Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122
Post translational modifications have a profound role in the regulation of several biological processes such as transcription, replication, and DNA repair. Acetylation and phosphorylation form a major class of post translational modifications involved in nucleosomal regulation by modifying its struc...
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| Veröffentlicht in: | European biophysics journal 2017-07, Vol.46 (5), p.471-484 |
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| creator | Rajagopalan, Muthukumaran Balasubramanian, Sangeetha Ioshikhes, Ilya Ramaswamy, Amutha |
| description | Post translational modifications have a profound role in the regulation of several biological processes such as transcription, replication, and DNA repair. Acetylation and phosphorylation form a major class of post translational modifications involved in nucleosomal regulation by modifying its structure. The effect of post translational modifications on nucleosome structure could be better explored when the molecular trajectories explaining the time dependent structural evolution over a period of time is examined at the atomic level. The present study attempts to highlight the importance of acetylation, especially at entry–exit (Lys56) and dyad (Lys115 and Lys122) regions in regulating the nucleosome accessibility and mobility using all atom simulations. It is evident from this study that acetylation at Lys56, Lys115, and Lys122 introduces local changes in the electrostatic nature of the lateral surface and thereby weakens the histone–DNA interactions. In addition, simulations also reveal significant changes in the dynamics of superhelical DNA. The acetylation at Lys56 promotes a high amplitude out-of-planar movement of entry–exit termini. Whereas, acetylation at Lys115 and Lys122 increases the flexibility of the superhelical DNA to facilitate the rolling of the superhelical DNA around the octameric histone. In essence, the present study highlights the role of acetylation at Lys56, Lys115, and Lys122 in transcriptional regulation by promoting high amplitude dynamics of superhelical DNA for a possible unwrapping as well as mobility of nucleosome. |
| doi_str_mv | 10.1007/s00249-016-1191-5 |
| format | Article |
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Acetylation and phosphorylation form a major class of post translational modifications involved in nucleosomal regulation by modifying its structure. The effect of post translational modifications on nucleosome structure could be better explored when the molecular trajectories explaining the time dependent structural evolution over a period of time is examined at the atomic level. The present study attempts to highlight the importance of acetylation, especially at entry–exit (Lys56) and dyad (Lys115 and Lys122) regions in regulating the nucleosome accessibility and mobility using all atom simulations. It is evident from this study that acetylation at Lys56, Lys115, and Lys122 introduces local changes in the electrostatic nature of the lateral surface and thereby weakens the histone–DNA interactions. In addition, simulations also reveal significant changes in the dynamics of superhelical DNA. The acetylation at Lys56 promotes a high amplitude out-of-planar movement of entry–exit termini. Whereas, acetylation at Lys115 and Lys122 increases the flexibility of the superhelical DNA to facilitate the rolling of the superhelical DNA around the octameric histone. In essence, the present study highlights the role of acetylation at Lys56, Lys115, and Lys122 in transcriptional regulation by promoting high amplitude dynamics of superhelical DNA for a possible unwrapping as well as mobility of nucleosome.</description><identifier>ISSN: 0175-7571</identifier><identifier>EISSN: 1432-1017</identifier><identifier>DOI: 10.1007/s00249-016-1191-5</identifier><identifier>PMID: 27933430</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Accessibility ; Acetylation ; Atomic structure ; Biochemistry ; Biological activity ; Biological and Medical Physics ; Biology ; Biomedical and Life Sciences ; Biophysics ; Cell Biology ; Chromatin ; Control ; Deoxyribonucleic acid ; DNA ; DNA biosynthesis ; DNA repair ; Dynamics ; Evolution ; Flexibility ; Gene regulation ; Histones - chemistry ; Histones - metabolism ; Life Sciences ; Lysine - metabolism ; Membrane Biology ; Mobility ; Molecular Dynamics Simulation ; Molecular structure ; Molecular trajectories ; Nanotechnology ; Neurobiology ; Nucleosomes - metabolism ; Original Article ; Phosphorylation ; Protein Multimerization ; Protein Stability ; Protein Structure, Quaternary ; Repair ; Replication ; Simulation ; Superhelical DNA ; Thermodynamics ; Time dependence ; Trajectories ; Transcription ; Translation</subject><ispartof>European biophysics journal, 2017-07, Vol.46 (5), p.471-484</ispartof><rights>European Biophysical Societies' Association 2016</rights><rights>European Biophysics Journal is a copyright of Springer, 2017.