Research

Protein-protein cross-linking applications

We have applied chemical cross-linking to numerous protein complexes, mostly in collaborative projects. Cross-linking data complements high-resolution structural biology techniques such as cryo-electron microscopy or NMR spectroscopy and can help to provide a better understanding of structure and function of protein assemblies of different sizes.

Selected publications:

• Trabjerg et al. Identification of a direct interaction between the Fab domains of IgG antibodies and human FcRn upon IgG-FcRn complex formation, Nat. Commun. 2025. external page Link
• von Rosen et al. Substrates bind to residues lining the ring of asymmetrically engaged bacterial proteasome activator Bpa, Nat. Commun. 2025. external page Link
• Usher et al. The sodium leak channel NALCN is regulated by neuronal SNARE complex proteins, Sci. Adv. 2025. external page Link
• Mohammadi et al. Characterization of the N- and C-terminal domain interface of the three main apoE isoforms: a combined quantitative cross-linking mass spectrometry and molecular modelling study, Biochim. Biophys. Acta – Gen. Subj. 2025. external page Link
• Portugal-Calisto et al. An inhibitory segment within G-patch activators tunes Prp43-ATPase activity during ribosome assembly, Nat. Commun. 2024. external page Link
• Zdanowicz et al. Stoichiometry and architecture of the human pyruvate dehydrogenase complex, Sci. Adv. 2024. external page Link
• Khanppnavar et al. Regulatory sites of CaM-sensitive adenylyl cyclase AC8 revealed by cryo-EM and structural proteomics, EMBO Rep. 2024. external page Link  
• Park et al. A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle, Nat. Commun. 2024. external page Link
• Selcuk et al. Transglutaminase 2 has higher affinity for relaxed than for stretched fibronectin fibers, Matrix Biol. 2024. external page Link 
• Kern et al. Cross-linking mass spectrometric analysis of the endogenous TREX complex from S. cerevisiae, RNA 2023. external page Link

Protein-RNA cross-linking

More recently, we have extended our cross-linking scope to study protein-RNA complexes. This opens up new possibilities to study interactions between these two important classes of biomolecules. In collaboration with Frédéric Allain’s group at ETH we have established CLIR-MS, a method based on photochemical cross-linking that allows the localization of interaction sites at single residue level for amino acids and nucleotides. Our follow-up work includes the development of refined methods, dedicated software, and applications of the technology.

Selected publications:

• Sarnowski et al. A highly sensitive protein-RNA cross-linking mass spectrometry workflow with enhanced structural modeling potential, Nucl. Acids Res. 2025. external page Link
• de Vries et al. Specific protein-RNA interactions are mostly preserved in biomolecular condensates, Sci. Adv. 2024. external page Link
• Sarnowski et al. RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein–RNA Cross-Linking/Mass Spectrometry Data, J. Proteome Res. 2023. external page Link
• Padroni et al. A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2, Nucl. Acids Res. 2023. external page Link
• Knörlein et al. Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes, Nat. Commun. 2022. external page Link
• Götze et al. Single Nucleotide Resolution RNA–Protein Cross-Linking Mass Spectrometry: A Simple Extension of the CLIR-MS Workflow, Anal. Chem. 2020. external page Link
• Dorn et al. Structural modeling of protein-RNA complexes using crosslinking of segmentally isotope labeled RNA and MS/MS, Nat. Methods 2017. external page Link

Data standards and best practices

The importance of data and reporting standards in science is often overlooked, but standards increase transparency and fulfil an important role in helping methods gain acceptance in the wider scientific community. Alexander has made contributions to standards established by the HUPO Proteomics Standard Initiative and the Protein Data Bank. The group participated in community initiatives such as CASP, and Alexander co-authored several position papers on the future development of cross-linking MS.

Selected publications:

• Rappsilber et al. A Roadmap for Improving Reliability and Data Sharing in Crosslinking Mass Spectrometry, Mol. Cell. Proteomics 2025. external page Link
• Combe et al. mzIdentML 1.3.0 – Essential progress on the support of crosslinking and other identifications based on multiple spectra, Proteomics 2024. external page Link
• Vallat et al. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods, J. Mol. Biol. 2024. external page Link
• Leitner et al. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry, Structure 2020. external page Link
• Berman et al. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures, Structure 2019. external page Link  
• Fajardo et al. Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13, Proteins 2019. external page Link

Funding sources

We currently receive funding from the external page Swiss National Science Foundation via the external page NCCR RNA & Disease and SNSF individual project funding. Roberta Florea is funded by a grant from the external page Vontobel Foundation.

Our work has previously been funded by an ETH Research Grant, the Strategic Focus Area Personalized Health and Related Technologies of the ETH Domain, the National Research Pogram "COVID-19" (NRP 78). Esben Trabjerg was funded by a fellowship from the Benzon Foundation.