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32 results on '"Ceylan, Betül"'

1. Personalized Protein-Protein Interaction Networks Towards Unraveling the Molecular Mechanisms of Alzheimer’s Disease

Author: CEYLAN, Betül, DÜZ, Elif, and ÇAKIR, Tunahan
Published: 2024
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2. 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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3. 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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4. 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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5. 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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6. ¹H, ¹³C and 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, Duchardt-Ferner, Elke, 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
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 and ¹⁵N and ³¹P resonance assignments of 5_SL4 as the basis for in-depth structural and ligand screening studies by solution NMR spectroscopy.
Published: 2024

7. 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, Wacker, Anna, 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
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.
Published: 2024

8. 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

9. Interprofessionelle Zusammenarbeit von Hausärzt_innen und Pflegefachpersonen in der Primärversorgung: Eine qualitative Studie.

Author: Zimansky, Manuel, Ceylan, Betül, Klukas, Eduard, Hamacher, Marie, van de Sand, Heike, Gustaevel, Malin, Wiegelmann, Saskia, and Hämel, Kerstin
Published: 2024
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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, 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

11. 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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12. 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

13. 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

14. 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

15. 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
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16. 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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17. 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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18. 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

19. 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

20. 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

21. 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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22. 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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23. 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

24. 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

25. 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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26. 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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27. The Philosophical Analysis of Reinhart P. A. Dozy's History of Islamic Works (Example İsmail Fenni, Manastirli İsmail Hakki, Filibeli Ahmet Hilmi)

Author: Ceylan, Betül, Çapku, Ahmet, and Felsefe Anabilim Dalı
Subjects: Philosophy, Dozy, Batıcılık, Positivism, Felsefe, Westernism, History of Islam, Materialism, Materyalizm, Pozitivizm, Tarih-i İslam
Abstract: Dozy'nin `Tarih-i İslamiyet` kitabında İslamiyet ve Müslümanlar hakkındaki ifadeleri bilimsel ve felsefi olarak birçok çelişik ifadeye sahiptir. Ancak bu durum ülkemizde bazı düşünürler tarafından normal karşılanırken, bazı milliyetçi ve İslamcı düşünürler tarafından yoğun şekilde eleştirilmiş ve bu düşüncelere reddiyeler yazılma ihtiyacı hissedilmiştir. Abdullah Cevdet'in Dozy'nin kitabını tercüme etmesi ve bu kitaba karşı yapmış olduğu aşırı övgüler, İsmail Fenni Ertuğrul, Filibeli Ahmet Hilmi, Manastırlı İsmail Hakkı gibi İslamcı ve milliyetçi düşünürleri harekete geçirmiştir. Tezimizde, bu düşünürlerin eleştirilerinin amacını, bunları hangi felsefi ve bilimsel yöntemler ile yapmaya çalıştıklarını ve Dozy'e eleştirilerini incelemeye çalıştık. In Dozy's `History of Islam` his statements about Islam and Muslims have many contradictory expressions, scientifically and philosophically. However, while this situation was considered normal by some thinkers in our country, it was extensively criticized by some nationalist and Islamist thinkers and it was felt the need to write rejections to these ideas. Abdullah Cevdet's translation of Dozy's book and the excessive praise he made against this book provoked Islamist and nationalist thinkers such as İsmail Fenni Ertuğrul, Ahmet Hilmi from Filibeli and İsmail Hakkı from Manastir. In our thesis, we tried to examine the purpose of the criticism of these thinkers, what philosophical and scientific methods they try to do and their criticism to Dozy. 192
Published: 2019

28. Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function.

Author: Bains, Jasleen Kaur, Qureshi, Nusrat Shahin, Ceylan, Betül, Wacker, Anna, and Schwalbe, Harald
Published: 2023
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29. 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., 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, 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, 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, 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, Almeida, Marcius Da Silva, 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
Subjects: NMR spectroscopy, SARS-CoV-2, nonstructural proteins, accessory proteins, COVID-19, structural proteins, intrinsically disordered region, cell-free protein synthesis, 3. Good health
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.

30. Optimization of Structure-Guided Development of Chemical Probes for the Pseudoknot RNA of the Frameshift Element in SARS-CoV-2.

