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Proteins associated with Cdc48A identified by LC-MS\MS data

ABSTRACT: His6-Cdc48a and associated proteins purified from H. volcanii. A) SDS- PAGE of proteins purified by Ni2+ -chromatography. H. volcanii carrying empty vector control (H1209-pJAM202c, lane 1) and ectopically expressing His6-Cdc48a (H1209- pJAM1409, lane 2). Red bars indicate regions of gel excised. B) Proteins identified in gel slices by LC-MS/MS analysis. Criteria for protein inclusion: FDR < 0.01%, normalized total spectra minus control > 50, protein threshold > 99% and 2 peptide minimum. Based on spectral counting, Cdc48a and DUF111 were most abundant in regions (a) and (b), respectively, as indicated. DHS1, deoxyhypusine synthase. DUF111, Cdc48a gene neighbor of unknown function. TnaA, tryptophanase; Rps3, ribosomal protein S3; n.d., not detected.

INSTRUMENT(S): LTQ Orbitrap XL

ORGANISM(S): Haloferax Volcanii Ds2

SUBMITTER: Swathi Dantuluri

LAB HEAD: Julie Maupin-Furlow

PROVIDER: PXD019906 | Pride | 2023-06-22

REPOSITORIES: Pride

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Project description:Cellular functional pathways have evolved through selection based on fitness benefits conferred through protein intra- and inter-molecular interactions that comprise all protein conformational features and protein-protein interactions, collectively referred to as the interactome. While the interactome is regulated by proteome levels, it is also regulated independently by, post translational modification, co-factor, and ligand levels, as well as local protein environmental factors, such as osmolyte concentration, pH, ionic strength, temperature and others. In modern biomedical research, cultivatable cell lines have become an indispensable tool, with selection of optimal cell lines that exhibit specific functional profiles being critical for success in many cases. While it is clear that cell lines derived from different cell types have differential proteome levels, increased understanding of large-scale functional differences requires additional information beyond abundance level measurements, including how protein conformations and interactions are altered in certain cell types to shape functional landscapes. Here, we employed quantitative in vivo protein cross-linking coupled to mass spectrometry to probe large-scale protein conformational and interaction changes among three commonly employed human cell lines, HEK293, MCF-7, and HeLa cells. Isobaric quantitative Protein Interaction Reporter (iqPIR) technologies were used to obtain quantitative values of cross-linked peptides across three cell lines. These data illustrated highly reproducible (R2 values larger than 0.8 for all biological replicates) quantitative interactome levels across multiple biological replicates. We also measured protein abundance levels in these cells using data independent acquisition quantitative proteomics methods. Combining quantitative interactome and proteomics information allowed visualization of cell type-specific interactome changes mediated by proteome level adaptations as well as independently regulated interactome changes to gain deeper insight into possible drivers of these changes. Among the biggest detected alterations in protein interactions and conformations are changes in cytoskeletal proteins, RNA-binding proteins, chromatin remodeling complexes, mitochondrial proteins, and others. Overall, these data demonstrate the utility and reproducibility of quantitative cross-linking to study systems-level interactome variations. Moreover, these results illustrate how combined quantitative interactomics and proteomics can provide unique insight on cellular functional landscapes.

			Action	DRS
	Control.raw	Raw
	Control__F021944_.mzid.gz	Mzid
	Control__F021944_.mzid_Control__F021944_.MGF	Mzid
	Sample-1.raw	Raw
	Sample-1__F021945_.mzid.gz	Mzid

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Proteins associated with Cdc48A identified by LC-MS\MS data

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