Publications

Selected Recent Publications

Saumer P, Scheffner M, Marx A, Stengel F (2024) Interactome of intact chromatosome variants with site-specifically ubiquitylated and acetylated linker histone H1.2, Nucleic Acids Res Jan 11;52(1):101-113. doi: 10.1093/nar/gkad1113.

Sailer C, Jansen J, Sekulski K, Cruz VE, Erzberger JP, Stengel F (2022) A comprehensive landscape of 60S ribosome biogenesis factors, Cell Rep. Feb 8;38(6):110353.

Fürsch J, Voormann C, Kammer KM, Stengel F (2021), Structural probing of Hsp26 activation and client binding by quantitative cross-linking mass spectrometry, Anal Chem, Oct 5;93(39):13226-13234. doi: 10.1021/acs.analchem.1c02282.

Boczek EE, Fürsch J, Jawerth L, Jahnel M, Niedermeier ML, Ruer-Gruß M, Kammer KM, Mediani L, Wang J, Yan X, Pozniakovski A, Poser I, Mateju D, Carra S, Alberti S, Hyman HH, Stengel F (2021), HspB8 prevents aberrant phase transitions of FUS by stabilizing its folded RNA binding domain, Elife Sep 6;10:e69377. doi: 10.7554/eLife.69377.

Höllmüller E, Geigges S, Niedermeier ML, Kammer KM, Kienle SM, Rösner D, Scheffner M, Marx A, Stengel F (2021) Site-specific ubiquitylation acts as a regulator of linker histone H1, Nat Commun, Jun 9;12(1):3497. doi:10.1038/s41467-021-23636-5.

Publications

Müller F, Jansen J, Offensperger F, Eichbichler D, Stengel F, Scheffner M (2024) Cobalamins function as allosteric activators of an Angelman syndrome-associated UBE3A/E6AP variant. Chembiochem. 2024 Apr 4:e202400184. doi: 10.1002/cbic.202400184. Online ahead of print. PMID: 38573110

Eichbichler D, Bernecker C, Stengel F, Scheffner M (2024) Phase separation promotes the activity of HECT E3 ligases-A word of caution. Proc Natl Acad Sci U S A. 2024 Apr 2;121(14):e2402551121. doi: 10.1073/pnas.2402551121. Epub 2024 Mar 25.

Rieth S, Spliesgar D, Orth J, Lehner M, Kasprzyk R, Stengel F, Marx A (2024) A desthiobiotin labelled NAD+ analogue to uncover Poly(ADP-ribose) polymerase 1 protein targets, Chembiochem, Jan 18:e202300797. doi: 10.1002/cbic.202300797.

Bongiovanni TR, Latario CJ, Le Cras Y, Trus E, Robitaille S, Swartz K, Schmidtke D, Vincent M, Kosta A, Orth J, Stengel F, Pellarin R, Rocha EPC, Ross BD, Durand E (2024) Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota, Nat Commun. Jan 10;15(1):429. doi: 10.1038/s41467-023-44426-1. PMID: 38200008.

Lambrecht R, Rudolf F, Ückert AK, Sladky VC, Phan TS, Jansen J, Naim S, Kaufmann T, Keogh A, Kirschnek S, Mangerich A, Stengel F, Leist M, Villunger A, Brunner T (2024) Non-canonical BIM-regulated energy metabolism determines drug-induced liver necrosis, Cell Death & Differ, Jan;31(1):119-131. doi: 10.1038/s41418-023-01245-7. Epub 2023 Nov 24. PMID: 38001256

Stengel F (2023) Measuring Changes in Protein Complex Membershipt at Scale, J Proteome Res. Aug 4;22(8):2539. doi: 10.1021/acs.jproteome.3c00413. PMID: 37538020

Goretzki B, Wiedemann C, McCray BA, Schäfer SL, Jansen J, Tebbe F, Mitrovic SA, Nöth J, Cabezudo AC, Donohue JK, Jeffries CM, Steinchen W, Stengel F, Sumner CJ, Hummer G, Hellmich UA (2023) Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity, Nat Commun. Jul 13;14(1):4165. doi: 10.1038/s41467-023-39808-4.

Yuan Y, Stumpf FM, Schlor LA, Schmidt OP, Saumer P, Huber LB, Frese M, Höllmüller E, Scheffner M, Stengel F, Diederichs K, Marx A (2023) Chemoproteomic discovery of a human RNA ligase, Nat Commun, Feb 15;14(1):842. doi: 10.1038/s41467-023-36451-x.

Albrecht CJ, Stumpf FM, Krüger L, Niedermeier ML, Stengel F, Marx A (2023) Chemical proteomics reveals interactors of the alarmone diadenosine triphosphate in the cancer cell line H1299, J Pept Sci. J Pept Sci. 2023 Mar;29(3):e3458. doi: 10.1002/psc.3458.

Chen X, Sailer C, Kammer KM, Fürsch J, Eisele MR, Sakata E, Pellarin R, Stengel F (2022) A mono- and intralink filter (mi-filter) to reduce false identifications in cross-linking mass spectrometry data, Anal Chem, Dec 27;94(51):17751-17756.

Cruz VE, Sekulski K, Peddada N, Sailer C, Balasubramanian S, Weirich CS, Stengel F, Erzberger JP (2022) Sequence-directed RNA remodeling within a topologically complex RNP substrate. Nat Struct Mol Biol., Dec;29(12):1228-1238.

Heim A, Niedermeier ML, Stengel F and Mayer TU (2022) The translation regulator Zar1l is required to control the timing of meiosis in Xenopus oocytes, Development, Nov 1;149(21):dev200900.

Kienle SM, Schneider T, Stuber K, Globisch C, Jansen J, Stengel F, Peter C, Marx A, Kovermann M, Scheffner M (2022) Electrostatic and steric effects underlie acetylation-induced changes in ubiquitin structure and function, Nat Commun. Sep 16;13(1):5435. doi: 10.1038/s41467-022-33087-1.

Prattes M, Grishkovskaya I, Hodirnau VV, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. (2022) Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1, Nat Struct Mol Biol. 2022 Sep 12. doi: 10.1038/s41594-022-00832-5. Online ahead of print.

Herzog D, Jansen J, Mißun M, Diederichs K, Stengel F, Marx A (2022) Chemical Proteomics of the Tumor Suppressor Fhit Covalently Bound to the Cofactor Ap 3 A Elucidates Its Inhibitory Action on Translation, J Am Chem Soc. May 6. doi: 10.1021/jacs.2c00815.

Lehner M, Rieth S, Höllmüller H, Spliesgar D, Mertes B, Stengel F, Marx A (2022) Profiling of the ADP-Ribolysome in Living Cells, Angew. Chem. Int. Ed., Feb 21. doi: 10.1002/anie.202200977.

Sailer C, Jansen J, Sekulski K, Cruz VE, Erzberger JP, Stengel F (2022) A comprehensive landscape of 60S ribosome biogenesis factors, Cell Rep. Feb 8;38(6):110353.

Krüger L, Albrecht CJ, Schammann HK, Stumpf F, Niedermeier ML, Yuan Y, Stuber K, Wimmer J, Stengel F, Scheffner M, Marx (2021) A, Chemical proteomics profiling of the alarmones diadenosine triphosphate and tetraphosphate reveals protein interactors, Nat Commun, Oct 4;12(1):5808. doi: 10.1038/s41467-021-26075-4.

Fürsch J, Voormann C, Kammer KM, Stengel F (2021), Structural probing of Hsp26 activation and client binding by quantitative cross-linking mass spectrometry, Anal Chem, Sep 20. doi: 10.1021/acs.analchem.1c02282. Online ahead of print.

Höllmüller E, Greiner K, Kienle SM, Scheffner M, Marx A, Stengel F (2021), The interactome of site-specifically acetylated linker histone H1, J Proteome Res, Aug 5. doi: 10.1021/acs.jproteome.1c00396.

Huang B, Guo Q, Niedermeier ML, Cheng J, Engler T, Maurer M, Pautsch A, Baumeister W, Stengel F^§, Kochanek S^§, Fernández-Busnadiego R^§, PolyQ expansion does not alter the Huntingtin-HAP40 complex, Structure, Apr 26:S0969-2126(21)00119-2. doi: 10.1016/j.str.2021.04.003. Online ahead of print. PMID: 33909994 § Shared corresponding authorship

Nicola Roverato, Carolin Sailer, Nicola Catone, Annette Aichem, Florian Stengel, Marcus Groettrup, Parkin is an E3 ligase for the ubiquitin-like modifier FAT10 which inhibits Parkin activation and mitophagy, Cell Reports, 2021, Mar 16;34(11):108857. doi: 10.1016/j.celrep.2021.108857.

Fabian Offensperger, Franziska Müller, Jasmin Jansen, Daniel Hammler, Andreas Marx, Stormy J. Chamberlain, Florian Stengel, Martin Scheffner, Identification of small molecule activators of the ubiquitin ligase E6AP/UBE3A and Angelman syndrome-derived E6AP/UBE3A mutants, Cell Chem Biol. 2020 Sep 14: S2451-9456(20)30339-1. doi: 10.1016/j.chembiol.2020.08.017.

Leitner at al., Towards Increased Reliability, Transparency and Accessibility in Cross-linking Mass Spectrometry, Structure. 2020 Oct 12:S0969-2126(20)30336-1. doi: 10.1016/j.str.2020.09.011. Online ahead of print. PMID: 33065067

Felix Ebner, Carolin Sailer, Daniela Eichbichler, Anna Sladewska-Marquardt, Florian Stengel, Martin Scheffner, A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6, J Biol Chem. 2020 Aug 27:jbc.RA120.015603. doi: 10.1074/jbc.RA120.015603. Online ahead of print. PMID: 32855237

Joachim Lutz, Eva Höllmüller, Martin Scheffner^§, Andreas Marx^§, Florian Stengel^§, The length of a ubiquitin chain is a determinant for selective recognition by ubiquitin-binding proteins, Angew. Chem. Int. Ed. 2020 Apr 17. doi: 10.1002/anie.202003058. [Epub ahead of print]

Julius Fürsch, Kai-Michael Kammer, Stefan Kreft, Martin Beck^§ and Florian Stengel^§, Proteome-wide structural probing of low-abundant protein interactions by crosslinking mass spectrometry, Anal Chem, 2020,10.1021/acs.analchem.9b05559.

Annette Aichem, Carolin Sailer, Stella Ryu, Nicola Catone, Nicolas Stankovic-Valentin, Gunter Schmidtke, Frauke Melchior, Florian Stengel, and Marcus Groettrup, Regulating the regulator: the ubiquitin-like modifier FAT10 thwarts SUMO activation, Nat Commun. 2019 Oct 1;10(1):4452. doi: 10.1038/s41467-019-12430-z.

Martin Gamerdinger, Kan Kobayashi, Annalena Wallisch, Stefan G. Kreft, Carolin Sailer, Renate Schlömer, Nadine Sachs, Ahmad Jomaa, Florian Stengel, Nenad Ban, Elke Deuerling, Early scanning of nascent polypeptides inside the ribosomal tunnel by NAC, Mol Cell, 2019 Jul 25. pii: S1097-2765(19)30487-3.

Kargas V, Castro-Hartmann P, Escudero-Urquijo N, Dent K, Hilcenko C, Sailer C, Zisser G, Carvalho M, Pellegrino S, Wawiórka L, Freund S, Wagstaff J, Andreeva A, Faille A, Chen E, Stengel F, Bergler H, Warren AJ, Mechanism of completion of peptidyltransferase centre assembly in eukaryotes, Elife. 2019 May 22;8. pii: e44904. doi: 10.7554/eLife.44904.

The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study, Iacobucci C et al, Anal Chem. 2019 May 2. doi: 10.1021/acs.analchem.9b00658.

Sailer, C., Offensperger, F., Julier, A., Kammer, K., Walker-Gray, R., Gold, M.G., Scheffner_,M.^§ and Stengel, F., ^§ Structural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex, Nat Commun., 2018 Oct 25;9(1):4441. doi: 10.1038/s41467-018-06953-0.

Henry N, Krammer EM, Stengel F, Adams Q, Van Liefferinge F, Hubin E, Chaves R, Efremov R, Aebersold R, Vandenbussche G, Prévost M, Raussens V, Deroo S., Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach. PLoS Comput Biol. 2018 Jun 22;14(6):e1006165. doi: 10.1371/journal.pcbi.1006165.

Identification of Proteins Interacting with Ubiquitin Chains, Zhao X, Lutz J, Höllmüller E, Scheffner M^§, Marx A^§, Stengel F^§., Angew Chem Int Ed Engl. 2017 Oct 17. doi: 10.1002/anie.201705898.

