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1. Analogical Transfer of Tool-Dependent Problem Solving in Toddlers: A Replication and Extension Study

Author: Bains, Jasleen, Chang, Kristen, Liu, Rachel, Pierce, Midori, and Vedagarbha, Namrata
Subjects: analogical transfer, functional tool-dependent problem-solving, long-term memory
Abstract: Analogical transfer, or the ability to use similar solutions to solve seemingly dissimilar problems, has been studied in children using tasks that require the support of long-term memory. However, the transfer of solutions that require the use of tools, or objects with certain functional parts, has not been studied in great depth. This paper replicates and extends upon data collected from a novel study that investigated the role of age and memory on analogical transfer across children who attend public preschools in southern Sweden (Bobrowicz et al., 2020). The purpose of this study was to integrate analogical transfer with functional tool-dependent problem solving and study how both skills develop in toddlerhood. The replication yielded similar results to the original experiment in all five hypotheses tested, with the main finding being that age is not a significant predictor of being able to display analogical transfer from task to task. As an extension to the variables examined in the study, two additional models were created to see whether spending more time with the functional tool or with the relevant apparatus leads to a greater percentage of successes in solving the test task, but there were no significant differences found in this model.
Published: 2022

2. Long-term Outcomes Among Patients Treated With Physician Modified Endograft for Juxtarenal Aortic Aneurysms

Author: Phocas, Alexandra, primary, Anderson, Gerald, additional, Bains, Jasleen, additional, Larimore, Allison, additional, Singh, Niten, additional, Starnes, Benjamin, additional, and Zettervall, Sara L., additional
Published: 2024
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3. Structure of an internal loop motif with three consecutive U•U mismatches from stem–loop 1 in the 3′-UTR of the SARS-CoV-2 genomic RNA

Author: Vögele, Jennifer, primary, Duchardt-Ferner, Elke, additional, Bains, Jasleen Kaur, additional, Knezic, Bozana, additional, Wacker, Anna, additional, Sich, Christian, additional, Weigand, Julia E, additional, Šponer, Jiří, additional, Schwalbe, Harald, additional, Krepl, Miroslav, additional, and Wöhnert, Jens, additional
Published: 2024
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4. 1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5′-UTR of SARS-CoV-2

Author: Mertinkus, Klara R., Grün, J. Tassilo, Altincekic, Nadide, Bains, Jasleen Kaur, Ceylan, Betül, Ferner, Jan-Peter, Frydman, Lucio, Fürtig, Boris, Hengesbach, Martin, Hohmann, Katharina F., Hymon, Daniel, Kim, Jihyun, Knezic, Božana, Novakovic, Mihajlo, Oxenfarth, Andreas, Peter, Stephen A., Qureshi, Nusrat S., Richter, Christian, Scherf, Tali, Schlundt, Andreas, Schnieders, Robbin, Schwalbe, Harald, Stirnal, Elke, Sudakov, Alexey, Vögele, Jennifer, Wacker, Anna, Weigand, Julia E., Wirmer-Bartoschek, Julia, Martin, Maria A. Wirtz, and Wöhnert, Jens
Published: 2022
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5. HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex

Author: Leisegang, Matthias S., Bains, Jasleen Kaur, Seredinski, Sandra, Oo, James A., Krause, Nina M., Kuo, Chao-Chung, Günther, Stefan, Sentürk Cetin, Nevcin, Warwick, Timothy, Cao, Can, Boos, Frederike, Izquierdo Ponce, Judit, Haydar, Shaza, Bednarz, Rebecca, Valasarajan, Chanil, Fuhrmann, Dominik C., Preussner, Jens, Looso, Mario, Pullamsetti, Soni S., Schulz, Marcel H., Jonker, Hendrik R. A., Richter, Christian, Rezende, Flávia, Gilsbach, Ralf, Pflüger-Müller, Beatrice, Wittig, Ilka, Grummt, Ingrid, Ribarska, Teodora, Costa, Ivan G., Schwalbe, Harald, and Brandes, Ralf P.
Published: 2022
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6. Farnesol induces protection against murine CNS inflammatory demyelination and modifies gut microbiome

Author: Sell, Lacey B., Ramelow, Christina C., Kohl, Hannah M., Hoffman, Kristina, Bains, Jasleen K., Doyle, William J., Strawn, Kevin D., Hevrin, Theresa, Kirby, Trevor O., Gibson, K. Michael, Roullet, Jean-Baptiste, and Ochoa-Repáraz, Javier
Published: 2022
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7. Recognition of Gurmukhi Signboard Image Classes Based on Static and Dynamic Feature Sets

Author: Bains, Jasleen Kaur, Singh, Sukhdeep, Sharma, Anuj, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Babu, R. Venkatesh, editor, Prasanna, Mahadeva, editor, and Namboodiri, Vinay P., editor
Published: 2020
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8. 1H, 13C, 15N and 31P chemical shift assignment for stem-loop 4 from the 5′-UTR of SARS-CoV-2

Author: Vögele, Jennifer, Ferner, Jan-Peter, Altincekic, Nadide, Bains, Jasleen Kaur, Ceylan, Betül, Fürtig, Boris, Grün, J. Tassilo, Hengesbach, Martin, Hohmann, Katharina F., Hymon, Daniel, Knezic, Bozana, Löhr, Frank, Peter, Stephen A., Pyper, Dennis, Qureshi, Nusrat S., Richter, Christian, Schlundt, Andreas, Schwalbe, Harald, Stirnal, Elke, Sudakov, Alexey, Wacker, Anna, Weigand, Julia E., Wirmer-Bartoschek, Julia, Wöhnert, Jens, and Duchardt-Ferner, Elke
Published: 2021
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9. 1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2

Author: Richter, Christian, Hohmann, Katharina F., Toews, Sabrina, Mathieu, Daniel, Altincekic, Nadide, Bains, Jasleen Kaur, Binas, Oliver, Ceylan, Betül, Duchardt-Ferner, Elke, Ferner, Jan, Fürtig, Boris, Grün, J. Tassilo, Hengesbach, Martin, Hymon, Daniel, Jonker, Hendrik R. A., Knezic, Bozana, Korn, Sophie M., Landgraf, Tom, Löhr, Frank, Peter, Stephen A., Pyper, Dennis J., Qureshi, Nusrat S., Schlundt, Andreas, Schnieders, Robbin, Stirnal, Elke, Sudakov, Alexey, Vögele, Jennifer, Weigand, Julia E., Wirmer-Bartoschek, Julia, Witt, Kerstin, Wöhnert, Jens, Schwalbe, Harald, and Wacker, Anna
Published: 2021
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10. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development

Author: Berg, Hannes, Wirtz Martin, Maria A., Altincekic, Nadide, Alshamleh, Islam, Kaur Bains, Jasleen, Blechar, Julius, Ceylan, Betül, Jesus, Vanessa de, Dhamotharan, Karthikeyan, Fuks, Christin, Gande, Santosh L., Hargittay, Bruno, Hohmann, Katharina F., Hutchison, Marie T., Korn, Sophie Marianne, Krishnathas, Robin, Kutz, Felicitas, Linhard, Verena, Matzel, Tobias, Meiser, Nathalie, Niesteruk, Anna, Pyper, Dennis J., Schulte, Linda, Trucks, Sven, Azzaoui, Kamal, Blommers, Marcel J. J., Gadiya, Yojana, Karki, Reagon, Zaliani, Andrea, Gribbon, Philip, Silva Almeida, Marcius da, Dinis Anobom, Cristiane, Bula, Anna L., Bütikofer, Matthias, Putinhon Caruso, Ícaro, Caterina Felli, Isabella, Da Poian, Andrea T., Cardoso de Amorim, Gisele, Fourkiotis, Nikolaos K., Gallo, Angelo, Ghosh, Dhiman, Gomes‐Neto, Francisco, Gorbatyuk, Oksana, Hao, Bing, Kurauskas, Vilius, Lecoq, Lauriane, Li, Yunfeng, Cunha Mebus‐Antunes, Nathane, Mompeán, Miguel, Cristtina Neves‐Martins, Thais, Ninot‐Pedrosa, Martí, Pinheiro, Anderson S., Pontoriero, Letizia, Pustovalova, Yulia, Riek, Roland, Robertson, Angus J., Jose Abi Saad, Marie, Treviño, Miguel Á., Tsika, Aikaterini C., Almeida, Fabio C. L., Bax, Ad, Henzler‐Wildman, Katherine, Hoch, Jeffrey C., Jaudzems, Kristaps, Laurents, Douglas V., Orts, Julien, Pierattelli, Roberta, Spyroulias, Georgios A., Duchardt‐Ferner, Elke, Ferner, Jan, Fürtig, Boris, Hengesbach, Martin, Löhr, Frank, Qureshi, Nusrat, Richter, Christian, Saxena, Krishna, Schlundt, Andreas, Sreeramulu, Sridhar, Wacker, Anna, Weigand, Julia E., Wirmer‐Bartoschek, Julia, Wöhnert, Jens, Schwalbe, Harald, Berg, Hannes, Wirtz Martin, Maria A., Altincekic, Nadide, Alshamleh, Islam, Kaur Bains, Jasleen, Blechar, Julius, Ceylan, Betül, Jesus, Vanessa de, Dhamotharan, Karthikeyan, Fuks, Christin, Gande, Santosh L., Hargittay, Bruno, Hohmann, Katharina F., Hutchison, Marie T., Korn, Sophie Marianne, Krishnathas, Robin, Kutz, Felicitas, Linhard, Verena, Matzel, Tobias, Meiser, Nathalie, Niesteruk, Anna, Pyper, Dennis J., Schulte, Linda, Trucks, Sven, Azzaoui, Kamal, Blommers, Marcel J. J., Gadiya, Yojana, Karki, Reagon, Zaliani, Andrea, Gribbon, Philip, Silva Almeida, Marcius da, Dinis Anobom, Cristiane, Bula, Anna L., Bütikofer, Matthias, Putinhon Caruso, Ícaro, Caterina Felli, Isabella, Da Poian, Andrea T., Cardoso de Amorim, Gisele, Fourkiotis, Nikolaos K., Gallo, Angelo, Ghosh, Dhiman, Gomes‐Neto, Francisco, Gorbatyuk, Oksana, Hao, Bing, Kurauskas, Vilius, Lecoq, Lauriane, Li, Yunfeng, Cunha Mebus‐Antunes, Nathane, Mompeán, Miguel, Cristtina Neves‐Martins, Thais, Ninot‐Pedrosa, Martí, Pinheiro, Anderson S., Pontoriero, Letizia, Pustovalova, Yulia, Riek, Roland, Robertson, Angus J., Jose Abi Saad, Marie, Treviño, Miguel Á., Tsika, Aikaterini C., Almeida, Fabio C. L., Bax, Ad, Henzler‐Wildman, Katherine, Hoch, Jeffrey C., Jaudzems, Kristaps, Laurents, Douglas V., Orts, Julien, Pierattelli, Roberta, Spyroulias, Georgios A., Duchardt‐Ferner, Elke, Ferner, Jan, Fürtig, Boris, Hengesbach, Martin, Löhr, Frank, Qureshi, Nusrat, Richter, Christian, Saxena, Krishna, Schlundt, Andreas, Sreeramulu, Sridhar, Wacker, Anna, Weigand, Julia E., Wirmer‐Bartoschek, Julia, Wöhnert, Jens, and Schwalbe, Harald
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.
Published: 2024

11. 1H, 13C and 15N chemical shift assignment of the stem-loop 5a from the 5′-UTR of SARS-CoV-2

Author: Schnieders, Robbin, Peter, Stephen A., Banijamali, Elnaz, Riad, Magdalena, Altincekic, Nadide, Bains, Jasleen Kaur, Ceylan, Betül, Fürtig, Boris, Grün, J. Tassilo, Hengesbach, Martin, Hohmann, Katharina F., Hymon, Daniel, Knezic, Bozana, Oxenfarth, Andreas, Petzold, Katja, Qureshi, Nusrat S., Richter, Christian, Schlagnitweit, Judith, Schlundt, Andreas, Schwalbe, Harald, Stirnal, Elke, Sudakov, Alexey, Vögele, Jennifer, Wacker, Anna, Weigand, Julia E., Wirmer-Bartoschek, Julia, and Wöhnert, Jens
Published: 2021
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12. Biophysical Investigation of RNA ⋅ DNA : DNA Triple Helix and RNA : DNA Heteroduplex Formation by the lncRNAs MEG3 and Fendrr.

