Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations
The positively charged N-terminal histone tails play a crucial role in chromatin compaction and are important modulators of DNA transcription, recombination, and repair. The detailed mechanism of the interaction of histone tails with DNA remains elusive. To model the unspecific interaction of histon...
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| Format: | Journal Article |
| Language: | English |
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2015
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| Online Access: | https://hdl.handle.net/10356/106867 http://hdl.handle.net/10220/25198 http://dx.doi.org/10.1002/bip.22499 |
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| author | Korolev, Nikolay Yu, Hang Lyubartsev, Alexander P. Nordenskiöld, Lars |
| author2 | Case, David A. |
| author_facet | Case, David A. Korolev, Nikolay Yu, Hang Lyubartsev, Alexander P. Nordenskiöld, Lars |
| author_sort | Korolev, Nikolay |
| collection | NTU |
| description | The positively charged N-terminal histone tails play a crucial role in chromatin compaction and are important modulators of DNA transcription, recombination, and repair. The detailed mechanism of the interaction of histone tails with DNA remains elusive. To model the unspecific interaction of histone tails with DNA, all-atom molecular dynamics (MD) simulations were carried out for systems of four DNA 22-mers in the presence of 20 or 16 short fragments of the H4 histone tail (variations of the 16-23 a. a. KRHRKVLR sequence, as well as the unmodified fragment a. a.13-20, GGAKRHRK). This setup with high DNA concentration, explicit presence of DNA-DNA contacts, presence of unstructured cationic peptides (histone tails) and K(+) mimics the conditions of eukaryotic chromatin. A detailed account of the DNA interactions with the histone tail fragments, K(+) and water is presented. Furthermore, DNA structure and dynamics and its interplay with the histone tail fragments binding are analysed. The charged side chains of the lysines and arginines play major roles in the tail-mediated DNA-DNA attraction by forming bridges and by coordinating to the phosphate groups and to the electronegative sites in the minor groove. Binding of all species to DNA is dynamic. The structure of the unmodified fully-charged H4 16-23 a.a. fragment KRHRKVLR is dominated by a stretched conformation. The H4 tail a. a. fragment GGAKRHRK as well as the H4 Lys16 acetylated fragment are highly flexible. The present work allows capturing typical features of the histone tail-counterion-DNA structure, interaction and dynamics. |
| first_indexed | 2024-10-01T05:20:33Z |
| format | Journal Article |
| id | ntu-10356/106867 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:20:33Z |
| publishDate | 2015 |
| record_format | dspace |
| spelling | ntu-10356/1068672019-12-06T22:19:59Z Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations Korolev, Nikolay Yu, Hang Lyubartsev, Alexander P. Nordenskiöld, Lars Case, David A. School of Biological Sciences DRNTU::Science::Biological sciences The positively charged N-terminal histone tails play a crucial role in chromatin compaction and are important modulators of DNA transcription, recombination, and repair. The detailed mechanism of the interaction of histone tails with DNA remains elusive. To model the unspecific interaction of histone tails with DNA, all-atom molecular dynamics (MD) simulations were carried out for systems of four DNA 22-mers in the presence of 20 or 16 short fragments of the H4 histone tail (variations of the 16-23 a. a. KRHRKVLR sequence, as well as the unmodified fragment a. a.13-20, GGAKRHRK). This setup with high DNA concentration, explicit presence of DNA-DNA contacts, presence of unstructured cationic peptides (histone tails) and K(+) mimics the conditions of eukaryotic chromatin. A detailed account of the DNA interactions with the histone tail fragments, K(+) and water is presented. Furthermore, DNA structure and dynamics and its interplay with the histone tail fragments binding are analysed. The charged side chains of the lysines and arginines play major roles in the tail-mediated DNA-DNA attraction by forming bridges and by coordinating to the phosphate groups and to the electronegative sites in the minor groove. Binding of all species to DNA is dynamic. The structure of the unmodified fully-charged H4 16-23 a.a. fragment KRHRKVLR is dominated by a stretched conformation. The H4 tail a. a. fragment GGAKRHRK as well as the H4 Lys16 acetylated fragment are highly flexible. The present work allows capturing typical features of the histone tail-counterion-DNA structure, interaction and dynamics. 2015-03-09T04:39:06Z 2019-12-06T22:19:59Z 2015-03-09T04:39:06Z 2019-12-06T22:19:59Z 2014 2014 Journal Article Korolev, N., Yu, H., Lyubartsev, A. P., & Nordenskiöld, L. (2014). Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations. Biopolymers, 101(10), 1051-1064. 0006-3525 https://hdl.handle.net/10356/106867 http://hdl.handle.net/10220/25198 http://dx.doi.org/10.1002/bip.22499 en Biopolymers © 2014 Wiley Periodicals, Inc. |
| spellingShingle | DRNTU::Science::Biological sciences Korolev, Nikolay Yu, Hang Lyubartsev, Alexander P. Nordenskiöld, Lars Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations |
| title | Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations |
| title_full | Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations |
| title_fullStr | Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations |
| title_full_unstemmed | Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations |
| title_short | Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations |
| title_sort | molecular dynamics simulations demonstrate the regulation of dna dna attraction by h4 histone tail acetylations and mutations |
| topic | DRNTU::Science::Biological sciences |
| url | https://hdl.handle.net/10356/106867 http://hdl.handle.net/10220/25198 http://dx.doi.org/10.1002/bip.22499 |
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