Mechanisms for restraining cAMP-dependent protein kinase revealed by subunit quantitation and novel crosslinking approaches, Ryan Walker-Gray, Florian Stengel, Matthew G. Gold, Proc Natl Acad Sci U S A. 2017 Sep 26;114(39):10414-10419. doi: 10.1073/pnas.1701782114.

Patel N, Stengel F, Aebersold R, Gold MG, Molecular basis of AKAP79 regulation by calmodulin, Nat Commun. 2017 Nov 22;8(1):1681. doi: 10.1038/s41467-017-01715-w

Obayashi E, Luna RE, Nagata T, Martin-Marcos P, Hiraishi H, Singh CR, Erzberger JP, Zhang F, Arthanari H, Morris J, Pellarin R, Moore C, Harmon I, Papadopoulos E, Yoshida H, Nasr ML, Unzai S, Thompson B, Aube E, Hustak S, Stengel F, Dagraca E, Ananbandam A, Gao P, Urano T, Hinnebusch AG, Wagner G, Asano K., Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5. Cell Rep. 2017 Mar 14;18(11):2651-2663. doi: 10.1016/j.celrep.2017.02.052.

Faini M, Stengel F, Aebersold R., The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology, J Am Soc Mass Spectrom. 2016 Apr 7.

Ruzbeh Mosadeghi, Kurt M Reichermeier, Martin Winkler, Anne Schreiber, Justin M Reitsma, Yaru Zhang, Florian Stengel, Junyue Cao, Minsoo Kim, Michael J Sweredoski, Sonja Hess, Alexander Leitner, Ruedi Aebersold, Matthias Peter Raymond, J Deshaies, Radoslav I Enchev, Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle, Elife. 2016 Mar 31;5.

Leitner A, Faini M, Stengel F, Aebersold R., Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines., Trends Biochem Sci. 2016 Jan;41(1):20-32.

Nadinath B. Nillegoda, Janine Kirstein, Anna Szlachcic, Mykhaylo Berynskyy, Antonia Stank, Florian Stengel, Kristin Arnsburg, Xuechao Gao, Annika Scior, Ruedi Aebersold, D. Lys Guilbride, Rebecca C. Wade, Richard I. Morimoto, Matthias P. Mayer and Bernd Bukau, Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation, Nature, 2015 Aug 5.

Aufderheide A, Beck F, Stengel F, Hartwig M, Schweitzer A, Pfeifer G, Goldberg AL, Sakata E, Baumeister W, Förster F., Structural characterization of the interaction of Ubp6 with the 26S proteasome, Proc Natl Acad Sci U S A. 2015 Jun 30.

Stéphanie Deroo, Florian Stengel, Azadeh Mohammadi, Nicolas Henry, Ellen Hubin, Eva-Maria Krammer, Ruedi Aebersold, and Vincent Raussens, Chemical crosslinking/mass spectrometry maps the amyloid peptide binding region on both apolipoprotein E domains, ACS Chem Biol. 2015 Jan 21.

Jan P. Erzberger*, Florian Stengel*, Riccardo Pellarin*, Suyang Zhang, Tanja Schaefer, Christopher H. S. Aylett, Peter Čimermančic, Daniel Boehringer, Andrej Sali, Ruedi Aebersold and Nenad Ban, Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex, Cell, 2014 Aug 28;158(5):1123-35. *equal contribution

Birol, M., Enchev, R.I., Yang, Y., Stengel F., Aebersold R., Betzi, S., Padilla, A. Hoh, F., Peter, M., Dumas, C., Echalier, A., Structural and Biochemical Characterization of the Cop9 Signalosome CSN5/CSN6 Heterodimer, PLoS One, 2014 Aug 21;9(8).

Florian Stengel*, Argyris Politis*, Zoe Hall, Helena Hernández, Alexander Leitner, Thomas Walzthoeni, Carol V. Robinson & Ruedi Aebersold, A mass-spectrometry based hybrid method for structural modelling of protein complexes, Nature Methods, 2014 Feb 9. doi: 10.1038/nmeth.2841. * Authors contributed equally to this work and are listed in alphabetical order in print.

Vu Q. Nguyen, Anand Ranjan, Florian Stengel, Debbie Wei, Ruedi Aebersold, Carl Wuand Andres E. Leschziner, Molecular Architecture of the ATP-Dependent Chromatin Remodeling Complex SWR1, Cell, Sep 12;154(6):1220-31.

