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

• Published in: Analytical chemistry (Washington) Vol. 94; no. 7; pp. 3203 - 3210
• Main Authors: Polák, Marek, Yassaghi, Ghazaleh, Kavan, Daniel, Filandr, František, Fiala, Jan, Kukačka, Zdeněk, Halada, Petr, Loginov, Dmitry S., Novák, Petr
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 22-02-2022
• Subjects: Amino Acids; Analytical chemistry; Binding; Chemistry; Coordination compounds; Deoxyribonucleic acid; DNA; FOXO4 protein; Fragmentation; Mass spectrometry; Mass Spectrometry - methods; Mass spectroscopy; Oxidation; Oxidation-Reduction; Peptide mapping; Phase separation; Photochemicals; Proteins; Residues; Scientific imaging; Spectroscopy; Structural analysis; Transcription Factors
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/acs.analchem.1c04746

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·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.