4. Crosslinking distances and restraints

Note

under construction.

Crosslinking coupled to mass spectrometry (XL-MS) is becoming an increasingly popular technique for modelling protein monomers and complexes. The distance restraints garnered from these experiments can be used alone or as part of an integrative modelling approach, incorporating data from many sources. We developed a new scoring procedure for models based on crosslink data - Matched and Non-accessible Crosslink score (MNXL). The distances between crosslinked lysines are calculated either as Euclidean distances or Solvent Accessible Surface Distances (SASD) using a newly-developed method (Jwalk). MNXL takes into account whether a crosslink is non-accessible, i.e., an experimentally observed crosslink has no corresponding SASD in a model due to buried lysines.


  • Bullock JMA, Schwab J, Thalassinos K, Topf M. (2016). The importance of non-accessible crosslinks and solvent accessible surface distance in modelling proteins with restraints from crosslinking mass spectrometry. MCP. 5(7):2491-500.
_images/crosslink_path.png

Fig: Solvant accessible crosslink paths.