Francesco A. Aprile, Anne Dhulesia, Florian Stengel, Cintia Roodveldt, Justin L. P. Benesch, Paolo Tortora, Carol V. Robinson, Xavier Salvatella, Christopher M. Dobson, Nunilo Cremades, Hsp70 Oligomerization Is Mediated by an Interaction between the Interdomain Linker and the Substrate-Binding Domain, PLoS One, 2013 Jun 28;8(6).

Thomas Walzthoeni, Alexander Leitner, Florian Stengel and RuediAebersold, Mass Spectrometry supported determination of protein complex structure, Curr Opin Struct Biol., 2013, 23:1-9.

Florian Stengel*, Andrew J. Baldwin*, Matthew F Bush, Gillian R Hilton, Hadi Lioe, Eman Basha, Nomalie Jaya, Elizabeth Vierling and Justin L.P. Benesch, Dissecting Heterogeneous Molecular Chaperone Complexes Using a Mass Spectrum Deconvolution Approach, Chem Biol., 2012 May 25;19(5):599-607. *equal contribution

Gillian R Hilton*, Hadi Lioe* Florian Stengel*, Andrew J. Baldwin, Justin L.P Benesch, Small Heat-Shock Proteins: Paramedics of the Cell, Top Curr Chem., 2012 May 11. *equal contribution

Florian Stengel, Ruedi Aebersold and Carol V. Robinson, Joining Forces: Integrating proteomics and crosslinking with the mass spectrometry of intact complexes, MCP, 2012 Mar,11(3):R111.014027. Epub 2011 Dec 16.

Francesco A. Aprile, Anne Dhulesia, Florian Stengel, Tommaso Eliseo, Cintia Roodvelt, Benedetta Bolognesi, Paolo Tortora, Xavier Salvatella, Nunilo Cremades, Christopher M. Dobson, Insights into the molecular mechanisms of Hsp70-mediated inhibition of amyloid formation, European Biophysics Journal with Biophysics Letters, 2011, 40,1, 87-87.

Eri Sakata*, Florian Stengel*, Keisuke Fukunaga, Min Zhou, Yasushi Saeki, Friedrich Förster, Wolfgang Baumeister, Keiji Tanaka and Carol V. Robinson, The catalytic activity of Ubp6 enhances maturation of the proteasomal regulatory particle, Mol Cell, 2011 June 10, 42, 637–649. *equal contribution

Matthew G Gold*, Florian Stengel*, Patrick J. Nygren, Chad R. Weisbrod, James E. Bruce, Carol V. Robinson, David Barford, John D. Scott, Architecture and dynamics of an AKAP79 signalling complex, Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6426-31. *equal contribution

Anne Schreiber, Florian Stengel, Ziguo Zhang, Radoslav I. Enchev, Eric Kong, Edward P. Morris, Carol V. Robinson, Paula C.A. da Fonseca and David Barford, Structural basis for the subunit assembly of the anaphase promoting complex, Nature, 2011 Feb 10, 470(7333):227-32.

Justin LP Benesch, J Andrew Aquilina, Andrew J Baldwin, Agata Rekas, Florian Stengel, Robyn A Lindner, Glyn L Devlin, Joseph Horwitz, Elizabeth Vierling, John A Carver& Carol V Robinson, Dynamic oligomerisation of HSP26 adjusts its quaternary dynamics and dispersity, Chem Biol. 2010Sep 24;17(9):1008-17.

Florian Stengel, Andrew J. Baldwin, Alexander J. Painter, Nomalie Jaya, EmanBasha, Lewis E. Kay, Elizabeth Vierling, Carol V. Robinson & Justin L.P. Benesch, Quaternary Dynamics and Plasticity underlie small Heat Shock Protein Chaperone Function, Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2007-12.

This article has been featured in the new edition of the text book Biochemistry by Garrett and Grisham to illustrate the role of these chaperones in protein homeostasis.

Luis M. Fidalgo, Graeme Whyte, Brandon T. Ruotolo, Justin L. P. Benesch, Florian Stengel, Chris Abell, Carol V. Robinson and Wilhelm T. S. Huck, Coupling MicrodropletMicroreactors with Mass Spectrometry, Reading the Contents of Single Droplets Online, Angew. Chem. Int. Ed. 2009, 48, (20):3665-8.

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