Author: Krause, Nina M., Bains, Jasleen K., Blechar, Julius, Richter, Christian, Bessi, Irene, Grote, Phillip, Leisegang, Matthias S., Brandes, Ralf P., and Schwalbe, Harald
Published: 2024
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13. Dynamic features based stroke recognition system for signboard images of Gurmukhi text

Author: Bains, Jasleen Kaur, Singh, Sukhdeep, and Sharma, Anuj
Published: 2021
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14. Switching at the ribosome: riboswitches need rProteins as modulators to regulate translation

Author: de Jesus, Vanessa, Qureshi, Nusrat S., Warhaut, Sven, Bains, Jasleen K., Dietz, Marina S., Heilemann, Mike, Schwalbe, Harald, and Fürtig, Boris
Published: 2021
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15. Fendrr synergizes with Wnt signalling to regulate fibrosis related genes during lung development via its RNA:dsDNA triplex element

Author: Ali, Tamer, primary, Rogala, Sandra, additional, Krause, Nina M, additional, Bains, Jasleen Kaur, additional, Melissari, Maria-Theodora, additional, Währisch, Sandra, additional, Schwalbe, Harald, additional, Herrmann, Bernhard G, additional, and Grote, Phillip, additional
Published: 2023
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16. Biophysical studies of RNA:DNA:DNA triplexes and characterization of riboswitches in cell-free transcription-translation systems

Author: Bains, Jasleen Kaur and Bains, Jasleen Kaur
Abstract: RNA research is very important since RNA molecules are involved in various gene regulatory mechanisms as well as pathways of cell physiology and disease development.1 RNAs have evolved from being considered as carriers of genetic information from DNA to proteins, with the three major types of RNA involved in protein synthesis, including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).2 In addition to the RNAs involved in protein synthesis numerous regulatory non-coding RNAs (ncRNAs) have been discovered in the transcriptome. The regulatory ncRNAs are classified into small ncRNAs (sncRNAs) with transcripts less than 200 nucleotides (nt) and long non-coding RNAs (lncRNAs) with more than 200 nt.3 LncRNAs represent the most diverse and versatile class of ncRNAs that can regulate cellular functions of chromatin modification, transcription, and post-transcription through multiple mechanisms.4 They are involved in the formation of RNA:protein, RNA:RNA and RNA:DNA complexes as part of their gene regulatory mechanism.4,5 The RNA:DNA interactions can be divided into RNA:DNA heteroduplex formation, also called R-loops, and RNA:DNA:DNA triplex formation. In triplex formation, RNA binds to the major groove of double-stranded DNA through Hoogsteen or reverse Hoogsteen hydrogen bonding, resulting in parallel or anti-parallel triplexes, respectively. In vitro studies have confirmed the formation of RNA:DNA:DNA triplexes.6 However, the extent to which these interactions occur in cells and their effects on cellular function are still not understood, which is why these structures are so exciting to study (Chapter I RNA:DNA:DNA Triplexes). This cumulative thesis investigates several functional and regulatory important RNAs. The first project involves the improved biochemical and biophysical characterization of RNA:DNA:DNA triplex formation between lncRNAs of interest and their target genes. Triplex formation was confirmed by a series of experiments including electro, Die Erforschung von RNAs ist von großer Bedeutung, da RNA-Moleküle an verschiedenen Mechanismen der Genregulation sowie an Signalwegen in der Zellphysiologie und bei der Entstehung von Krankheiten beteiligt sind.1 RNAs haben sich von Trägern der genetischen Information von der DNA zu Proteinen entwickelt, wobei die drei wichtigsten RNA-Typen an der Proteinsynthese beteiligt sind: Boten-RNA (mRNA), Transfer-RNA (tRNA) und ribosomale RNA (rRNA).2 Neben den an der Proteinsynthese beteiligten RNAs wurden im Transkriptom zahlreiche regulatorische nicht-kodierende RNAs (ncRNAs) entdeckt. Die regulatorischen ncRNAs werden unterteilt in kurze ncRNAs (sncRNAs) mit Transkripten kürzer als 200 Nukleotide (nt) und lange ncRNAs (lncRNAs) mit Transkripten länger als 200 nt.3 LncRNAs stellen die vielfältigste und vielseitigste Klasse von ncRNAs dar, die durch verschiedene Mechanismen zelluläre Funktionen der Chromatinmodifikation, Transkription und Posttranskription regulieren können.4 Sie sind an der Bildung von RNA:Protein-, RNA:RNA- und RNA:DNA-Komplexen als Teil ihrer Genregulationsmechanismen beteiligt.4,5 Die RNA:DNA Interaktionen können in die Bildung von RNA:DNA Heteroduplexen, auch R-Schleifen genannt und die Bildung von RNA:DNA:DNA Triplexen unterteilt werden. Bei der Triplexbildung bindet die RNA über Hoogsteen oder inverse Hoogsteen Wasserstoffbrücken an die große Furche der doppelsträngigen DNA, was zu parallelen oder anti-parallelen Triplexen führt. In vitro Studien haben die Bildung von RNA:DNA:DNA Triplexen bestätigt. 6 Inwieweit diese Wechselwirkungen in Zellen auftreten und sich auf die Zellfunktionen auswirken, ist noch nicht geklärt, weshalb diese Strukturen für die Forschung von großem Interesse sind (Kapitel I RNA:DNA:DNA Triplexe). In dieser kumulativen Dissertation werden verschiedene funktionell und regulatorisch wichtige RNAs untersucht. Das erste Projekt umfasst die verbesserte biochemische und biophysikalische Charakterisierung von RNA:DNA:DNA Triplexen
Published: 2023

17. Sodium-Glucose Cotransporter 2 (SGLT2) Inhibitors: Benefits Versus Risk

Author: Bains Jasleen, Gupta K Vishal, Malepati Sameera, Molla Fahad, O'Brien Brendan, Santander Deion, and Sudhakar Pemminati
Subjects: General Engineering
Published: 2023

18. Comprehensive Fragment Screening of the SARS-CoV-2 Proteome Explores Novel Chemical Space for Drug Development

Author: Berg, Hannes, Wirtz Martin, Maria A., Altincekic, Nadide, Alshamleh, Islam, Kaur Bains, Jasleen, Blechar, Julius, Ceylan, Betül, de Jesus, Vanessa, Dhamotharan, Karthikeyan, Fuks, Christin, Gande, Santosh L., Hargittay, Bruno, Hohmann, Katharina F., Hutchison, Marie T., Korn, Sophie Marianne, Krishnathas, Robin, Kutz, Felicitas, Linhard, Verena, Matzel, Tobias, Meiser, Nathalie, Bütikofer, Matthias, Ghosh, Dhiman, and Riek, Roland
Subjects: Fragment Screening, SARS-CoV-2, COVID19-NMR, Drug Discovery, NMR Spectroscopy, Protein
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., Angewandte Chemie. International Edition, 61 (46), ISSN:1433-7851, ISSN:1521-3773, ISSN:0570-0833
Published: 2022

19. A universal model of RNA.DNA:DNA triplex formation accurately predicts genome-wide RNA–DNA interactions

Author: Warwick, Timothy, primary, Seredinski, Sandra, additional, Krause, Nina M, additional, Bains, Jasleen Kaur, additional, Althaus, Lara, additional, Oo, James A, additional, Bonetti, Alessandro, additional, Dueck, Anne, additional, Engelhardt, Stefan, additional, Schwalbe, Harald, additional, Leisegang, Matthias S, additional, Schulz, Marcel H, additional, and Brandes, Ralf P, additional
Published: 2022
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20. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development

Author: Berg, Hannes, primary, Wirtz Martin, Maria A., additional, Altincekic, Nadide, additional, Alshamleh, Islam, additional, Kaur Bains, Jasleen, additional, Blechar, Julius, additional, Ceylan, Betül, additional, de Jesus, Vanessa, additional, Dhamotharan, Karthikeyan, additional, Fuks, Christin, additional, Gande, Santosh L., additional, Hargittay, Bruno, additional, Hohmann, Katharina F., additional, Hutchison, Marie T., additional, Marianne Korn, Sophie, additional, Krishnathas, Robin, additional, Kutz, Felicitas, additional, Linhard, Verena, additional, Matzel, Tobias, additional, Meiser, Nathalie, additional, Niesteruk, Anna, additional, Pyper, Dennis J., additional, Schulte, Linda, additional, Trucks, Sven, additional, Azzaoui, Kamal, additional, Blommers, Marcel J. J., additional, Gadiya, Yojana, additional, Karki, Reagon, additional, Zaliani, Andrea, additional, Gribbon, Philip, additional, da Silva Almeida, Marcius, additional, Dinis Anobom, Cristiane, additional, Bula, Anna L., additional, Bütikofer, Matthias, additional, Putinhon Caruso, Ícaro, additional, Caterina Felli, Isabella, additional, Da Poian, Andrea T., additional, Cardoso de Amorim, Gisele, additional, Fourkiotis, Nikolaos K., additional, Gallo, Angelo, additional, Ghosh, Dhiman, additional, Gomes‐Neto, Francisco, additional, Gorbatyuk, Oksana, additional, Hao, Bing, additional, Kurauskas, Vilius, additional, Lecoq, Lauriane, additional, Li, Yunfeng, additional, Cunha Mebus‐Antunes, Nathane, additional, Mompeán, Miguel, additional, Cristtina Neves‐Martins, Thais, additional, Ninot‐Pedrosa, Martí, additional, Pinheiro, Anderson S., additional, Pontoriero, Letizia, additional, Pustovalova, Yulia, additional, Riek, Roland, additional, Robertson, Angus J., additional, Jose Abi Saad, Marie, additional, Treviño, Miguel Á., additional, Tsika, Aikaterini C., additional, Almeida, Fabio C. L., additional, Bax, Ad, additional, Henzler‐Wildman, Katherine, additional, Hoch, Jeffrey C., additional, Jaudzems, Kristaps, additional, Laurents, Douglas V., additional, Orts, Julien, additional, Pierattelli, Roberta, additional, Spyroulias, Georgios A., additional, Duchardt‐Ferner, Elke, additional, Ferner, Jan, additional, Fürtig, Boris, additional, Hengesbach, Martin, additional, Löhr, Frank, additional, Qureshi, Nusrat, additional, Richter, Christian, additional, Saxena, Krishna, additional, Schlundt, Andreas, additional, Sreeramulu, Sridhar, additional, Wacker, Anna, additional, Weigand, Julia E., additional, Wirmer‐Bartoschek, Julia, additional, Wöhnert, Jens, additional, and Schwalbe, Harald, additional
Published: 2022
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21. Prediction of RNA:DNA:DNA triple helix formation using next-generation sequencing data

Author: Warwick, Timothy, primary, Seredinski, Sandra, additional, Krause, Nina, additional, Bains, Jasleen Kaur, additional, Althaus, Lara, additional, Oo, James, additional, Bonetti, Alessandro, additional, Dueck, Anne, additional, Engelhardt, Stefan, additional, Schwalbe, Harald, additional, Leisegang, Matthias, additional, Schulz, Marcel, additional, and Brandes, Ralf, additional
Published: 2022
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22. Farnesol induces protection against CNS inflammatory demyelination and decreases spinal infiltration of CD4+ T-Cells

