NMR investigation of FOXO4-DNA interaction for discriminating target and non-target DNA sequences

• Published in: Communications biology 2024-11, Vol.7 (1), p.1425-10, Article 1425
• Main Authors: Kang, Donghoon, Yang, Min June, Cheong, Hae-Kap, Park, Chin-Ju
• Format: Article
• Language: English
• Subjects: 631/45/535/878/1263; 631/45/612/1229; 82/6; 82/80; 82/83; Base Sequence; Binding Sites; Biology; Biomedical and Life Sciences; Cell cycle; Cell Cycle Proteins - chemistry; Cell Cycle Proteins - genetics; Cell Cycle Proteins - metabolism; Diabetes; DNA - chemistry; DNA - metabolism; DNA methylation; Electrostatic properties; Foreign exchange rates; Forkhead protein; Forkhead Transcription Factors - chemistry; Forkhead Transcription Factors - genetics; Forkhead Transcription Factors - metabolism; FOXO4 protein; Humans; Life Sciences; Magnetic Resonance Spectroscopy - methods; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Nucleotide sequence; Protein Binding; Transcription factors
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-024-07133-1

Forkhead box O4 (FOXO4), a human transcription factor, recognizes target DNA through its forkhead domain (FHD) while maintaining comparable binding affinity to non-target DNA. The conserved region 3 (CR3), a transactivation domain, modulates DNA binding kinetics to FHD and contributes to target DNA selection, but the underlying mechanism of this selection remains elusive. Using paramagnetic relaxation enhancement analysis, we observed a minor state of CR3 close to FHD in the presence of non-target DNA, a state absent when FHD interacts with target DNA. This minor state suggests that CR3 effectively masks the non-target DNA-binding interface on FHD. The interaction weakens significantly under high salt concentration, implying that CR3 or high salt concentrations can modulate electrostatic interactions with non-target DNA. Our 15 N relaxation measurements revealed FHD’s flexibility with non-target DNA and increased rigidity with target DNA binding. Our findings offer insights into the role of FOXO4 as a transcription initiator. FOXO4 CR3 masks the non-target DNA binding interface of FHD. FHD increases flexibility with non-target DNA and rigidity with target DNA, releasing CR3. Salt modulates the rate of FHD-DNA binding, discriminating between target and non-target DNA.