publications of the research group NMR-based structural chemistry(NBSC)
http://hdl.handle.net/10033/621053
2024-03-28T16:02:30ZPhosphotyrosine couples peptide binding and SHP2 activation via a dynamic allosteric network.
http://hdl.handle.net/10033/623025
Phosphotyrosine couples peptide binding and SHP2 activation via a dynamic allosteric network.
Marasco, Michelangelo; Kirkpatrick, John; Nanna, Vittoria; Sikorska, Justyna; Carlomagno, Teresa
SHP2 is a ubiquitous protein tyrosine phosphatase, whose activity is regulated by phosphotyrosine (pY)-containing peptides generated in response to extracellular stimuli. Its crystal structure reveals a closed, auto-inhibited conformation in which the N-terminal Src homology 2 (N-SH2) domain occludes the catalytic site of the phosphatase (PTP) domain. High-affinity mono-phosphorylated peptides promote catalytic activity by binding to N-SH2 and disrupting the interaction with the PTP. The mechanism behind this process is not entirely clear, especially because N-SH2 is incapable of accommodating complete peptide binding when SHP2 is in the auto-inhibited state. Here, we show that pY performs an essential role in this process; in addition to its contribution to overall peptide-binding energy, pY-recognition leads to enhanced dynamics of the N-SH2 EF and BG loops via an allosteric communication network, which destabilizes the N-SH2–PTP interaction surface and simultaneously generates a fully accessible binding pocket for the C-terminal half of the phosphopeptide. Subsequently, full binding of the phosphopeptide is associated with the stabilization of activated SHP2. We demonstrate that this allosteric network exists only in N-SH2, which is directly involved in the regulation of SHP2 activity, while the C-terminal SH2 domain (C-SH2) functions primarily to recruit high-affinity bidentate phosphopeptides.
2021-04-20T00:00:00ZLarge-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications.
http://hdl.handle.net/10033/622936
Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications.
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; 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.
2021-05-10T00:00:00ZHigh-resolution structure of eukaryotic Fibrillarin interacting with Nop56 amino-terminal domain.
http://hdl.handle.net/10033/622934
High-resolution structure of eukaryotic Fibrillarin interacting with Nop56 amino-terminal domain.
Höfler, Simone; Lukat, Peer; Blankenfeldt, Wulf; Carlomagno, Teresa
Ribosomal RNA (rRNA) carries extensive 2'-O-methyl marks at functionally important sites. This simple chemical modification is thought to confer stability, promote RNA folding, and contribute to generate a heterogenous ribosome population with a yet-uncharacterized function. 2'-O-methylation occurs both in archaea and eukaryotes and is accomplished by the Box C/D RNP enzyme in an RNA-guided manner. Extensive and partially conflicting structural information exists for the archaeal enzyme, while no structural data is available for the eukaryotic enzyme. The yeast Box C/D RNP consists of a guide RNA, the RNA-primary binding protein Snu13, the two scaffold proteins Nop56 and Nop58, and the enzymatic module Nop1. Here we present the high-resolution structure of the eukaryotic Box C/D methyltransferase Nop1 from Saccharomyces cerevisiae bound to the amino-terminal domain of Nop56. We discuss similarities and differences between the interaction modes of the two proteins in archaea and eukaryotes and demonstrate that eukaryotic Nop56 recruits the methyltransferase to the Box C/D RNP through a protein-protein interface that differs substantially from the archaeal orthologs. This study represents a first achievement in understanding the evolution of the structure and function of these proteins from archaea to eukaryotes.
2021-01-22T00:00:00ZSpecificity and regulation of phosphotyrosine signaling through SH2 domains.
http://hdl.handle.net/10033/622930
Specificity and regulation of phosphotyrosine signaling through SH2 domains.
Marasco, Michelangelo; Carlomagno, Teresa
Phosphotyrosine (pY) signaling is instrumental to numerous cellular processes. pY recognition occurs through specialized protein modules, among which the Src-homology 2 (SH2) domain is the most common. SH2 domains are small protein modules with an invariant fold, and are present in more than a hundred proteins with different function. Here we ask the question of how such a structurally conserved, small protein domain can recognize distinct phosphopeptides with the breath of binding affinity, specificity and kinetic parameters necessary for proper control of pY-dependent signaling and rapid cellular response. We review the current knowledge on structure, thermodynamics and kinetics of SH2-phosphopeptide complexes and conclude that selective phosphopeptide recognition is governed by both structure and dynamics of the SH2 domain, as well as by the kinetics of the binding events. Further studies on the thermodynamic and kinetic properties of SH2-phosphopeptide complexes, beyond their structure, are required to understand signaling regulation.
2020-05-27T00:00:00Z