Electrostatic interactions in nucleosome and higher-order structures are regulated by protonation state of histone ionizable residue Article Swipe
Heng Zhang
,
Wenhan Guo
,
Wang Xu
,
Anbang Li
,
Lijun Jiang
,
Lin Li
,
Yunhui Peng
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.06.07.597724
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.06.07.597724
The nucleosome serves as the fundamental unit of chromatin organization, with electrostatic interactions acting as the driving forces in the folding of nucleosomes into chromatin. Perturbations in cellular pH conditions can lead to changes in the protonation states of titratable histone residues, impacting nucleosome surface electrostatic potentials and interactions. However, the effects of proton uptake or release of histone ionizable groups on nucleosome-partner protein interactions and higher-order chromatin structures remain largely unexplored. Here, we conducted comprehensive analyses of histone titratable residue pKa values in various nucleosome contexts, utilizing 96 experimentally determined structures. We revealed that pH-induced changes in histone residue protonation states modulated nucleosome surface electrostatic potentials and significantly influenced nucleosome-partner protein interactions. Furthermore, we observed that proton uptake or release often accompanied nucleosome-partner protein interactions, facilitating their binding processes. Additionally, using a dataset of 1266 recurrent histone cancer mutations, we systematically characterized their impact on nucleosome surface electrostatics, demonstrating their profound effects on electrostatic interactions between nucleosomes and partner proteins. Finally, our findings suggest that alterations in histone protonation or cancer mutations can also regulate nucleosome self-association, thereby modulating the organization and dynamics of higher-order chromatin structure.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.06.07.597724
- https://www.biorxiv.org/content/biorxiv/early/2024/06/09/2024.06.07.597724.full.pdf
- OA Status
- green
- Cited By
- 1
- References
- 60
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4399469300
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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- DOI
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https://doi.org/10.1101/2024.06.07.597724Digital Object Identifier
- Title
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Electrostatic interactions in nucleosome and higher-order structures are regulated by protonation state of histone ionizable residueWork title
- Type
-
preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-06-09Full publication date if available
- Authors
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Heng Zhang, Wenhan Guo, Wang Xu, Anbang Li, Lijun Jiang, Lin Li, Yunhui PengList of authors in order
- Landing page
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https://doi.org/10.1101/2024.06.07.597724Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2024/06/09/2024.06.07.597724.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2024/06/09/2024.06.07.597724.full.pdfDirect OA link when available
- Concepts
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Protonation, Residue (chemistry), Nucleosome, Histone, Chemistry, Biophysics, Biochemistry, Organic chemistry, DNA, Biology, IonTop concepts (fields/topics) attached by OpenAlex
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1Total citation count in OpenAlex
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2025: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.We | 93 |
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| abstract_inverted_index.of | 8, 22, 39, 53, 58, 78, 135, 185 |
| abstract_inverted_index.on | 62, 146, 154 |
| abstract_inverted_index.or | 56, 120, 171 |
| abstract_inverted_index.pH | 29 |
| abstract_inverted_index.to | 33 |
| abstract_inverted_index.we | 74, 115, 141 |
| abstract_inverted_index.The | 1 |
| abstract_inverted_index.and | 48, 66, 108, 159, 183 |
| abstract_inverted_index.can | 31, 174 |
| abstract_inverted_index.our | 163 |
| abstract_inverted_index.pKa | 82 |
| abstract_inverted_index.the | 5, 16, 20, 36, 51, 181 |
| abstract_inverted_index.1266 | 136 |
| abstract_inverted_index.also | 175 |
| abstract_inverted_index.into | 24 |
| abstract_inverted_index.lead | 32 |
| abstract_inverted_index.that | 95, 117, 166 |
| abstract_inverted_index.unit | 7 |
| abstract_inverted_index.with | 11 |
| abstract_inverted_index.Here, | 73 |
| abstract_inverted_index.often | 122 |
| abstract_inverted_index.their | 128, 144, 151 |
| abstract_inverted_index.using | 132 |
| abstract_inverted_index.acting | 14 |
| abstract_inverted_index.cancer | 139, 172 |
| abstract_inverted_index.forces | 18 |
| abstract_inverted_index.groups | 61 |
| abstract_inverted_index.impact | 145 |
| abstract_inverted_index.proton | 54, 118 |
| abstract_inverted_index.remain | 70 |
| abstract_inverted_index.serves | 3 |
| abstract_inverted_index.states | 38, 102 |
| abstract_inverted_index.uptake | 55, 119 |
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| abstract_inverted_index.binding | 129 |
| abstract_inverted_index.changes | 34, 97 |
| abstract_inverted_index.dataset | 134 |
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| abstract_inverted_index.folding | 21 |
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| abstract_inverted_index.largely | 71 |
| abstract_inverted_index.partner | 160 |
| abstract_inverted_index.protein | 64, 112, 125 |
| abstract_inverted_index.release | 57, 121 |
| abstract_inverted_index.residue | 81, 100 |
| abstract_inverted_index.suggest | 165 |
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| abstract_inverted_index.thereby | 179 |
| abstract_inverted_index.various | 85 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.Finally, | 162 |
| abstract_inverted_index.However, | 50 |
| abstract_inverted_index.analyses | 77 |
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| abstract_inverted_index.observed | 116 |
| abstract_inverted_index.profound | 152 |
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| abstract_inverted_index.revealed | 94 |
| abstract_inverted_index.chromatin | 9, 68, 187 |
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| abstract_inverted_index.contexts, | 87 |
| abstract_inverted_index.impacting | 43 |
| abstract_inverted_index.ionizable | 60 |
| abstract_inverted_index.modulated | 103 |
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| abstract_inverted_index.proteins. | 161 |
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| abstract_inverted_index.influenced | 110 |
| abstract_inverted_index.modulating | 180 |
| abstract_inverted_index.mutations, | 140 |
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| abstract_inverted_index.potentials | 47, 107 |
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| abstract_inverted_index.protonation | 37, 101, 170 |
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| abstract_inverted_index.unexplored. | 72 |
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| abstract_inverted_index.facilitating | 127 |
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| abstract_inverted_index.Additionally, | 131 |
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| abstract_inverted_index.demonstrating | 150 |
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| cited_by_percentile_year.max | 95 |
| cited_by_percentile_year.min | 91 |
| corresponding_author_ids | https://openalex.org/A5082796473 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 7 |
| corresponding_institution_ids | https://openalex.org/I40963666, https://openalex.org/I4210112540 |
| citation_normalized_percentile.value | 0.58875262 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |