Publications

2025

    Journal articles

  • Kazi, Nafizul Haque; Klink, Nikolas; Gallant, Kai; Kipka, Gian-Marvin; Gersch, Malte
    Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30
    In: Nature Structural & Molecular Biology 2025 , in press
    DOI (Open Access)
  • Sander, Pascal; Schwalm, Martin P.; Krämer, Andreas; Elson, Lewis; Rasch, Alexander; Masberg, Benedikt; Selig, Roland; Sievers-Engler, Adrian; Lämmerhofer, Michael; Müller, Susanne; Knapp, Stefan; Albrecht, Wolfgang; Laufer, Stefan A.
    Design, Synthesis, and Biochemical Evaluation of Novel MLK3 Inhibitors: A Target Hopping Example
    In: Journal of Medicinal Chemistry , Vol. 68 2025, Nr. 1, pp. 674 – 694
    DOI
  • Haag, Adrian; Němec, Václav; Janovská, Pavlína; Bartošíková, Jana; Adhikari, Bikash; Müller, Juliane; Schwalm, Martin P.; Čada, Štěpán; Ohmayer, Uli; Daub, Henrik; Kim, Yeojin; Born, Florian; Wolf, Elmar; Bryja, Vítězslav; Knapp, Stefan
    Development and Discovery of a Selective Degrader of Casein Kinases 1 δ/ϵ
    In: Journal of Medicinal Chemistry , Vol. 68 2025, Nr. 1, pp. 506 – 530
    DOI
  • Wendrich, Kim; Gallant, Kai; Recknagel, Sarah; Petroulia, Stavroula; Kazi, Nafizul Haque; Hane, Jan André; Führer, Siska; Bezstarosti, Karel; O’Dea, Rachel; Demmers, Jeroen; Gersch, Malte
    Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53
    In: Nature Chemical Biology , Vol. 21 2025, Nr. 5, pp. 746 – 757
    DOI (Open Access)
  • Schwalm, Martin P.; Menge, Amelie; Elson, Lewis; Greco, Francesco A.; Robers, Matthew B.; Müller, Susanne; Knapp, Stefan
    Functional Characterization of Pathway Inhibitors for the Ubiquitin-Proteasome System (UPS) as Tool Compounds for CRBN and VHL-Mediated Targeted Protein Degradation
    In: ACS Chemical Biology , Vol. 20 2025, Nr. 1, pp. 94 – 104
    DOI (Open Access)
  • Stubenvoll, Antonia; Schmidt, Maria; Moeller, Johanna; Chango, Max Alexander Lingner; Schultz, Carolyn; Antoniadou, Olga; Loeffler-Wirth, Henry; Bernhart, Stephan; Große, Florian; Thier, Beatrice; Paschen, Annette; Anderegg, Ulf; Simon, Jan C.; Ziemer, Mirjana; Schoeder, Clara T.; Binder, Hans; Kunz, Manfred
    Single-cell transcriptomics and epigenomics point to CD58-CD2 interaction in controlling primary melanoma growth and immunity
    In: Cancer Communications , Vol. 45 2025, Nr. 4, pp. 465 – 470
    DOI (Open Access)
  • Schwalm, Martin P.; Knapp, Stefan
    Single-plate kinome screening in live-cells to enable highly cost-efficient kinase inhibitor profiling
    In: SLAS Discovery , Vol. 31 2025, 100214
    DOI (Open Access)
  • Führer, Siska; Gallant, Kai; Kaschani, Farnusch; Kaiser, Markus; Janning, Petra; Waldmann, Herbert; Gersch, Malte
    Small Molecule-Induced Alterations of Protein Polyubiquitination Revealed by Mass-Spectrometric Ubiquitome Analysis
    In: Angewandte Chemie International Edition 2025 , in press
    DOI (Open Access)
  • Sewald, Leonard; Tabak, Werner W. A.; Fehr, Lorenz; Zolg, Samuel; Najdzion, Maja; Verhoef, Carlo J. A.; Podlesainski, David; Geiss-Friedlander, Ruth; Lammens, Alfred; Kaschani, Farnusch; Hellerschmied, Doris; Huber, Robert; Kaiser, Markus
    Sulphostin-inspired N-phosphonopiperidones as selective covalent DPP8 and DPP9 inhibitors
    In: Nature Communications , Vol. 16 2025, Nr. 1, 3208
    DOI (Open Access)
  • Dudziak, Alexander; Pleuger, Richard; Schmidt, Jasmin; Hamm, Frederik; Tendulkar, Sharvari Gurudatta; Jänen, Karolin; Vetter, Ingrid R; Singh, Sylvia; Fischböck, Josef; Herzog, Franz; Westermann, Stefan
    The Spc105/Kre28 complex promotes mitotic error correction by outer kinetochore recruitment of Ipl1/Sli15
    In: The EMBO Journal 2025 , in press
    DOI (Open Access)
  • Miletić, Nebojša; Weckesser, Janik; Mosler, Thorsten; Rathore, Rajeshwari; Hoffmann, Marina E.; Gehrtz, Paul; Schlesiger, Sarah; Hartung, Ingo V.; Berner, Nicola; Wilhelm, Stephanie; Müller, Juliane; Adhikari, Bikash; Němec, Václav; Sivashanmugam, Saran Aswathaman; Elson, Lewis; Holzmann, Hanna; Schwalm, Martin P.; Hoffmann, Lasse; Abdul Azeez, Kamal Rayees; Müller, Susanne; Kuster, Bernhard; Wolf, Elmar; Đikić, Ivan; Knapp, Stefan
    Workflow for E3 Ligase Ligand Validation for PROTAC Development
    In: ACS Chemical Biology , Vol. 20 2025, Nr. 2, pp. 507 – 521
    DOI (Open Access)

    • Preprints

  • Reinders, Maike; Kravic, Bojana; Gahlot, Pinki; van den Boom, Johannes; Schulze, Nina; Levantovsky, Sophie; Kleine, Stefan; Kaiser, Markus; Kulathu, Yogesh; Behrends, Christian; Meyer, Hemmo
    ATXN3 regulates lysosome regeneration after damage by targeting K48-K63-branched ubiquitin chains
    2025
    DOI (Open Access)
  • Zaffar, Eman; Vieyto-Nuñez, Julio; Pravi, Katerina; Aslam, Mohammed Faidh; Almeida-Hernández, Yasser; Mieres-Pérez, Joel; Kaschani, Farnusch; Kaiser, Markus; Kroesen, Anika; Boos, Dominik; Sánchez-García, Elsa
    MTBP allosterically activates Cdk8-CycC kinase activity
    2025
    DOI (Open Access)
  • Wagner, Jessica; Feller, Konstantina; Schrenke, Nicole; Schulze, Nina; Paschen, Annette; Dehmelt, Leif; Nalbant, Perihan
    Optogenetic stimulation of Lbc GEF-mediated Rho activity dynamics promotes cell invasion
    2025
    DOI (Open Access)
  • Egetemaier, Stefanie; Chauvistré, Heike; Váraljai, Renáta; Hua, Yichao; Lueong, Smiths; Makhzami, Samira; Srinivas, Nalini; Forster, Jan; Ullrich, Vivien; Stupia, Simone; Schroeder, Valéria; Scharfenberg, Sarah; Hoewner, Anna; Shannan, Batool; Siveke, Jens; Baietti, Maria Francesca; Leucci, Eleonora; Marine, Jean-Christophe; Paschen, Annette; Scheffler, Björn; Engel, Daniel R.; Becker, Lisa; Nensa, Felix; Köster, Johannes; Grünwald, Barbara; Poepsel, Simon; Ninck, Sabrina; Kaschani, Farnusch; Schadendorf, Dirk; Becker, Jürgen; Tasdogan, Alpaslan; Rambow, Florian; Rösch, Alexander
    Redirecting resistance evolution in BRAFV600 melanoma by inhibition of the peroxiredoxin-thioredoxin system
    2025
    DOI (Open Access)
  • Daniilidis, Melina; Günsel, Umut; Broutzakis, Georgios; Janowski, Robert; Leitl, Kira D.; Fredriksson, Kai; Niessing, Dierk; Gatsogiannis, Christos; Hagn, Franz
    Structural basis of apoptosis induction by the mitochondrial voltage dependent anion channel
    2025
    DOI (Open Access)
  • Cmentowski, Verena; Musacchio, Andrea
    The BUB1 and BUBR1 paralogs scaffold the kinetochore fibrous corona
    2025
    DOI (Open Access)
  • Kitanovski, Simo; Conroy, Shannon; Sonneck, Justin; Dorsch, Madeleine; Urban, Sebastian; Chen, Jianxu; Grüner, Barbara M.; Hoffmann, Daniel
    Uncertainty-aware quantitative analysis of high-throughput live cell migration data
    2025
    DOI (Open Access)

2024

    Journal articles

  • Owens, Dominic D. G.; Maitland, Matthew E. R.; Khalili Yazdi, Aliakbar; Song, Xiaosheng; Reber, Viviane; Schwalm, Martin P.; Machado, Raquel A. C.; Bauer, Nicolas; Wang, Xu; Szewczyk, Magdalena M.; Dong, Cheng; Dong, Aiping; Loppnau, Peter; Calabrese, Matthew F.; Dowling, Matthew S.; Lee, Jisun; Montgomery, Justin I.; O’Connell, Thomas N.; Subramanyam, Chakrapani; Wang, Feng; Adamson, Ella C.; Schapira, Matthieu; Gstaiger, Matthias; Knapp, Stefan; Vedadi, Masoud; Min, Jinrong; Lajoie, Gilles A.; Barsyte-Lovejoy, Dalia; Owen, Dafydd R.; Schild-Poulter, Caroline; Arrowsmith, Cheryl H.
    A chemical probe to modulate human GID4 Pro/N-degron interactions
    In: Nature Chemical Biology , Vol. 20 2024, Nr. 9, pp. 1164 – 1175
    DOI
  • Huang, Jing; Jaekel, Andreas; van den Boom, Johannes; Podlesainski, David; Elnaggar, M.; Heuer-Jungemann, A.; Kaiser, Markus; Meyer, Hemmo; Saccà, Barbara
    A modular DNA origami nanocompartment for engineering a cell-free, protein unfolding and degradation pathway
    In: Nature Nanotechnology , Vol. 19 2024, Nr. 10, pp. 1521 – 1531
    DOI (Open Access)
  • Ibruli, Olta; Rose, France; Beleggia, Filippo; Schmitt, Anna; Cartolano, Maria; Fernandez, Lucia Torres; Saggau, Julia; Bonasera, Debora; Kiljan, Martha; Gozum, Gokcen; Lichius, Luca; Cai, Jiali; Niu, Li-Na; Caiaffa, Manoela Iannicelli; Herter, Jan M.; Walczak, Henning; Liccardi, Gianmaria; Grüll, Holger; Büttner, Reinhard; Bosco, Graziella; George, Julie; Thomas, Roman K.; Bozek, Kasia; Reinhardt, Hans Christian; Herter-Sprie, Grit S.
    A novel mouse model recapitulating the MMR-defective SCLC subtype uncovers an actionable sensitivity to immune checkpoint blockade
    In: Journal of Cancer Research and Clinical Oncology , Vol. 150 2024, Nr. 11, 496
    DOI (Open Access)
  • Kück, Anja; van den Boom, Johannes; Koska, Sandra; Ron, David; Meyer, Hemmo
    Alternating binding and p97-mediated dissociation of SDS22 and I3 recycles active PP1 between holophosphatases
    In: Proceedings of the National Academy of Sciences of the United States of America (PNAS) , Vol. 121 2024, Nr. 36, e2408787121
    DOI (Open Access)
  • Flümann, Ruth; Hansen, Julia; Meinel, Jörn; Pfeiffer, Pauline; Wittkopf, Hannah Goldfarb; Lütz, Anna; Wirtz, Jessica; Möllmann, Michael; Zhou, Tanja; Tabatabai, Areya; Lohmann, Tim; Jauch, Maximilian; Beleggia, Filippo; Pelzer, Benedikt; Ullrich, Fabian; Höfmann, Svenja; Arora, Aastha; Persigehl, Thorsten; Büttner, Reinhard; von Tresckow, Bastian; Klein, Sebastian; Jachimowicz, Ron D.; Reinhardt, Hans Christian; Knittel, Gero
    An inducible Cd79b mutation confers ibrutinib sensitivity in mouse models of Myd88-driven diffuse large B-cell lymphoma
    In: Blood Advances , Vol. 8 2024, Nr. 5, pp. 1063 – 1074
    DOI (Open Access)
  • Dobersalske, Celia; Rauschenbach, Laurèl; Hua, Yichao; Berliner, Christoph; Steinbach, Anita; Grüneboom, Anika; Kokkaliaris, Konstantinos D.; Heiland, Dieter H.; Berger, Pia; Langer, Sarah; Tan, Chin L.; Stenzel, Martin; Landolsi, Somaya; Weber, Flora; Darkwah Oppong, Marvin; Werner, Rudolf A.; Gull, Hanah; Schröder, Thomas; Linsenmann, Thomas; Buck, Andreas K.; Gunzer, Matthias; Stuschke, Martin; Keyvani, Kathy; Forsting, Michael; Glas, Martin; Kipnis, Jonathan; Steindler, Dennis A.; Reinhardt, Hans Christian; Green, Edward W.; Platten, Michael; Tasdogan, Alpaslan; Herrmann, Ken; Rambow, Florian; Cima, Igor; Sure, Ulrich; Scheffler, Björn
    Cranioencephalic functional lymphoid units in glioblastoma
    In: Nature Medicine , Vol. 30 2024, Nr. 10, pp. 2947 – 2956
    DOI (Open Access)
  • Schwalm, Martin P.; Dopfer, Johannes; Kumar, Adarsh; Greco, Francesco A.; Bauer, Nicolas; Löhr, Frank; Heering, Jan; Cano-Franco, Sara; Lechner, Severin; Hanke, Thomas; Jaser, Ivana; Morasch, Viktoria; Lenz, Christopher; Fearon, Daren; Marples, Peter G.; Tomlinson, Charles W. E.; Brunello, Lorene; Saxena, Krishna; Adams, Nathan B. P.; von Delft, Frank; Müller, Susanne; Stolz, Alexandra; Proschak, Ewgenij; Kuster, Bernhard; Knapp, Stefan; Rogov, Vladimir V.
    Critical assessment of LC3/GABARAP ligands used for degrader development and ligandability of LC3/GABARAP binding pockets
    In: Nature Communications , Vol. 15 2024, Nr. 1, 10204
    DOI (Open Access)
  • Shah Zaib Saleem, Rahman; Schwalm, Martin P.; Knapp, Stefan
    Expanding the ligand spaces for E3 ligases for the design of protein degraders
    In: Bioorganic and Medicinal Chemistry , Vol. 105 2024, 117718
    DOI (Open Access)
  • Schillinger, Jasmin; Koci, Michelle; Bravo-Rodriguez, Kenny; Heilmann, Geronimo; Kaschani, Farnusch; Kaiser, Markus; Beuck, Christine; Luecke, Hartmut; Huber, Robert; Hellerschmied-Jelinek, Doris; Burston, Steven G.; Ehrmann, Michael
    High resolution analysis of proteolytic substrate processing
    In: The Journal of Biological Chemistry (JBC) , Vol. 300 2024, Nr. 11, 107812
    DOI (Open Access)
  • Pol, Savina Abraham; Liljenberg, Sara; Barr, Jack; Simon, Gina; Wong-Dilworth, Luis; Paterson, Danielle L.; Berishvili, Vladimir P.; Bottanelli, Francesca; Kaschani, Farnusch; Kaiser, Markus; Pettersson, Mariell; Hellerschmied, Doris
    Induced degradation of SNAP-fusion proteins
    In: RSC Chemical Biology , Vol. 5 2024, Nr. 12, pp. 1232 – 1247
    DOI (Open Access)
  • Fischer, Kim Denise; Tiwari, Shashank; Thier, Beatrice; Qiu, Lin Christina; Lin, Tzu-Chen; Paschen, Annette; Imig, Jochen
    Long non-coding RNA GRASLND links melanoma differentiation and interferon-gamma response
    In: Frontiers in Molecular Biosciences , Vol. 11 2024, 1471100
    DOI (Open Access)
  • Schwalm, Martin P.; Saxena, Krishna; Müller, Susanne; Knapp, Stefan
    Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells
    In: Nature Protocols , Vol. 19 2024, Nr. 8, pp. 2317 – 2357
    DOI
  • Gahlot, Pinki; Kravic, Bojana; Rota, Giulia; van den Boom, Johannes; Levantovsky, Sophie; Schulze, Nina; Maspero, Elena; Polo, Simona; Behrends, Christian; Meyer, Hemmo
    Lysosomal damage sensing and lysophagy initiation by SPG20-ITCH
    In: Molecular Cell 2024, pp. 1556 – 1569.e10
    DOI, Online Full Text (Open Access)
  • Pleuger, Richard; Cozma, Christian; Hohoff, Simone; Denkhaus, Christian; Dudziak, Alexander; Kaschani, Farnusch; Kaiser, Markus; Musacchio, Andrea; Vetter, Ingrid R.; Westermann, Stefan
    Microtubule end-on attachment maturation regulates Mps1 association with its kinetochore receptor
    In: Current Biology , Vol. 34 2024, Nr. 11, pp. 2279 – 2293.e6
    DOI (Open Access)
  • Schmidt, Mirko; Grethe, Christian; Recknagel, Sarah; Kipka, Gian-Marvin; Klink, Nikolas; Gersch, Malte
    N-Cyanopiperazines as Specific Covalent Inhibitors of the Deubiquitinating Enzyme UCHL1
    In: Angewandte Chemie International Edition , Vol. 63 2024, Nr. 12, e202318849
    DOI (Open Access)
  • Heger, Jan-Michel; d'Hargues, Yannick; Kleinert, Fanni; Mattlener, Julia; Weiss, Jonathan; Franzen, Fabian; Becker, Christian; Becker, Kerstin; Gödel, Philipp; Schmiel, Marcel; Meinel, Jörn; Flümann, Ruth; Simon, Florian; Reinhardt, H. Christian; Borchmann, Peter; Borchmann, Sven; Balke-Want, Hyatt; Knittel, Gero; von Tresckow, Bastian
    Noninvasive minimal residual disease assessment in relapsed/refractory large B-cell lymphoma using digital droplet PCR
    In: European Journal of Haematology , Vol. 112 2024, Nr. 6, pp. 957 – 963
    DOI (Open Access)
  • Beaufort, Nathalie; Ingendahl, Linda; Merdanovic, Melisa; Schmidt, Andree; Podlesainski, David; Richter, Tim; Neumann, Thorben; Kuszner, Michael; Vetter, Ingrid R.; Stege, Patricia; Burston, Steven G.; Filipovic, Anto; Ruiz-Blanco, Yasser B.; Bravo Rodriguez, Kenny; Mieres-Perez, Joel; Beuck, Christine; Uebel, Stephan; Zobawa, Monika; Schillinger, Jasmin; Malik, Rainer; Todorov-Völgyi, Katalin; Rey, Juliana; Roberti, Annabell; Hagemeier, Birte; Wefers, Benedikt; Müller, Stephan A.; Wurst, Wolfgang; Sanchez-Garcia, Elsa; Zimmermann, Alexander; Hu, Xiao-Yu; Clausen, Tim; Huber, Robert; Lichtenthaler, Stefan F.; Schmuck, Carsten; Giese, Michael; Kaiser, Markus; Ehrmann, Michael; Dichgans, Martin
    Rational correction of pathogenic conformational defects in HTRA1
    In: Nature Communications , Vol. 15 2024, Nr. 1, 5944
    DOI (Open Access)
  • Conti, Duccio; Verza, Arianna Esposito; Pesenti, Marion E.; Cmentowski, Verena; Vetter, Ingrid R.; Pan, Dongqing; Musacchio, Andrea
    Role of protein kinase PLK1 in the epigenetic maintenance of centromeres
    In: Science , Vol. 385 2024, Nr. 6713, pp. 1091 – 1097
    DOI
  • Gybeľ, Tomáš; Čada, Štěpán; Klementová, Darja; Schwalm, Martin P.; Berger, Benedict-Tilman; Šebesta, Marek; Knapp, Stefan; Bryja, Vítězslav
    Splice variants of CK1α and CK1α-like : Comparative analysis of subcellular localization, kinase activity, and function in the Wnt signaling pathway
    In: The Journal of Biological Chemistry (JBC) , Vol. 300 2024, Nr. 7, 107407
    DOI (Open Access)
  • Polley, Soumitra; Raisch, Tobias; Ghetti, Sabrina; Körner, Marie; Terbeck, Melina; Gräter, Frauke; Raunser, Stefan; Aponte-Santamaría, Camilo; Vetter, Ingrid R.; Musacchio, Andrea
    Structure of the human KMN complex and implications for regulation of its assembly
    In: Nature Structural & Molecular Biology , Vol. 31 2024, Nr. 6, pp. 861 – 873
    DOI (Open Access)
  • Meyer, Hemmo; Kravic, Bojana
    The Endo-Lysosomal Damage Response
    In: Annual Review of Biochemistry , Vol. 93 2024, Nr. 1, pp. 367 – 387
    DOI (Open Access)
  • Musacchio, Andrea
    Thirty years of structural changes
    In: Nature Structural & Molecular Biology , Vol. 31 2024, Nr. 1, pp. 4 – 5
    DOI
  • Day, Matthew; Tetik, Bilal; Parlak, Milena; Almeida-Hernández, Yasser; Räschle, Markus; Kaschani, Farnusch; Siegert, Heike; Marko, Anika; Sanchez-Garcia, Elsa; Kaiser, Markus; Barker, Isabel A.; Pearl, Laurence H.; Oliver, Antony W.; Boos, Dominik
    TopBP1 utilises a bipartite GINS binding mode to support genome replication
    In: Nature Communications , Vol. 15 2024, Nr. 1, 1797
    DOI, Online Full Text (Open Access)
  • Schwalm, Martin P.; Knapp, Stefan; Rogov, Vladimir V.
    Toward effective Atg8-based ATTECs : Approaches and perspectives
    In: Journal of Cellular Biochemistry , Vol. 125 2024, Nr. 11: Special Issue: New Horizons in Selective Autophagy, e30380
    DOI (Open Access)
  • Mirsanaye, Ann Schirin; Hoffmann, Saskia; Weisser, Melanie; Mund, Andreas; Lopez Mendez, Blanca; Typas, Dimitris; van den Boom, Johannes; Benedict, Bente; Hendriks, Ivo A.; Nielsen, Michael Lund; Meyer, Hemmo; Duxin, Julien P.; Montoya, Guillermo; Mailand, Niels
    VCF1 is a p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates
    In: Nature Communications , Vol. 15 2024, Nr. 1, 2459
    DOI (Open Access)
  • Dopfer, Johannes; Vasta, James D.; Müller, Susanne; Knapp, Stefan; Robers, Matthew B.; Schwalm, Martin P.
    tracerDB : a crowdsourced fluorescent tracer database for target engagement analysis
    In: Nature Communications , Vol. 15 2024, Nr. 1, 5646
    DOI (Open Access)

