Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies.
Chemical cross-linking and mass spectrometry is of growing use for establishment of distance constraints on protein conformations and interactions. Whereas intraprotein cross-links can arise from proteins in isolation, interprotein cross-links reflect proximity of two interacting proteins in the sample. Prediction of expected ratios of the number of interprotein to intraprotein cross-links is hindered by lacking comprehensive knowledge on the interactome network and global occupancy levels for all interacting complex subunits. Here we determine the theoretical number of possible inter- and intraprotein cross-links in available PDB structures of proteins bound in complexes to predict a maximum expected fraction of interprotein cross-links in large scale in vivo cross-linking studies. We show how the maximum fraction can guide interpretation of reported interprotein fractions with respect to the extent of sample protein binding, comparing whole cell and lysate cross-linked samples as an example. We also demonstrate how an observation of interprotein cross-link fractions greater than the maximum value can result from the presence of false positive cross-links which are predominantly interprotein, their number estimable from the observed surplus fraction of interprotein cross-links.
['Keller|Andrew|A|', 'Chavez|Juan D|JD|', 'Felt|Kevin C|KC|', 'Bruce|James E|JE|0000-0001-6441-6089']
D003432:Cross-Linking Reagents D030562:Databases, Protein D008958:Models, Molecular D011485:Protein Binding D011487:Protein Conformation D025941:Protein Interaction Mapping D060066:Protein Interaction Maps D011506:Proteins
cross-linking mass spectrometry interactomics DSSO FDR lower bound PIR cross-linker span extent of binding maximum interprotein quality check