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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A90127%2F22%3A00140007" target="_blank" >RIV/00216224:90127/22:00140007 - isvavai.cz</a>

Alternative codes found

RIV/61388971:_____/22:00556153 RIV/00216208:11310/22:10445307

Result on the web

<a href="https://pubs.acs.org/doi/10.1021/acs.analchem.1c04746" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.analchem.1c04746</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.analchem.1c04746" target="_blank" >10.1021/acs.analchem.1c04746</a>

Result language

angličtina

Original language name

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

Original language description

A combination of covalent labeling techniques and mass spectrometry (MS) is currently a progressive approach for deriving insights related to the mapping of protein surfaces or protein-ligand interactions. In this study, we mapped an interaction interface between the DNA binding domain (DBD) of FOXO4 protein and the DNA binding element (DAF16) using fast photochemical oxidation of proteins (FPOP). Residues involved in protein-DNA interaction were identified using the bottom-up approach. To confirm the findings and avoid a misinterpretation of the obtained data, caused by possible multiple radical oxidations leading to the protein surface alteration and oxidation of deeply buried amino acid residues, a top-down approach was employed for the first time in FPOP analysis. An isolation of singly oxidized ions enabled their gas-phase separation from multiply oxidized species followed by CID and ECD fragmentation. Application of both fragmentation techniques allowed generation of complementary fragment sets, out of which the regions shielded in the presence of DNA were deduced. The findings obtained by bottom-up and top-down approaches were highly consistent. Finally, FPOP results were compared with those of the HDX study of the FOXO4-DBD center dot DAF16 complex. No contradictions were found between the methods. Moreover, their combination provides complementary information related to the structure and dynamics of the protein-DNA complex. Data are available via ProteomeXchange with identifier PXD027624.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10406 - Analytical chemistry

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

—

Publication year

2022

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Analytical chemistry

ISSN

0003-2700

e-ISSN

—

Volume of the periodical

94

Issue of the periodical within the volume

7

Country of publishing house

US - UNITED STATES

Number of pages

8

Pages from-to

3203-3210

UT code for WoS article

000758042700001

EID of the result in the Scopus database

2-s2.0-85124911406