    • Preprints

  • Blümke, Anika; Hagemeier, Birte; Ripkens, Kamilla; Schulze, Nina; Strzala, Michal; Koci, Michelle; Kaschani, Farnusch; Kaiser, Markus; Erkelenz, Michael; Schlücker, Sebastian; Merdanovic, Melisa; Poepsel, Simon; Hellerschmied-Jelinek, Doris; Burston, Steve; Ehrmann, Michael
    A non-autonomous protein quality control mechanism targeting tau aggregate propagation
    2024
    DOI (Open Access)
  • Brenner, Joel Cyrille; Zirden, Linda; Almeida-Hernandez, Yasser; Kaschani, Farnusch; Kaiser, Markus; Sanchez-Garcia, Elsa; Poepsel, Simon; Hellerschmied-Jelinek, Doris
    Conformational plasticity of a BiP-GRP94 chaperone complex
    2024
    DOI (Open Access)
  • Broutzakis, George; Pyrris, Yiannis; Akrani, Ifigeneia; Neuhaus, Alexander; Mikros, Emmanuel; Diallinas, George; Gatsogiannis, Christos
    High-resolution structures of the UapA purine transporter reveal unprecedented aspects of the elevator-type transport mechanism
    2024
    DOI (Open Access)
  • Scholes, Natalie S.; Bertoni, Martino; Comajuncosa-Creus, Arnau; Kladnik, Katharina; Frommelt, Fabian; Hinterndorfer, Matthias; Razumkov, Hlib; Prokofeva, Polina; Schwalm, Martin P.; Imrichova, Hana; Barone, Eleonora; Schätz, Caroline; Rukavina, Andrea; Koren, Anna; Kubicek, Stefan; Knapp, Stefan; Gray, Nathanael S.; Superti-Furga, Giulio; Kuster, Bernhard; Aloy, Patrick; Winter, Georg E.
    Inhibitor-induced supercharging of kinase turnover via endogenous proteolytic circuits
    2024
    DOI (Open Access)

    • Book articles / Proceedings papers

  • Schwalm, Martin P.; Dopfer, Johannes; Knapp, Stefan; Rogov, Vladimir V.
    High-Throughput Screening for LC3/GABARAP Binders Utilizing the Fluorescence Polarization Assay
    In: Selective Autophagy: Methods and Protocols / Nezis, Ioannis P. (Eds.) 2024, pp. 203 – 218
    DOI
  • Schwalm, Martin P.; Babaahmadi, Atoosa Karimi; Ackloo, Suzanne; Knapp, Stefan
    Targeting the Acetylation Reader Family : Bromodomain Proteins
    In: Epigenetic Drug Discovery / Chan, Ho Man; Arrowsmith, Cheryl (Eds.) 2024, pp. 404 – 439
    DOI
  • Dopfer, Johannes; Schwalm, Martin P.; Knapp, Stefan; Rogov, Vladimir V.
    Thermodynamic Characterization of LC3/GABARAP : Ligand Interactions by Isothermal Titration Calorimetry
    In: Selective Autophagy / Nezis, Ioannis P. (Eds.) 2024, pp. 219 – 235
    DOI

2023

    Journal articles

  • Sauer, Paul V.; Pavlenko, Egor; Cookis, Trinity; Zirden, Linda C.; Renn, Juliane; Singhal, Ankush; Hunold, Pascal; Hoehne, Michaela N.; van Ray, Olivia; Hänsel-Hertsch, Robert; Sanbonmatsu, Karissa Y.; Nogales, Eva; Poepsel, Simon
    Activation of automethylated PRC2 by dimerization on chromatin
    In: Molecular Cell , Vol. 84 2023, Nr. 20, pp. 3885 – 3898.e8
    DOI (Open Access)
  • Patwardhan, Rutuja; Nanda, Suchet; Wagner, Jessica; Stockter, Tom; Dehmelt, Leif; Nalbant, Perihan; Li, Rong (Eds.)
    Cdc42 activity in the trailing edge is required for persistent directional migration of keratinocytes
    In: Molecular Biology of the Cell , Vol. 35 2023, Nr. 1, br1
    DOI (Open Access)
  • Hoi, David M.; Junker, Sabryna; Junk, Lukas; Schwechel, Kristin; Fischel, Katharina; Podlesainski, David; Hawkins, Paige M.E.; van Geelen, Lasse; Kaschani, Farnusch; Leodolter, Julia; Morreale, Francesca Ester; Kleine, Stefan; Guha, Somraj; Rumpel, Klaus; Schmiedel, Volker M.; Weinstabl, Harald; Meinhart, Anton; Payne, Richard J.; Kaiser, Markus; Hartl, Markus; Boehmelt, Guido; Kazmaier, Uli; Kalscheuer, Rainer; Clausen, Tim
    Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival
    In: Cell , Vol. 186 2023, Nr. 10, pp. 2176 – 2192.e22
    DOI (Open Access)
  • Flümann, Ruth; Hansen, Julia; Pelzer, Benedikt W.; Nieper, Pascal; Lohmann, Tim; Kisis, Ilmars; Riet, Tobias; Kohlhas, Viktoria; Nguyen, Phuong-Hien; Peifer, Martin; Abedpour, Nima; Bosco, Graziella; Thomas, Roman K.; Kochanek, Moritz; Knüfer, Jacqueline; Jonigkeit, Lorenz; Beleggia, Filippo; Holzem, Alessandra; Büttner, Reinhard; Lohneis, Philipp; Meinel, Jörn; Ortmann, Monika; Persigehl, Thorsten; Hallek, Michael; Calado, Dinis Pedro; Chmielewski, Markus; Klein, Sebastian; Göthert, Joachim R.; Chapuy, Bjoern; Zevnik, Branko; Wunderlich, F. Thomas; von Tresckow, Bastian; Jachimowicz, Ron D.; Melnick, Ari M.; Reinhardt, Hans Christian; Knittel, Gero
    Distinct genetically-determined origins of Myd88/Bcl2-driven aggressive lymphoma rationalize targeted therapeutic intervention strategies
    In: Blood Cancer Discovery , Vol. 4 2023, Nr. 1, pp. 78 – 97
    DOI (Open Access)
  • Fehr, Lorenz; Sewald, Leonard; Huber, Robert; Kaiser, Markus
    Facile Multicomponent Synthesis of Oxazolidinones from Primary Amines and Cesium (Hydrogen)Carbonate
    In: European Journal of Organic Chemistry , Vol. 26 2023, Nr. 27, e202300135
    DOI (Open Access)
  • Stupia, Simone; Heeke, Christina; Brüggemann, Alicia; Zaremba-Montenari, Anne; Thier, Beatrice; Kretz, Julia; Sucker, Antje; Philip, Manuel; Zelinskyy, Gennadiy; Ferrone, Soldano; Rösch, Alexander; Horn, Susanne; Hadaschik, Eva; Schadendorf, Dirk; Trilling, Mirko; Dittmer, Ulf; Griewank, Klaus; Zhao, Fang; Paschen, Annette
    HLA class II loss and JAK1/2 deficiency coevolve in melanoma leading to CD4 T cell and IFNγ cross-resistance
    In: Clinical Cancer Research , Vol. 29 2023, Nr. 15, pp. 2894 – 2907
    DOI
  • Váraljai, Renáta; Zimmer, Lisa; Al-Matary, Yahya; Kaptein, Paulien; Albrecht, Lea J.; Shannan, Batool; Brase, Jan C.; Gusenleitner, Daniel; Amaral, Teresa; Wyss, Nina; Utikal, Jochen; Flatz, Lukas; Rambow, Florian; Reinhardt, Hans Christian; Dick, Jenny; Engel, Daniel R.; Horn, Susanne; Ugurel, Selma; Sondermann, Wiebke; Livingstone, Elisabeth; Sucker, Antje; Paschen, Annette; Zhao, Fang; Placke, Jan-Malte; Klose, Jasmin M.; Fendler, Wolfgang; Thommen, Daniela S.; Helfrich, Iris; Schadendorf, Dirk; Rösch, Alexander
    Interleukin 17 signaling supports clinical benefit of dual CTLA-4 and PD-1 checkpoint inhibition in melanoma
    In: Nature Cancer , Vol. 4 2023, Nr. 9, pp. 1292 – 1308
    DOI (Open Access)
  • O’Dea, Rachel; Kazi, Nafizul; Hoffmann-Benito, Alicia; Zhao, Zhou; Recknagel, Sarah; Wendrich, Kim; Janning, Petra; Gersch, Malte
    Molecular basis for ubiquitin/Fubi cross-reactivity in USP16 and USP36
    In: Nature Chemical Biology , Vol. 19 2023, Nr. 11, pp. 1394 – 1405
    DOI (Open Access)
  • Zhao, Zhou; O’Dea, Rachel; Wendrich, Kim; Kazi, Nafizul; Gersch, Malte
    Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases
    In: Journal of the American Chemical Society: JACS , Vol. 145 2023, Nr. 38, pp. 20801 – 20812
    DOI (Open Access)
  • Cmentowski, Verena; Ciossani, Giuseppe; d'Amico, Ennio; Wohlgemuth, Sabine; Owa, Mikito; Dynlacht, Brian; Musacchio, Andrea
    RZZ‐Spindly and CENP‐E form an integrated platform to recruit dynein to the kinetochore corona
    In: The EMBO Journal , Vol. 42 2023, Nr. 24, e114838
    DOI (Open Access)
  • van den Boom, Johannes; Marini, Guendalina; Meyer, Hemmo; Saibil, Helen R
    Structural basis of ubiquitin-independent PP1 complex disassembly by p97
    In: The EMBO Journal , Vol. 42 2023, Nr. 14, e113110
    DOI (Open Access)
  • Rüttermann, Maximilian; Koci, Michelle; Lill, Pascal; Geladas, Ermis Dionysios; Kaschani, Farnusch; Klink, Björn Udo; Erdmann, Ralf; Gatsogiannis, Christos
    Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate
    In: Nature Communications , Vol. 14 2023, Nr. 1, 5942
    DOI (Open Access)
  • Kornakov, Nikolay; Westermann, Stefan
    Systematic analysis of microtubule plus-end networks defines EB-cargo complexes critical for mitosis in budding yeast
    In: Molecular Biology of the Cell , Vol. 34 2023, Nr. 5, ar37
    DOI (Open Access)
  • Meyer, Hemmo; van den Boom, Johannes
    Targeting of client proteins to the VCP/p97/Cdc48 unfolding machine
    In: Frontiers in Molecular Biosciences , Vol. 10 2023, 1142989
    DOI, Online Full Text (Open Access)
  • Blüggel, Mike; Kröning, Alexander; Kracht, Matthias; van den Boom, Johannes; Dabisch, Matthias; Göhring, Anna; Kaschani, Farnusch; Kaiser, Markus; Bayer, Peter; Meyer, Hemmo; Beuck, Christine
    The UBX domain in UBXD1 organizes ubiquitin binding at the C-terminus of the VCP/p97 AAA-ATPase
    In: Nature Communications , Vol. 14 2023, Nr. 1, 3258
    DOI, Online Full Text (Open Access)
  • Schwalm, Martin P.; Krämer, Andreas; Dölle, Anja; Weckesser, Janik; Yu, Xufen; Jin, Jian; Saxena, Krishna; Knapp, Stefan
    Tracking the PROTAC degradation pathway in living cells highlights the importance of ternary complex measurement for PROTAC optimization
    In: Cell Chemical Biology , Vol. 30 2023, Nr. 7, pp. 753 – 765.e8
    DOI (Open Access)
  • Buzuk, Lana; Hellerschmied-Jelinek, Doris
    Ubiquitin-mediated degradation at the Golgi apparatus
    In: Frontiers in Molecular Biosciences , Vol. 10 2023, 1197921
    DOI, Online Full Text (Open Access)

    • Prefaces/Postfaces

  • Venturutti, Leandro; Rivas, Martin A.; Pelzer, Benedikt W.; Flümann, Ruth; Hansen, Julia; Karagiannidis, Ioannis; Xia, Min; McNally, Dylan R.; Isshiki, Yusuke; Lytle, Andrew; Teater, Matt; Chin, Christopher R.; Meydan, Cem; Knittel, Gero; Ricker, Edd; Mason, Christopher E.; Ye, Xiaofei; Pan-Hammarström, Qiang; Steidl, Christian; Scott, David W.; Reinhardt, Hans Christian; Pernis, Alessandra B.; Béguelin, Wendy; Melnick, Ari M.
    An Aged/Autoimmune B-cell Program Defines the Early Transformation of Extranodal Lymphomas
    In: Cancer Discovery , Vol. 13 2023, Nr. 1, pp. 216 – 243
    DOI (Open Access)

    • Preprints

  • Pleuger, Richard; Cozma, Christian; Hohoff, Simone; Denkhaus, Christian; Dudziak, Alexander; Kaschani, Farnusch; Musacchio, Andrea; Vetter, Ingrid R.; Westermann, Stefan
    Ipl1-controlled attachment maturation regulates Mps1 association with its kinetochore receptor
    2023
    DOI (Open Access)

    • Posters / Proceedings posters

  • Lama, Soni; Koch, Johannes; Schulze, Nina; Rehwald, Stephanie
    Sharing, storing and analysing cell image data in a Collaborative Research Centre using OMERO
    Data Steward goes Germany 2023, 25.-26.09.2023, Dresden,
    2023
    DOI (Open Access)

2022

    Journal articles

  • Schwalm, Martin P.; Berger, Lena M.; Meuter, Maximilian N.; Vasta, James D.; Corona, Cesear R.; Röhm, Sandra; Berger, Benedict-Tilman; Farges, Frederic; Beinert, Sebastian M.; Preuss, Franziska; Morasch, Viktoria; Rogov, Vladimir V.; Mathea, Sebastian; Saxena, Krishna; Robers, Matthew B.; Müller, Susanne; Knapp, Stefan
    A Toolbox for the Generation of Chemical Probes for Baculovirus IAP Repeat Containing Proteins
    In: Frontiers in Cell and Developmental Biology , Vol. 10 2022, 886537
    DOI (Open Access)
  • Ruiz-Blanco, Yasser B.; Agüero-Chapin, Guillermin; Romero-Molina, Sandra; Antunes, Agostinho; Olari, Lia-Raluca; Spellerberg, Barbara; Münch, Jan; Sanchez-Garcia, Elsa
    ABP-Finder : A Tool to Identify Antibacterial Peptides and the Gram-Staining Type of Targeted Bacteria
    In: Antibiotics , Vol. 11 2022, Nr. 12, 1708
    DOI (Open Access)
  • Rey, Juliana; Breiden, Maike; Lux, Vanda; Bluemke, Anika; Steindel, Maike; Ripkens, Kamilla; Möllers, Bastian; Bravo Rodriguez, Kenny; Boisguerin, Prisca; Volkmer, Rudolf; Mieres-Perez, Joel; Clausen, Tim; Sánchez-García, Elsa; Ehrmann, Michael
    An allosteric HTRA1-calpain 2 complex with restricted activation profile
    In: Proceedings of the National Academy of Sciences of the United States of America (PNAS) , Vol. 119 2022, Nr. 14, e2113520119
    DOI (Open Access)
  • Schwalm, Martin P.; Knapp, Stefan
    BET bromodomain inhibitors
    In: Current Opinion in Chemical Biology , Vol. 68 2022, 102148
    DOI
  • Carvalho, Luís A. R.; Ross, Breyan; Fehr, Lorenz; Bolgi, Oguz; Wöhrle, Svenja; Lum, Kenneth M.; Podlesainski, David; Vieira, Andreia C.; Kiefersauer, Reiner; Félix, Rita; Rodrigues, Tiago; Lucas, Susana D.; Groß, Olaf; Geiss‐Friedlander, Ruth; Cravatt, Benjamin F.; Huber, Robert; Kaiser, Markus; Moreira, Rui
    Chemoproteomics‐Enabled Identification of 4‐Oxo‐β‐Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9
    In: Angewandte Chemie International Edition , Vol. 61 2022, Nr. 47, e202210498
    DOI (Open Access)
  • d'Amico, Ennio A.; Ud Din Ahmad, Misbha; Cmentowski, Verena; Girbig, Mathias; Müller, Franziska; Wohlgemuth, Sabine; Brockmeyer, Andreas; Maffini, Stefano; Janning, Petra; Vetter, Ingrid R.; Carter, Andrew P.; Perrakis, Anastassis; Musacchio, Andrea
    Conformational transitions of the Spindly adaptor underlie its interaction with Dynein and Dynactin
    In: The Journal of Cell Biology (JCB) , Vol. 221 2022, Nr. 11, e202206131
    DOI (Open Access)
  • Harms, Mirja; Hansson, Rikke Fabech; Carmali, Sheiliza; Almeida-Hernández, Yasser; Sanchez-Garcia, Elsa; Münch, Jan; Zelikin, Alexander N.
    Dimerization of the Peptide CXCR4-Antagonist on Macromolecular and Supramolecular Protraction Arms Affords Increased Potency and Enhanced Plasma Stability
    In: Bioconjugate Chemistry , Vol. 33 2022, Nr. 4, pp. 594 – 607
    DOI
  • Pavlenko, Egor; Ruengeler, Till; Engel, Paulina; Poepsel, Simon
    Functions and Interactions of Mammalian KDM5 Demethylases
    In: Frontiers in Genetics , Vol. 13 2022
    DOI (Open Access)
  • Thier, Beatrice; Zhao, Fang; Stupia, Simone; Brüggemann, Alicia; Koch, Johannes; Schulze, Nina; Horn, Susanne; Coch, Christoph; Hartmann, Gunther; Sucker, Antje; Schadendorf, Dirk; Paschen, Annette
    Innate immune receptor signaling induces transient melanoma dedifferentiation while preserving immunogenicity
    In: Journal for ImmunoTherapy of Cancer , Vol. 10 2022, Nr. 6, e003863
    DOI (Open Access)
  • Stejerean-Todoran, Ioana; Zimmermann, Katharina; Gibhardt, Christine S; Vultur, Adina; Ickes, Christian; Shannan, Batool; Bonilla del Rio, Zuriñe; Wölling, Anna; Cappello, Sabrina; Sung, Hsu-Min; Shumanska, Magdalena; Zhang, Xin; Nanadikar, Maithily; Latif, Muhammad U; Wittek, Anna; Lange, Felix; Waters, Andrea; Brafford, Patricia; Wilting, Jörg; Urlaub, Henning; Katschinski, Dörthe M; Rehling, Peter; Lenz, Christof; Jakobs, Stefan; Ellenrieder, Volker; Rösch, Alexander; Schön, Michael P; Herlyn, Meenhard; Stanisz, Hedwig; Bogeski, Ivan
    MCU controls melanoma progression through a redox-controlled phenotype switch
    In: EMBO Reports , Vol. 23 2022, Nr. 11, e54746
    DOI (Open Access)
  • Bozilovic, Jelena; Eing, Lorenz; Berger, Benedict-Tilman; Adhikari, Bikash; Weckesser, Janik; Berner, Nicola B.; Wilhelm, Stephanie; Kuster, Bernhard; Wolf, Elmar; Knapp, Stefan
    Novel, highly potent PROTACs targeting AURORA-A kinase
    In: Current Research in Chemical Biology , Vol. 2 2022, 100032
    DOI (Open Access)
  • Musacchio, Andrea
    On the role of phase separation in the biogenesis of membraneless compartments
    In: The EMBO Journal , Vol. 41 2022, Nr. 5, e109952
    DOI (Open Access)
  • Romero-Molina, Sandra; Ruiz-Blanco, Yasser B.; Mieres-Perez, Joel; Harms, Mirja; Münch, Jan; Ehrmann, Michael; Sanchez-Garcia, Elsa
    PPI-Affinity : A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity
    In: Journal of Proteome Research , Vol. 21 2022, Nr. 8, pp. 1829 – 1841
    DOI (Open Access)
  • Němec, Václav; Schwalm, Martin P.; Müller, Susanne; Knapp, Stefan
    PROTAC degraders as chemical probes for studying target biology and target validation
    In: Chemical Society Reviews , Vol. 51 2022, Nr. 18, pp. 7971 – 7993
    DOI
  • Chauvistré, Heike; Shannan, Batool; Daignault-Mill, Sheena M.; Ju, Robert J.; Picard, Daniel; Egetemaier, Stefanie; Váraljai, Renáta; Gibhardt, Christine S.; Sechi, Antonio; Kaschani, Farnusch; Keminer, Oliver; Stehbens, Samantha J.; Liu, Qin; Yin, Xiangfan; Jeyakumar, Kirujan; Vogel, Felix C. E.; Krepler, Clemens; Rebecca, Vito W.; Kubat, Linda; Lueong, Smiths S.; Forster, Jan; Horn, Susanne; Remke, Marc; Ehrmann, Michael; Paschen, Annette; Becker, Jürgen; Helfrich, Iris; Rauh, Daniel; Kaiser, Markus; Gul, Sheraz; Herlyn, Meenhard; Bogeski, Ivan; Rodríguez-López, José Neptuno; Haass, Nikolas K.; Schadendorf, Dirk; Rösch, Alexander
    Persister state-directed transitioning and vulnerability in melanoma
    32. Deutscher Hautkrebskongress (ADO-Jahrestagung), 14.–17. September 2022, Hannover, Germany,
    In: Nature Communications , Vol. 13 2022, Nr. 1, pp. 35 – 36
    DOI, Online Full Text (Open Access)
  • Grethe, Christian; Schmidt, Mirko; Kipka, Gian-Marvin; O’Dea, Rachel; Gallant, Kai; Janning, Petra; Gersch, Malte
    Structural basis for specific inhibition of the deubiquitinase UCHL1
    In: Nature Communications , Vol. 13 2022, Nr. 1, 5950
    DOI (Open Access)
  • Raisch, Tobias; Ciossani, Giuseppe; d’Amico, Ennio; Cmentowski, Verena; Carmignani, Sara; Maffini, Stefano; Merino, Felipe; Wohlgemuth, Sabine; Vetter, Ingrid R.; Raunser, Stefan; Musacchio, Andrea
    Structure of the RZZ complex and molecular basis of Spindly‐driven corona assembly at human kinetochores
    In: The EMBO Journal , Vol. 41 2022, Nr. 9, e110411
    DOI (Open Access)
  • Kravić, Bojana; Bionda, Tihana; Siebert, Alexander; Gahlot, Pinki; Levantovsky, Sophie; Behrends, Christian; Meyer, Hemmo
    Ubiquitin profiling of lysophagy identifies actin stabilizer CNN2 as a target of VCP/p97 and uncovers a link to HSPB1
    In: Molecular Cell , Vol. 82 2022, Nr. 14, pp. 2633 – 2649.e7
    DOI (Open Access)
  • Kröning, Alexander; van den Boom, Johannes; Kracht, Matthias; Kück, Anja; Meyer, Hemmo
    Ubiquitin-directed AAA+ ATPase p97/VCP unfolds stable proteins crosslinked to DNA for proteolysis by SPRTN
    In: The Journal of Biological Chemistry (JBC) , Vol. 298 2022, Nr. 6, 101976
    DOI (Open Access)

