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bioRxiv · 10.1101/2022.05.03.490500

Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation

Meshcheryakov, V. A.·Pan, W.·Li, T.·Wang, Y.·Ghosh, G.·Wang, V. Y.-F.
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Abstract

The mammalian NF-{kappa}B p52:p52 homodimer together with its cofactor Bcl3 activates transcription of {kappa}B sites with a central G/C base pair (bp), while it is inactive toward {kappa}B sites with a central A/T bp. To understand the molecular basis for this unique property of p52, we have determined its structure in complex with a P-selectin(PSel)-{kappa}B DNA (5-GGGGTGACCCC-3) (central bp is underlined) and variants changing the central bp to A/T or swapping the flanking bp. The structures reveal a nearly two-fold widened minor groove in the central region of the DNA as compared to all other currently available NF-{kappa}B-DNA complex structures, which have a central A/T bp. Molecular dynamics (MD) simulations show free DNAs exist in distinct preferred conformations, and p52:p52 homodimer induces the least amount of conformational changes on the more transcriptionally active natural PSel-{kappa}B DNA in the bound form. Our binding assays further demonstrate that the fast kinetics driven by entropy is correlated with higher transcriptional activity. Overall, our studies have revealed a novel conformation for {kappa}B DNA in complex with NF-{kappa}B and suggest the importance of binding kinetics, dictated by free DNA conformational and dynamic states, in controlling transcriptional activation for NF-{kappa}B.

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Meshcheryakov, V. A., Pan, W., Li, T., Wang, Y., Ghosh, G., Wang, V. Y.-F.. 2022-05-03. Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation. https://doi.org/10.1101/2022.05.03.490500

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