Research Unit

Fan Liu

Structural Interactomics

Fan Liu

Our group is interested in developing and applying tools to characterize the complexity of protein interactions within the cell. Using state-of-the-art mass spectrometric technologies, in particular cross-linking mass spectrometry (XL-MS), we aim to chart the protein interactomes of complex biological systems.


Better understanding of protein interactions

Nearly every process in the living cell is based on proteins. To precisely execute this plethora of tasks, proteins are highly organized in a variety of assemblies, ranging from stable protein complexes, well-regulated pathways, to extended protein interaction networks. Perturbation of these well-balanced systems is linked to many different physiological and pathological conditions. Our group is interested in developing and applying tools to characterize the complexity of protein interactions within the cell. Using state-of-the-art mass spectrometric technologies, in particular cross-linking mass spectrometry, we aim to gain a better understanding of protein interactomes in complex biological systems. These studies will offer enormous opportunities to elucidate the fundamental organization principles of proteins and discover previously unrecognized protein interactions in health and disease.

 

Research Overview

Proteins are the primary effectors of cells. They are highly organized in a variety of assemblies, forming the basis of well-regulated pathways and networks to precisely execute a plethora of cellular processes. Alternations of proteins expression, and their interaction networks are linked to many physiological and pathological conditions. Our main interest is to develop and apply mass spectrometry-based approaches to understand the spatial organization and dynamic regulation of protein complexes in space and time during cellular processes such as signaling and differentiation.

Publications

Contact

Prof. Dr. Fan Liu

Head, Fan Liu (SI) Group,
Head Mass Spectrometry


Research Section

Structural Biology

Cooperations

Theliulab


Publications via ORCID

An extended interaction site determines binding between AP180 and AP2 in clathrin mediated endocytosis

  • Samuel Naudi-Fabra; Carlos A. Elena-Real; Ida Marie Vedel; Maud Tengo; Kathrin Motzny; Pin-Lian Jiang; Peter Schmieder; Fan Liu; Sigrid Milles

Nature Communications 2024

read online

Extensive protein pyrophosphorylation revealed in human cell lines

  • Jeremy Morgan; Arpita Singh; Leonie Kurz; Michal Nadler-Holly; Max Ruwolt; Shubhra Ganguli; Sheenam Sharma; Martin Penkert; Eberhard Krause; Fan Liu; Rashna Bhandari; Dorothea Fiedler

Nature Chemical Biology 2024

read online

RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control

  • Louise Ulrich Kurt; Milan Avila Clasen; Ísis Venturi Biembengut; Max Ruwolt; Fan Liu; Fabio Gozzo; Diogo Borges Lima; Paulo Carvalho

Journal of Proteome Research 2024

read online

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

  • Samira Klössel; Ying Zhu; Lucia Amado; Daniel D Bisinski; Julia Ruta; Fan Liu; Ayelén González Montoro

The EMBO Journal 2024

read online

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

  • Ying Zhu; Kerem C. Akkaya; Julia Ruta; Nanako Yokoyama; Cong Wang; Max Ruwolt; Diogo Borges Lima; Martin Lehmann; Fan Liu

Nature Communications 2024

read online

Molecular architecture of synaptic vesicles

  • Uljana Kravcenko; Max Ruwolt; Jana Kroll; Artsemi Yushkevich; Martina Zenkner; Julia Ruta; Rowaa Lotfy; Erich Wanker; Christian Rosenmund; Fan Liu; Misha Kudryashev

Proceedings of the National Academy of Sciences 2024

read online

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

  • Boris Bogdanow; Max Ruwolt; Julia Ruta; Lars Mühlberg; Cong Wang; Wen-feng Zeng; Arne Elofsson; Fan Liu

Molecular Systems Biology 2024

read online

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

  • Milan Avila Clasen; Max Ruwolt; Cong Wang; Julia Ruta; Boris Bogdanow; Louise U. Kurt; Zehong Zhang; Shuai Wang; Fabio C. Gozzo; Tao Chen; Paulo Carvalho; Diogo Borges Lima; Fan Liu

Nature Methods 2024

read online

The nuclear GYF protein CD2BP2/U5–52K is required for T cell homeostasis

  • Miriam Bertazzon; Almudena Hurtado-Pico; Carlos Plaza-Sirvent; Marc Schuster; Marco Preußner; Benno Kuropka; Fan Liu; Andor Zenon Amandus Kirsten; Xiao Jakob Schmitt; Benjamin König; Miguel Álvaro-Benito; Esam T. Abualrous; Gesa I. Albert; Stefanie Kliche; Florian Heyd; Ingo Schmitz; Christian Freund

Frontiers in Immunology 2024

read online
of 9

PROTEOME-SCALE RECOMBINANT STANDARDS AND A ROBUST HIGH-SPEED SEARCH ENGINE TO ADVANCE CROSS-LINKING MS-BASED INTERACTOMICS

  • Milan Avila Clasen; Max Ruwolt; Louise U. Kurt; Fabio C Gozzo; Shuai Wang; Tao Chen; Paulo C Carvalho; Diogo Borges Lima; Fan Liu
read online

Real-Time Library Search Increases Cross-Link Identification Depth across All Levels of Sample Complexity

  • Max Ruwolt; Yi He; Diogo Borges Lima; William Barshop; Johannes Broichhagen; Romain Huguet; Rosa Viner; Fan Liu

Analytical Chemistry 2023

read online

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

  • Max Ruwolt; Ilaria Piazza; Fan Liu

Current Opinion in Structural Biology 2023

read online

An antagonism between Spinophilin and Syd-1 operates upstream of memory-promoting presynaptic long-term plasticity

  • Niraja Ramesh; Marc Escher; Oriane Turrel; Janine Lützkendorf; Tanja Matkovic; Fan Liu; Stephan Sigrist

eLife 2023

read online

CaMKII autophosphorylation can occur between holoenzymes without subunit exchange

  • Iva Lučić; Léonie Héluin; Pin-Lian Jiang; Alejandro G Castro Scalise; Cong Wang; Andreas Franz; Florian Heyd; Markus Wahl; Fan Liu; Andrew Plested

eLife 2023

read online

Spatially resolved protein map of intact human cytomegalovirus virions

  • Boris Bogdanow; Iris Gruska; Lars Mühlberg; Jonas Protze; Svea Hohensee; Barbara Vetter; Jens B. Bosse; Martin Lehmann; Mohsen Sadeghi; Lüder Wiebusch; Fan Liu

Nature Microbiology 2023

read online

Structural Host-Virus Interactome Profiling of Intact Infected Cells

  • Boris Bogdanow; Lars Mühlberg; Iris Gruska; Barbara Vetter; Julia Ruta; Arne Elofsson; Lüder Wiebusch; Fan Liu
read online
of 7
of 4
of 5