Targeted Protein Degradation

Publications

Selected Publications

  • 2020 Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation Science Sawa-Makarska J, Baumann V, Coudevylle N, von Bülow S, Nogellova V, Abert C, Schuschnig M, Graef M, Hummer G, Martens S Go to publication →
  • 2020 A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress eLife Stephani M, Picchianti L, Gajic A, Beveridge R, Skarwan R, Sanchez de Medina Hernandez V, Mohseni A, Clavel M, Zeng Y, Naumann C, Matuszkiewicz M, Turco E, Loefke C, Li B, Durnberger G, Schutzbier M, Chen HT, Abdrakhmanov A, Savova A, Chia KS, Djamei A, Schaffner I, Abel S, Jiang L, Mechtler K, Ikeda F, Martens S, Clausen T, Dagdas Y Go to publication →
  • 2020 Rational discovery of molecular glue degraders via scalable chemical profiling Nature Chemical Biology Mayor-Ruiz C, Bauer S, Brand M, Kozicka Z, Siklos M, Imrichova H, Kaltheuner IH, Hahn E, Seiler K, Koren A, Petzold G, Fellner M, Bock C, Müller AC, Zuber J, Geyer M, Thomä NH, Kubicek S, Winter GE Go to publication →
  • 2020 Native Mass Spectrometry Can Effectively Predict PROTAC Efficacy ACS Central Science Beveridge R, Kessler D, Rumpel K, Ettmayer P, Meinhart A, Clausen T Go to publication →
  • 2020 Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism eLife Ahel J, Lehner A, Vogel A, Schleiffer A, Meinhart A, Haselbach D, Clausen T Go to publication →
  • 2020 Quantifying the heterogeneity of macromolecular machines by mass photometry Nature Communications Sonn-Segev A, Belacic K, Bodrug T, Young G, VanDerLindern R, Schulman BA, Schimpf J, Friedrich T, Dip PV, Schwartz TU, Bauer B, Peters JM, Struwe WB, Benesch JLP, Brown NG#, Haselbach D#, Kukura P# (#co-corresponding authors) Go to publication →
  • 2020 The linear ubiquitin chain assembly complex generates heterotypic ubiquitin chains bioRxiv Rodriguez Carvajal A, Gomez Diaz C, Vogel A, Sonn-Segev A, Schodl K, Deszcz L, Orban-Nemeth Z, Sakamoto S, Mechtler K, Kukura P, Clausen T, Haselbach D, Ikeda F Go to publication →
  • 2020 Selective Mediator dependence of cell-type-specifying transcription Nature Genetics Jaeger MG, Schwalb B, Mackowiak SD, Velychko T, Hanzl A, Imrichova H, Brand M, Agerer B, Chorn S, Nabet B, Ferguson FM, Müller AC, Bergthaler A, Gray NS, Bradner JE, Bock C, Hnisz D, Cramer P, Winter GE Go to publication →
  • 2020 A PI3K-WIPI2 positive feedback loop allosterically activates LC3 lipidation in autophagy Journal of Cell Biology Fracchiolla D, Chang C, Hurley JH, Martens S Go to publication →
  • 2020 The Irish potato famine pathogen subverts host vesicle trafficking to channel starvation-induced autophagy to the pathogen interface bioRxiv Pandey P, Leary AY, Tümtas Y, Savage Z, Dagvadorj B, Tan E, Khandare V, Duggan C, Yusunov T, Madalinski M, Mirkin FG, Schornack S, Dagdas Y, Kamoun S, Bozkurt TO Go to publication →
  • 2020 Phase separation directs ubiquitination of gene-body nucleosomes Nature Gallego LD, Schneider M, Mittal C, Romanauska A, Gudino Carrillo RM, Schubert T, Pugh BF, Köhler A Go to publication →
