PXD005210

PXD005210 is an original dataset announced via ProteomeXchange.

Title	Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins using Limited Proteolysis
Description	Conformational changes in proteins can lead to disease. Thus, methods for identifying conformational changes in proteins can further improve our understanding and facilitate detection of disease states. Here we combine limited proteolysis (LiP) with Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) to characterize breast cancer-related conformational changes in proteins on the proteomic scale. Studied here are the conformational properties of proteins in two cell culture models of breast cancer, including the MCF-10A and MCF-7 cell lines. The SILAC-LiP approach described here identified ~200 proteins with cell-line dependent conformational changes, as determined by their differential susceptibility to proteolytic digestion using the non-specific protease, proteinase K. The protease susceptibility profiles of the proteins in these cell lines were compared to thermodynamic stability and expression level profiles previously generated for proteins in these same breast cancer cell lines. The comparisons revealed that there was little overlap between the proteins with protease susceptibility changes and the proteins with thermodynamic stability and/or expression level changes. Thus, the large-scale conformational analysis described here provides unique insight into the molecular basis of the breast cancer phenotypes in this study.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_03:40:48.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fang Liu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue; 6x(13)C labeled residue; monohydroxylated residue; acetylated residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-10-24 02:11:10	ID requested
1	2016-12-23 08:07:47	announced
⏵ 2	2017-10-24 03:40:49	announced	Updated project metadata.

Liu F, Fitzgerald MC, Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins Using Limited Proteolysis. J Proteome Res, 15(12):4666-4674(2016) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Mass Spectrometry, SILAC, proteomics, MCF-7, MCF-10A, protein folding, limited proteolysis

Michael C. Fitzgerald
contact affiliation	Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
contact email	michael.c.fitzgerald@duke.edu
lab head
Fang Liu
contact affiliation	Duke university
contact email	fang.liu@duke.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005210
     1. Label: PRIDE project
     2. Name: Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins using Limited Proteolysis