Project description:The pH dependency of the reaction of the cross-linking reagent, disuccinimidyl suberate (DSS), was studied on a set of eight model proteins.
Project description:These data sets are part of a large study aimed at the comparison of experimental and computational workflows used in chemical cross-linking coupled to mass spectrometry. Bovine serum albumin (BSA) was used as a model protein. Two different cross-linking chemistries were used: disuccinimidyl suberate (DSS) and a combination of pimelic acid dihydrazide (PDH) and the coupling reagent, DMTMM. See related publication: Iacobucci et al., First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study, Analytical Chemistry, 91 (2019) 6953-6961, DOI: 10.1021/acs.analchem.9b00658 This project is a reanalysis of these datasets with the two Labeled Cross-Linking MS identification tools OpenPepXL and xQuest.
Project description:Chemical cross-linking of proteins coupled with mass spectrometry (CXMS) is widely used in protein structural analysis. In this study we develop a new class of non-hydrolyzable amine-selective di-ortho-phthalaldehyde (DOPA) cross-linkers, one of which is DOPA2. Cross-linking of proteins with DOPA2 is 60-120 times faster than that with the N-hydroxysuccinimide ester cross-linker DSS. Compared with DSS cross-links, DOPA2 cross-links have a higher degree of agreement with the crystal structures of tested proteins. More importantly, DOPA2 has unique advantages of working at low pH, low temperature, or in the presence of denaturants such as 8 M urea or 6 M guanidine hydrochloride. Using staphylococcal nuclease, bovine serum albumin, and bovine pancreatic ribonuclease A, we demonstrate that DOPA2 cross-linking provides abundant spatial information about the conformations of proteins denatured to varying degrees. Lastly, we show that CXMS with only 10 seconds of DOPA cross-linking uncovers conformational changes ass
Project description:Chemical cross-linking coupled to mass spectrometry was used to study binary and ternary complexes involving cyclin-dependent kinase 19 (CDK19), cyclin-C, and an N-terminal fragment of subunit 12 of the Mediator complex (MED12 1-100). Cross-linking was performed using disuccinimidyl suberate (DSS). These results were generated in the context of the study published as Klatt et al., A precisely positioned MED12 activation helix stimulates CDK8 kinase activity, Proc. Natl. Acad. Sci. USA 2020 (DOI: 10.1073/pnas.1917635117) with the associated data set PXD015394, but were not included in the article.
Project description:Chemical cross-linking coupled to mass spectrometry was used to study the folding of the client protein, beta-tubulin, by the chaperonin TRiC/CCT. Different complexes containing TRiC/CCT and/or the chaperone prefoldin were cross-linked in absence or presence of nucleotides with the homobifunctional, noncleavable reagent, disuccinimidyl suberate (DSS).
Project description:Chemical cross-linking coupled to mass spectrometry was used to study the architecture of the co-complex between TRiC/CCT, PFD and PhLP2A. The complex was cross-linked with the homobifunctional, noncleavable reagent, disuccinimidyl suberate (DSS).