Abstract
The dimeric nuclear factor kappa B (NF- κB) transcription factors (TFs) regulate gene expression by binding to a variety of κB DNA elements with conserved G:C-rich flanking sequences enclosing a degenerate central region. Toward defining mechanistic principles of affinity regulated by degeneracy, we observed an unusual dependence of the affinity of RelA on the identity of the central base pair, which appears to be noncontacted in the complex crystal structures. The affinity of κB sites with A or T at the central position is ~10- fold higher than with G or C. The crystal structures of neither the complexes nor the free κB DNAs could explain the differences in affinity. Interestingly, differential dynamics of several residues were revealed in molecular dynamics simulation studies, where simulation replicates totaling 148 μs were performed on NF-κB:DNA complexes and free κB DNAs. Notably, Arg187 and Arg124 exhibited selectivity in transient inter- actions that orchestrated a complex interplay among several DNA-interacting residues in the central region. Binding and simulation studies with mutants supported these observations of transient interactions dictating specificity. In combination with pub- lished reports, this work provides insights into the nuanced mechanisms governing the discriminatory binding of NF- κB family TFs to κB DNA elements and sheds light on cancer pathogenesis of cRel, a close homolog of RelA.
Document Type
Article
Publication Date
2024
Digital Object Identifier (DOI)
https://doi.org/10.1073/pnas.2405555121
Funding Information
This research is supported by NIH GM085490 to G.G. Y.W. acknowledges funding support from the Research Grants Council Areas of Excellence Scheme (AoE/P-705/16) and computing resources of the X-GPU cluster supported by the Hong Kong Research Grants Council Collaborative Research Fund C6021-19EF. V.Y.-F.W. was supported by the Science and Technology Development Fund, Macao S.A.R. (FDCT) [project 0104/2019/A2 and 0089/2022/AFJ] and the Multi-Year Research Grant from University of Macau [MYRG2018-00093-FHS].
Repository Citation
Li, Tianjie; Shahabi, Shandy; Biswas, Tapan; Tsodikov, Oleg V.; Pan, Wenfei; Huang, De-Bin; Wang, Vivien Ya-Fan; Wang, Yi; and Ghosh, Gourisankar, "Transient interactions modulate the affinity of NF-κB transcription factors for DNA" (2024). Biology Faculty Publications. 228.
https://uknowledge.uky.edu/biology_facpub/228
Notes/Citation Information
Copyright © 2024 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution- NonCommercial-NoDerivatives License 4.0 (CC BY- NC- ND).