Author: Doyle, William Jerome, primary, Sell, Lacey B., additional, Ramelow, Christina C., additional, Kohl, Hannah M., additional, Hoffman, Kristina R., additional, Bains, Jasleen K., additional, Strawn, Kevin D., additional, Hervin, Theresa, additional, Kirby, Trevor O., additional, Gibson, K Michael, additional, Roullet, Jean-Babtiste, additional, and Ochoa-Repárez, Javier, additional
Published: 2022
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23. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

Author: Altincekic, Nadide, Korn, Sophie Marianne, Qureshi, Nusrat Shahin, Dujardin, Marie, Ninot-Pedrosa, Martí, Abele, Rupert, Abi Saad, Marie Jose, Alfano, Caterina, Almeida, Fabio C. L., Alshamleh, Islam, de Amorim, Gisele Cardoso, Anderson, Thomas K., Anobom, Cristiane D., Anorma, Chelsea, Bains, Jasleen Kaur, Bax, Adriaan, Blackledge, Martin, Blechar, Julius, Böckmann, Anja, Brigandat, Louis, Bula, Anna, Bütikofer, Matthias, Camacho-Zarco, Aldo R., Carlomagno, Teresa, Caruso, Icaro Putinhon, Ceylan, Betül, Chaikuad, Apirat, Chu, Feixia, Cole, Laura, Crosby, Marquise G., Jesus, Vanessa de, Dhamotharan, Karthikeyan, Felli, Isabella C., Ferner, Jan, Fleischmann, Yanick, Fogeron, Marie-Laure, Fourkiotis, Nikolaos K., Fuks, Christin, Fürtig, Boris, Gallo, Angelo, Gande, Santosh L., Gerez, Juan Atilio, Ghosh, Dhiman, Gomes-Neto, Francisco, Gorbatyuk, Oksana, Guseva, Serafima, Hacker, Carolin, Häfner, Sabine, Hao, Bing, Hargittay, Bruno, Henzler-Wildman, K., Hoch, Jeffrey C., Hohmann, Katharina F., Hutchison, Marie T., Jaudzems, Kristaps, Jović, Katarina, Kaderli, Janina, Kalniņš, Gints, Kaņepe, Iveta, Kirchdoerfer, Robert N., Kirkpatrick, John, Knapp, Stefan, Krishnathas, Robin, Kutz, Felicitas, Lage, Susanne zur, Lambertz, Roderick, Lang, Andras, Laurents, Douglas, Lecoq, Lauriane, Linhard, Verena, Löhr, Frank, Malki, Anas, Bessa, Luiza Mamigonian, Martin, Rachel W., Matzel, Tobias, Maurin, Damien, McNutt, Seth W., Mebus-Antunes, Nathane Cunha, Meier, Beat H., Meiser, Nathalie, Mompeán, Miguel, Monaca, Elisa, Montserret, Roland, Mariño Perez, Laura, Moser, Celine, Muhle-Goll, Claudia, Neves-Martins, Thais Cristtina, Ni, Xiamonin, Norton-Baker, Brenna, Pierattelli, Roberta, Pontoriero, Letizia, Pustovalova, Yulia, Ohlenschläger, Oliver, Orts, Julien, Da Poian, Andrea T., Pyper, Dennis J., Richter, Christian, Riek, Roland, Rienstra, Chad M., Robertson, Angus, Pinheiro, Anderson S., Sabbatella, Raffaele, Salvi, Nicola, Saxena, Krishna, Schulte, Linda, Schiavina, Marco, Schwalbe, Harald, Silber, Mara, da Silva Almeida, Marcius, Sprague-Piercy, Marc A., Spyroulias, Georgios A., Sreeramulu, Sridhar, Tants, Jan-Niklas, Tārs, Kaspars, Torres, Felix, Töws, Sabrina, Treviño, Miguel Á., Trucks, Sven, Tsika, Aikaterini C., Varga, Krisztina, Wang, Ying, Weber, Marco E., Weigand, Julia E., Wiedemann, Christoph, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Zehnder, Johannes, Hengesbach, Martin, Schlundt, Andreas, Altincekic, Nadide, Korn, Sophie Marianne, Qureshi, Nusrat Shahin, Dujardin, Marie, Ninot-Pedrosa, Martí, Abele, Rupert, Abi Saad, Marie Jose, Alfano, Caterina, Almeida, Fabio C. L., Alshamleh, Islam, de Amorim, Gisele Cardoso, Anderson, Thomas K., Anobom, Cristiane D., Anorma, Chelsea, Bains, Jasleen Kaur, Bax, Adriaan, Blackledge, Martin, Blechar, Julius, Böckmann, Anja, Brigandat, Louis, Bula, Anna, Bütikofer, Matthias, Camacho-Zarco, Aldo R., Carlomagno, Teresa, Caruso, Icaro Putinhon, Ceylan, Betül, Chaikuad, Apirat, Chu, Feixia, Cole, Laura, Crosby, Marquise G., Jesus, Vanessa de, Dhamotharan, Karthikeyan, Felli, Isabella C., Ferner, Jan, Fleischmann, Yanick, Fogeron, Marie-Laure, Fourkiotis, Nikolaos K., Fuks, Christin, Fürtig, Boris, Gallo, Angelo, Gande, Santosh L., Gerez, Juan Atilio, Ghosh, Dhiman, Gomes-Neto, Francisco, Gorbatyuk, Oksana, Guseva, Serafima, Hacker, Carolin, Häfner, Sabine, Hao, Bing, Hargittay, Bruno, Henzler-Wildman, K., Hoch, Jeffrey C., Hohmann, Katharina F., Hutchison, Marie T., Jaudzems, Kristaps, Jović, Katarina, Kaderli, Janina, Kalniņš, Gints, Kaņepe, Iveta, Kirchdoerfer, Robert N., Kirkpatrick, John, Knapp, Stefan, Krishnathas, Robin, Kutz, Felicitas, Lage, Susanne zur, Lambertz, Roderick, Lang, Andras, Laurents, Douglas, Lecoq, Lauriane, Linhard, Verena, Löhr, Frank, Malki, Anas, Bessa, Luiza Mamigonian, Martin, Rachel W., Matzel, Tobias, Maurin, Damien, McNutt, Seth W., Mebus-Antunes, Nathane Cunha, Meier, Beat H., Meiser, Nathalie, Mompeán, Miguel, Monaca, Elisa, Montserret, Roland, Mariño Perez, Laura, Moser, Celine, Muhle-Goll, Claudia, Neves-Martins, Thais Cristtina, Ni, Xiamonin, Norton-Baker, Brenna, Pierattelli, Roberta, Pontoriero, Letizia, Pustovalova, Yulia, Ohlenschläger, Oliver, Orts, Julien, Da Poian, Andrea T., Pyper, Dennis J., Richter, Christian, Riek, Roland, Rienstra, Chad M., Robertson, Angus, Pinheiro, Anderson S., Sabbatella, Raffaele, Salvi, Nicola, Saxena, Krishna, Schulte, Linda, Schiavina, Marco, Schwalbe, Harald, Silber, Mara, da Silva Almeida, Marcius, Sprague-Piercy, Marc A., Spyroulias, Georgios A., Sreeramulu, Sridhar, Tants, Jan-Niklas, Tārs, Kaspars, Torres, Felix, Töws, Sabrina, Treviño, Miguel Á., Trucks, Sven, Tsika, Aikaterini C., Varga, Krisztina, Wang, Ying, Weber, Marco E., Weigand, Julia E., Wiedemann, Christoph, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Zehnder, Johannes, Hengesbach, Martin, and Schlundt, Andreas
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.
Published: 2022

