PXD030245

PXD030245 is an original dataset announced via ProteomeXchange.

Title	Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues
Description	The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications and it is therefore important to delineate factors that influence methionine oxidation rates within a protein. Previously, neighboring residue effects and solvent accessibility (SA) had been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of the domains where they reside. We surveyed the E. coli proteome using several proteomic methodologies and globally measured oxidation rates of methionines in the presence and absence of tertiary structure as well as folding stabilities of methionione containing domains. The data indicate that buried methionines have a wide range of protection factors (PFs) against oxidation that correlate strongly with folding stabilities. Concordantly, we show that in comparison to E. coli, the proteome of the thermophile T. thermophilus is significantly more stable and thus more resistant to methionine oxidation. These results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and suggest a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures.
HostingRepository	PRIDE
AnnounceDate	2022-04-22
AnnouncementXML	Submission_2022-04-22_10:00:03.515.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ethan Walker
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Thermus thermophilus HB8; NCBI TaxID: 300852;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-08 07:45:59	ID requested
⏵ 1	2022-04-22 10:00:04	announced

Walker EJ, Bettinger JQ, Welle KA, Hryhorenko JR, Molina Vargas AM, O'Connell MR, Ghaemmaghami S, Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues. J Biol Chem, 298(5):101872(2022) [pubmed]

submitter keyword: methionine, protein stability, oxidation-reduction, quantitative proteomics, Lumos

Sina Ghaemmaghami
contact affiliation	Associate professor, department of Biology. University of Rochester,NY, USA University of Rochester Mass Spectrometry Resource Laboratory, NY, USA ( lab head )
contact email	sina.ghaemmaghami@rochester.edu
lab head
Ethan Walker
contact affiliation	University of Rochester
contact email	Ethan_walker@urmc.rochester.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD030245
     1. Label: PRIDE project
     2. Name: Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues