Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails.
Identifieur interne : 002265 ( PubMed/Corpus ); précédent : 002264; suivant : 002266Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails.
Auteurs : Nikolay Korolev ; Alexander P. Lyubartsev ; Lars NordenskiöldSource :
- Biophysical journal [ 0006-3495 ] ; 2006.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, HMGN Proteins, Histones, Nucleosomes.
- Binding Sites, Computer Simulation, Models, Chemical, Models, Molecular, Nucleic Acid Conformation, Protein Binding, Static Electricity, Stress, Mechanical.
Abstract
We conducted molecular dynamics computer simulations of charged histone tail-DNA interactions in systems mimicking nucleosome core particles (NCP) . In a coarse-grained model, the NCP is modeled as a negatively charged spherical particle with flexible polycationic histone tails attached to it in a dielectric continuum with explicit mobile counterions and added salt. The size, charge, and distribution of the tails relative to the core were built to mimick real NCP. In this way, we incorporate attractive ion-ion correlation effects due to fluctuations in the ion cloud and the attractive entropic and energetic tail-bridging effects. In agreement with experimental data, increase of monovalent salt content from salt-free to physiological concentration leads to the formation of NCP aggregates; likewise, in the presence of MgCl2, the NCPs form condensed systems via histone-tail bridging and accumulation of counterions. More detailed mechanisms of the histone tail-DNA interactions and dynamics have been obtained from all-atom molecular dynamics simulations (including water), comprising three DNA 22-mers and 14 short fragments of the H4 histone tail (amino acids 5-12) carrying three positive charges on lysine+ interacting with DNA. We found correlation of the DNA-DNA distance with the presence and association of the histone tail between the DNA molecules.
DOI: 10.1529/biophysj.105.080226
PubMed: 16565063
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pubmed:16565063Le document en format XML
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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="2006">2006</date><idno type="RBID">pubmed:16565063</idno><idno type="pmid">16565063</idno><idno type="doi">10.1529/biophysj.105.080226</idno><idno type="wicri:Area/PubMed/Corpus">002265</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002265</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails.</title><author><name sortKey="Korolev, Nikolay" sort="Korolev, Nikolay" uniqKey="Korolev N" first="Nikolay" last="Korolev">Nikolay Korolev</name><affiliation><nlm:affiliation>School of Biological Sciences, Nanyang Technological University, Nanyang, Singapore.</nlm:affiliation></affiliation></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">Biophysical journal</title><idno type="ISSN">0006-3495</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Computer Simulation</term><term>DNA (chemistry)</term><term>HMGN Proteins (chemistry)</term><term>Histones (chemistry)</term><term>Models, Chemical</term><term>Models, Molecular</term><term>Nucleic Acid Conformation</term><term>Nucleosomes (chemistry)</term><term>Protein Binding</term><term>Static Electricity</term><term>Stress, Mechanical</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>HMGN Proteins</term><term>Histones</term><term>Nucleosomes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Computer Simulation</term><term>Models, Chemical</term><term>Models, Molecular</term><term>Nucleic Acid Conformation</term><term>Protein Binding</term><term>Static Electricity</term><term>Stress, Mechanical</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We conducted molecular dynamics computer simulations of charged histone tail-DNA interactions in systems mimicking nucleosome core particles (NCP) . In a coarse-grained model, the NCP is modeled as a negatively charged spherical particle with flexible polycationic histone tails attached to it in a dielectric continuum with explicit mobile counterions and added salt. The size, charge, and distribution of the tails relative to the core were built to mimick real NCP. In this way, we incorporate attractive ion-ion correlation effects due to fluctuations in the ion cloud and the attractive entropic and energetic tail-bridging effects. In agreement with experimental data, increase of monovalent salt content from salt-free to physiological concentration leads to the formation of NCP aggregates; likewise, in the presence of MgCl2, the NCPs form condensed systems via histone-tail bridging and accumulation of counterions. More detailed mechanisms of the histone tail-DNA interactions and dynamics have been obtained from all-atom molecular dynamics simulations (including water), comprising three DNA 22-mers and 14 short fragments of the H4 histone tail (amino acids 5-12) carrying three positive charges on lysine+ interacting with DNA. We found correlation of the DNA-DNA distance with the presence and association of the histone tail between the DNA molecules.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16565063</PMID><DateCompleted><Year>2006</Year><Month>07</Month><Day>27</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0006-3495</ISSN><JournalIssue CitedMedium="Print"><Volume>90</Volume><Issue>12</Issue><PubDate><Year>2006</Year><Month>Jun</Month><Day>15</Day></PubDate></JournalIssue><Title>Biophysical journal</Title><ISOAbbreviation>Biophys. J.</ISOAbbreviation></Journal><ArticleTitle>Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails.</ArticleTitle><Pagination><MedlinePgn>4305-16</MedlinePgn></Pagination><Abstract><AbstractText>We conducted molecular dynamics computer simulations of charged histone tail-DNA interactions in systems mimicking nucleosome core particles (NCP) . In a coarse-grained model, the NCP is modeled as a negatively charged spherical particle with flexible polycationic histone tails attached to it in a dielectric continuum with explicit mobile counterions and added salt. The size, charge, and distribution of the tails relative to the core were built to mimick real NCP. In this way, we incorporate attractive ion-ion correlation effects due to fluctuations in the ion cloud and the attractive entropic and energetic tail-bridging effects. In agreement with experimental data, increase of monovalent salt content from salt-free to physiological concentration leads to the formation of NCP aggregates; likewise, in the presence of MgCl2, the NCPs form condensed systems via histone-tail bridging and accumulation of counterions. More detailed mechanisms of the histone tail-DNA interactions and dynamics have been obtained from all-atom molecular dynamics simulations (including water), comprising three DNA 22-mers and 14 short fragments of the H4 histone tail (amino acids 5-12) carrying three positive charges on lysine+ interacting with DNA. We found correlation of the DNA-DNA distance with the presence and association of the histone tail between the DNA molecules.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Korolev</LastName><ForeName>Nikolay</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, Nanyang Technological University, Nanyang, Singapore.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lyubartsev</LastName><ForeName>Alexander P</ForeName><Initials>AP</Initials></Author><Author ValidYN="Y"><LastName>Nordenskiöld</LastName><ForeName>Lars</ForeName><Initials>L</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>03</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Biophys J</MedlineTA><NlmUniqueID>0370626</NlmUniqueID><ISSNLinking>0006-3495</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D024001">HMGN Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D006657">Histones</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009707">Nucleosomes</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>Biophys J. 2006 Jul 15;91(2):777</RefSource></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D024001" MajorTopicYN="N">HMGN Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006657" MajorTopicYN="N">Histones</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008956" MajorTopicYN="Y">Models, Chemical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="Y">Models, 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