PXD000858

PXD000858 is an original dataset announced via ProteomeXchange.

Title	SILAC-Based Strategy for Proteome-Wide Analysis of Protein-Ligand Binding Interactions (Part 1/2)
Description	A quantitative mass spectrometry-based proteomics method for the large-scale thermodynamic analysis of protein-ligand binding interactions is described here. The methodology utilizes a chemical modification strategy termed, Stability of Proteins from Rates of Oxidation (SPROX), in combination with a Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) approach to compare the equilibrium folding/unfolding properties of proteins in the absence and presence of target ligands. The method, which is general with respect to ligand, measures the ligand-induced changes in protein stability associated with protein-ligand binding. The methodology is demonstrated in a proof-of-principle study in which the well-characterized protein-drug interaction between cyclosporine A and cyclophilin A is analyzed in the context of a yeast cell lysate. The method is also utilized for the global analysis of adenosine triphosphate (ATP) binding to proteins in the yeast proteome using the non-hydrolyzable ATP analogue, adenylyl imidodiphosphate (AMP-PNP), and the proteins in a yeast cell lysate.
HostingRepository	PRIDE
AnnounceDate	2014-10-23
AnnouncementXML	Submission_2014-10-23_03:08:17.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000858
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jagat Adhikari
SpeciesList	scientific name: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); NCBI TaxID: 559292;
ModificationList	iodoacetamide - site C: 57.021464; monohydroxylated residue: 15.994915; deamidated L-asparagine: 0.984016; L-cysteine methyl disulfide: 45.987721; 6x(13)C: 2x(15)N labeled L-lysine
Instrument	6520 Quadrupole Time-of-Flight LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2014-03-26 02:49:42	ID requested
1	2014-07-31 08:37:02	announced
⏵ 2	2014-10-23 03:08:18	announced	Updated project metadata.

Tran DT, Adhikari J, Fitzgerald MC, StableIsotope Labeling with Amino Acids in Cell Culture (SILAC)-based strategy for proteome-wide thermodynamic analysis of protein-ligand binding interactions. Mol Cell Proteomics, 13(7):1800-13(2014) [pubmed]

curator keyword: Biological

submitter keyword: ATP, Cyclosporine A, Shot-gun proteomics,Yeast

Michael C. Fitzgerald
contact affiliation	Chemistry Department, Duke University, Durham, NC, 27705, USA
contact email	michael.c.fitzgerald@duke.edu
lab head
Jagat Adhikari
contact affiliation	Duke University
contact email	ja117@duke.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000858
     1. Label: PRIDE project
     2. Name: SILAC-Based Strategy for Proteome-Wide Analysis of Protein-Ligand Binding Interactions (Part 1/2)