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.Základní údaje
Originální název
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
Autoři
POLAK, Marek, Ghazaleh YASSAGHI, Daniel KAVAN, Frantisek FILANDR, Jan FIALA, Zdenek KUKACKA, Petr HALADA, Dmitry S LOGINOV a Petr NOVAK
Vydání
Analytical chemistry, WASHINGTON, AMER CHEMICAL SOC, 2022, 0003-2700
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10406 Analytical chemistry
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Odkazy
Impakt faktor
Impact factor: 7.400
Kód RIV
RIV/00216224:14740/22:00128777
Organizační jednotka
Středoevropský technologický institut
UT WoS
000758042700001
Klíčová slova anglicky
DNA; Mass spectrometry; Oxidation; Phase separation; Transcription
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 3. 4. 2023 17:37, Mgr. Pavla Foltynová, Ph.D.
Anotace
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.
Návaznosti
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