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Year of publication
Has Fulltext
- yes (47)
Is part of the Bibliography
- no (47)
Keywords
- SARS-CoV-2 (7)
- BESIII (5)
- Solution NMR-spectroscopy (4)
- COVID19-NMR (3)
- Covid19-NMR (3)
- Non-structural protein (3)
- Branching fractions (2)
- Hadronic decays (2)
- Lexicalized Tree Adjoining Grammar (2)
- Protein drugability (2)
Institute
Zirafi, Onofrio ; Kim, Kyeong-Ae ; Ständker, Ludger ; Mohr, Katharina B. ; Sauter, Daniel ; Heigele, Anke ; Kluge, Silvia F. ; Wiercinska, Eliza ; Chudziak, Doreen ; Richter, Rudolf ; Moepps, Barbara ; Gierschik, Peter ; Vas, Virag ; Geiger, Hartmut ; Lamla, Markus ; Weil, Tanja ; Burster, Timo ; Zgraja, Andreas ; Daubeuf, Francois ; Frossard, Nelly ; Hachet-Haas, Muriel ; Heunisch, Fabian ; Reichetzeder, Christoph ; Galzi, Jean-Luc ; Pérez-Castells, Javier ; Canales-Mayordomo, Angeles ; Jiménez-Barbero, Jesus ; Giménez-Gallego, Guillermo ; Schneider, Marion ; Shorter, James ; Telenti, Amalio ; Hocher, Berthold ; Forssmann, Wolf-Georg ; Bönig, Halvard-Björn ; Kirchhoff, Frank ; Münch, Jan
CXCL12-CXCR4 signaling controls multiple physiological processes and its dysregulation is associated with cancers and inflammatory diseases. To discover as-yet-unknown endogenous ligands of CXCR4, we screened a blood-derived peptide library for inhibitors of CXCR4-tropic HIV-1 strains. This approach identified a 16 amino acid fragment of serum albumin as an effective and highly specific CXCR4 antagonist. The endogenous peptide, termed EPI-X4, is evolutionarily conserved and generated from the highly abundant albumin precursor by pH-regulated proteases. EPI-X4 forms an unusual lasso-like structure and antagonizes CXCL12-induced tumor cell migration, mobilizes stem cells, and suppresses inflammatory responses in mice. Furthermore, the peptide is abundant in the urine of patients with inflammatory kidney diseases and may serve as a biomarker. Our results identify EPI-X4 as a key regulator of CXCR4 signaling and introduce proteolysis of an abundant precursor protein as an alternative concept for chemokine receptor regulation.
In this paper we will explore the similarities and differences between two feature logic-based approaches to the composition of semantic representations. The first approach is formulated for Lexicalized Tree Adjoining Grammar (LTAG, Joshi and Schabes 1997), the second is Lexical Ressource Semantics (LRS, Richter and Sailer 2004) and was first defined in Head-driven Phrase Structure Grammar. The two frameworks have several common characteristics that make them easy to compare: 1 They use languages of two sorted type theory for semantic representations. 2. They allow underspecification. LTAG uses scope constraints while LRS provides component-of contraints. 3 They use feature logics for computing semantic representations. 4. they are designed for computational applications. By comparing the two frameworks we will also point outsome characteristics and advantages of feature logic-based semantic computation in genereal.
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 ; 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
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.
Triebskorn, Rita ; Amler, Klaus ; Blaha, Ludek ; Gallert, Claudia ; Giebner, Sabrina ; Güde, Hans ; Henneberg, Anja ; Hess, Stefanie ; Hetzenauer, Harald ; Jedele, Klaus ; Jung, Ralph-Michael ; Kneipp, Sven ; Köhler, Heinz-R. ; Krais, Stefanie ; Kuch, Bertram ; Lange, Claudia ; Löffler, Herbert ; Maier, Diana ; Metzger, Jörg ; Müller, Michael ; Oehlmann, Jörg ; Osterauer, Raphaela ; Peschke, Katharina ; Raizner, Jürgen ; Rey, Peter ; Rault, Magali ; Richter, Doreen ; Sacher, Frank ; Scheurer, Marco ; Schneider-Rapp, Jutta ; Seifan, Merav ; Spieth, Markus ; Vogel, Hans-Joachim ; Weyhmüller, Michael ; Winter, Josef ; Wurm, Karl
The project focuses on the efficiency of combined technologies to reduce the release of micropollutants and bacteria into surface waters via sewage treatment plants of different size and via stormwater overflow basins of different types. As a model river in a highly populated catchment area, the river Schussen and, as a control, the river Argen, two tributaries of Lake Constance, Southern Germany, are under investigation in this project. The efficiency of the different cleaning technologies is monitored by a wide range of exposure and effect analyses including chemical and microbiological techniques as well as effect studies ranging from molecules to communities.
1H, 13C, and 15N backbone chemical shift assignments of coronavirus-2 non-structural protein Nsp10
(2020)
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
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.
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
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.