Author: Ceylan B, Adam J, Toews S, Kaiser F, Dörr J, Scheppa D, Tants JN, Smart A, Schoth J, Philipp S, Stirnal E, Ferner J, Richter C, Sreeramulu S, Caliskan N, Schlundt A, Weigand JE, Göbel M, Wacker A, and Schwalbe H
Abstract: Targeting the RNA genome of SARS-CoV-2 is a viable option for antiviral drug development. We explored three ligand binding sites of the core pseudoknot RNA of the SARS-CoV-2 frameshift element. We iteratively optimized ligands, based on improved affinities, targeting these binding sites and report on structural and dynamic properties of the three identified binding sites. Available experimental 3D structures of the pseudoknot element were compared to SAXS and NMR data to validate its dominant folding state in solution. In order to experimentally map in silico predicted binding sites, NMR assignments of the majority of nucleobases were achieved by segmental labeling of the pseudoknot RNA and isotope-filtered NMR experiments at 1.2 GHz, demonstrating the value of NMR spectroscopy to supplement modelling and docking data. Optimized ligands with enhanced affinity were shown to specifically inhibit frameshifting without affecting 0-frame translation in cell-free translation assays, establishing the frameshift element as target for drug-like ligands of low molecular weight., (© 2025 The Author(s). Angewandte Chemie International Edition published by Wiley-VCH GmbH.)
Published: 2025
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31. [Interprofessional collaboration of general practitioners and nurses in primary care: A qualitative study].

Author: Zimansky M, Ceylan B, Klukas E, Hamacher M, van de Sand H, Gustaevel M, Wiegelmann S, and Hämel K
Subjects: Humans, Interprofessional Relations, Qualitative Research, Primary Health Care, General Practitioners, Nursing Care
Abstract: Interprofessional collaboration of general practitioners and nurses in primary care: A qualitative study Abstract. Background: There is a need to strengthen interprofessional collaboration of general practitioners and home care nurses in the primary care of people with chronic diseases and long-term care needs. Aim: This study investigated a) how general practitioners and nurses in Germany perceive their collaboration in primary care and b) which development perspectives of collaboration exist from their point of view. Methods: Expert interviews were conducted with seven general practitioners and eight home care nurses. The data were analysed using thematic-structured qualitative content analysis. Results: The interviewees from both professional groups report that their collaboration is hindered by poor mutual accessibility. At the same time, they emphasise their appreciation of the professional exchange with the other professional group. Nevertheless, the perceptions of the professional competence of home care nurses differ. To improve their cooperation, the interviewees recommend the establishment of interprofessional meetings and cooperation in spatial proximity for regular professional exchange. They expect this to lead to a joint development of trust and competence and to an expansion of the area of responsibility of home care nurses in primary care. Conclusions: Binding communication structures, cooperation in spatial proximity and an expansion of the area of responsibility of home care nurses offer high potential for strengthening primary care in Germany.
Published: 2024
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32. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications.

