A dynamic perspective on cross-linking data XL-MS

The XL-MS cross-linking experiment consists of the promotion of interresidual bonds and their identification in a protein. By knowing the cross-linking agent used, relevant information about the structure of the protein can be obtained. In this study, experimental crosslinking data and structures obtained by simulation for SalBIII and Calmodulin were analyzed. The compatibility of the cross-links with the simulation structures as a function of the spectra quality parameters showed us a positive correlation, indicating the score parameter as most significant for the selection of cross-links compatible with both the crystallographic structure and the simulation structures. In the crosslink compatibility analysis with simulation structures it was shown to be important to study the topological and Euclidean distances together, both being relevant and pertinent in many of the cases where the results deviated from what was expected. In the case of Calmodulin, the simulations showed that the change in conformation of the protein, upon complexation with calcium, restricts the compatibility of the structure with cross-links related to the connection of domains separated by the formation of the $\alpha$-helix. This study provides a greater understanding of the scope of the results and the consequences of the conditions we expose the protein to in the XL-MS experiment.