Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations.
Identifieur interne : 001B41 ( Main/Exploration ); précédent : 001B40; suivant : 001B42Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations.
Auteurs : Nikolay Korolev [Singapour] ; Hang Yu ; Alexander P. Lyubartsev ; Lars NordenskiöldSource :
- Biopolymers [ 1097-0282 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Histone, Mutation.
- métabolisme : Histone.
- ADN, Acétylation, Cations, Histone, Peptides, Simulation de dynamique moléculaire.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Histones, Peptides.
- chemical , genetics : Histones.
- chemical , metabolism : Histones.
- chemical : Cations.
- genetics : Mutation.
- Acetylation, Molecular Dynamics Simulation.
Abstract
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.
DOI: 10.1002/bip.22499
PubMed: 24740714
Affiliations:
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Lyubartsev</name></author><author><name sortKey="Nordenskiold, Lars" sort="Nordenskiold, Lars" uniqKey="Nordenskiold L" first="Lars" last="Nordenskiöld">Lars Nordenskiöld</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24740714</idno><idno type="pmid">24740714</idno><idno type="doi">10.1002/bip.22499</idno><idno type="wicri:Area/PubMed/Corpus">001A06</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001A06</idno><idno type="wicri:Area/PubMed/Curation">001A06</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001A06</idno><idno type="wicri:Area/PubMed/Checkpoint">001797</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001797</idno><idno type="wicri:Area/Ncbi/Merge">000D38</idno><idno type="wicri:Area/Ncbi/Curation">000D38</idno><idno type="wicri:Area/Ncbi/Checkpoint">000D38</idno><idno type="wicri:Area/Main/Merge">001B50</idno><idno type="wicri:Area/Main/Curation">001B41</idno><idno type="wicri:Area/Main/Exploration">001B41</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations.</title><author><name sortKey="Korolev, Nikolay" sort="Korolev, Nikolay" uniqKey="Korolev N" first="Nikolay" last="Korolev">Nikolay Korolev</name><affiliation wicri:level="1"><nlm:affiliation>Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551</wicri:regionArea><wicri:noRegion>637551</wicri:noRegion></affiliation></author><author><name sortKey="Yu, Hang" sort="Yu, Hang" uniqKey="Yu H" first="Hang" last="Yu">Hang Yu</name></author><author><name sortKey="Lyubartsev, Alexander P" sort="Lyubartsev, Alexander P" uniqKey="Lyubartsev A" first="Alexander P" last="Lyubartsev">Alexander P. Lyubartsev</name></author><author><name sortKey="Nordenskiold, Lars" sort="Nordenskiold, Lars" uniqKey="Nordenskiold L" first="Lars" last="Nordenskiöld">Lars Nordenskiöld</name></author></analytic><series><title level="j">Biopolymers</title><idno type="eISSN">1097-0282</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Acetylation</term><term>Cations</term><term>DNA (chemistry)</term><term>Histones (chemistry)</term><term>Histones (genetics)</term><term>Histones (metabolism)</term><term>Molecular Dynamics Simulation</term><term>Mutation (genetics)</term><term>Peptides (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>Acétylation</term><term>Cations</term><term>Histone ()</term><term>Histone (génétique)</term><term>Histone (métabolisme)</term><term>Mutation (génétique)</term><term>Peptides ()</term><term>Simulation de dynamique moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>Histones</term><term>Peptides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Histones</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Histones</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Cations</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mutation</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Histone</term><term>Mutation</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Histone</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Acetylation</term><term>Molecular Dynamics Simulation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Acétylation</term><term>Cations</term><term>Histone</term><term>Peptides</term><term>Simulation de dynamique moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><affiliations><list><country><li>Singapour</li></country></list><tree><noCountry><name sortKey="Lyubartsev, Alexander P" sort="Lyubartsev, Alexander P" uniqKey="Lyubartsev A" first="Alexander P" last="Lyubartsev">Alexander P. Lyubartsev</name><name sortKey="Nordenskiold, Lars" sort="Nordenskiold, Lars" uniqKey="Nordenskiold L" first="Lars" last="Nordenskiöld">Lars Nordenskiöld</name><name sortKey="Yu, Hang" sort="Yu, Hang" uniqKey="Yu H" first="Hang" last="Yu">Hang Yu</name></noCountry><country name="Singapour"><noRegion><name sortKey="Korolev, Nikolay" sort="Korolev, Nikolay" uniqKey="Korolev N" first="Nikolay" last="Korolev">Nikolay Korolev</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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