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

  1. Wenfei Pan
  2. Vladimir A Meshcheryakov
  3. Tianjie Li
  4. Yi Wang
  5. Gourisankar Ghosh
  6. Vivien Ya-Fan Wang  Is a corresponding author
  1. University of Macau, China
  2. Chinese University of Hong Kong, Hong Kong
  3. University of California, San Diego, United States
  4. University of Macau, Macao

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

  1. Wenfei Pan

    Faculty of Health Sciences, University of Macau, Taipa, China
    Competing interests
    The authors declare that no competing interests exist.
  2. Vladimir A Meshcheryakov

    Faculty of Health Sciences, University of Macau, Taipa, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Tianjie Li

    Chinese University of Hong Kong, Shatin, Hong Kong
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4734-1577
  4. Yi Wang

    Chinese University of Hong Kong, Shatin, Hong Kong
    Competing interests
    The authors declare that no competing interests exist.
  5. 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.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6311-7351
  6. 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.
    ORCID icon "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.

Reviewing Editor

  1. Volker Dötsch, Goethe University, Germany

Version history

  1. Preprint posted: May 3, 2022 (view preprint)
  2. Received: January 18, 2023
  3. Accepted: February 7, 2023
  4. Accepted Manuscript published: February 13, 2023 (version 1)
  5. Version of Record published: March 7, 2023 (version 2)

Copyright

© 2023, Pan et al.

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.

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  1. Wenfei Pan
  2. Vladimir A Meshcheryakov
  3. Tianjie Li
  4. Yi Wang
  5. Gourisankar Ghosh
  6. Vivien Ya-Fan Wang
(2023)
Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation
eLife 12:e86258.
https://doi.org/10.7554/eLife.86258

Share this article

https://doi.org/10.7554/eLife.86258

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