Author: Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, Bula A, Bütikofer M, Camacho-Zarco AR, Carlomagno T, Caruso IP, Ceylan B, Chaikuad A, Chu F, Cole L, Crosby MG, de Jesus V, Dhamotharan K, Felli IC, Ferner J, Fleischmann Y, Fogeron ML, Fourkiotis NK, Fuks C, Fürtig B, Gallo A, Gande SL, Gerez JA, Ghosh D, Gomes-Neto F, Gorbatyuk O, Guseva S, Hacker C, Häfner S, Hao B, Hargittay B, Henzler-Wildman K, Hoch JC, Hohmann KF, Hutchison MT, Jaudzems K, Jović K, Kaderli J, Kalniņš G, Kaņepe I, Kirchdoerfer RN, Kirkpatrick J, Knapp S, Krishnathas R, Kutz F, Zur Lage S, Lambertz R, Lang A, Laurents D, Lecoq L, Linhard V, Löhr F, Malki A, Bessa LM, Martin RW, Matzel T, Maurin D, McNutt SW, Mebus-Antunes NC, Meier BH, Meiser N, Mompeán M, Monaca E, Montserret R, Mariño Perez L, Moser C, Muhle-Goll C, Neves-Martins TC, Ni X, Norton-Baker B, Pierattelli R, Pontoriero L, Pustovalova Y, Ohlenschläger O, Orts J, Da Poian AT, Pyper DJ, Richter C, Riek R, Rienstra CM, Robertson A, Pinheiro AS, Sabbatella R, Salvi N, Saxena K, Schulte L, Schiavina M, Schwalbe H, Silber M, Almeida MDS, Sprague-Piercy MA, Spyroulias GA, Sreeramulu S, Tants JN, Tārs K, Torres F, Töws S, Treviño MÁ, Trucks S, Tsika AC, Varga K, Wang Y, Weber ME, Weigand JE, Wiedemann C, Wirmer-Bartoschek J, Wirtz Martin MA, Zehnder J, Hengesbach M, and Schlundt A
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., Competing Interests: CH was employed by Signals GmbH & Co. KG. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Altincekic, Korn, Qureshi, Dujardin, Ninot-Pedrosa, Abele, Abi Saad, Alfano, Almeida, Alshamleh, de Amorim, Anderson, Anobom, Anorma, Bains, Bax, Blackledge, Blechar, Böckmann, Brigandat, Bula, Bütikofer, Camacho-Zarco, Carlomagno, Caruso, Ceylan, Chaikuad, Chu, Cole, Crosby, de Jesus, Dhamotharan, Felli, Ferner, Fleischmann, Fogeron, Fourkiotis, Fuks, Fürtig, Gallo, Gande, Gerez, Ghosh, Gomes-Neto, Gorbatyuk, Guseva, Hacker, Häfner, Hao, Hargittay, Henzler-Wildman, Hoch, Hohmann, Hutchison, Jaudzems, Jović, Kaderli, Kalniņš, Kaņepe, Kirchdoerfer, Kirkpatrick, Knapp, Krishnathas, Kutz, zur Lage, Lambertz, Lang, Laurents, Lecoq, Linhard, Löhr, Malki, Bessa, Martin, Matzel, Maurin, McNutt, Mebus-Antunes, Meier, Meiser, Mompeán, Monaca, Montserret, Mariño Perez, Moser, Muhle-Goll, Neves-Martins, Ni, Norton-Baker, Pierattelli, Pontoriero, Pustovalova, Ohlenschläger, Orts, Da Poian, Pyper, Richter, Riek, Rienstra, Robertson, Pinheiro, Sabbatella, Salvi, Saxena, Schulte, Schiavina, Schwalbe, Silber, Almeida, Sprague-Piercy, Spyroulias, Sreeramulu, Tants, Tārs, Torres, Töws, Treviño, Trucks, Tsika, Varga, Wang, Weber, Weigand, Wiedemann, Wirmer-Bartoschek, Wirtz Martin, Zehnder, Hengesbach and Schlundt.)
Published: 2021
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32 results on '"Ceylan, Betül"'

1. Personalized Protein-Protein Interaction Networks Towards Unraveling the Molecular Mechanisms of Alzheimer’s Disease

2. 1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5′-UTR of SARS-CoV-2

3. 1H, 13C, 15N and 31P chemical shift assignment for stem-loop 4 from the 5′-UTR of SARS-CoV-2

4. 1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2

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

6. ¹H, ¹³C and ¹⁵N and ³¹P chemical shift assignment for stem-loop 4 from the 5′-UTR of SARS-CoV-2

7. ¹H, ¹³C and ¹⁵N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2

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

9. Interprofessionelle Zusammenarbeit von Hausärzt_innen und Pflegefachpersonen in der Primärversorgung: Eine qualitative Studie.

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

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

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

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

14. Exploring the druggability of conserved RNA regulatory elements in the SARS-CoV-2 genome

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

16. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome

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

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

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

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

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

22. 1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5′-UTR of SARS-CoV-2.

23. 1H, 13C, and 15N backbone chemical shift assignments of coronavirus-2 non-structural protein Nsp10

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

25. 1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2.

26. 1H, 13C, 15N and 31P chemical shift assignment for stem-loop 4 from the 5′-UTR of SARS-CoV-2.

27. The Philosophical Analysis of Reinhart P. A. Dozy's History of Islamic Works (Example İsmail Fenni, Manastirli İsmail Hakki, Filibeli Ahmet Hilmi)

28. Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function.

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

30. Optimization of Structure-Guided Development of Chemical Probes for the Pseudoknot RNA of the Frameshift Element in SARS-CoV-2.

31. [Interprofessional collaboration of general practitioners and nurses in primary care: A qualitative study].

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

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32 results on '"Ceylan, Betül"'

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