PXD027624

PXD027624 is an original dataset announced via ProteomeXchange.

Title	Structural aspects of FOXO4 binding to DAF16 investigated with FPOP using both bottom-up and top-down MS.
Description	A combination of covalent labelling techniques and mass spectrometry (MS) is currently a progressive approach for the de-riving insights relating to the mapping of protein surfaces or protein-ligand interactions. In this study, we mapped an interac-tion interface between DNA binding domain (DBD) of FOXO4 protein and DNA binding element (DAF16) using the Fast Photochemical Oxidation of Protein (FPOP). Residues involved in protein – DNA interaction were identified using bottom-up approach. To avoid a misinterpretation of obtained data, caused by possible multiple radical oxidation leading to the alter-ing a protein surface and oxidation of deep-buried amino acid residues, a top-down approach was employed for the first time in FPOP analysis. An isolation of singly-oxidized ions allowed their gas-phase separation from multiply oxidized species followed by CID and ECD fragmentation. Application of both fragmentation techniques allowed to obtained complemen-tary fragment sets, out of which the regions shielded in the presence of DNA were deduced. The results obtained by bottom-up and top-down approaches were in a high consistency. Lastly, FPOP results were compared with HDX study of FOXO4-DBD•DAF16 complex. No contradictions were found between both methods. Moreover, their combination provide com-plementary information related to the structure and dynamics of the protein-DNA complex.
HostingRepository	PRIDE
AnnounceDate	2023-05-14
AnnouncementXML	Submission_2023-05-14_14:20:34.676.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	MarekPolak
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	solariX

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-28 04:38:35	ID requested
1	2022-02-14 02:30:05	announced
⏵ 2	2023-05-14 14:20:35	announced	2023-05-14: Updated project metadata.

Pol, á, k M, Yassaghi G, Kavan D, Filandr F, Fiala J, Kuka, č, ka Z, Halada P, Loginov DS, Nov, á, k P, Utilization of Fast Photochemical Oxidation of Proteins and Both Bottom-up and Top-down Mass Spectrometry for Structural Characterization of a Transcription Factor-dsDNA Complex. Anal Chem, 94(7):3203-3210(2022) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: bottom-up proteomics, DNA, transcription factors,Protein, FOXO4, Fast photochemical oxidation of proteins, top-dow proteomics

PetrNovak
contact affiliation	Biocev-Institute of Microbiology, The Czech Academy of Sciences, Prague, Czech Republic
contact email	pnovak@biomed.cas.cz
lab head
MarekPolak
contact affiliation	Biocev - Institute of Microbiology of the Czech Academy of Science, Vestec, Czech Republic
contact email	marek.polak@biomed.cas.cz
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD027624

PRIDE project URI

• PRIDE
  1. PXD027624
     1. Label: PRIDE project
     2. Name: Structural aspects of FOXO4 binding to DAF16 investigated with FPOP using both bottom-up and top-down MS.