Targeted Protein Degradation

Publications

Selected Publications

  • 2025 TRIM52 maintains cellular fitness and is under tight proteolytic control by multiple giant E3 ligases Nature Communications Shulkina A, Hacker K, Ehrmann JF, Budroni V, Mandlbauer A, Bock J, Grabarczyk DB, Edobor G, Cochella L, Clausen T, Versteeg GA Go to publication →
  • 2025 Convergent Assembly of Homo- and Heterotypic Ubiquitin Chains from Functionalized, Expressed Monomers via Thiol-Ene Chemistry Angew Chem Int Ed Engl Urschbach M, Huhmann S, Appel D, Ferrari L, Vogl D, Martens S, Becker CFW Go to publication →
  • 2025 Autophagy in Plant Health and Disease Annual Review of Plant Biology Gross AS, Raffeiner M, Zeng Y, Üstün S, Dagdas Y Go to publication →
  • 2025 The coordinated action of UFMylation and ribosome-associated quality control pathway clears arrested nascent chains at the endoplasmic reticulum bioRxiv Mihailovic M, Anisimova AS, Erte B, Zhan N, Styliara I, Dagdas Y, Karagöz GE Go to publication →
  • 2025 The UBR domain of plant Ubr1 homolog PRT6 accommodates basic and hydrophobic amino termini for substrate recognition Journal of Molecular Biology Rudi O, Hodakova Z, Saad CF, Winter N, Grishkovskaya I, Böhm J, Jarck G, Schleiffer A, Haselbach D, Bachmair A Go to publication →
  • 2024 PITHD1: An Endogenous Inhibitor of the 26S Proteasome During Cellular Dormancy bioRxiv Amann SJ, Dong K, Roehsner J, Krall D, Grishkovskaya I, Kotisch H, Schleiffer A, Roitinger E, Pauli A, Martin A, Haselbach D Go to publication →
  • 2024 Seipin governs phosphatidic acid homeostasis at the inner nuclear membrane Nature Communications Romanauska A, Stankunas E, Schuldiner M, Köhler A Go to publication →
  • 2024 A multivalent adaptor mechanism drives the nuclear import of proteasomes bioRxiv Brunner HL, Kalis RW, Grundmann L, Hodáková Z, Koskova Z, Grishkovskaya I, de Almeida M, Hinterndorfer M, Höfflin S, Andersch F, Kotisch H, Dickmanns A, Cuylen-Häring S, Zuber J, Haselbach D Go to publication →
  • 2024 Degradome analysis to identify direct protein substrates of small-molecule degraders Cell Chemical Biology Jochem M, Schrempf A, Wagner LM, Segal D, Cisneros J, Ng A, Winter GE, Krijgsveld J Go to publication →
  • 2024 Recruitment of autophagy initiator TAX1BP1 advances aggrephagy from cargo collection to sequestration EMBO Journal Bauer B, Idinger J, Schuschnig M, Ferrari L, Martens S Go to publication →
  • 2024 IGF2BP1 phosphorylation in the disordered linkers regulates ribonucleoprotein condensate formation and RNA metabolism Nature Communications Hornegger H, Anisimova AS, Muratovic A, Bourgeois B, Spinetti E, Niedermoser I, Covino R, Madl T, Karagöz GE Go to publication →
  • 2024 Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants bioRxiv Sánchez de Medina Hernández V, Nava García MM, Clavel M, Papareddy RK, Andreev VI, Mathur V, Mohseni A, García-León M, Gao P, de la Concepción JC, Picchianti L, Grujic N, Kobylinska R, Abdrakhmanov A, Duvergé H, Anand G, Leibrock G, Bianchi A, Raffeiner M, Crawford TC, Argirò L, Matuszkiewicz M, Wun CL, Kanne JV, Meinhart A, Roitinger E, Bäurle I, Kang BH, Petersen M, Üstün S, Kulathu Y, Clausen T, Ramundo S, Dagdas Y Go to publication →
  • 2024 Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering EMBO Journal Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser I, Fischer I, Versteeg GA, Loose M, Covino R, Karagöz GE Go to publication →
  • 2024 Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape bioRxiv De la Concepcion JC, Duverge G, Kim Y, Julian J, Xu HD, Ikene SA, Bianchi A, Grujic N, Papareddy RK, Grishkovskaya I, Haselbach D, Murray DH, Irwin NAT, Dagdas Y Go to publication →
  • 2024 Inhibitor-induced supercharging of kinase turnover via endogenous proteolytic circuits bioRxiv Scholes NS, Bertoni M, Comajuncosa-Creus A, Kladnik K, Frommelt F, Hinterndorfer M, Razumkov H, Prokofeva P, Schwalm MP, Imrichova H, Barone E, Schätz C, Rukavina A, Koren A, Kubicek S, Knapp S, Gray MS, Superti-Furga G, Küster B, Aloy P, Winter GE Go to publication →
  • 2024 Monovalent Pseudo-Natural Product Degraders Supercharge the Native Degradation of IDO1 by KLHDC3 bioRxiv Hennes E, Lucas B, Scholes NS, Cheng XF, Scott DC, Bischoff M, Reich K, Gasper R, Luca M, Xu TT, Pulvermacher LM, Dötsch L, Imrichova H, Brause A, Naredla KS, Sievers S, Kumar K, Janning P, Gersch M, Murray PJ, Schulman BA, Winter GE, Ziegler S, Waldmann H Go to publication →
  • 2024 Alkylamine-tethered molecules recruit FBXO22 for targeted protein degradation Nature Communication Kagiou C, Cisneros JA, Farnung J, Liwocha J, Offensperger F, Dong K, Yang K, Tin G, Horstmann CS, Hinterndorfer M, Paulo JA, Scholes NS, Sanchez Avila J, Fellner M, Andersch F, Hannich JT, Zuber J, Kubicek S, Gygi SP, Schulman BA, Winter GE Go to publication →
  • 2024 Orpinolide disrupts a leukemic dependency on cholesterol transport by inhibiting OSBP Nature Chemical Biology Cigler M, Imrichova H, Frommelt F, Caramelle L, Depta L, Rukavina A, Kagiou C, Hannich JT, Mayor-Ruiz C, Superti-Furga G, Sievers S, Forrester A, Laraia L, Waldmann H, Winter GE Go to publication →
  • 2024 Tau fibrils evade autophagy by excessive p62 coating and TAX1BP1 exclusion Science Advances Ferrari L, Bauer B, Qiu Y, Schuschnig M, Klotz S, Anrather D, Juretschke T, Beli P, Gelpi E, Martens S Go to publication →
  • 2024 Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity bioRxiv Schwartz I, Budroni V, Meyenberg M, Hornegger H, Hacker K, Schwartz S, Hodakova Z, Grabarczyk DB, Ehrmann JF, Scinicariello S, Haselbach D, Menche J, Clausen T, Karagöz GE, Versteeg GA Go to publication →
  • 2024 A RabGAP negatively regulates plant autophagy and immune trafficking Current Biology Yuen ELH, Leary AY, Clavel M, Tumtas Y, Mohseni A, Zhao J, Picchianti L, Jamshidiha M, Pandey P, Duggan C, Cota E, Dagdas Y, Bozkurt TO Go to publication →
  • 2024 Endoplasmic reticulum: Monitoring and maintaining protein and membrane homeostasis in the endoplasmic reticulum by the unfolded protein response Int J Biochem Cell Biol Kettel P, Karagöz GE Go to publication →
  • 2024 Metabolic enzymes moonlight as selective autophagy receptors to protect plants against viral-induced cellular damage bioRxiv Clavel M, Bianchi A, Kobylinska R, Groh R, Ma J, Papareddy RK, Grujic N, Picchianti L, Stewart E, Schutzbier M, Stejskal K, de la Concepcion JC, Sanchez de Medina Hernandez V, Yoichek Y, Clauw P, Gunis J, Durnberger G, Muelders JC, Grimm A, Sedivy A, Erhardt M, Vyboishchikov V, Gao P, Lechner E, Vantard E, Jez J, Roitinger E, Genschik P, Kang BG, Dagdas Y Go to publication →
  • 2024 Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells Science Offensperger F, Tin G, Duran-Frigola M, Hahn E, Dobner S, Ende CWA, Strohbach JW, Rukavina A, Brennsteiner V, Ogilvie K, Marella N, Kladnik K, Ciuffa R, Majmudar JD, Field SD, Bensimon A, Ferrari L, Ferrada E, Ng A, Zhang Z, Degliesposti G, Boeszoermenyi A, Martens S, Stanton R, Müller AC, Hannich JT, Hepworth D, Superti-Furga G, Kubicek S, Schenone M, Winter GE Go to publication →