    • Book articles / Proceedings papers

  • Schillinger, Jasmin; Hellerschmied-Jelinek, Doris
    Targeted Protein Unfolding at the Golgi Apparatus
    In: Golgi: Methods and Protocols / Wang, Yanzhuang; Lupashin, Vladimir V.; Graham, Todd R. (Eds.) 2022, pp. 645 – 659
    DOI

2021

    Journal articles

  • Böhm, Miriam; Killinger, Kerstin; Dudziak, Alexander; Pant, Pradeep; Jänen, Karolin; Hohoff, Simone; Mechtler, Karl; Örd, Mihkel; Loog, Mart; Sánchez-García, Elsa; Westermann, Stefan
    Cdc4 phospho-degrons allow differential regulation of ame1ceⁿp⁻u protein stability across the cell cycle
    In: eLife , Vol. 10 2021, e67390
    DOI (Open Access)
  • Dudziak, Alexander; Engelhard, Lena; Bourque, Cole; Klink, Björn Udo; Rombaut, Pascaline; Kornakov, Nikolay; Jänen, Karolin; Herzog, Franz; Gatsogiannis, Christos; Westermann, Stefan
    Phospho-regulated Bim1/EB1 interactions trigger Dam1c ring assembly at the budding yeast outer kinetochore
    In: The EMBO Journal , Vol. 40 2021, Nr. 18, e108004
    DOI (Open Access)
  • Dorsch, Madeleine; Kowalczyk, Manuela; Planque, Mélanie; Heilmann, Geronimo; Urban, Sebastian; Dujardin, Philip; Forster, Jan; Ueffing, Kristina; Nothdurft, Silke; Oeck, Sebastian; Paul, Annika; Liffers, Sven T.; Kaschani, Farnusch; Kaiser, Markus; Schramm, Alexander; Siveke, Jens; Winslow, Monte M.; Fendt, Sarah-Maria; Nalbant, Perihan; Grüner, Barbara M.
    Statins affect cancer cell plasticity with distinct consequences for tumor progression and metastasis
    In: Cell Reports , Vol. 37 2021, Nr. 8, 110056
    DOI, Online Full Text (Open Access)