24. Comprehensive Fragment Screening of the SARS-CoV-2 Proteome Explores Novel Chemical Space for Drug Development

Author: State of Hesse, German Research Foundation, European Commission, Ministero dell'Istruzione, dell'Università e della Ricerca, Agence Nationale de la Recherche (France), Centre National de la Recherche Scientifique (France), National Institutes of Health (US), National Science Foundation (US), Latvian Council of Science, Berg, Hannes [0000-0002-2060-4296], Wirtz Martin, Maria A. [0000-0002-0318-7785], Altincekic, Nadide [0000-0001-6370-3414], Alshamleh, Islam [0000-0001-6714-3602], Dhamotharan, Karthikeyan [0000-0003-0226-7350], Marianne Korn, Sophie [0000-0003-3798-3277], Schulte, Linda [0000-0002-9334-8908], da Silva Almeida, Marcius [0000-0003-4921-8185], Caterina Felli, Isabella [0000-0002-6018-9090], Fourkiotis, Nikolaos K. [0000-0002-5197-4142], Gallo, Angelo [0000-0001-9778-4822], Ninot-Pedrosa, Martí [0000-0003-2851-9990], Pontoriero, Letizia [0000-0002-5586-1305], Treviño, Miguel A. [0000-0002-0738-5973], Tsika, Aikaterini C. [000-0002-3723-0606], Almeida, Fabio C.L. [0000-0001-6046-7006], Bax, Ad [0000-0002-9809-5700], Henzler-Wildman, Katherine [0000-0002-5295-2121], Hoch, Jeffrey C. [0000-0002-9230-2019], Jaudzems, Kristaps [0000-0003-3922-2447], Laurents, D.V. [0000-0002-4187-165X], Ferner, Jan [0000-0002-2009-3203], Hengesbach, Martin [0000-0001-9414-1602], Löhr, Frank [0000-0001-6399-9497], Qureshi, Nusrat [0000-0002-5753-5984], Richter, Christian [0000-0002-5420-2826], Schlundt, Andreas [0000-0003-2254-7560], Weigand, Julia E. [0000-0003-4247-1348], Wirmer-Bartoschek, Julia [0000-0002-0642-1311], Schwalbe, Harald [0000-0001-5693-7909], Berg, Hannes, Wirtz Martin, Maria A., Altincekic, Nadide, Alshamleh, Islam, Kaur Bains, Jasleen, Blechar, Julius, Ceylan, Betül, Jesus, Vanessa de, Dhamotharan, Karthikeyan, Fuks, Christin, Gande, Santosh L., Hargittay, Bruno, Hohmann, Katharina F., Hutchison, Marie T., Marianne Korn, Sophie, Krishnathas, Robin, Kutz, Felicitas, Linhard, Verena, Matzel, Tobias, Meiser, Nathalie, Niesteruk, Anna, Pyper, Dennis J., Schulte, Linda, Trucks, Sven, Azzaoui, Kamal, Blommers, Marcel J.J., Gadiya, Yojana, Karki, Reagon, Zaliani, Andrea, Gribbon, Philip, da Silva Almeida, Marcius, Dinis Anobom, Cristiane, Bula, Anna L., Bütikofer, Matthias, Putinhon Caruso, Ícaro, Caterina Felli, Isabella, Da Poian, Andrea T., Cardoso de Amorim, Gisele, Fourkiotis, Nikolaos K., Gallo, Angelo, Ghosh, Dhiman, Gomes-Neto, Francisco, Gorbatyuk, Oksana, Hao, Bing, Kurauskas, Vilius, Lecoq, Lauriane, Li, Yunfeng, Cunha Mebus-Antunes, Nathane, Mompeán, Miguel, Cristtina Neves-Martins, Thais, Ninot-Pedrosa, Martí, Pinheiro, Anderson S.., Pontoriero, Letizia, Pustovalova, Yulia, Riek, Roland, Robertson, Angus J., Jose Abi Saad, Marie, Treviño, Miguel A., Tsika, Aikaterini C., Almeida, Fabio C.L., Bax, Ad, Henzler-Wildman, Katherine, Hoch, Jeffrey C., Jaudzems, Kristaps, Laurents, Douglas V., Orts, Julien, Pierattelli, Roberta, Spyroulias, Georgios A., Duchardt-Ferner, Elke, Ferner, Jan, Fürtig, Boris, Hengesbach, Martin, Löhr, Frank, Qureshi, Nusrat, Richter, Christian, Saxena, Krishna, Schlundt, Andreas, Sreeramulu, Sridhar, Wacker, Anna, Weigand, Julia E., Wirmer-Bartoschek, Julia, Wöhnert, Jens, Schwalbe, Harald, State of Hesse, German Research Foundation, European Commission, Ministero dell'Istruzione, dell'Università e della Ricerca, Agence Nationale de la Recherche (France), Centre National de la Recherche Scientifique (France), National Institutes of Health (US), National Science Foundation (US), Latvian Council of Science, Berg, Hannes [0000-0002-2060-4296], Wirtz Martin, Maria A. [0000-0002-0318-7785], Altincekic, Nadide [0000-0001-6370-3414], Alshamleh, Islam [0000-0001-6714-3602], Dhamotharan, Karthikeyan [0000-0003-0226-7350], Marianne Korn, Sophie [0000-0003-3798-3277], Schulte, Linda [0000-0002-9334-8908], da Silva Almeida, Marcius [0000-0003-4921-8185], Caterina Felli, Isabella [0000-0002-6018-9090], Fourkiotis, Nikolaos K. [0000-0002-5197-4142], Gallo, Angelo [0000-0001-9778-4822], Ninot-Pedrosa, Martí [0000-0003-2851-9990], Pontoriero, Letizia [0000-0002-5586-1305], Treviño, Miguel A. [0000-0002-0738-5973], Tsika, Aikaterini C. [000-0002-3723-0606], Almeida, Fabio C.L. [0000-0001-6046-7006], Bax, Ad [0000-0002-9809-5700], Henzler-Wildman, Katherine [0000-0002-5295-2121], Hoch, Jeffrey C. [0000-0002-9230-2019], Jaudzems, Kristaps [0000-0003-3922-2447], Laurents, D.V. [0000-0002-4187-165X], Ferner, Jan [0000-0002-2009-3203], Hengesbach, Martin [0000-0001-9414-1602], Löhr, Frank [0000-0001-6399-9497], Qureshi, Nusrat [0000-0002-5753-5984], Richter, Christian [0000-0002-5420-2826], Schlundt, Andreas [0000-0003-2254-7560], Weigand, Julia E. [0000-0003-4247-1348], Wirmer-Bartoschek, Julia [0000-0002-0642-1311], Schwalbe, Harald [0000-0001-5693-7909], Berg, Hannes, Wirtz Martin, Maria A., Altincekic, Nadide, Alshamleh, Islam, Kaur Bains, Jasleen, Blechar, Julius, Ceylan, Betül, Jesus, Vanessa de, Dhamotharan, Karthikeyan, Fuks, Christin, Gande, Santosh L., Hargittay, Bruno, Hohmann, Katharina F., Hutchison, Marie T., Marianne Korn, Sophie, Krishnathas, Robin, Kutz, Felicitas, Linhard, Verena, Matzel, Tobias, Meiser, Nathalie, Niesteruk, Anna, Pyper, Dennis J., Schulte, Linda, Trucks, Sven, Azzaoui, Kamal, Blommers, Marcel J.J., Gadiya, Yojana, Karki, Reagon, Zaliani, Andrea, Gribbon, Philip, da Silva Almeida, Marcius, Dinis Anobom, Cristiane, Bula, Anna L., Bütikofer, Matthias, Putinhon Caruso, Ícaro, Caterina Felli, Isabella, Da Poian, Andrea T., Cardoso de Amorim, Gisele, Fourkiotis, Nikolaos K., Gallo, Angelo, Ghosh, Dhiman, Gomes-Neto, Francisco, Gorbatyuk, Oksana, Hao, Bing, Kurauskas, Vilius, Lecoq, Lauriane, Li, Yunfeng, Cunha Mebus-Antunes, Nathane, Mompeán, Miguel, Cristtina Neves-Martins, Thais, Ninot-Pedrosa, Martí, Pinheiro, Anderson S.., Pontoriero, Letizia, Pustovalova, Yulia, Riek, Roland, Robertson, Angus J., Jose Abi Saad, Marie, Treviño, Miguel A., Tsika, Aikaterini C., Almeida, Fabio C.L., Bax, Ad, Henzler-Wildman, Katherine, Hoch, Jeffrey C., Jaudzems, Kristaps, Laurents, Douglas V., Orts, Julien, Pierattelli, Roberta, Spyroulias, Georgios A., Duchardt-Ferner, Elke, Ferner, Jan, Fürtig, Boris, Hengesbach, Martin, Löhr, Frank, Qureshi, Nusrat, Richter, Christian, Saxena, Krishna, Schlundt, Andreas, Sreeramulu, Sridhar, Wacker, Anna, Weigand, Julia E., Wirmer-Bartoschek, Julia, Wöhnert, Jens, and Schwalbe, Harald
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.
Published: 2022

25. Fendrr synergizes with Wnt signalling to regulate fibrosis related genes during lung development via its RNA:dsDNA Triplex Element

Author: Ali, Tamer, primary, Rogala, Sandra, additional, Krause, Nina M, additional, Bains, Jasleen K, additional, Melissari, Maria-Theodora, additional, Waehrisch, Sandra, additional, Herrmann, Bernhard G, additional, Schwalbe, Harald, additional, and Grote, Phillip, additional
Published: 2021
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26. Exploring the druggability of conserved RNA regulatory elements in the SARS-CoV-2 genome

Author: Sreeramulu, Sridhar, Richter, Christian, Berg, Hannes, Wirtz Martin, Maria A., Ceylan, Betül, Matzel, Tobias, Adam, Jennifer, Altincekic, Nadide, Azzaoui, Kamal, Bains, Jasleen Kaur, Blommers, Marcel Jules José, Ferner, Jan, Fürtig, Boris, Göbel, Michael, Grün, J. Tassilo, Hengesbach, Martin, Hohmann, Katharina F., Hymon, Daniel, Knezic, Bozana, Martins, Jason N., Mertinkus, Klara R., Niesteruk, Anna, Peter, Stephen A., Pyper, Dennis J., Qureshi, Nusrat, Scheffer, Ute, Schlundt, Andreas, Schnieders, Robbin, Stirnal, Elke, Sudakov, Alexey, Tröster, Alix Friederike, Vögele, Jennifer, Wacker, Anna, Weigand, Julia, Wirmer-Bartoschek, Julia, Wöhnert, Jens, and Schwalbe, Harald
Subjects: ddc:570, ddc:540, ddc:610
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 1H-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.
Published: 2021

27. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

Author: Altincekic, Nadide, Korn, Sophie Marianne, Qureshi, Nusrat Shahin, Dujardin, Marie, Ninot-Pedrosa, Martí, Abele, Rupert, Abi Saad, Marie Jose, Alfano, Caterina, Almeida, Fabio, Alshamleh, Islam, de Amorim, Gisele Cardoso, Anderson, Thomas, Anobom, Cristiane, Anorma, Chelsea, Bains, Jasleen Kaur, Bax, Adriaan, Blackledge, Martin, Blechar, Julius, Böckmann, Anja, Brigandat, Louis, Bula, Anna, Bütikofer, Matthias, Camacho-Zarco, Aldo, Carlomagno, Teresa, Caruso, Icaro Putinhon, Ceylan, Betül, Chaikuad, Apirat, Chu, Feixia, Cole, Laura, Crosby, Marquise, de Jesus, Vanessa, Dhamotharan, Karthikeyan, Felli, Isabella, Ferner, Jan, Fleischmann, Yanick, Fogeron, Marie-Laure, Fourkiotis, Nikolaos, Fuks, Christin, Fürtig, Boris, Gallo, Angelo, Gande, Santosh, Gerez, Juan Atilio, Ghosh, Dhiman, GOMES-NETO, Francisco, Gorbatyuk, Oksana, Guseva, Serafima, Hacker, Carolin, Häfner, Sabine, Hao, Bing, Hargittay, Bruno, Henzler-Wildman, K., Hoch, Jeffrey, Hohmann, Katharina, Hutchison, Marie, Jaudzems, Kristaps, Jović, Katarina, Kaderli, Janina, Kalniņš, Gints, Kaņepe, Iveta, Kirchdoerfer, Robert, Kirkpatrick, John, Knapp, Stefan, Krishnathas, Robin, Kutz, Felicitas, zur Lage, Susanne, Lambertz, Roderick, Lang, Andras, Laurents, Douglas, Lecoq, Lauriane, Linhard, Verena, Löhr, Frank, Malki, Anas, Bessa, Luiza Mamigonian, Martin, Rachel, Matzel, Tobias, Maurin, Damien, McNutt, Seth, Mebus-Antunes, Nathane Cunha, Meier, Beat, Meiser, Nathalie, Mompeán, Miguel, Monaca, Elisa, Montserret, Roland, Mariño Perez, Laura, Moser, Celine, Muhle-Goll, Claudia, Neves-Martins, Thais Cristtina, Ni, Xiamonin, Norton-Baker, Brenna, Pierattelli, Roberta, Pontoriero, Letizia, Pustovalova, Yulia, Ohlenschläger, Oliver, Orts, Julien, Da Poian, Andrea, Pyper, Dennis, Richter, Christian, Riek, Roland, Rienstra, Chad, Robertson, Angus, Pinheiro, Anderson, Sabbatella, Raffaele, Salvi, Nicola, Saxena, Krishna, Schulte, Linda, Schiavina, Marco, Schwalbe, Harald, Silber, Mara, Almeida, Marcius da Silva, Sprague-Piercy, Marc, Spyroulias, Georgios, Sreeramulu, Sridhar, Tants, Jan-Niklas, Tārs, Kaspars, Torres, Felix, Töws, Sabrina, Treviño, Miguel, Trucks, Sven, Tsika, Aikaterini, Varga, Krisztina, Wang, Ying, Weber, Marco, Weigand, Julia, Wiedemann, Christoph, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Zehnder, Johannes, Hengesbach, Martin, Schlundt, Andreas, Treviño, Miguel Á., Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), Goethe University Frankfurt am Main, German Research Foundation, Cassa di Risparmio di Firenze, European Commission, University of New Hampshire, The Free State of Thuringia, National Institutes of Health (US), National Science Foundation (US), Howard Hughes Medical Institute, Latvian Council of Science, Ministry of Development and Investments (Greece), Helmholtz Association, Centre National de la Recherche Scientifique (France), Agence Nationale de la Recherche (France), Fondation pour la Recherche Médicale, Swiss National Science Foundation, Fonds National Suisse de la Recherche Scientifique, ETH Zurich, European Research Council, Université Grenoble Alpes, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación 'la Caixa', Instituto de Salud Carlos III, Boehringer Ingelheim Fonds, Ministero dell'Istruzione, dell'Università e della Ricerca, Polytechnic Foundation of Frankfurt am Main, Goethe University Frankfurt, CNRS/Lyon University, Fondazione Ri.MED, Federal University of Rio de Janeiro, Caxias Federal University of Rio de Janeiro, University of Wisconsin-Madison, University of California, NIDDK, IBS, Latvian Institute of Organic Synthesis, Leibniz University Hannover, Helmholtz Centre for Infection Research, Universidade Estadual Paulista (Unesp), Buchmann Institute for Molecular Life Sciences, University of Florence, University of Patras, Oswaldo Cruz Foundation (FIOCRUZ), UConn Health, Signals GmbH Co. KG, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Latvian Biomedical Research and Study Centre, Spanish National Research Council (CSIC), Karlsruhe Institute of Technology, Technical University of Darmstadt, Martin Luther University Halle-Wittenberg, Altincekic N., Korn S.M., Qureshi N.S., Dujardin M., Ninot-Pedrosa M., Abele R., Abi Saad M.J., Alfano C., Almeida F.C.L., Alshamleh I., de Amorim G.C., Anderson T.K., Anobom C.D., Anorma C., Bains J.K., Bax A., Blackledge M., Blechar J., Bockmann A., Brigandat L., Bula A., Butikofer M., Camacho-Zarco A.R., Carlomagno T., Caruso I.P., Ceylan B., Chaikuad A., Chu F., Cole L., Crosby M.G., de Jesus V., Dhamotharan K., Felli I.C., Ferner J., Fleischmann Y., Fogeron M.-L., Fourkiotis N.K., Fuks C., Furtig B., Gallo A., Gande S.L., Gerez J.A., Ghosh D., Gomes-Neto F., Gorbatyuk O., Guseva S., Hacker C., Hafner S., Hao B., Hargittay B., Henzler-Wildman K., Hoch J.C., Hohmann K.F., Hutchison M.T., Jaudzems K., Jovic K., Kaderli J., Kalnins G., Kanepe I., Kirchdoerfer R.N., Kirkpatrick J., Knapp S., Krishnathas R., Kutz F., zur Lage S., Lambertz R., Lang A., Laurents D., Lecoq L., Linhard V., Lohr F., Malki A., Bessa L.M., Martin R.W., Matzel T., Maurin D., McNutt S.W., Mebus-Antunes N.C., Meier B.H., Meiser N., Mompean M., Monaca E., Montserret R., Marino Perez L., Moser C., Muhle-Goll C., Neves-Martins T.C., Ni X., Norton-Baker B., Pierattelli R., Pontoriero L., Pustovalova Y., Ohlenschlager O., Orts J., Da Poian A.T., Pyper D.J., Richter C., Riek R., Rienstra C.M., Robertson A., Pinheiro A.S., Sabbatella R., Salvi N., Saxena K., Schulte L., Schiavina M., Schwalbe H., Silber M., Almeida M.D.S., Sprague-Piercy M.A., Spyroulias G.A., Sreeramulu S., Tants J.-N., Tars K., Torres F., Tows S., Trevino M.A., Trucks S., Tsika A.C., Varga K., Wang Y., Weber M.E., Weigand J.E., Wiedemann C., Wirmer-Bartoschek J., Wirtz Martin M.A., Zehnder J., Hengesbach M., Schlundt A., HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany., and Obra Social la Caixa
Subjects: Life sciences, biology, SARS-COV-2, COVID-19, protein production, structural biology, NMR, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, Accessory proteins, NMR spectroscopy, ddc:570, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Molecular Biosciences, ddc:610, Nonstructural proteins, Molecular Biology, Original Research, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], SARS-CoV-2, Intrinsically disordered region, nonstructural proteins, structural proteins, Cell-free protein synthesis, intrinsically disordered region, cell-free protein synthesis, accessory proteins, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Structural proteins
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., This work was supported by Goethe University (Corona funds), the DFG-funded CRC: “Molecular Principles of RNA-Based Regulation,” DFG infrastructure funds (project numbers: 277478796, 277479031, 392682309, 452632086, 70653611), the state of Hesse (BMRZ), the Fondazione CR Firenze (CERM), and the IWB-EFRE-program 20007375. This project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 871037. AS is supported by DFG Grant SCHL 2062/2-1 and by the JQYA at Goethe through project number 2019/AS01. Work in the lab of KV was supported by a CoRE grant from the University of New Hampshire. The FLI is a member of the Leibniz Association (WGL) and financially supported by the Federal Government of Germany and the State of Thuringia. Work in the lab of RM was supported by NIH (2R01EY021514) and NSF (DMR-2002837). BN-B was supported by theNSF GRFP.MCwas supported byNIH (R25 GM055246 MBRS IMSD), and MS-P was supported by the HHMI Gilliam Fellowship. Work in the labs of KJ and KT was supported by Latvian Council of Science Grant No. VPP-COVID 2020/1-0014. Work in the UPAT’s lab was supported by the INSPIRED (MIS 5002550) project, which is implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and cofinanced by Greece and the EU (European Regional Development Fund) and the FP7 REGPOT CT-2011- 285950–“SEE-DRUG” project (purchase of UPAT’s 700MHz NMR equipment). Work in the CM-G lab was supported by the Helmholtz society. Work in the lab of ABö was supported by the CNRS, the French National Research Agency (ANR, NMRSCoV2- ORF8), the Fondation de la Recherche Médicale (FRM, NMR-SCoV2-ORF8), and the IR-RMN-THC Fr3050 CNRS. Work in the lab of BM was supported by the Swiss National Science Foundation (Grant number 200020_188711), the Günthard Stiftung für Physikalische Chemie, and the ETH Zurich. Work in the labs of ABö and BM was supported by a common grant from SNF (grant 31CA30_196256). This work was supported by the ETHZurich, the grant ETH40 18 1, and the grant Krebsliga KFS 4903 08 2019. Work in the lab of the IBS Grenoble was supported by the Agence Nationale de Recherche (France) RA-COVID SARS2NUCLEOPROTEIN and European Research Council Advanced Grant DynamicAssemblies. Work in the CA lab was supported by Patto per il Sud della Regione Siciliana–CheMISt grant (CUP G77B17000110001). Part of this work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UMS 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-05-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE- 0003). Work at the UW-Madison was supported by grant numbers NSF MCB2031269 and NIH/NIAID AI123498. MM is a Ramón y Cajal Fellow of the Spanish AEI-Ministry of Science and Innovation (RYC2019-026574-I), and a “La Caixa” Foundation (ID 100010434) Junior Leader Fellow (LCR/BQ/PR19/11700003). Funded by project COV20/00764 fromthe Carlos III Institute of Health and the SpanishMinistry of Science and Innovation to MMand DVL. VDJ was supported by the Boehringer Ingelheim Fonds. Part of this work used the resources of the Italian Center of Instruct-ERIC at the CERM/ CIRMMP infrastructure, supported by the Italian Ministry for University and Research (FOE funding). CF was supported by the Stiftung Polytechnische Gesellschaft. Work in the lab of JH was supported by NSF (RAPID 2030601) and NIH (R01GM123249).
Published: 2021

28. HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex

Author: Leisegang, Matthias S., primary, Bains, Jasleen Kaur, additional, Seredinski, Sandra, additional, Oo, James A., additional, Krause, Nina M., additional, Kuo, Chao-Chung, additional, Günther, Stefan, additional, Cetin, Nevcin Sentürk, additional, Warwick, Timothy, additional, Cao, Can, additional, Boos, Frederike, additional, Ponce, Judit Izquierdo, additional, Bednarz, Rebecca, additional, Valasarajan, Chanil, additional, Fuhrmann, Dominik, additional, Preussner, Jens, additional, Looso, Mario, additional, Pullamsetti, Soni S., additional, Schulz, Marcel H., additional, Rezende, Flávia, additional, Gilsbach, Ralf, additional, Pflüger-Müller, Beatrice, additional, Wittig, Ilka, additional, Grummt, Ingrid, additional, Ribarska, Teodora, additional, Costa, Ivan G., additional, Schwalbe, Harald, additional, and Brandes, Ralf P., additional
Published: 2021
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29. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome

Author: Sreeramulu, Sridhar, primary, Richter, Christian, additional, Berg, Hannes, additional, Wirtz Martin, Maria A., additional, Ceylan, Betül, additional, Matzel, Tobias, additional, Adam, Jennifer, additional, Altincekic, Nadide, additional, Azzaoui, Kamal, additional, Bains, Jasleen Kaur, additional, Blommers, Marcel J. J., additional, Ferner, Jan, additional, Fürtig, Boris, additional, Göbel, Michael, additional, Grün, J. Tassilo, additional, Hengesbach, Martin, additional, Hohmann, Katharina F., additional, Hymon, Daniel, additional, Knezic, Bozana, additional, Martins, Jason N., additional, Mertinkus, Klara R., additional, Niesteruk, Anna, additional, Peter, Stephen A., additional, Pyper, Dennis J., additional, Qureshi, Nusrat S., additional, Scheffer, Ute, additional, Schlundt, Andreas, additional, Schnieders, Robbin, additional, Stirnal, Elke, additional, Sudakov, Alexey, additional, Tröster, Alix, additional, Vögele, Jennifer, additional, Wacker, Anna, additional, Weigand, Julia E., additional, Wirmer‐Bartoschek, Julia, additional, Wöhnert, Jens, additional, and Schwalbe, Harald, additional
Published: 2021
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30. Structural and Biophysical Characterization of BoxC from Burkholderia xenovorans LB400: A NOVEL RING-CLEAVING ENZYME IN THE CROTONASE SUPERFAMILY

Author: Bains, Jasleen, Leon, Rafael, and Boulanger, Martin J.
Published: 2009
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31. Wavelength-Selective Uncaging of Two Different Photoresponsive Groups on One Effector Molecule for Light-Controlled Activation and Deactivation

Author: Elamri, Isam, primary, Abdellaoui, Chahinez, additional, Bains, Jasleen Kaur, additional, Hohmann, Katharina Felicitas, additional, Gande, Santosh Lakshmi, additional, Stirnal, Elke, additional, Wachtveitl, Josef, additional, and Schwalbe, Harald, additional
Published: 2021
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32. Correction to ‘Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy’

Author: Wacker, Anna, primary, Weigand, Julia E, additional, Akabayov, Sabine R, additional, Altincekic, Nadide, additional, Bains, Jasleen Kaur, additional, Banijamali, Elnaz, additional, Binas, Oliver, additional, Castillo-Martinez, Jesus, additional, Cetiner, Erhan, additional, Ceylan, Betül, additional, Chiu, Liang-Yuan, additional, Davila-Calderon, Jesse, additional, Dhamotharan, Karthikeyan, additional, Duchardt-Ferner, Elke, additional, Ferner, Jan, additional, Frydman, Lucio, additional, Fürtig, Boris, additional, Gallego, José, additional, Grün, J Tassilo, additional, Hacker, Carolin, additional, Haddad, Christina, additional, Hähnke, Martin, additional, Hengesbach, Martin, additional, Hiller, Fabian, additional, Hohmann, Katharina F, additional, Hymon, Daniel, additional, de Jesus, Vanessa, additional, Jonker, Henry, additional, Keller, Heiko, additional, Knezic, Bozana, additional, Landgraf, Tom, additional, Löhr, Frank, additional, Luo, Le, additional, Mertinkus, Klara R, additional, Muhs, Christina, additional, Novakovic, Mihajlo, additional, Oxenfarth, Andreas, additional, Palomino-Schätzlein, Martina, additional, Petzold, Katja, additional, Peter, Stephen A, additional, Pyper, Dennis J, additional, Qureshi, Nusrat S, additional, Riad, Magdalena, additional, Richter, Christian, additional, Saxena, Krishna, additional, Schamber, Tatjana, additional, Scherf, Tali, additional, Schlagnitweit, Judith, additional, Schlundt, Andreas, additional, Schnieders, Robbin, additional, Schwalbe, Harald, additional, Simba-Lahuasi, Alvaro, additional, Sreeramulu, Sridhar, additional, Stirnal, Elke, additional, Sudakov, Alexey, additional, Tants, Jan-Niklas, additional, Tolbert, Blanton S, additional, Vögele, Jennifer, additional, Weiß, Lena, additional, Wirmer-Bartoschek, Julia, additional, Wirtz Martin, Maria A, additional, Wöhnert, Jens, additional, and Zetzsche, Heidi, additional
Published: 2021
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33. Switching at the ribosome: riboswitches need rProteins as modulators to regulate translation

Author: Jesus, Vanessa de, Qureshi, Nusrat, Warhaut, Sven, Bains, Jasleen Kaur, Dietz, Marina, Heilemann, Mike, Schwalbe, Harald, Fürtig, Boris, Jesus, Vanessa de, Qureshi, Nusrat, Warhaut, Sven, Bains, Jasleen Kaur, Dietz, Marina, Heilemann, Mike, Schwalbe, Harald, and Fürtig, Boris
Abstract: Translational riboswitches are cis-acting RNA regulators that modulate the expression of genes during translation initiation. Their mechanism is considered as an RNA-only gene-regulatory system inducing a ligand-dependent shift of the population of functional ON- and OFF-states. The interaction of riboswitches with the translation machinery remained unexplored. For the adenine-sensing riboswitch from Vibrio vulnificus we show that ligand binding alone is not sufficient for switching to a translational ON-state but the interaction of the riboswitch with the 30S ribosome is indispensable. Only the synergy of binding of adenine and of 30S ribosome, in particular protein rS1, induces complete opening of the translation initiation region. Our investigation thus unravels the intricate dynamic network involving RNA regulator, ligand inducer and ribosome protein modulator during translation initiation.
Published: 2021