  • 2024 ATG8ylation of vacuolar membrane protects plants against cell wall damage bioRxiv Julian J, Gao P, Del Chiaro A, De La Concepcion JC, Armengot L, Somssich M, Duverge H, Clavel M, Grujic N, Kobylinska R, Polivka I, Besten M, Dank C, Korbei B, Bachmair A, Coll NS, Sprakel J, Dagdas Y. Go to publication →
  • 2024 BIG enhances Arg/N-degron pathway-mediated protein degradation to regulate Arabidopsis hypoxia responses and suberin deposition Plant Cell Zhang H, Rundle C, Winter N, Miricescu A, Mooney BC, Bachmair A, Graciet E, Theodoulou FL Go to publication →
  • 2024 A metabolite sensor subunit of the Atg1/ULK complex regulates selective autophagy Nature Cell Biology Gross AS, Ghillebert R, Schuetter M, Reinartz E, Rowland A, Bishop BC, Stumpe M, Dengjel J, Graef M Go to publication →
  • 2024 Targeted protein degradation via intramolecular bivalent glues Nature Hsia O*, Hinterndorfer M*, Cowan AD*, Iso K, Ishida T, Sundaramoorthy R, Nakasone MA, Imrichova H, Schätz C, Rukavina A, Husnjak K, Wegner M, Correa-Sáez A, Craigon C, Casement R, Maniaci C, Testa A, Kaulich M, Dikic I, Winter GE†, Ciulli A† Go to publication →
  • 2023 Sequestration of translation initiation factors in p62 condensates Cell Reports Danieli A, Vucak G, Baccarini M, Martens S Go to publication →
  • 2023 Discovery of Molecular Glue Degraders via Isogenic Morphological Profiling ASC Chemical Biology Ng A, Offensperger F, Cisneros JA, Scholes NS, Malik M, Villanti L, Rukavina A, Ferrada E, Hannich JT, Koren A, Kubicek S, Superti-Furga G, Winter GE Go to publication →
  • 2023 Adult neural stem cells and neurogenesis are resilient to intermittent fasting EMBO Journal Gabarró-Solanas R, Davaatseren A, Kleifeld J, Kepčija T, Köcher T, Giralt A, Crespo-Enríquez I, Urbán N Go to publication →
  • 2023 Discovery of a Drug-like, Natural Product-Inspired DCAF11 Ligand Chemotype Nature Communication Xue G, Xie J, Hinterndorfer M, Cigler M, Dötsch L, Imrichova H, Lampe P, Cheng X, Adariani SR, Winter GE, Waldmann H Go to publication →
  • 2023 Optimized infrared photoactivatable ribonucleoside enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells. RNA Anisimova AS, Karagöz GE Go to publication →
  • 2023 The potential of cross-linking mass spectrometry in the development of protein–protein interaction modulators Current Opinion in Structural Biology Ruwolt M, Piazza I, Liu F Go to publication →
  • 2023 SPOP targets the immune transcription factor IRF1 for proteasomal degradation eLife Schwartz I, Vunjak M, Budroni V, Cantoran García A, Mastrovito M, Soderholm A, Hinterndorfer M, de Almeida M, Hacker K, Wang J, Froussios K, Jude J, Decker T, Zuber J, Versteeg GA. Go to publication →
  • 2023 p62 and NBR1 functions are dispensable for aggrephagy in mouse ESCs and ESC-derived neurons Life Science Alliance Trapannone R, Romanov J, Martens S Go to publication →
  • 2023 Lipid saturation controls nuclear envelope function Nature Cell Biology Romanauska A, Köhler A Go to publication →
  • 2023 The membrane surface as a platform that organizes cellular and biochemical processes Developmental Cell Leonard TA, Loose M, Martens S Go to publication →
  • 2023 Analysis of higher plant N-degron pathway components and substrates via expression in S. cerevisiae Methods in Enzymology Böhm J, Winter N, Kozlic A, Telser T, Nehlin L, Bachmair A Go to publication →
  • 2023 Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales eLife Polyansky AA, Gallego LD, Efremov RG, Köhler A, Zagrovic B Go to publication →
  • 2023 Light-Cleavable Auxiliary for Diselenide–Selenoester Ligations of Peptides and Proteins Chemistry Europe Schrems M, Kravchuk AV, Niederacher G, Exler F, Bello C, Becker CFW. Go to publication →
  • 2023 Aggrephagy at a glance Journal of Cell Science Bauer B, Martens S, Ferrari L Go to publication →
  • 2023 Atg8 family proteins, LIR/AIM motifs and other interaction modes Autophagy Reports Rogov VV, Nezis IP, Tsapras P, Zhang H, Dagdas Y, Noda NN, Nakatogawa H, Wirth M, Mouilleron S, McEwan DG, Behrends C, Deretic V, Elazar Z, Tooze SA, Dikic I, Lamark T, Johansen T Go to publication →
  • 2023 HUWE1 controls tristetraprolin proteasomal degradation by regulating its phosphorylation eLife Scinicariello S, Söderholm A, Schäfer M, Shulkina A, Schwartz I, Hacker K, Gogova R, Kalis RW, Froussios K, Budroni V, Bestehorn A, Clausen T, Kovarik P, Zuber J, Versteeg GA. Go to publication →
  • 2023 Structural basis of how the BIRC6/SMAC complex regulates apoptosis and autophagy Science Ehrmann JF, Grabarczyk DB, Heinke M, Deszcz L, Kurzbauer R, Hudecz O, Shulkina A, Gogova R, Meinhart A, Versteeg GA, Clausen T Go to publication →
  • 2023 NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy EMBO Journal Kataura T, Otten EG, Rabanal-Ruiz Y, Adriaenssens E, Urselli F, Scialo F, Fan L, Smith GR, Dawson WM, Chen X, Yue WW, Bronowska AK, Carroll B, Martens S, Lazarou M, Korolchuk VI Go to publication →
  • 2023 Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and C53-mediated autophagy EMBO Journal Picchianti L, Sánchez de Medina Hernández V, Zhan N, Irwin NAT, Stephani M, Hornegger H, Beveridge R, Sawa-Makarska J, Lendl T, Grujic N, Martens S, Richards TA, Clausen T, Ramundo S, Karagöz E, Dagdas Y Go to publication →
  • 2023 Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence Journal of American Chemical Society Duran-Frigola* M, Cigler M, and Winter GE* Go to publication →
  • 2023 E3-Specific Degrader Discovery by Dynamic Tracing of Substrate Receptor Abundance Journal of American Chemical Society Hanzl A, Barone E, Bauer S, Yue H, Nowak RP, Hahn E, Pankevich EV, Koren A, Kubicek S, Fischer ES, Winter GE Go to publication →
  • 2022 Orchestration of selective autophagy by cargo receptors Current Biology Adriaenssens E, Ferrari L, Martens S Go to publication →
  • 2023 SUMO Conjugation and SUMO Chain Formation by Plant Enzymes Methods in Molecular Biology Tomanov K, Julian J, Ziba I, Bachmair A Go to publication →
  • 2022 Characterization of ATG8-Family Interactors by Isothermal Titration Calorimetry Methods in Molecular Biology Picchianti L, Sedivy A, Dagdas Y Go to publication →
  • 2022 POLθ processes ssDNA gaps and promotes replication fork progression in BRCA1 deficient cells Cell Reports Schrempf A*, Bernardo S*, Arasa-Verge EA, Ramirez-Otero MA, Wilson J, Kirchhofer D, Timelthaler G, Ambros AM, Kaya A, Wieder M, Ecker GF, Winter GE, Costanzo V, Loizou JI Go to publication →
  • 2022 Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine Nature Communications Dowman LJ, Kulkarni SS, Alegre-Requena JV, Giltrap AM, Norman AR, Sharma A, Gallegos LC, Mackay AS, Welegedara AP, Watson EE, van Raad D, Niederacher G, Huhmann S, Proschogo N, Patel K, Larance M, Becker CFW, Mackay JP, Lakhwani G, Huber T, Paton RS, Payne RJ Go to publication →
  • 2022 Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders Nature Chemical Biology Hanzl A, Casement R, Imrichova H, Hughes SJ, Barone E, Testa A, Bauer S, Wright J, Brand M, Ciulli A, Winter GE Go to publication →
