Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation
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 s...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2023-02-01
|
| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/86258 |
| _version_ | 1811158627841474560 |
|---|---|
| author | Wenfei Pan Vladimir A Meshcheryakov Tianjie Li Yi Wang Gourisankar Ghosh Vivien Ya-Fan Wang |
| author_facet | Wenfei Pan Vladimir A Meshcheryakov Tianjie Li Yi Wang Gourisankar Ghosh Vivien Ya-Fan Wang |
| author_sort | Wenfei Pan |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-10T05:27:19Z |
| format | Article |
| id | doaj.art-c5abdd016ec542a0b07b3d9999e58e5b |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-10T05:27:19Z |
| publishDate | 2023-02-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-c5abdd016ec542a0b07b3d9999e58e5b2023-03-07T15:55:39ZengeLife Sciences Publications LtdeLife2050-084X2023-02-011210.7554/eLife.86258Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activationWenfei Pan0Vladimir A Meshcheryakov1Tianjie Li2https://orcid.org/0000-0003-4734-1577Yi Wang3Gourisankar Ghosh4https://orcid.org/0000-0001-6311-7351Vivien Ya-Fan Wang5https://orcid.org/0000-0002-1984-2713Faculty of Health Sciences, University of Macau, Taipa, ChinaFaculty of Health Sciences, University of Macau, Taipa, ChinaDepartment of Physics, Chinese University of Hong Kong, Shatin, Hong KongDepartment of Physics, Chinese University of Hong Kong, Shatin, Hong KongDepartment of Chemistry and Biochemistry, University of California, San Diego, La Jolla, United StatesFaculty of Health Sciences, University of Macau, Taipa, China; MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macao; Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, ChinaThe 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.https://elifesciences.org/articles/86258DNA conformationNF-κBcrystal structureMD simulationtranscriptional regulationthermodynamics |
| spellingShingle | Wenfei Pan Vladimir A Meshcheryakov Tianjie Li Yi Wang Gourisankar Ghosh Vivien Ya-Fan Wang Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation eLife DNA conformation NF-κB crystal structure MD simulation transcriptional regulation thermodynamics |
| title | Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation |
| title_full | Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation |
| title_fullStr | Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation |
| title_full_unstemmed | Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation |
| title_short | Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation |
| title_sort | structures of nf κb p52 homodimer dna complexes rationalize binding mechanisms and transcription activation |
| topic | DNA conformation NF-κB crystal structure MD simulation transcriptional regulation thermodynamics |
| url | https://elifesciences.org/articles/86258 |
| work_keys_str_mv | AT wenfeipan structuresofnfkbp52homodimerdnacomplexesrationalizebindingmechanismsandtranscriptionactivation AT vladimirameshcheryakov structuresofnfkbp52homodimerdnacomplexesrationalizebindingmechanismsandtranscriptionactivation AT tianjieli structuresofnfkbp52homodimerdnacomplexesrationalizebindingmechanismsandtranscriptionactivation AT yiwang structuresofnfkbp52homodimerdnacomplexesrationalizebindingmechanismsandtranscriptionactivation AT gourisankarghosh structuresofnfkbp52homodimerdnacomplexesrationalizebindingmechanismsandtranscriptionactivation AT vivienyafanwang structuresofnfkbp52homodimerdnacomplexesrationalizebindingmechanismsandtranscriptionactivation |