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

J 2022

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

POLAK, Marek, Ghazaleh YASSAGHI, Daniel KAVAN, Frantisek FILANDR, Jan FIALA et. al.

Basic information

Original 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

Authors

POLAK, Marek, Ghazaleh YASSAGHI, Daniel KAVAN, Frantisek FILANDR, Jan FIALA, Zdenek KUKACKA, Petr HALADA, Dmitry S LOGINOV and Petr NOVAK

Edition

Analytical chemistry, WASHINGTON, AMER CHEMICAL SOC, 2022, 0003-2700

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10406 Analytical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 7.400

RIV identification code

RIV/00216224:14740/22:00128777

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/acs.analchem.1c04746

UT WoS

000758042700001

Keywords in English

DNA; Mass spectrometry; Oxidation; Phase separation; Transcription

Abstract

V originále

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.

Links

90127, large research infrastructures

Name: CIISB II

Citovat

POLAK, Marek, Ghazaleh YASSAGHI, Daniel KAVAN, Frantisek FILANDR, Jan FIALA, Zdenek KUKACKA, Petr HALADA, Dmitry S LOGINOV and Petr NOVAK. 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. Analytical chemistry. WASHINGTON: AMER CHEMICAL SOC, 2022, vol. 94, No 7, p. 3203-3210. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.1c04746.

@article{2262564,
   author = {Polak, Marek and Yassaghi, Ghazaleh and Kavan, Daniel and Filandr, Frantisek and Fiala, Jan and Kukacka, Zdenek and Halada, Petr and Loginov, Dmitry S and Novak, Petr},
   article_location = {WASHINGTON},
   article_number = {7},
   doi = {http://dx.doi.org/10.1021/acs.analchem.1c04746},
   keywords = {DNA; Mass spectrometry; Oxidation; Phase separation; Transcription},
   language = {eng},
   issn = {0003-2700},
   journal = {Analytical chemistry},
   title = {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},
   url = {https://pubs.acs.org/doi/10.1021/acs.analchem.1c04746},
   volume = {94},
   year = {2022}
}

TY  - JOUR
ID  - 2262564
AU  - Polak, Marek - Yassaghi, Ghazaleh - Kavan, Daniel - Filandr, Frantisek - Fiala, Jan - Kukacka, Zdenek - Halada, Petr - Loginov, Dmitry S - Novak, Petr
PY  - 2022
TI  - 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
JF  - Analytical chemistry
VL  - 94
IS  - 7
SP  - 3203-3210
EP  - 3203-3210
PB  - AMER CHEMICAL SOC
SN  - 00032700
KW  - DNA
KW  - Mass spectrometry
KW  - Oxidation
KW  - Phase separation
KW  - Transcription
UR  - https://pubs.acs.org/doi/10.1021/acs.analchem.1c04746
N2  - 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.
ER  -

POLAK, Marek, Ghazaleh YASSAGHI, Daniel KAVAN, Frantisek FILANDR, Jan FIALA, Zdenek KUKACKA, Petr HALADA, Dmitry S LOGINOV and Petr NOVAK. 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. \textit{Analytical chemistry}. WASHINGTON: AMER CHEMICAL SOC, 2022, vol.~94, No~7, p.~3203-3210. ISSN~0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.1c04746.

Detailed Information on Publication Record