  • 2022 Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole Journal of Cell Biology Zhao J, Bui MT, Ma J, Künzl F, Picchianti L, De La Concepcion JC, Chen Y, Petsangouraki S, Mohseni A, García-Leon M, Gomez MS, Giannini C, Gwennogan D, Kobylinska R, Clavel M, Schellmann S, Jaillais Y, Friml J, Kang BH, Dagdas Y Go to publication →
  • 2021 E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP bioRxiv Ahel J, Fletcher A, Grabarczyk DB, Roitinger E, Deszcz L, Lehner A, Virdee S, Clausen T Go to publication →
  • 2022 Transcriptome, metabolome and suppressor analysis reveal an essential role for the ubiquitin-proteasome system in seedling chloroplast development BMC Plant Biology Talloji P, Nehlin L, Hüttel B, Winter N, Černý M, Dufková H, Hamali B, Hanczaryk K, Novák J, Hermanns M, Drexler N, Eifler K, Schlaich N, Brzobohatý B, Bachmair A Go to publication →
  • 2022 Autophagy promotes programmed cell death and corpse clearance in specific cell types of the Arabidopsis root cap Current Biology Feng Q, De Rycke R, Dagdas Y, Nowack MK Go to publication →
  • 2022 Could a Different View of Quiescence Help Us Understand How Neurogenesis Is Regulated? Frontiers in Neuroscience Urbán N Go to publication →
  • 2022 Expressed Protein Selenoester Ligation Angewandte Chemie International Ed. Kulkarni SS, Watson EE, Maxwell JWC, Niederacher G, Johansen-Leete J, Huhmann S, Mukherjee S, Norman AR, Kriegesmann J, Becker CFW, Payne RJ Go to publication →
  • 2022 Molecular mechanisms of endomembrane trafficking in plants Plant Cell Aniento F, Sánchez de Medina Hernández V, Dagdas Y, Rojas-Pierce M, Russinova E Go to publication →
  • 2022 A yeast-based functional assay to study plant N-degron – N-recognin interactions Frontiers in Plant Science Kozlic A, Winter N, Telser T, Reimann J, Rose K, Nehlin L, Berckhan S, Sharma G, Dambire C, Boeckx T, Holdsworth MJ, Bachmair A Go to publication →
  • 2021 Stem cell quiescence: the challenging path to activation Development Noelia Urbán and Tom H. Cheung Go to publication →
  • 2021 Decomposing the mutational landscape of cancer genomes with RepairSig Cell Systems Bernardo S, Meyenberg M and Loizou JI Go to publication →
  • 2021 Wnt/beta-catenin signalling is dispensable for adult neural stem cell homeostasis and activation Development Austin SHL, Gabarró-Solanas R, Rigo P, Paun O, Harris L, Guillemot F, Urbán N Go to publication →
  • 2021 Proteasome and selective autophagy: Brothers-in-arms for organelle quality control Current Opinion in Plant Biology Clavel M, Dagdas Y Go to publication →
  • 2021 Reconstitution defines the roles of p62, NBR1 and TAX1BP1 in ubiquitin condensate formation and autophagy initiation Nature Communications Turco E, Savova A, Gere F, Ferrari L, Romanov J, Schuschnig M, Martens S Go to publication →
  • 2021 The rise of proteome‐wide biophysics Molecular Systems Biology Mateus A, Savitski MM, Piazza I Go to publication →
  • 2021 HUWE1 employs a giant substrate-binding ring to feed and regulate its HECT E3 domain Nature Chemical Biology Grabarczyk DB, Petrova OA, Deszcz L, Kurzbauer R, Murphy P, Ahel J, Vogel A, Gogova R, Faas V, Kordic D, Schleiffer A, Meinhart A, Imre R, Lehner A, Neuhold J, Bader G, Stolt-Bergner P, Böttcher J, Wolkerstorfer B, Fischer G, Grishkovskaya I, Haselbach D, Kessler D, Clausen T Go to publication →
  • 2021 Identification and selectivity profiling of small-molecule degraders via multi-omics approaches Cell Chemical Biology Scholes NS, Mayor-Ruiz C, Winter GE Go to publication →
  • 2021 Cellular control of protein turnover via modification of the amino terminus International Journal of Molecular Sciences Winter N, Novatchkova M and Bachmair A Go to publication →