  • 2020 Highly Precise Protein Semisynthesis through Ligation–Desulfurization Chemistry in Combination with Phenacyl Protection of Native Cysteines Methods in Mol. Biol. Mukherjee S, Matveenko M, Becker CFW Go to publication →
  • 2020 EXO70D isoforms mediate selective autophagic degradation of Type-A ARR proteins to regulate cytokinin sensitivity bioRxiv Acheampong AK, Shanks C, Chang CY, Schaller E, Dagdas Y, Kieber JJ Go to publication →
  • 2020 Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells EMBO J. Rodriguez E, Chevalier J, Olsen J, Ansbøl J, Kapousidou V, Zuo Z, Svenning S, Loefke C, Koemeda S, Drozdowskyj PS, Jez J, Durnberger G, Kuenzl F, Schutzbier M, Mechtler K, Ebstrup EN, Lolle S, Dagdas Y*, Petersen M* Go to publication →
  • 2020 Targeted protein degradation: current and future challenges Curr. Opin. Chem. Biol. Hanzl A. Winter GE Go to publication →
  • 2019 Quiescence of Adult Mammalian Neural Stem Cells: A Highly Regulated Rest Neuron Urbán N, Blomfield IM, Guillemot F Go to publication →
  • 2019 The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation Genome Biol. Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant JY, Zarnack K, König J, Beli P Go to publication →
  • 2019 Id4 promotes the elimination of the pro-activation factor Ascl1 to maintain quiescence of adult hippocampal stem cells eLife Blomfield IM, Rocamonde B, Masdeu MDM, Mulugeta E, Vaga S, van den Berg DL, Huillard E, Guillemot F, Urbán N Go to publication →
  • 2019 Labeling and Natural Post-Translational Modification of Peptides and Proteins via Chemoselective Pd-Catalyzed Prenylation of Cysteine J. Am. Chem. Soc. Schlatzer T, Kriegesmann J, Schröder H, Trobe M, Lembacher-Fadum C, Santner S, Kravchuk AV, Becker CFW, Breinbauer R Go to publication →
  • 2019 Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site Proc. Natl. Acad. Sci. USA Watson ER, Grace CRR, Zhang W, Miller DJ, Davidson IF, Prabu JR, Yu S, Bolhuis DL, Kulko ET, Vollrath R, Haselbach D, Stark H, Peters JM, Brown NG, Sidhu SS, Schulman BA Go to publication →
  • 2019 N-terminal β-strand underpins biochemical specialization of an ATG8 isoform PLoS Biol. Zess EK, Jensen C, Cruz-Mireles N, De la Concepcion JC, Sklenar J, Stephani M, Imre R, Roitinger E, Hughes R, Belhaj K, Mechtler K, Menke FLH, Bozkurt T, Banfield MJ, Kamoun S, Maqbool A, Dagdas YF Go to publication →
  • 2019 Plasticity of the cullin-RING ligase repertoire shapes sensitivity to ligand-induced protein degradation Mol. Cell Mayor-Ruiz C, Jaeger MG, Bauer S, Brand M, Sin C, Hanzl A, Mueller AC, Menche J, Winter GE Go to publication →
  • 2019 A repetitive acidic region contributes to the extremely rapid degradation of the cell-context essential protein TRIM52 Scientific Reports Hacker K, Benke S, Agerer B, Scinicariello S, Budroni V, Versteeg GA Go to publication →
  • 2019 MTHFD1 interaction with BRD4 links folate metabolism to transcriptional regulation Nature Genetics Sdelci S, Rendeiro AF, Rathert P, You W, Lin JG, Ringler A, Hofstätter G, Moll HP, Gürtl B, Farlik M, Schick S, Klepsch F, Oldach M, Buphamalai P, Schischlik F, Májek P, Parapatics K, Schmidl C, Schuster M, Penz T, Buckley DL, Hudecz O, Imre R, Wang SY, Maric HM, Kralovics R, Bennett KL, Müller AC, Mechtler K, Menche J, Bradner JE, Winter GE, Klavins K, Casanova E, Bock C, Zuber J, Kubicek S Go to publication →
  • 2019 FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates Mol. Cell Turco E, Witt M, Abert C, Bock-Bierbaum T, Su MY, Trapannone R, Sztacho M, Danieli A, Shi X, Zaffagnini G, Gamper A, Schuschnig M, Fracchiolla D, Bernklau D, Romanov J, Hartl M, Hurley JH, Daumke O, Martens S Go to publication →
  • 2019 Structure of McsB, a protein kinase for regulated arginine phosphorylation Nat. Chem. Biol. Suskiewicz MJ, Hajdusits B, Beveridge R, Heuck A, Vu LD, Kurzbauer R, Hauer K, Thoeny V, Rumpel K, Mechtler K, Meinhart A, Clausen T Go to publication →
  • 2019 Locus-Specific Knock-in of a degradable tag for target validation studies Methods Mol. Biol. Brand M, Winter GE Go to publication →
  • 2019 Homolog-Selective Degradation as a Strategy to Probe the Function of CDK6 in AML Cell Chem. Biology Brand M, Jiang B, Bauer S, Donovan KA, Liang Y, Wang ES, Nowak RP, Yuan JC, Zhang T, Kwiatkowski N, Müller AC, Fischer ES, Gray NS, Winter GE Go to publication →
  • 2019 The Scope, Functions, and Dynamics of Posttranslational Protein Modifications Annu. Rev. Plant Biol. Millar AH, Heazlewood JL, Giglione C, Holdsworth MJ, Bachmair A, Schulze WX Go to publication →
  • 2019 Identification and characterization of cancer vulnerabilities via targeted protein degradation Drug Discov. Today Technol. Mayor-Ruiz C, Winter GE Go to publication →
  • 2018 The unfolded protein response and endoplasmic reticulum protein targeting machineries converge on the stress sensor IRE1 eLife Acosta-Alvear D, Karagöz GE, Fröhlich F, Li H, Walther TC, Walter P Go to publication →
  • 2019 Single Posttranslational Modifications in the Central Repeat Domains of Tau4 Impact its Aggregation and Tubulin Binding Angew. Chem. Int. Ed. Ellmer D, Brehs M, Haj-Yahya M, Lashuel HA, Becker CFW Go to publication →
  • 2018 LZTR1 is a regulator of RAS ubiquitination and signaling Science Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G Go to publication →
  • 2018 Native chemical ligation in protein synthesis and semi-synthesis Chem. Soc. Rev. Conibear AC, Watson EE, Payne RJ, Becker CFW Go to publication →
  • 2019 Distinct branches of the N-end rule pathway modulate the plant immune response New Phytol. Vicente J, Mendiondo GM, Pauwels J, Pastor V, Izquierdo Y, Naumann C, Movahedi M, Rooney D, Gibbs DJ, Smart K, Bachmair A, Gray JE, Dissmeyer N, Castresana C, Ray RV, Gevaert K, Holdsworth MJ Go to publication →
  • 2018 The inner nuclear membrane is a metabolically active territory that generates nuclear lipid droplets Cell Romanauska A, Köhler A Go to publication →
  • 2018 Host autophagy machinery is diverted to the pathogen interface to mediate focal defense responses against the Irish potato famine pathogen eLife Dagdas YF*, Pandey P*, Tumtas Y, Sanguankiattichai N, Belhaj K, Duggan C, Leary AY, Segretin ME, Contreras MP, Savage Z, Khandare VS, Kamoun S, Bozkurt TO Go to publication →
  • 2018 Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48 Nat. Commun. Velimezi G, Robinson-Garcia L, Muñoz-Martínez F, Wiegant WW, Ferreira da Silva J, Owusu M, Moder M, Wiedner M, Rosenthal SB, Fisch KM, Moffat J, Menche J, van Attikum H, Jackson SP, Loizou JI Go to publication →
  • 2018 Targetable BET proteins- and E2F1-dependent transcriptional program maintains the malignancy of glioblastoma Proc. Natl. Acad. Sci. USA Xu L, Chen Y, Mayakonda A, Koh L, Chong YK, Buckley DL, Sandanaraj E, Lim SW, Lin RY, Ke XY, Huang ML, Chen J, Sun W, Wang LZ, Goh BC, Dinh HQ, Kappei D, Winter GE, Ding LW, Ang BT, Berman BP, Bradner JE, Tang C, Koeffler HP Go to publication →
  • 2018 The dTAG system for immediate and target-specific protein degradation Nat. Chem. Biol. Nabet B, Roberts JM, Buckley DL, Paulk J, Dastjerdi S, Yang A, Leggett AL, Erb MA, Lawlor MA, Souza A, Scott TG, Vittori S, Perry JA, Qi J, Winter GE, Wong KK, Gray NS, Bradner JE Go to publication →
  • 2018 p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage Nat. Commun. Borisova ME, Voigt A, Tollenaere MAX, Sahu SK, Juretschke T, Kreim N, Mailand N, Choudhary C, Bekker-Jensen S, Akutsu M, Wagner SA, Beli P Go to publication →
  • 2018 Functional TRIM24 degrader via conjugation of ineffectual bromodomain and VHL ligands Nat. Chem. Biol. Gechijian LN, Buckley DL, Lawlor MA, Reyes JM, Paulk J, Ott CJ, Winter GE, Erb MA, Scott TG, Xu M, Seo HS, Dhe-Paganon S, Kwiatkowski NP, Perry JA, Qi J, Gray NS, Bradner JE Go to publication →
  • 2018 Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function EMBO Rep. Heidelberger JB, Voigt A, Borisova ME, Petrosino G, Ruf S, Wagner SA, Beli P Go to publication →
  • 2018 Human tripartite motif protein 52 is required for cell context-dependent proliferation Oncotarget Benke S, Agerer B, Haas L, Stöger M, Lercher A, Gabler L, Kiss I, Scinicariello S, Berger W, Bergthaler A, Obenauf AC, Versteeg GA Go to publication →
  • 2018 UFD-2 is an adaptor-assisted E3 ligase targeting unfolded proteins Nat. Commun. Hellerschmied D, Roessler M, Lehner A, Gazda L, Stejskal K, Imre R, Mechtler K, Dammermann A, Clausen T Go to publication →
  • 2018 Translation Termination Factor GSPT1 Is a Phenotypically Relevant Off-Target of Heterobifunctional Phthalimide Degraders ACS Chem. Biol. Ishoey M, Chorn S, Singh N, Jaeger MG, Brand M, Paulk J, Bauer S, Erb MA, Parapatics K, Müller AC, Bennett KL, Ecker GF, Bradner JE, Winter GE Go to publication →
  • 2018 p62 filaments capture and present ubiquitinated cargos for autophagy EMBO J. Zaffagnini G, Savova A, Danieli A, Romanov J, Tremel S, Ebner M, Peterbauer T, Sztacho M, Trapannone R, Tarafder AK, Sachse C, Martens S Go to publication →
  • 2018 SUMO chain formation relies on the amino-terminal region of SUMO conjugating enzyme and has dedicated substrates in plants Biochemical J. Tomanov, K., Nehlin, L., Ziba, I., Bachmair, A. Go to publication →
  • 2018 Acute Pharmacologic Degradation of a Stable Antigen Enhances Its Direct Presentation on MHC Class I Molecules Front. Immunol. Moser SC, Voerman JSA, Buckley DL, Winter GE, Schliehe C Go to publication →
  • 2018 Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation Nat. Chem. Biol. Olson CM, Jiang B, Erb MA, Liang Y, Doctor ZM, Zhang Z, Zhang T, Kwiatkowski N, Boukhali M, Green JL, Haas W, Nomanbhoy T, Fischer ES, Young RA, Bradner JE, Winter GE, Gray NS Go to publication →
  • 2017 Repair of UV-Induced DNA Damage Independent of Nucleotide Excision Repair Is Masked by MUTYH Mol. Cell Mazouzi A, Battistini F, Moser SC, Ferreira da Silva, Wiedner M, Owusu M, Lardeau C-H, Ringler A, Weil B, Neesen J, Orozco M, Kubicek S, Loizou JI Go to publication →
  • 2017 Parallel genome-wide screens identify a synthetic viable interaction between the BLM helicase complex and Fanconi anemia Nat. Commun. Moder M, Velimezi G, Owusu M, Mazouzi A, Wiedner M, Ferreira da Silva J, Robinson-Garcia L, Schischlik F, Slavkovsky R, Kralovics R, Schuster M, Bock C, Ideker T, Jackson SP, Menche J, Loizou JI Go to publication →
  • 2017 An unfolded protein-induced conformational switch activates mammalian IRE1 eLife Karagöz GE, Acosta-Alvear D, Nguyen HT, Lee CP, Chu F, Walter P Go to publication →
  • 2017 MELK is not necessary for the proliferation of basal-like breast cancer cells eLife Huang HT, Seo HS, Zhang T, Wang Y, Jiang B, Li Q, Buckley DL, Nabet B, Roberts JM, Paulk J, Dastjerdi S, Winter GE, McLauchlan H, Moran J, Bradner JE, Eck MJ, Dhe-Paganon S, Zhao JJ, Gray NS Go to publication →
  • 2017 Long-range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs Nat. Commun. Haselbach D , Schrader J, Lambrecht F, Henneberg F, Chari A, Stark H Go to publication →
  • 2017 Semisynthetic prion protein (PrP) variants carrying glycan mimics at position 181 and 197 do not form fibrils Chem. Sci. Araman C, Thompson RE, Wang S, Hackl S, Payne RJ, Becker CFW Go to publication →
  • 2017 BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment Mol. Cell Winter GE, Mayer A, Buckley DL, Erb MA, Roderick JE, Vittori S, Reyes JM, di Iulio J, Souza A, Ott CJ, Roberts JM, Zeid R, Scott TG, Paulk J, Lachance K, Olson CM, Dastjerdi S, Bauer S, Lin CY, Gray NS, Kelliher MA, Churchman LS, Bradner JE Go to publication →
  • 2017 Transcription control by the ENL YEATS domain in acute leukaemia Nature Erb MA, Scott TG, Li BE, Xie H, Paulk J, Seo HS, Souza A, Roberts JM, Dastjerdi S, Buckley DL, Sanjana NE, Shalem O, Nabet B, Zeid R, Offei-Addo NK, Dhe-Paganon S, Zhang F, Orkin SH, Winter GE, Bradner JE Go to publication →
  • 2016 Mechanism of cargo-directed Atg8 conjugation during selective autophagy eLife Fracchiolla D, Sawa-Makarska J, Zens B, Ruiter A, Zaffagnini G, Brezovich A, Romanov J, Runggatscher K, Kraft C, Zagrovic B, Martens S Go to publication →
  • 2016 Arginine phosphorylation marks proteins for degradation by a Clp protease Nature Trentini DB, Suskiewicz MJ, Heuck A, Kurzbauer R, Deszcz L, Mechtler K, Clausen T Go to publication →
  • 2016 Cryo-EM of Mitotic Checkpoint Complex-Bound APC/C Reveals Reciprocal and Conformational Regulation of Ubiquitin Ligation Mol. Cell Yamaguchi M, VanderLinden R, Weissmann F, Qiao R, Dube P, Brown NG, Haselbach D, Zhang W, Sidhu SS, Peters JM, Stark H, Schulman BA Go to publication →
  • 2016 Structural Basis of Host Autophagy-related Protein 8 (ATG8) Binding by the Irish Potato Famine Pathogen Effector Protein PexRD54 J. Biol. Chem. Maqbool A, Hughes RK, Dagdas YF, Tregidgo N, Zess E, Belhaj K, Round A, Bozkurt TO, Kamoun S, Banfield MJ Go to publication →
