Three-dimensional dynamic views of proteomes as a novel readout for physiological and pathological alterations

Project Information

Proteomes-in-3D

Grant agreement ID: 866004

DOI

10.3030/866004

Project closed

EC signature date 19 February 2020

Start date 1 March 2020

End date 28 February 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 000 000,00

EU contribution

€ 2 000 000,00

Coordinated by

EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Switzerland

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (21)

Mechanism of connexin channel inhibition by mefloquine and 2-aminoethoxydiphenyl borate

Author(s): Pia Lavriha, Yufei Han, Xinyue Ding, Dina Schuster, Chao Qi, Anand Vaithia, Paola Picotti, Volodymyr M. Korkhov
Published in: PLOS ONE, Issue 19, 2024, Page(s) e0315510, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0315510

Systematic detection of functional proteoform groups from bottom-up proteomic datasets

Author(s): Bludau, Isabell Frank, Max Dörig, Christian Cai, Yujia Heusel, Moritz Rosenberger, George Picotti, Paola Collins, Ben C. Röst, Hannes Aebersold, Ruedi
Published in: Nature Communications, Issue 20411723, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-24030-x

An approach to characterize mechanisms of action of anti-amyloidogenic compounds in vitro and in situ

Author(s): P. Stalder, T. Serdiuk, D. Ghosh, Y. Fleischmann, N. Ait-Bouziad, J.-P. Quast, L. Malinovska, A. Ouared, A. Davranche, W. Haenseler, C. Boudou, E. Tsika, J. Stöhr, R. Melki, R. Riek, N. de Souza, P. Picotti
Published in: npj Parkinson's Disease, Issue 11, 2025, ISSN 2373-8057
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41531-025-00966-5

Molecular and functional landscape of malignant serous effusions for precision oncology

Author(s): Rebekka Wegmann, Lorenz Bankel, Yasmin Festl, Kate Lau, Sohyon Lee, Fabian Arnold, Valentina Cappelletti, Aaron Fehr, Paola Picotti, Konstantin J. Dedes, Daniel Franzen, Daniela Lenggenhager, Peter K. Bode, Martin Zoche, Holger Moch, Christian Britschgi, Berend Snijder
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-52694-8

Comparative analysis of the intracellular responses to disease-related aggregation-prone proteins

Author(s): Melnik, Andre Cappelletti, Valentina Vaggi, Federico Piazza, Ilaria Tognetti, Marco Schwarz, Carmen Cereghetti, Gea Ahmed, Mennat A. Soste, Martin Matlack, Kent de Souza, Natalie Csikasz-Nagy, Attila Picotti, Paola
Published in: Journal of Proteomics, Issue 18743919, 2020, ISSN 1874-3919
Publisher: Elsevier BV
DOI: 10.1016/j.jprot.2020.103862

USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit

Author(s): Montellese, Christian van den Heuvel, Jasmin Ashiono, Caroline Dörner, Kerstin Melnik, André Jonas, Stefanie Zemp, Ivo Picotti, Paola Gillet, Ludovic C. Kutay, Ulrike
Published in: eLife, Issue 2050084X, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.54435

Analysis of Limited Proteolysis-Coupled Mass Spectrometry Data

Author(s): Luise Nagel, Jan Grossbach, Valentina Cappelletti, Christian Dörig, Paola Picotti, Andreas Beyer
Published in: Molecular & Cellular Proteomics, Issue 24, 2025, Page(s) 100934, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2025.100934

Global profiling of protein complex dynamics with an experimental library of protein interaction markers

Author(s): Christian Dörig, Cathy Marulli, Thomas Peskett, Norbert Volkmar, Lorenzo Pantolini, Gabriel Studer, Camilla Paleari, Fabian Frommelt, Torsten Schwede, Natalie de Souza, Yves Barral, Paola Picotti
Published in: Nature Biotechnology, 2024, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-024-02432-8

Combining data integration and molecular dynamics for target identification in α-Synuclein-aggregating neurodegenerative diseases: Structural insights on Synaptojanin-1 (Synj1).

Author(s): Kirsten Jenkins; Teodora Mateeva; István Szabó; Andre Melnik; Paola Picotti; Attila Csikász-Nagy; Attila Csikász-Nagy; Edina Rosta
Published in: Computational and Structural Biotechnology Journal, Vol 18, Iss , Pp 1032-1042 (2020), Issue 20010370, 2020, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.3929/ethz-b-000465810

Comparative analysis of cancer cell responses to targeted radionuclide therapy (TRT) and external beam radiotherapy (EBRT)

Author(s): Grzmil, Michal Boersema, Paul Sharma, Ashish Blanc, Alain Imobersteg, Stefan Pruschy, Martin Picotti, Paola Schibli, Roger Behe, Martin
Published in: Journal of Hematology & Oncology, Issue 17568722, 2022, ISSN 1756-8722
Publisher: BioMed Central
DOI: 10.1186/s13045-022-01343-y

Combining CRISPRi and metabolomics for functional annotation of compound libraries

Author(s): Miquel Anglada-Girotto; Gabriel Handschin; Karin Ortmayr; Adrian I. Campos; Ludovic Gillet; Pablo Manfredi; Claire V. Mulholland; Michael Berney; Urs Jenal; Paola Picotti; Mattia Zampieri
Published in: Nature Chemical Biology, 18 (5), Issue 15524469, 2022, ISSN 1552-4469
Publisher: Springer Nature
DOI: 10.1038/s41589-022-00970-3

Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ

Author(s): Valentina Cappelletti, Thomas Hauser, Ilaria Piazza, Monika Pepelnjak, Liliana Malinovska, Tobias Fuhrer, Yaozong Li, Christian Dörig, Paul Boersema, Ludovic Gillet, Jan Grossbach, Aurelien Dugourd, Julio Saez-Rodriguez, Andreas Beyer, Nicola Zamboni, Amedeo Caflisch, Natalie de Souza, Paola Picotti
Published in: Cell, Issue 184/2, 2021, Page(s) 545-559.e22, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2020.12.021

Systematic detection of functional proteoform groups from bottom-up proteomic datasets

Author(s): Isabell Bludau; Isabell Bludau; Max Frank; Christian Dörig; Yujia Cai; Moritz Heusel; Moritz Heusel; George Rosenberger; George Rosenberger; Paola Picotti; Ben C. Collins; Ben C. Collins; Hannes L. Röst; Ruedi Aebersold; Ruedi Aebersold
Published in: Nature Communications, 12 (1), Issue 5, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.3929/ethz-b-000491987

Detecting Protein-Small Molecule Interactions Using Limited Proteolysis-Mass Spectrometry (LiP-MS).

Author(s): Monika Pepelnjak; Natalie de Souza; Natalie de Souza; Paola Picotti
Published in: Trends in Biochemical Sciences, Issue 3, 2020, ISSN 0968-0004
Publisher: Elsevier BV
DOI: 10.3929/ethz-b-000441347

A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes

Author(s): Ilaria Piazza, Nigel Beaton, Roland Bruderer, Thomas Knobloch, Crystel Barbisan, Lucie Chandat, Alexander Sudau, Isabella Siepe, Oliver Rinner, Natalie de Souza, Paola Picotti, Lukas Reiter
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-18071-x

Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker

Author(s): Mackmull, Marie-Therese Nagel, Luise Sesterhenn, Fabian Muntel, Jan Grossbach, Jan Stalder, Patrick Bruderer, Roland Reiter, Lukas van de Berg, Wilma D.J. de Souza, Natalie Beyer, Andreas Picotti, Paola
Published in: Nature Structural & Molecular Biology, Issue 14764687, 2022, ISSN 1476-4687
Publisher: Springer Nature
DOI: 10.1038/s41594-022-00837-0

Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance

Author(s): Kamrad, Stephan Grossbach, Jan Rodríguez-López, Maria Mülleder, Michael Townsend, StJohn Cappelletti, Valentina Stojanovski, Gorjan Correia-Melo, Clara Picotti, Paola Beyer, Andreas Ralser, Markus Bähler, Jürg
Published in: Molecular Systems Biology, Issue 17444292, 2020, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20199270

Deciphering the signaling network of breast cancer improves drug sensitivity prediction.

Author(s): Marco Tognetti; Attila Gábor; Attila Gábor; Mi Yang; Mi Yang; Valentina Cappelletti; Jonas Windhager; Oscar M. Rueda; Konstantina Charmpi; Elham Esmaeilishirazifard; Elham Esmaeilishirazifard; Alejandra Bruna; Natalie de Souza; Natalie de Souza; Carlos Caldas; Carlos Caldas; Andreas Beyer; Paola Picotti; Julio Saez-Rodriguez; Julio Saez-Rodriguez; Bernd Bodenmiller
Published in: Cell Systems, 12 (5), Issue 24054720, 2021, ISSN 2405-4720
Publisher: CellPress
DOI: 10.3929/ethz-b-000485506

Structure of Mycobacterium tuberculosis Cya, an evolutionary ancestor of the mammalian membrane adenylyl cyclases

Author(s): Mehta, Ved Khanppnavar, Basavraj Schuster, Dina Kantarci, Ilayda Vercellino, Irene Kosturanova, Angela Iype, Tarun Stefanic, Sasa Picotti, Paola Korkhov, Volodymyr M.
Published in: eLife, Issue 2050084X, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.77032

In situ analysis of osmolyte mechanisms of proteome thermal stabilization

Author(s): Monika Pepelnjak, Britta Velten, Nicolas Näpflin, Tatjana von Rosen, Umberto Capasso Palmiero, Jeong Hoon Ko, Heather D. Maynard, Paolo Arosio, Eilika Weber-Ban, Natalie de Souza, Wolfgang Huber, Paola Picotti
Published in: Nature Chemical Biology, Issue 20, 2024, Page(s) 1053-1065, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-024-01568-7

Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule disassembly

Author(s): Gea Cereghetti, Caroline Wilson-Zbinden, Vera M. Kissling, Maren Diether, Alexandra Arm, Haneul Yoo, Ilaria Piazza, Shady Saad, Paola Picotti, D. Allan Drummond, Uwe Sauer, Reinhard Dechant, Matthias Peter
Published in: Nature Cell Biology, Issue 23/10, 2021, Page(s) 1085-1094, ISSN 1465-7392
Publisher: Nature Publishing Group
DOI: 10.1038/s41556-021-00760-4

Monographic books (1)

Limited Proteolysis-Mass Spectrometry to Identify Metabolite-Protein Interactions

Author(s): Aleš Holfeld, Jan-Philipp Quast, Roland Bruderer, Lukas Reiter, Natalie de Souza & Paola Picotti
Published in: Cell-Wide Identification of Metabolite-Protein Interactions, 2022, ISBN 978-1-0716-2624-5
Publisher: Springer Nature