34. Correction to 'Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy’

Author: Wacker, Anna, Weigand, Julia, Akabayov, Sabine R, Altınçekiç, Nadide, Bains, Jasleen Kaur, Banijamali, Elnaz, Binas, Oliver, Castillo-Martinez, Jesus, Çetiner, Erhan Can, Ceylan, Betül, Chiu, Liang-Yuan, Davila-Calderon, Jesse, Dhamotharan, Karthikeyan, Duchardt-Ferner, Elke, Ferner, Jan, Frydman, Lucio, Fürtig, Boris, Gallego, José, Grün, J. Tassilo, Hacker, Carolin, Haddad, Christina, Hähnke, Martin Jens, Hengesbach, Martin, Hiller, Fabian, Hohmann, Katharina Felicitas, Hymon, Daniel, Jesus, Vanessa de, Jonker, Henry, Keller, Heiko, Knežić, Božana, Landgraf, Tom, Löhr, Frank, Luo, Le, Mertinkus, Klara Rebecca, Muhs, Christina, Novakovic, Mihajlo, Oxenfarth, Andreas, Palomino-Schätzlein, Martina, Petzold, Katja, Peter, Stephen, Pyper, Dennis Joshua, Qureshi, Nusrat, Riad, Magdalena, Richter, Christian, Saxena, Krishna, Schamber, Tatjana, Scherf, Tali, Schlagnitweit, Judith, Schlundt, Andreas, Schnieders, Robbin, Schwalbe, Harald, Simba-Lahuasi, Alvaro, Sreeramulu, Sridhar, Stirnal, Elke, Sudakov, Alexey, Tants, Jan-Niklas, Tolbert, Blanton S, Vögele, Jennifer, Weiß, Lena, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Wöhnert, Jens, Zetzsche, Heidi, Wacker, Anna, Weigand, Julia, Akabayov, Sabine R, Altınçekiç, Nadide, Bains, Jasleen Kaur, Banijamali, Elnaz, Binas, Oliver, Castillo-Martinez, Jesus, Çetiner, Erhan Can, Ceylan, Betül, Chiu, Liang-Yuan, Davila-Calderon, Jesse, Dhamotharan, Karthikeyan, Duchardt-Ferner, Elke, Ferner, Jan, Frydman, Lucio, Fürtig, Boris, Gallego, José, Grün, J. Tassilo, Hacker, Carolin, Haddad, Christina, Hähnke, Martin Jens, Hengesbach, Martin, Hiller, Fabian, Hohmann, Katharina Felicitas, Hymon, Daniel, Jesus, Vanessa de, Jonker, Henry, Keller, Heiko, Knežić, Božana, Landgraf, Tom, Löhr, Frank, Luo, Le, Mertinkus, Klara Rebecca, Muhs, Christina, Novakovic, Mihajlo, Oxenfarth, Andreas, Palomino-Schätzlein, Martina, Petzold, Katja, Peter, Stephen, Pyper, Dennis Joshua, Qureshi, Nusrat, Riad, Magdalena, Richter, Christian, Saxena, Krishna, Schamber, Tatjana, Scherf, Tali, Schlagnitweit, Judith, Schlundt, Andreas, Schnieders, Robbin, Schwalbe, Harald, Simba-Lahuasi, Alvaro, Sreeramulu, Sridhar, Stirnal, Elke, Sudakov, Alexey, Tants, Jan-Niklas, Tolbert, Blanton S, Vögele, Jennifer, Weiß, Lena, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Wöhnert, Jens, and Zetzsche, Heidi
Published: 2021

35. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

Author: Altınçekiç, Nadide, Korn, Sophie Marianne, Qureshi, Nusrat Shahin, Dujardin, Marie, Ninot-Pedrosa, Martí, Abele, Rupert, Abi Saad, Marie Jose, Alfano, Caterina, Almeida, Fabio C. L., Alshamleh, Islam, Amorim, Gisele Cardoso de, Anderson, Thomas K., Anobom, Cristiane D., Anorma, Chelsea, Bains, Jasleen Kaur, Bax, Adriaan, Blackledge, Martin, Blechar, Julius, Böckmann, Anja, Brigandat, Louis, Bula, Anna, Bütikofer, Matthias, Camacho-Zarco, Aldo R., Carlomagno, Teresa, Caruso, Icaro Putinhon, Ceylan, Betül, Chaikuad, Apirat, Chu, Feixia, Cole, Laura, Crosby, Marquise G., De Jesus, Vanessa, Dhamotharan, Karthikeyan, Felli, Isabella C., Ferner, Jan, Fleischmann, Yanick, Fogeron, Marie-Laure, Fourkiotis, Nikolaos K., Fuks, Christin, Fürtig, Boris, Gallo, Angelo, Gande, Santosh L., Gerez, Juan Atilio, Ghosh, Dhiman, Gomes-Neto, Francisco, Gorbatyuk, Oksana, Guseva, Serafima, Hacker, Carolin, Häfner, Sabine, Hao, Bing, Hargittay, Bruno, Henzler-Wildman, Katherine, Hoch, Jeffrey C., Hohmann, Katharina Felicitas, Hutchison, Marie T., Jaudzems, Kristaps, Jović, Katarina, Kaderli, Janina, Kalnins, Gints, Kanepe, Iveta, Kirchdoerfer, Robert N., Kirkpatrick, John, Knapp, Stefan, Krishnathas, Robin, Kutz, Felicitas, Zur Lage, Susanne, Lambertz, Roderick, Lang, Andras, Laurents, Douglas, Lecoq, Lauriane, Linhard, Verena, Löhr, Frank, Malki, Anas, Bessa, Luiza Mamigonian, Martin, Rachel W., Matzel, Tobias, Maurin, Damien, McNutt, Seth W., Mebus-Antunes, Nathane Cunha, Meier, Beat H., Meiser, Nathalie, Mompeán, Miguel, Monaca, Elisa, Montserret, Roland, Perez, Laura Mariño, Moser, Celine, Muhle-Goll, Claudia, Neves-Martins, Thais Cristtina, Ni, Xiamonin, Norton-Baker, Brenna, Pierattelli, Roberta, Pontoriero, Letizia, Pustovalova, Yulia, Ohlenschläger, Oliver, Orts, Julien, Poian, Andrea T. da, Pyper, Dennis Joshua, Richter, Christian, Riek, Roland, Rienstra, Chad M., Robertson, Angus, Pinheiro, Anderson S., Sabbatella, Raffaele, Salvi, Nicola, Saxena, Krishna, Schulte, Linda, Schiavina, Marco, Schwalbe, Harald, Silber, Mara, Almeida, Marcius da Silva, Sprague-Piercy, Marc A., Spyroulias, Georgios A., Sreeramulu, Sridhar, Tants, Jan-Niklas, Tars, Kaspars, Torres, Felix, Töws, Sabrina, Trevino, Miguel A., Trucks, Sven, Tsika, Aikaterini C., Varga, Krisztina, Wang, Ying, Weber, Marco E., Weigand, Julia E., Wiedemann, Christoph, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Zehnder, Johannes, Hengesbach, Martin, Schlundt, Andreas, Altınçekiç, Nadide, Korn, Sophie Marianne, Qureshi, Nusrat Shahin, Dujardin, Marie, Ninot-Pedrosa, Martí, Abele, Rupert, Abi Saad, Marie Jose, Alfano, Caterina, Almeida, Fabio C. L., Alshamleh, Islam, Amorim, Gisele Cardoso de, Anderson, Thomas K., Anobom, Cristiane D., Anorma, Chelsea, Bains, Jasleen Kaur, Bax, Adriaan, Blackledge, Martin, Blechar, Julius, Böckmann, Anja, Brigandat, Louis, Bula, Anna, Bütikofer, Matthias, Camacho-Zarco, Aldo R., Carlomagno, Teresa, Caruso, Icaro Putinhon, Ceylan, Betül, Chaikuad, Apirat, Chu, Feixia, Cole, Laura, Crosby, Marquise G., De Jesus, Vanessa, Dhamotharan, Karthikeyan, Felli, Isabella C., Ferner, Jan, Fleischmann, Yanick, Fogeron, Marie-Laure, Fourkiotis, Nikolaos K., Fuks, Christin, Fürtig, Boris, Gallo, Angelo, Gande, Santosh L., Gerez, Juan Atilio, Ghosh, Dhiman, Gomes-Neto, Francisco, Gorbatyuk, Oksana, Guseva, Serafima, Hacker, Carolin, Häfner, Sabine, Hao, Bing, Hargittay, Bruno, Henzler-Wildman, Katherine, Hoch, Jeffrey C., Hohmann, Katharina Felicitas, Hutchison, Marie T., Jaudzems, Kristaps, Jović, Katarina, Kaderli, Janina, Kalnins, Gints, Kanepe, Iveta, Kirchdoerfer, Robert N., Kirkpatrick, John, Knapp, Stefan, Krishnathas, Robin, Kutz, Felicitas, Zur Lage, Susanne, Lambertz, Roderick, Lang, Andras, Laurents, Douglas, Lecoq, Lauriane, Linhard, Verena, Löhr, Frank, Malki, Anas, Bessa, Luiza Mamigonian, Martin, Rachel W., Matzel, Tobias, Maurin, Damien, McNutt, Seth W., Mebus-Antunes, Nathane Cunha, Meier, Beat H., Meiser, Nathalie, Mompeán, Miguel, Monaca, Elisa, Montserret, Roland, Perez, Laura Mariño, Moser, Celine, Muhle-Goll, Claudia, Neves-Martins, Thais Cristtina, Ni, Xiamonin, Norton-Baker, Brenna, Pierattelli, Roberta, Pontoriero, Letizia, Pustovalova, Yulia, Ohlenschläger, Oliver, Orts, Julien, Poian, Andrea T. da, Pyper, Dennis Joshua, Richter, Christian, Riek, Roland, Rienstra, Chad M., Robertson, Angus, Pinheiro, Anderson S., Sabbatella, Raffaele, Salvi, Nicola, Saxena, Krishna, Schulte, Linda, Schiavina, Marco, Schwalbe, Harald, Silber, Mara, Almeida, Marcius da Silva, Sprague-Piercy, Marc A., Spyroulias, Georgios A., Sreeramulu, Sridhar, Tants, Jan-Niklas, Tars, Kaspars, Torres, Felix, Töws, Sabrina, Trevino, Miguel A., Trucks, Sven, Tsika, Aikaterini C., Varga, Krisztina, Wang, Ying, Weber, Marco E., Weigand, Julia E., Wiedemann, Christoph, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Zehnder, Johannes, Hengesbach, Martin, and Schlundt, Andreas
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.
Published: 2021

36. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

Author: Goethe University Frankfurt am Main, German Research Foundation, Cassa di Risparmio di Firenze, European Commission, University of New Hampshire, The Free State of Thuringia, National Institutes of Health (US), National Science Foundation (US), Howard Hughes Medical Institute, Latvian Council of Science, Ministry of Development and Investments (Greece), Helmholtz Association, Centre National de la Recherche Scientifique (France), Agence Nationale de la Recherche (France), Fondation pour la Recherche Médicale, Swiss National Science Foundation, Fonds National Suisse de la Recherche Scientifique, ETH Zurich, European Research Council, Université Grenoble Alpes, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación la Caixa, Instituto de Salud Carlos III, Boehringer Ingelheim Fonds, Ministero dell'Istruzione, dell'Università e della Ricerca, Polytechnic Foundation of Frankfurt am Main, Altincekic, Nadide, Korn, Sophie Marianne, Qureshi, Nusrat Shahin, Dujardin, Marie, Ninot-Pedrosa, Martí, Abele, Rupert, Abi Saad, Marie Jose, Alfano, Caterina, Almeida, Fabio C. L., Alshamleh, Islam, Cardoso de Amorim, Gisele, Anorma, Chelsea, Bains, Jasleen Kaur, Bax, Andriaan, Blackledge, Martin, Blechar, Julius, Böckmann, Anja, Brigandat, Louis, Bula, Anna, Bütikofer, Matthias, Camacho-Zarco, Aldo R., Ghosh, Dhiman, Carlomagno, Teresa, Caruso, Icaro Putinhon, Ceylan, Betül, Chaikuad, Apirat, Chu, Feixia, Cole, Laura, Crosby, Marquise G., Jesus, Vanessa de, Dhamotharan, Karthikeyan, Felli, Isabella C., Gomes-Neto, Francisco, Ferner, Jan, Fleischmann, Yanick, Fogeron, Marie-Laure, Fourkiotis, Nikolaos K., Fuks, Christin, Fürtig, Boris, Gallo, Angelo, Gande, Santosh L., Gerez, Juan Atilio, Gorbatyuk, Oksana, Guseva, Serafima, Hacker, Carolin, Häfner, Sabine, Hao, Bing, Hargittay, Bruno, Henzler-Wildman, K., Hoch, Jeffrey C., Malki, Anas, Hohmann, Katharina F., Hutchison, Marie T., Jaudzems, Kristaps, Jović, Katarina, Kaderli, Janina, Kalniņš, Gints, Kaņepe, Iveta, Kirchdoerfer, Robert N., Kirkpatrick, John, Knapp, Stefan, Bessa, Luiza Mamigonian, Krishnathas, Robin, Kutz, Felicitas, Lage, Susanne zur, Lambertz, Roderick, Lang, Andras, Laurents, Douglas V., Lecoq, Lauriane, Linhard, Verena, Löhr, Frank, Martin, Rachel W., Matzel, Tobias, Maurin, Damien, McNutt, Seth W., Mebus-Antunes, Nathane Cunha, Meier, Beat H., Meiser, Nathalie, Mompeán, Miguel, Pinheiro, Anderson S.., Monaca, Elisa, Montserret, Roland, Mariño Perez, Laura, Moser, Celine, Muhle-Goll, Claudia, Neves-Martins, Thais Cristtina, Ni, Xiamonin, Norton-Baker, Brenna, Pierattelli, Roberta, Pontoriero, Letizia, Sabbatella, Raffaele, Pustovalova, Yulia, Ohlenschläger, Oliver, Orts, Julien, Da Poian, Andrea T., Pyper, Dennis J., Richter, Christian, Riek, Roland, Rienstra, Chad M., Robertson, Angus, Salvi, Nicola, Saxena, Krishna, Schulte, Linda, Schiavina, Marco, Schwalbe, Harald, Silber, Mara, Silva Almeida, Marcius da, Sprague-Piercy, Marc A., Anderson, Thomas K., Spyroulias, Georgios A., Sreeramulu, Sridhar, Tants, Jan-Niklas, Tārs, Kaspars, Torres, Felix, Töws, Sabrina, Treviño, Miguel A., Trucks, Sven, Tsika, Aikaterini C., Varga, Krisztina, Anobom, Cristiane D., Wang, Ying, Weber, Marco E., Weigand, Julia E., Wiedemann, Christoph, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Zehnder, Johannes, Hengesbach, Martin, Schlundt, Andreas, Goethe University Frankfurt am Main, German Research Foundation, Cassa di Risparmio di Firenze, European Commission, University of New Hampshire, The Free State of Thuringia, National Institutes of Health (US), National Science Foundation (US), Howard Hughes Medical Institute, Latvian Council of Science, Ministry of Development and Investments (Greece), Helmholtz Association, Centre National de la Recherche Scientifique (France), Agence Nationale de la Recherche (France), Fondation pour la Recherche Médicale, Swiss National Science Foundation, Fonds National Suisse de la Recherche Scientifique, ETH Zurich, European Research Council, Université Grenoble Alpes, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación la Caixa, Instituto de Salud Carlos III, Boehringer Ingelheim Fonds, Ministero dell'Istruzione, dell'Università e della Ricerca, Polytechnic Foundation of Frankfurt am Main, Altincekic, Nadide, Korn, Sophie Marianne, Qureshi, Nusrat Shahin, Dujardin, Marie, Ninot-Pedrosa, Martí, Abele, Rupert, Abi Saad, Marie Jose, Alfano, Caterina, Almeida, Fabio C. L., Alshamleh, Islam, Cardoso de Amorim, Gisele, Anorma, Chelsea, Bains, Jasleen Kaur, Bax, Andriaan, Blackledge, Martin, Blechar, Julius, Böckmann, Anja, Brigandat, Louis, Bula, Anna, Bütikofer, Matthias, Camacho-Zarco, Aldo R., Ghosh, Dhiman, Carlomagno, Teresa, Caruso, Icaro Putinhon, Ceylan, Betül, Chaikuad, Apirat, Chu, Feixia, Cole, Laura, Crosby, Marquise G., Jesus, Vanessa de, Dhamotharan, Karthikeyan, Felli, Isabella C., Gomes-Neto, Francisco, Ferner, Jan, Fleischmann, Yanick, Fogeron, Marie-Laure, Fourkiotis, Nikolaos K., Fuks, Christin, Fürtig, Boris, Gallo, Angelo, Gande, Santosh L., Gerez, Juan Atilio, Gorbatyuk, Oksana, Guseva, Serafima, Hacker, Carolin, Häfner, Sabine, Hao, Bing, Hargittay, Bruno, Henzler-Wildman, K., Hoch, Jeffrey C., Malki, Anas, Hohmann, Katharina F., Hutchison, Marie T., Jaudzems, Kristaps, Jović, Katarina, Kaderli, Janina, Kalniņš, Gints, Kaņepe, Iveta, Kirchdoerfer, Robert N., Kirkpatrick, John, Knapp, Stefan, Bessa, Luiza Mamigonian, Krishnathas, Robin, Kutz, Felicitas, Lage, Susanne zur, Lambertz, Roderick, Lang, Andras, Laurents, Douglas V., Lecoq, Lauriane, Linhard, Verena, Löhr, Frank, Martin, Rachel W., Matzel, Tobias, Maurin, Damien, McNutt, Seth W., Mebus-Antunes, Nathane Cunha, Meier, Beat H., Meiser, Nathalie, Mompeán, Miguel, Pinheiro, Anderson S.., Monaca, Elisa, Montserret, Roland, Mariño Perez, Laura, Moser, Celine, Muhle-Goll, Claudia, Neves-Martins, Thais Cristtina, Ni, Xiamonin, Norton-Baker, Brenna, Pierattelli, Roberta, Pontoriero, Letizia, Sabbatella, Raffaele, Pustovalova, Yulia, Ohlenschläger, Oliver, Orts, Julien, Da Poian, Andrea T., Pyper, Dennis J., Richter, Christian, Riek, Roland, Rienstra, Chad M., Robertson, Angus, Salvi, Nicola, Saxena, Krishna, Schulte, Linda, Schiavina, Marco, Schwalbe, Harald, Silber, Mara, Silva Almeida, Marcius da, Sprague-Piercy, Marc A., Anderson, Thomas K., Spyroulias, Georgios A., Sreeramulu, Sridhar, Tants, Jan-Niklas, Tārs, Kaspars, Torres, Felix, Töws, Sabrina, Treviño, Miguel A., Trucks, Sven, Tsika, Aikaterini C., Varga, Krisztina, Anobom, Cristiane D., Wang, Ying, Weber, Marco E., Weigand, Julia E., Wiedemann, Christoph, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Zehnder, Johannes, Hengesbach, Martin, and Schlundt, Andreas
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.
Published: 2021

37. 19F NMR-based fragment screening for 14 different biologically active RNAs and 10 DNA and protein counter-screens

Author: Binas, Oliver, Jesus, Vanessa de, Landgraf, Tom, Völklein, Albrecht Eduard, Martins, Jason, Hymon, Daniel, Bains, Jasleen Kaur, Berg, Hannes, Biedenbänder, Thomas, Fürtig, Boris, Gande, Santosh Lakshmi, Niesteruk, Anna, Oxenfarth, Andreas, Qureshi, Nusrat, Schamber, Tatjana, Schnieders, Robbin, Tröster, Alix Friederike, Wacker, Anna, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Stirnal, Elke, Azzaoui, Kamal, Richter, Christian, Sreeramulu, Sridhar, Blommers, Marcel Jules José, and Schwalbe, Harald
Subjects: ddc:570
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.
Published: 2020

38. 1H, 13C, and 15N backbone chemical shift assignments of coronavirus-2 non-structural protein Nsp10

Author: Kubatova, Nina, Qureshi, Nusrat, Altınçekiç, Nadide, Abele, Rupert, Bains, Jasleen Kaur, Ceylan, Betül, Ferner, Jan, Fuks, Christin, Hargittay, Bruno, Hutchison, Marie, de Jesus, Vanessa, Kutz, Felicitas, Wirtz Martin, Maria Alexandra, Meiser, Nathalie, Linhard, Verena, Pyper, Dennis Joshua, Trucks, Sven, Fürtig, Boris, Hengesbach, Martin, Löhr, Frank, Richter, Christian, Saxena, Krishna, Schlundt, Andreas, Schwalbe, Harald, Sreeramulu, Sridhar, Wacker, Anna, Weigand, Julia, Wirmer-Bartoschek, Julia, Wöhnert, Jens, Kubatova, Nina, Qureshi, Nusrat, Altınçekiç, Nadide, Abele, Rupert, Bains, Jasleen Kaur, Ceylan, Betül, Ferner, Jan, Fuks, Christin, Hargittay, Bruno, Hutchison, Marie, de Jesus, Vanessa, Kutz, Felicitas, Wirtz Martin, Maria Alexandra, Meiser, Nathalie, Linhard, Verena, Pyper, Dennis Joshua, Trucks, Sven, Fürtig, Boris, Hengesbach, Martin, Löhr, Frank, Richter, Christian, Saxena, Krishna, Schlundt, Andreas, Schwalbe, Harald, Sreeramulu, Sridhar, Wacker, Anna, Weigand, Julia, Wirmer-Bartoschek, Julia, and Wöhnert, Jens
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.
Published: 2020

39. 1H, 13C, and 15N backbone chemical shift assignments of the apo and the ADP-ribose bound forms of the macrodomain of SARS-CoV-2 non-structural protein 3b

