PXD029353

PXD029353 is an original dataset announced via ProteomeXchange.

Title	Discovery of the Xenon-Protein Interactome using Large-Scale Measurements of Protein Folding and Stability
Description	The intermolecular interactions of noble gases in biological systems are associated with numerous biochemical responses, including apoptosis, inflammation, anesthesia, analgesia, and neuroprotection. The molecular modes of action underlying these responses are largely unknown. This is in large part due to the limited experimental techniques to study protein-gas interactions. The few techniques that are amenable to such studies are relatively low throughput and require large amounts of purified proteins. Thus, they do not enable the large-scale analyses that are useful for protein-target discovery. Here we report the application of Stability of Proteins from Rates of Oxidation (SPROX) and limited proteolysis (LiP) methodologies to detect protein-xenon interactions on the proteomic scale using protein folding stability measurements. Over 5,000 methionine-containing peptides and semi-tryptic peptides, mapping to ~1,500 and ~950 proteins in a yeast cell lysate, respectively, were assayed for Xe-interacting activity using the SPROX and LiP techniques. The SPROX and LiP analyses identified 31 and 60 Xe-interacting proteins, respectively, none of which were previously known to bind Xe. A bioinformatics analysis of the proteomic results revealed that these Xe-interacting proteins were enriched in those involved in ATP-driven processes. A fraction of the protein targets that were identified is tied to previously established modes of action related to xenon’s anesthetic and organoprotective properties. These results enrich our knowledge and understanding of biologically relevant xenon interactions, and the sample preparation protocols and analytical methodologies developed here for xenon should be applicable to the discovery of a wide range of protein-gas interactions in complex biological mixtures, including cell lysates.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:54:36.229.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nancy Corsi
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; methylthiolated residue; acetylated residue; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-26 01:24:17	ID requested
1	2023-07-20 10:38:22	announced
2	2023-11-14 09:02:28	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:54:38	announced	2024-10-22: Updated project metadata.

10.1021/jacs.1c11900;

Wiebelhaus N, Singh N, Zhang P, Craig SL, Beratan DN, Fitzgerald MC, Discovery of the Xenon-Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability. J Am Chem Soc, 144(9):3925-3938(2022) [pubmed]

submitter keyword: Noble Gases,Protein Stability, SPROX, Limited Proteolysis

Michael C. Fitzgerald
contact affiliation	Professor, Department of Chemistry, Duke University, Lab Head: Fitzgerald Lab
contact email	michael.c.fitzgerald@duke.edu
lab head
Nancy Corsi
contact affiliation	Duke University
contact email	njw23@duke.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD029353
     1. Label: PRIDE project
     2. Name: Discovery of the Xenon-Protein Interactome using Large-Scale Measurements of Protein Folding and Stability