7682991 DOI: 10.7554/elife.59306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 05/25/2020] [Accepted: 10/22/2020] [Indexed: 01/24/2023] Open
Abstract
The formation of oligomers of the amyloid-β peptide plays a key role in the onset of Alzheimer's disease. We describe herein the investigation of disease-relevant small amyloid-β oligomers by mass spectrometry and ion mobility spectrometry, revealing functionally relevant structural attributes. In particular, we can show that amyloid-β oligomers develop in two distinct arrangements leading to either neurotoxic oligomers and fibrils or non-toxic amorphous aggregates. Comprehending the key-attributes responsible for those pathways on a molecular level is a pre-requisite to specifically target the peptide's tertiary structure with the aim to promote the emergence of non-toxic aggregates. Here, we show for two fibril inhibiting ligands, an ionic molecular tweezer and a hydrophobic peptide that despite their different interaction mechanisms, the suppression of the fibril pathway can be deduced from the disappearance of the corresponding structure of the first amyloid-β oligomers.
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Affiliation(s)
- Tobias Lieblein
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Rene Zangl
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Janosch Martin
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Jan Hoffmann
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Marie J Hutchison
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Tina Stark
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Elke Stirnal
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Thomas Schrader
- University of Duisburg-Essen, Institute of Organic Chemistry, Essen, Germany
| | - Harald Schwalbe
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Nina Morgner
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
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13
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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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14
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Elamri I, Heumüller M, Herzig L, Stirnal E, Wachtveitl J, Schuman EM, Schwalbe H. Cover Feature: A New Photocaged Puromycin for an Efficient Labeling of Newly Translated Proteins in Living Neurons (ChemBioChem 23/2018). Chembiochem 2018. [DOI: 10.1002/cbic.201800691] [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: 11/10/2022]
Affiliation(s)
- Isam Elamri
- Center for Biomolecular Magnetic ResonanceInstitute of Organic Chemistry and Chemical BiologyGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Maximilian Heumüller
- Department of Synaptic Plasticity, MPI for Brain ResearchGoethe-University Frankfurt am Main Max-von-Laue-Strasse 4 60438 Frankfurt am Mail Germany
| | - Lisa‐M. Herzig
- Institute of Physical and Theoretical ChemistryGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Elke Stirnal
- Center for Biomolecular Magnetic ResonanceInstitute of Organic Chemistry and Chemical BiologyGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical ChemistryGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Erin M. Schuman
- Department of Synaptic Plasticity, MPI for Brain ResearchGoethe-University Frankfurt am Main Max-von-Laue-Strasse 4 60438 Frankfurt am Mail Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic ResonanceInstitute of Organic Chemistry and Chemical BiologyGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
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15
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Elamri I, Heumüller M, Herzig L, Stirnal E, Wachtveitl J, Schuman EM, Schwalbe H. A New Photocaged Puromycin for an Efficient Labeling of Newly Translated Proteins in Living Neurons. Chembiochem 2018; 19:2458-2464. [DOI: 10.1002/cbic.201800408] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/11/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Isam Elamri
- Center for Biomolecular Magnetic ResonanceInstitute of Organic Chemistry and Chemical BiologyGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Maximilian Heumüller
- Department of Synaptic Plasticity, MPI for Brain ResearchGoethe-University Frankfurt am Main Max-von-Laue-Strasse 4 60438 Frankfurt am Mail Germany
| | - Lisa‐M. Herzig
- Institute of Physical and Theoretical ChemistryGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Elke Stirnal
- Center for Biomolecular Magnetic ResonanceInstitute of Organic Chemistry and Chemical BiologyGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical ChemistryGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Erin M. Schuman
- Department of Synaptic Plasticity, MPI for Brain ResearchGoethe-University Frankfurt am Main Max-von-Laue-Strasse 4 60438 Frankfurt am Mail Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic ResonanceInstitute of Organic Chemistry and Chemical BiologyGoethe-University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
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Schnorr KA, Gophane DB, Helmling C, Cetiner E, Pasemann K, Fürtig B, Wacker A, Qureshi NS, Gränz M, Barthelmes D, Jonker HRA, Stirnal E, Sigurdsson ST, Schwalbe H. Impact of spin label rigidity on extent and accuracy of distance information from PRE data. J Biomol NMR 2017; 68:53-63. [PMID: 28500543 DOI: 10.1007/s10858-017-0114-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Paramagnetic relaxation enhancement (PRE) is a versatile tool for NMR spectroscopic structural and kinetic studies in biological macromolecules. Here, we compare the quality of PRE data derived from two spin labels with markedly different dynamic properties for large RNAs using the I-A riboswitch aptamer domain (78 nt) from Mesoplamsa florum as model system. We designed two I-A aptamer constructs that were spin-labeled by noncovalent hybridization of short spin-labeled oligomer fragments. As an example of a flexible spin label, UreidoU-TEMPO was incorporated into the 3' terminal end of helix P1 while, the recently developed rigid spin-label Çm was incorporated in the 5' terminal end of helix P1. We determined PRE rates obtained from aromatic 13C bound proton intensities and compared these rates to PREs derived from imino proton intensities in this sizeable RNA (~78 nt). PRE restraints derived from both imino and aromatic protons yielded similar data quality, and hence can both be reliably used for PRE determination. For NMR, the data quality derived from the rigid spin label Çm is slightly better than the data quality for the flexible UreidoTEMPO as judged by comparison of the structural agreement with the I-A aptamer crystal structure (3SKI).
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Affiliation(s)
- K A Schnorr
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - D B Gophane
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| | - C Helmling
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - E Cetiner
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - K Pasemann
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - B Fürtig
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - A Wacker
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - N S Qureshi
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - M Gränz
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - D Barthelmes
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - H R A Jonker
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - E Stirnal
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - S Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| | - H Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany.
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Noeske J, Richter C, Stirnal E, Schwalbe H, Wöhnert J. Phosphate-Group Recognition by the Aptamer Domain of the Thiamine Pyrophosphate Sensing Riboswitch. Chembiochem 2006; 7:1451-6. [PMID: 16871614 DOI: 10.1002/cbic.200600151] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [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: 12/29/2022]
Abstract
Riboswitches are highly structured RNA elements that control gene expression by binding directly to small metabolite molecules. Remarkably, many of these metabolites contain negatively charged phosphate groups that contribute significantly to the binding affinity. An example is the thiamine pyrophosphate-sensing riboswitch in the 5'-untranslated region of the E. coli thiM mRNA. This riboswitch binds, in order of decreasing affinity, to thiamine pyrophosphate (TPP), thiamine monophosphate (TMP), and thiamine, which contain two, one, and no phosphate groups, respectively. We examined the binding of TPP and TMP to this riboswitch by using (31)P NMR spectroscopy. Chemical-shift changes were observed for the alpha- and beta-phosphate group of TPP and the phosphate group of TMP upon RNA binding; this indicates that they are in close contact with the RNA. Titration experiments with paramagnetic Mn(2+) ions revealed strong line-broadening effects for both (31)P signals of the bound TPP; this indicates a Mg(2+) binding site in close proximity and suggests that the phosphate group(s) of the ligand is/are recognized in a magnesium ion-mediated manner by the RNA.
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Affiliation(s)
- Jonas Noeske
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann-Wolfgang-Goethe-University, 60438 Frankfurt am Main, Germany
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