Projects

Fibrin clots

Fibrin clots are important for stopping bleeding. However, runaway clot formation leads to thrombosis, with often fatal consequences. To develop new anti-coagulants a deeper understanding at the molecular level of how clots form is urgently needed.

Relevant literature:

Klykov et al; Flexible regions in the molecular architecture of Human fibrin clots structurally resolved by XL-MS and integrative structural modeling, bioRxiv, 2019

We studied the structure of fully formed clots with XL-MS to gain a deeper understanding of these molecular details on the structure of Fibrin(ogen). Uncovering almost 300 distance constraints on the fully formed clots allowed us to reconstruct molecular details of regions so far unresolved by other techniques like cryo-EM.

Based on this new structure we aim to uncover the interactions of whole Platelets and Red Blood Cells to Fibrin clots. Knowledge of these interactions we believe are key as it has recently become clear that these cells play an important role in runaway clot formation.


Single cell proteomics / interactomics

Coming soon…


Mass spectrometry

Focusing the mass spectrometer on the job at hand is beneficial for reaching more analytical depth. For XL-MS, even with PhoX, focusing of the mass spectrometer on cross-linked peptides is beneficial for samples of any complexity.

Relevant literature:

Steigenberger et al; Finding and using diagnostic ions in collision induced crosslinked peptide fragmentation spectra, IJMS, 2019

Depicted above is the set of diagnostic ions produced for the cross-linking reagent DSS; the mechanism is however universal for lysine reactive cross-linking reagents yielding different masses depending on the spacer region. We are developing data acquisition routines making heavy use of these ions to focus the mass spectrometer in real-time on the cross-linked peptides.