High Sensitivity Crosslink Detection Coupled With Integrative Structure Modeling in the Mass Spec Studio *
By Vladimir Sarpe, Atefeh Rafiei, Morgan Hepburn, Nicholas K H Ostan, A. Schryvers, David C. Schriemer. 2016
36 citations recorded by the source corpus.
The Mass Spec Studio package was designed to support the extraction of hydrogen-deuterium exchange and covalent labeling data for a range of mass spectrometry (MS)-based workflows, to integrate with restraint-driven protein modeling activities. In this report, we present an extension of the underlying Studio framework and provide a plug-in for crosslink (XL) detection. To accommodate flexibility in XL methods and applications, while maintaining efficient data processing, the plug-in employs a peptide library reduction strategy via a presearch of the tandem-MS data. We demonstrate that prescoring linear unmodified peptide tags using a probabilistic approach substantially reduces search space by requiring both crosslinked peptides to generate sparse data attributable to their linear forms. The method demonstrates highly sensitive crosslink peptide identification with a low false positive rate. Integration with a Haddock plug-in provides a resource that can combine multiple sources of data for protein modeling activities. We generated a structural model of porcine transferrin bound to TbpB, a membrane-bound receptor essential for iron acquisition in Actinobacillus pleuropneumoniae. Using mutational data and crosslinking restraints, we confirm the mechanism by which TbpB recognizes the iron-loaded form of transferrin, and note the requirement for disparate sources of restraint data for accurate model construction. The software plugin is freely available at www.msstudio.ca.
Subfields: Molecular Biology, Spectroscopy
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In Molecular Biology
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- Structural basis for loading and inhibition of a bacterial T6SS phospholipase effector by the VgrG spike (2020, methodology): “0 (Sarpe et al , 2016) with methionine oxidation as a variable modification and NNP9 modification sites: lysine, serine, threonine and tyrosine.”