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c372t-d8b6694ee805ad056774b5b03a87f0ce1814f6ee2fa22a790fbe0b67d810c2213</citedby><cites>FETCH-LOGICAL-c372t-d8b6694ee805ad056774b5b03a87f0ce1814f6ee2fa22a790fbe0b67d810c2213</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00249-016-1191-5$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00249-016-1191-5$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27933430$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Rajagopalan, Muthukumaran</creatorcontrib><creatorcontrib>Balasubramanian, Sangeetha</creatorcontrib><creatorcontrib>Ioshikhes, Ilya</creatorcontrib><creatorcontrib>Ramaswamy, Amutha</creatorcontrib><title>Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122</title><title>European biophysics journal</title><addtitle>Eur Biophys J</addtitle><addtitle>Eur Biophys J</addtitle><description>Post translational modifications have a profound role in the regulation of several biological processes such as transcription, replication, and DNA repair. Acetylation and phosphorylation form a major class of post translational modifications involved in nucleosomal regulation by modifying its structure. The effect of post translational modifications on nucleosome structure could be better explored when the molecular trajectories explaining the time dependent structural evolution over a period of time is examined at the atomic level. The present study attempts to highlight the importance of acetylation, especially at entry–exit (Lys56) and dyad (Lys115 and Lys122) regions in regulating the nucleosome accessibility and mobility using all atom simulations. It is evident from this study that acetylation at Lys56, Lys115, and Lys122 introduces local changes in the electrostatic nature of the lateral surface and thereby weakens the histone–DNA interactions. In addition, simulations also reveal significant changes in the dynamics of superhelical DNA. The acetylation at Lys56 promotes a high amplitude out-of-planar movement of entry–exit termini. Whereas, acetylation at Lys115 and Lys122 increases the flexibility of the superhelical DNA to facilitate the rolling of the superhelical DNA around the octameric histone. In essence, the present study highlights the role of acetylation at Lys56, Lys115, and Lys122 in transcriptional regulation by promoting high amplitude dynamics of superhelical DNA for a possible unwrapping as well as mobility of nucleosome.</description><subject>Accessibility</subject><subject>Acetylation</subject><subject>Atomic structure</subject><subject>Biochemistry</subject><subject>Biological activity</subject><subject>Biological and Medical Physics</subject><subject>Biology</subject><subject>Biomedical and Life Sciences</subject><subject>Biophysics</subject><subject>Cell Biology</subject><subject>Chromatin</subject><subject>Control</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA biosynthesis</subject><subject>DNA repair</subject><subject>Dynamics</subject><subject>Evolution</subject><subject>Flexibility</subject><subject>Gene regulation</subject><subject>Histones - chemistry</subject><subject>Histones - metabolism</subject><subject>Life Sciences</subject><subject>Lysine - metabolism</subject><subject>Membrane Biology</subject><subject>Mobility</subject><subject>Molecular Dynamics Simulation</subject><subject>Molecular structure</subject><subject>Molecular trajectories</subject><subject>Nanotechnology</subject><subject>Neurobiology</subject><subject>Nucleosomes - metabolism</subject><subject>Original Article</subject><subject>Phosphorylation</subject><subject>Protein Multimerization</subject><subject>Protein Stability</subject><subject>Protein Structure, Quaternary</subject><subject>Repair</subject><subject>Replication</subject><subject>Simulation</subject><subject>Superhelical DNA</subject><subject>Thermodynamics</subject><subject>Time dependence</subject><subject>Trajectories</subject><subject>Transcription</subject><subject>Translation</subject><issn>0175-7571</issn><issn>1432-1017</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNp1kE1r3DAQhkVJ6W62-QG5BEEuOdTNjGRZ8jGEpFu6UEias5DlcfHij0SyD_vvo2U3JQR6kQR63neGh7FzhO8IoK8jgMjLDLDIEEvM1Ce2xFyKDAH1CVumU2VaaVyw0xi3ALlCNF_YQuhSylzCkj08TmH20xxcx-vd4PrWRz42fJh9R2Mce-I91a2bqObVjjtP065zUzsOkbuJr-UvVXA31PsXovqGQnxlnxvXRTo73iv2dH_353adbX7_-Hl7s8m81GLKalMVRZkTGVCuBlVonVeqAumMbsATGsybgkg0TginS2gqgqrQtUHwQqBcsatD73MYX2aKk-3b6Knr3EDjHC2aXJtSojYJvfyAbsc5DGk7iyVojYVROlF4oHwYYwzU2OfQ9i7sLILdC7cH4TYJt3vhVqXMxbF5rpKof4k3wwkQByCmr-EvhXej_9v6Ctk7h-k</recordid><startdate>20170701</startdate><enddate>20170701</enddate><creator>Rajagopalan, Muthukumaran</creator><creator>Balasubramanian, Sangeetha</creator><creator>Ioshikhes, Ilya</creator><creator>Ramaswamy, Amutha</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope></search><sort><creationdate>20170701</creationdate><title>Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122</title><author>Rajagopalan, Muthukumaran ; Balasubramanian, Sangeetha ; Ioshikhes, Ilya ; Ramaswamy, Amutha</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c372t-d8b6694ee805ad056774b5b03a87f0ce1814f6ee2fa22a790fbe0b67d810c2213</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Accessibility</topic><topic>Acetylation</topic><topic>Atomic structure</topic><topic>Biochemistry</topic><topic>Biological activity</topic><topic>Biological and Medical Physics</topic><topic>Biology</topic><topic>Biomedical and Life Sciences</topic><topic>Biophysics</topic><topic>Cell Biology</topic><topic>Chromatin</topic><topic>Control</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA biosynthesis</topic><topic>DNA repair</topic><topic>Dynamics</topic><topic>Evolution</topic><topic>Flexibility</topic><topic>Gene regulation</topic><topic>Histones - chemistry</topic><topic>Histones - metabolism</topic><topic>Life Sciences</topic><topic>Lysine - metabolism</topic><topic>Membrane Biology</topic><topic>Mobility</topic><topic>Molecular Dynamics Simulation</topic><topic>Molecular structure</topic><topic>Molecular trajectories</topic><topic>Nanotechnology</topic><topic>Neurobiology</topic><topic>Nucleosomes - metabolism</topic><topic>Original Article</topic><topic>Phosphorylation</topic><topic>Protein Multimerization</topic><topic>Protein Stability</topic><topic>Protein Structure, Quaternary</topic><topic>Repair</topic><topic>Replication</topic><topic>Simulation</topic><topic>Superhelical DNA</topic><topic>Thermodynamics</topic><topic>Time dependence</topic><topic>Trajectories</topic><topic>Transcription</topic><topic>Translation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Rajagopalan, Muthukumaran</creatorcontrib><creatorcontrib>Balasubramanian, Sangeetha</creatorcontrib><creatorcontrib>Ioshikhes, Ilya</creatorcontrib><creatorcontrib>Ramaswamy, Amutha</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><jtitle>European biophysics journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Rajagopalan, Muthukumaran</au><au>Balasubramanian, Sangeetha</au><au>Ioshikhes, Ilya</au><au>Ramaswamy, Amutha</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122</atitle><jtitle>European biophysics journal</jtitle><stitle>Eur Biophys J</stitle><addtitle>Eur Biophys J</addtitle><date>2017-07-01</date><risdate>2017</risdate><volume>46</volume><issue>5</issue><spage>471</spage><epage>484</epage><pages>471-484</pages><issn>0175-7571</issn><eissn>1432-1017</eissn><abstract>Post translational modifications have a profound role in the regulation of several biological processes such as transcription, replication, and DNA repair. Acetylation and phosphorylation form a major class of post translational modifications involved in nucleosomal regulation by modifying its structure. The effect of post translational modifications on nucleosome structure could be better explored when the molecular trajectories explaining the time dependent structural evolution over a period of time is examined at the atomic level. The present study attempts to highlight the importance of acetylation, especially at entry–exit (Lys56) and dyad (Lys115 and Lys122) regions in regulating the nucleosome accessibility and mobility using all atom simulations. It is evident from this study that acetylation at Lys56, Lys115, and Lys122 introduces local changes in the electrostatic nature of the lateral surface and thereby weakens the histone–DNA interactions. In addition, simulations also reveal significant changes in the dynamics of superhelical DNA. The acetylation at Lys56 promotes a high amplitude out-of-planar movement of entry–exit termini. Whereas, acetylation at Lys115 and Lys122 increases the flexibility of the superhelical DNA to facilitate the rolling of the superhelical DNA around the octameric histone. In essence, the present study highlights the role of acetylation at Lys56, Lys115, and Lys122 in transcriptional regulation by promoting high amplitude dynamics of superhelical DNA for a possible unwrapping as well as mobility of nucleosome.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>27933430</pmid><doi>10.1007/s00249-016-1191-5</doi><tpages>14</tpages></addata></record> |
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| subjects | Accessibility Acetylation Atomic structure Biochemistry Biological activity Biological and Medical Physics Biology Biomedical and Life Sciences Biophysics Cell Biology Chromatin Control Deoxyribonucleic acid DNA DNA biosynthesis DNA repair Dynamics Evolution Flexibility Gene regulation Histones - chemistry Histones - metabolism Life Sciences Lysine - metabolism Membrane Biology Mobility Molecular Dynamics Simulation Molecular structure Molecular trajectories Nanotechnology Neurobiology Nucleosomes - metabolism Original Article Phosphorylation Protein Multimerization Protein Stability Protein Structure, Quaternary Repair Replication Simulation Superhelical DNA Thermodynamics Time dependence Trajectories Transcription Translation |
| title | Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122 |
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