Author: Cantini, F., Banci, L., Altincekic, Nadide, Bains, Jasleen Kaur, Dhamotharan, Karthikeyan, Fuks, Christin, Fürtig, Boris, Gande, S. L., Hargittay, Bruno, Hengesbach, Martin, Hutchison, Marie, Korn, Sophie M., Kubatova, Nina, Kutz, Felicitas, Linhard, Verena, Löhr, Frank, Meiser, Nathalie, Pyper, Dennis Joshua, Qureshi, Nusrat, Richter, Christian, Saxena, Krishna, Schlundt, Andreas, Schwalbe, Harald, Sreeramulu, Sridhar, Tants, Jan-Niklas, Wacker, Anna, Weigand, Julia E., Wöhnert, Jens, Tsika, A. C., Fourkiotis, N. K., Spyroulias, G. A., Cantini, F., Banci, L., Altincekic, Nadide, Bains, Jasleen Kaur, Dhamotharan, Karthikeyan, Fuks, Christin, Fürtig, Boris, Gande, S. L., Hargittay, Bruno, Hengesbach, Martin, Hutchison, Marie, Korn, Sophie M., Kubatova, Nina, Kutz, Felicitas, Linhard, Verena, Löhr, Frank, Meiser, Nathalie, Pyper, Dennis Joshua, Qureshi, Nusrat, Richter, Christian, Saxena, Krishna, Schlundt, Andreas, Schwalbe, Harald, Sreeramulu, Sridhar, Tants, Jan-Niklas, Wacker, Anna, Weigand, Julia E., Wöhnert, Jens, Tsika, A. C., Fourkiotis, N. K., and Spyroulias, G. A.
Abstract: The SARS-CoV-2 genome encodes for approximately 30 proteins. Within the international project COVID19-NMR, we distribute the spectroscopic analysis of the viral proteins and RNA. Here, we report NMR chemical shift assignments for the protein Nsp3b, a domain of Nsp3. The 217-kDa large Nsp3 protein contains multiple structurally independent, yet functionally related domains including the viral papain-like protease and Nsp3b, a macrodomain (MD). In general, the MDs of SARS-CoV and MERS-CoV were suggested to play a key role in viral replication by modulating the immune response of the host. The MDs are structurally conserved. They most likely remove ADP-ribose, a common posttranslational modification, from protein side chains. This de-ADP ribosylating function has potentially evolved to protect the virus from the anti-viral ADP-ribosylation catalyzed by poly-ADP-ribose polymerases (PARPs), which in turn are triggered by pathogen-associated sensing of the host immune system. This renders the SARS-CoV-2 Nsp3b a highly relevant drug target in the viral replication process. We here report the near-complete NMR backbone resonance assignment (1H, 13C, 15N) of the putative Nsp3b MD in its apo form and in complex with ADP-ribose. Furthermore, we derive the secondary structure of Nsp3b in solution. In addition, 15N-relaxation data suggest an ordered, rigid core of the MD structure. These data will provide a basis for NMR investigations targeted at obtaining small-molecule inhibitors interfering with the catalytic activity of Nsp3b.
Published: 2020

40. Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy

Author: Wacker, Anna, Weigand, Julia, Akabayov, Sabine R., Altınçekiç, Nadide, Bains, Jasleen Kaur, Banijamali, Elnaz, Binas, Oliver, Castillo-Martinez, Jesus, Çetiner, Erhan Can, Ceylan, Betül, Chiu, Liang-Yuan, Davila-Calderon, Jesse, Dhamotharan, Karthikeyan, Duchardt-Ferner, Elke, Ferner, Jan, Frydman, Lucio, Fürtig, Boris, Gallego, José, Grün, J. Tassilo, Hacker, Carolin, Haddad, Christina, Hähnke, Martin Jens, Hengesbach, Martin, Hiller, Fabian, Hohmann, Katharina Felicitas, Hymon, Daniel, de Jesus, Vanessa, Jonker, Henry, Keller, Heiko, Knežić, Božana, Landgraf, Tom, Löhr, Frank, Luo, Le, Mertinkus, Klara Rebecca, Muhs, Christina, Novakovic, Mihajlo, Oxenfarth, Andreas, Palomino-Schätzlein, Martina, Petzold, Katja, Peter, Stephen, Pyper, Dennis Joshua, Qureshi, Nusrat, Riad, Magdalena, Richter, Christian, Saxena, Krishna, Schamber, Tatjana, Scherf, Tali, Schlagnitweit, Judith, Schlundt, Andreas, Schnieders, Robbin, Schwalbe, Harald, Simba-Lahuasi, Alvaro, Sreeramulu, Sridhar, Stirnal, Elke, Sudakov, Alexey, Tants, Jan-Niklas, Tolbert, Blanton S., Vögele, Jennifer, Weiß, Lena, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Wöhnert, Jens, Zetzsche, Heidi, Wacker, Anna, Weigand, Julia, Akabayov, Sabine R., Altınçekiç, Nadide, Bains, Jasleen Kaur, Banijamali, Elnaz, Binas, Oliver, Castillo-Martinez, Jesus, Çetiner, Erhan Can, Ceylan, Betül, Chiu, Liang-Yuan, Davila-Calderon, Jesse, Dhamotharan, Karthikeyan, Duchardt-Ferner, Elke, Ferner, Jan, Frydman, Lucio, Fürtig, Boris, Gallego, José, Grün, J. Tassilo, Hacker, Carolin, Haddad, Christina, Hähnke, Martin Jens, Hengesbach, Martin, Hiller, Fabian, Hohmann, Katharina Felicitas, Hymon, Daniel, de Jesus, Vanessa, Jonker, Henry, Keller, Heiko, Knežić, Božana, Landgraf, Tom, Löhr, Frank, Luo, Le, Mertinkus, Klara Rebecca, Muhs, Christina, Novakovic, Mihajlo, Oxenfarth, Andreas, Palomino-Schätzlein, Martina, Petzold, Katja, Peter, Stephen, Pyper, Dennis Joshua, Qureshi, Nusrat, Riad, Magdalena, Richter, Christian, Saxena, Krishna, Schamber, Tatjana, Scherf, Tali, Schlagnitweit, Judith, Schlundt, Andreas, Schnieders, Robbin, Schwalbe, Harald, Simba-Lahuasi, Alvaro, Sreeramulu, Sridhar, Stirnal, Elke, Sudakov, Alexey, Tants, Jan-Niklas, Tolbert, Blanton S., Vögele, Jennifer, Weiß, Lena, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Wöhnert, Jens, and Zetzsche, Heidi
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.
Published: 2020

41. Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy

Author: Wacker, Anna, primary, Weigand, Julia E, additional, Akabayov, Sabine R, additional, Altincekic, Nadide, additional, Bains, Jasleen Kaur, additional, Banijamali, Elnaz, additional, Binas, Oliver, additional, Castillo-Martinez, Jesus, additional, Cetiner, Erhan, additional, Ceylan, Betül, additional, Chiu, Liang-Yuan, additional, Davila-Calderon, Jesse, additional, Dhamotharan, Karthikeyan, additional, Duchardt-Ferner, Elke, additional, Ferner, Jan, additional, Frydman, Lucio, additional, Fürtig, Boris, additional, Gallego, José, additional, Grün, J Tassilo, additional, Hacker, Carolin, additional, Haddad, Christina, additional, Hähnke, Martin, additional, Hengesbach, Martin, additional, Hiller, Fabian, additional, Hohmann, Katharina F, additional, Hymon, Daniel, additional, de Jesus, Vanessa, additional, Jonker, Henry, additional, Keller, Heiko, additional, Knezic, Bozana, additional, Landgraf, Tom, additional, Löhr, Frank, additional, Luo, Le, additional, Mertinkus, Klara R, additional, Muhs, Christina, additional, Novakovic, Mihajlo, additional, Oxenfarth, Andreas, additional, Palomino-Schätzlein, Martina, additional, Petzold, Katja, additional, Peter, Stephen A, additional, Pyper, Dennis J, additional, Qureshi, Nusrat S, additional, Riad, Magdalena, additional, Richter, Christian, additional, Saxena, Krishna, additional, Schamber, Tatjana, additional, Scherf, Tali, additional, Schlagnitweit, Judith, additional, Schlundt, Andreas, additional, Schnieders, Robbin, additional, Schwalbe, Harald, additional, Simba-Lahuasi, Alvaro, additional, Sreeramulu, Sridhar, additional, Stirnal, Elke, additional, Sudakov, Alexey, additional, Tants, Jan-Niklas, additional, Tolbert, Blanton S, additional, Vögele, Jennifer, additional, Weiß, Lena, additional, Wirmer-Bartoschek, Julia, additional, Wirtz Martin, Maria A, additional, Wöhnert, Jens, additional, and Zetzsche, Heidi, additional
Published: 2020
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42. Laccase from a non-melanogenic, alkalotolerant γ-proteobacterium JB isolated from industrial wastewater drained soil

Author: Bains, Jasleen, Capalash, Neena, and Sharma, Prince
Published: 2003
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43. 1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5′-UTR of SARS-CoV-2.

Author: Mertinkus, Klara R., Grün, J. Tassilo, Altincekic, Nadide, Bains, Jasleen Kaur, Ceylan, Betül, Ferner, Jan-Peter, Frydman, Lucio, Fürtig, Boris, Hengesbach, Martin, Hohmann, Katharina F., Hymon, Daniel, Kim, Jihyun, Knezic, Božana, Novakovic, Mihajlo, Oxenfarth, Andreas, Peter, Stephen A., Qureshi, Nusrat S., Richter, Christian, Scherf, Tali, and Schlundt, Andreas
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. [ABSTRACT FROM AUTHOR]
Published: 2022
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44. Elucidating the reaction mechanism of the benzoate oxidation pathway encoded aldehyde dehydrogenase from Burkholderia xenovorans LB400

Author: Bains, Jasleen, Leon, Rafael, Temke, Kevin G., and Boulanger, Martin J.
Published: 2011
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45. 19 F NMR‐Based Fragment Screening for 14 Different Biologically Active RNAs and 10 DNA and Protein Counter‐Screens

Author: Binas, Oliver, primary, Jesus, Vanessa, additional, Landgraf, Tom, additional, Völklein, Albrecht Eduard, additional, Martins, Jason, additional, Hymon, Daniel, additional, Kaur Bains, Jasleen, additional, Berg, Hannes, additional, Biedenbänder, Thomas, additional, Fürtig, Boris, additional, Lakshmi Gande, Santosh, additional, Niesteruk, Anna, additional, Oxenfarth, Andreas, additional, Shahin Qureshi, Nusrat, additional, Schamber, Tatjana, additional, Schnieders, Robbin, additional, Tröster, Alix, additional, Wacker, Anna, additional, Wirmer‐Bartoschek, Julia, additional, Wirtz Martin, Maria Alexandra, additional, Stirnal, Elke, additional, Azzaoui, Kamal, additional, Richter, Christian, additional, Sreeramulu, Sridhar, additional, José Blommers, Marcel Jules, additional, and Schwalbe, Harald, additional
Published: 2020
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46. Dynamic features based stroke recognition system for signboard images of Gurmukhi text

Author: Bains, Jasleen Kaur, primary, Singh, Sukhdeep, additional, and Sharma, Anuj, additional
Published: 2020
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47. Characterization of DNA:DNA:RNA triplex and DNA:RNA heteroduplex formation by lncRNAs using NMR spectroscopy

Author: Kaur Bains, Jasleen, primary
Published: 2020
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48. 1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2.

Author: Richter, Christian, Hohmann, Katharina F., Toews, Sabrina, Mathieu, Daniel, Altincekic, Nadide, Bains, Jasleen Kaur, Binas, Oliver, Ceylan, Betül, Duchardt-Ferner, Elke, Ferner, Jan, Fürtig, Boris, Grün, J. Tassilo, Hengesbach, Martin, Hymon, Daniel, Jonker, Hendrik R. A., Knezic, Bozana, Korn, Sophie M., Landgraf, Tom, Löhr, Frank, and Peter, Stephen A.
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. [ABSTRACT FROM AUTHOR]
Published: 2021
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49. 1H, 13C, 15N and 31P chemical shift assignment for stem-loop 4 from the 5′-UTR of SARS-CoV-2.

Author: Vögele, Jennifer, Ferner, Jan-Peter, Altincekic, Nadide, Bains, Jasleen Kaur, Ceylan, Betül, Fürtig, Boris, Grün, J. Tassilo, Hengesbach, Martin, Hohmann, Katharina F., Hymon, Daniel, Knezic, Bozana, Löhr, Frank, Peter, Stephen A., Pyper, Dennis, Qureshi, Nusrat S., Richter, Christian, Schlundt, Andreas, Schwalbe, Harald, Stirnal, Elke, and Sudakov, Alexey
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. [ABSTRACT FROM AUTHOR]
Published: 2021
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50. Combined smFRET and NMR analysis of riboswitch structural dynamics

Author: Bains, Jasleen Kaur, primary, Blechar, Julius, additional, de Jesus, Vanessa, additional, Meiser, Nathalie, additional, Zetzsche, Heidi, additional, Fürtig, Boris, additional, Schwalbe, Harald, additional, and Hengesbach, Martin, additional
Published: 2019
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