  • 2016 Return to quiescence of mouse neural stem cells by degradation of a proactivation protein Science Urbán N, van den Berg DL, Forget A, Andersen J, Demmers JA, Hunt C, Ayrault O, Guillemot F Go to publication →
  • 2016 Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C Cell Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau Am Wu KP, Zhang W, Yu S, Mercedi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CR, Miller DJ, Haselbach D, Jarvis MA, Yamaguchi M, Yanisheski D, Petzold G, Sidhu SS, Kuhlmann B, Kirschner MW, Harper JW, Peters JM, Stark H, Schulman BA Go to publication →
  • 2016 Mechanism of APC/CCDC20 activation by mitotic phosphorylation Proc. Natl. Acad. Sci. USA Qiao R, Weissmann F, Yamaguchi M, Brown NG, VanderLinden R, Imre R, Jarvis MA, Brunner MR, Davidson IF, Litos G, Haselbach D , Mechtler K, Stark H, Schulman BA, Peters JM Go to publication →
  • 2016 An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor eLife Dagdas YF*, Belhaj K*, Maqbool A, Chaparro-Garcia A, Pandey P, Petre B, Tabassum N, Cruz-Mireles N, Hughes RK, Sklenar J, Win J, Menke F, Findlay K, Banfield MJ, Kamoun S, Bozkurt TO Go to publication →
  • 2015 Oligomerization of p62 allows for selection of ubiquitinated cargo and isolation membrane during selective autophagy eLife Wurzer B, Zaffagnini G, Fracchiolla D, Turco E, Abert C, Romanov J, Martens S Go to publication →
  • 2015 ProteoPlex: stability optimization of macromolecular complexes by sparse-matrix screening of chemical space Nat. Methods Chari A*, Haselbach D *, Kirves JM*, Ohmer J, Paknia E, Fischer N, Ganichkin O,Möller V, Frye JJ, Petzold G, Jarvis M, Tietzel M, Grimm C, Peters JM, Schulman BA, Tittmann K, Markl J, Fischer U, Stark H. (*equal contribution) Go to publication →
  • 2015 DRUG DEVELOPMENT. Phthalimide conjugation as a strategy for in vivo target protein degradation Science Winter GE, Buckley DL, Paulk J, Roberts JM, Souza A, Dhe-Paganon S, Bradner JE Go to publication →
  • 2014 The eukaryotic N-end rule pathway: conserved mechanisms and diverse functions Trends in Cell Biol. Gibbs DJ, Bacardit J, Bachmair A, Holdsworth MJ Go to publication →
  • 2014 Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane–cargo apposition during selective autophagy Nat. Cell Biol. Sawa-Makarska J, Abert C, Romanov J, Zens B, Ibiricu I, Martens S Go to publication →
  • 2014 Hsp90-Tau complex reveals molecular basis for specificity in chaperone action Cell Karagöz GE, Duarte AM, Akoury E, Ippel H, Biernat J, Morán Luengo T, Radli M, Didenko T, Nordhues BA, Veprintsev DB, Dickey CA, Mandelkow E, Zweckstetter M, Boelens R, Madl T, Rüdiger SG Go to publication →
  • 2014 Nitric oxide sensing in plants is mediated by proteolytic control of group VII ERF transcription factors Mol. Cell Gibbs DJ, Md Isa N, Movahedi M, Lozano-Juste J, Mendiondo GM, Berckhan S, Marín-de la Rosa N, Vicente Conde J, Sousa Correia C, Pearce SP, Bassel GW, Hamali B, Talloji P, Tomé DF, Coego A, Beynon J, Alabadí D, Bachmair A, León J, Gray JE, Theodoulou FL, Holdsworth MJ Go to publication →