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

Abstract
Data availability
Article and author information
Metrics

Abstract

The mammalian NF-κB p52:p52 homodimer together with its cofactor Bcl3 activates transcription of κB sites with a central G/C base pair (bp), while it is inactive toward κB sites with a central A/T bp. To understand the molecular basis for this unique property of p52, we have determined the crystal structures of recombinant human p52 protein in complex with a P-selectin(PSel)-κB 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-κB-DNA complex structures, which have a central A/T bp. Microsecond molecular dynamics (MD) simulations of free DNAs and p52 bound complexes reveal that free DNAs exhibit distinct preferred conformations, and p52:p52 homodimer induces the least amount of DNA conformational changes when bound to the more transcriptionally active natural G/C-centric PSel-κB, but adopts closed conformation when bound to the mutant A/T and swap DNAs due to their narrowed minor grooves. Our binding assays further demonstrate that the fast kinetics favored by entropy is correlated with higher transcriptional activity. Overall, our studies have revealed a novel conformation for κB DNA in complex with NF-κB and pinpoint the importance of binding kinetics, dictated by DNA conformational and dynamic states, in controlling transcriptional activation for NF-κB.

Data availability

The atomic coordinates have been deposited in the Protein Data Bank, www.wwpdb.org (PDB ID codes 7CLI, 7VUQ, 7VUP and 7W7L).

Article and author information

Author details

Wenfei Pan

Faculty of Health Sciences, University of Macau, Taipa, China

Competing interests
The authors declare that no competing interests exist.
Vladimir A Meshcheryakov

Faculty of Health Sciences, University of Macau, Taipa, China

Competing interests
The authors declare that no competing interests exist.
Tianjie Li

Chinese University of Hong Kong, Shatin, Hong Kong

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4734-1577
Yi Wang

Chinese University of Hong Kong, Shatin, Hong Kong

Competing interests
The authors declare that no competing interests exist.
Gourisankar Ghosh

Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-6311-7351
Vivien Ya-Fan Wang

Faculty of Health Sciences, University of Macau, Taipa, Macao

For correspondence
vivienwang@um.edu.mo

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1984-2713

Funding

Science and Technology Development Fund, Macao SAR (0104/2019/A2)

Vivien Ya-Fan Wang

Science and Technology Development Fund, Macao SAR (0089/2022/AFJ)

Vivien Ya-Fan Wang

Multi Year Research Grant, University of Macau (MYRG2018-00093-FHS)

Vivien Ya-Fan Wang

Hong Kong Research Grant Council Collaborative Research Fund (C6021-19EF)

Yi Wang

Chinese University of Hong Kong

Tianjie Li
Yi Wang

National Institutes of Health (GM085490)

Gourisankar Ghosh

National Institutes of Health (CA142642)

Gourisankar Ghosh

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.