Leveraging the Entirety of the Protein Data Bank to Enable Improved Structure Prediction Based on Cross-Link Data

XLinkDB is a fast-expanding public database now storing more than 100 000 distinct identified cross-linked protein residue pairs acquired by chemical cross-linking with mass spectrometry from samples of 12 species (J. Proteome Res. 2019, 18 (2), 753-758). Mapping identified cross-links to protein structures, when available, provides valuable guidance on protein conformations detected in the cross-linked samples. As more and more structures become available in the Protein Data Bank (Nucleic Acids Res. 2000, 28 (1), 235-242), we sought to leverage their utility for cross-link studies by automatically mapping identified cross-links to structures based on sequence homology of the cross-linked proteins with those within structures. This enables use of structures derived from organisms different from those of samples, including large multiprotein complexes and complexes in alternative states. We demonstrate utility of mapping to orthologous structures, highlighting a cross-link between two subunits of mouse mitochondrial Complex I that was mapped to 15 structures derived from five mammals, its distances there of 16.2 +/- 0.4 angstrom indicating strong conservation of the protein interaction. We also show how multimeric structures enable reassessment of cross-links presumed to be intraprotein as potentially homodimeric interprotein in origin.

Automated summary

XLinkDB is a rapidly expanding public database storing over 100,000 identified cross-linked protein residue pairs acquired by chemical cross-linking with mass spectrometry from samples of 12 species. By mapping identified cross-links to protein structures, valuable guidance on protein conformations detected in the cross-linked samples can be provided. Leveraging available structures in the Protein Data Bank, cross-links can be mapped to structures based on sequence homology of the cross-linked proteins, enabling analysis of protein interactions across different organisms and states.