Revealing the Synapse Architecture and Plasticity by Structural Interactomics

Project Information

SynLink

Grant agreement ID: 949184

DOI

10.3030/949184

EC signature date 26 October 2020

Start date 1 January 2021

End date 31 December 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 243,00

EU contribution

€ 1 499 243,00

Coordinated by

FORSCHUNGSVERBUND BERLIN EV
Germany

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 (14)

Integrative Molecular Dynamics Simulations Untangle Cross‐Linking Data to Unveil Mitochondrial Protein Distributions

Author(s): Fabian Schuhmann, Kerem Can Akkaya, Dmytro Puchkov, Svea Hohensee, Martin Lehmann, Fan Liu, Weria Pezeshkian
Published in: Angewandte Chemie International Edition, Issue 64, 2025, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202417804

Redesigning error control in cross-linking mass spectrometry enables more robust and sensitive protein-protein interaction studies

Author(s): Boris Bogdanow, Max Ruwolt, Julia Ruta, Lars Mühlberg, Cong Wang, Wen-feng Zeng, Arne Elofsson, Fan Liu
Published in: Molecular Systems Biology, Issue 21, 2025, Page(s) 90-106, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.1038/s44320-024-00079-w

Controlling the interaction between <scp>CaMKII</scp> and Calmodulin with a photocrosslinking unnatural amino acid

Author(s): Iva Lučić, Pin‐Lian Jiang, Andreas Franz, Yuval Bursztyn, Fan Liu, Andrew J. R. Plested
Published in: Protein Science, Issue 32, 2023, ISSN 0961-8368
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.4798

Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies

Author(s): Ying Zhu, Kerem Can Akkaya, Julia Ruta, Nanako Yokoyama, Cong Wang, Max Ruwolt, Diogo Borges Lima, Martin Lehmann, Fan Liu
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-47569-x

The potential of cross-linking mass spectrometry in the development of protein–protein interaction modulators

Author(s): Max Ruwolt; Ilaria Piazza; Fan Liu
Published in: Current Opinion in Structural Biology, Issue 2, 2023, ISSN 1879-033X
Publisher: elsevier
DOI: 10.1016/j.sbi.2023.102648

Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics

Author(s): Milan Avila Clasen, Max Ruwolt, Cong Wang, Julia Ruta, Boris Bogdanow, Louise U. Kurt, Zehong Zhang, Shuai Wang, Fabio C. Gozzo, Tao Chen, Paulo C. Carvalho, Diogo Borges Lima, Fan Liu
Published in: Nature Methods, Issue 21, 2024, Page(s) 2327-2335, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-024-02478-1

CaMKII autophosphorylation can occur between holoenzymes without subunit exchange

Author(s): Iva Lučić; Léonie Héluin; Pin-Lian Jiang; Alejandro G Castro Scalise; Cong Wang; Andreas Franz; Florian Heyd; Markus C Wahl; Fan Liu; Andrew JR Plested
Published in: elife, Issue 2, 2023, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.86090

A Membrane‐Permeable and Immobilized Metal Affinity Chromatography (IMAC) Enrichable Cross‐Linking Reagent to Advance In Vivo Cross‐Linking Mass Spectrometry

Author(s): Pin‐Lian Jiang; Cong Wang; Anne Diehl; Rosa Viner; Chris Etienne; Premchendar Nandhikonda; Leigh Foster; Ryan D. Bomgarden; Fan Liu
Published in: Angewandte Chemie, Issue 1, 2021, ISSN 1521-3757
Publisher: wiley
DOI: 10.1002/anie.202113937

Real-time library search increases cross-link identification depth across all levels of sample complexity

Author(s): Ruwolt M., He Y, Lima D.B., Barshop W., Broichhagen J., Huguet R., Viner R., Liu F.
Published in: Analytical Chemistry, 2023, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.2c05141

Integrative Molekulardynamiksimulationen entwirren cross‐linking Daten und zeigen Verteilungen von mitochondrialen Proteinen

Author(s): Fabian Schuhmann, Kerem Can Akkaya, Dmytro Puchkov, Svea Hohensee, Martin Lehmann, Fan Liu, Weria Pezeshkian
Published in: Angewandte Chemie, Issue 137, 2025, ISSN 0044-8249
Publisher: Wiley
DOI: 10.1002/ange.202417804

Molecular architecture of synaptic vesicles

Author(s): Uljana Kravcenko, Max Ruwolt, Jana Kroll, Artsemi Yushkevich, Martina Zenkner, Julia Ruta, Rowaa Lotfy, Erich E. Wanker, Christian Rosenmund, Fan Liu, Mikhail Kudryashev
Published in: PNAS, 2025, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1101/2024.04.11.588828

Yeast TLDc domain proteins regulate assembly state and subcellular localization of the V-ATPase

Author(s): Samira Klössel, Ying Zhu, Lucia Amado, Daniel D Bisinski, Julia Ruta, Fan Liu, Ayelén González Montoro
Published in: The EMBO Journal, Issue 43, 2024, Page(s) 1870-1897, ISSN 1460-2075
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s44318-024-00097-2

Optimized TMT-based quantitative cross-linking mass spectrometry strategy for large-scale interactomic studies

Author(s): Ruwolt M., Schnirch L., Lima D.B., Nadler-Holly M., Viner R., Liu F.
Published in: Analytical Chemistry, 2022, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c04812

Q2C: A oftware for anaging ass pectrometry acilities

Author(s): Diogo B. Lima, Max Ruwolt, Marlon D.M. Santos, Ke Pu, Fan Liu, Paulo C. Carvalho
Published in: Journal of Proteomics, Issue 321, 2025, Page(s) 105511, ISSN 1874-3919
Publisher: Elsevier BV
DOI: 10.1016/j.jprot.2025.105511

Non-peer reviewed articles (1)

Integrative structural interactomics reveals protein organization and structure in a giant virus

Author(s): Lars Mühlberg, Julia Ruta, Vasilii Mikirtumov, Raymond Burton-Smith, Kazuyoshi Murata, Mikhail Kudryashev, Kenta Okamoto, Boris Bogdanow, Fan Liu
Published in: bioRxiv, 2025, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.06.16.659922