Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT
Integration and calibration of molecular dynamics simulations with experimental data remain a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2'-hydrox...
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| Veröffentlicht in: | Methods in enzymology 2015, Vol.553, p.215-234 |
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| container_title | Methods in enzymology |
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| creator | Kirmizialtin, Serdal Hennelly, Scott P Schug, Alexander Onuchic, Jose N Sanbonmatsu, Karissa Y |
| description | Integration and calibration of molecular dynamics simulations with experimental data remain a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2'-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the force field according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. |
| doi_str_mv | 10.1016/bs.mie.2014.10.061 |
| format | Article |
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We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2'-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the force field according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations.</description><identifier>ISSN: 0076-6879</identifier><identifier>EISSN: 1557-7988</identifier><identifier>DOI: 10.1016/bs.mie.2014.10.061</identifier><identifier>PMID: 25726467</identifier><language>eng</language><publisher>United States</publisher><subject>Acylation ; Computational Biology - methods ; Hydroxyl Radical - chemistry ; Ligands ; Models, Molecular ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; RNA - chemistry</subject><ispartof>Methods in enzymology, 2015, Vol.553, p.215-234</ispartof><rights>2015 Elsevier Inc. 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We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2'-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the force field according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations.</description><subject>Acylation</subject><subject>Computational Biology - methods</subject><subject>Hydroxyl Radical - chemistry</subject><subject>Ligands</subject><subject>Models, Molecular</subject><subject>Molecular Dynamics Simulation</subject><subject>Nucleic Acid Conformation</subject><subject>RNA - chemistry</subject><issn>0076-6879</issn><issn>1557-7988</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkE9Lw0AQxRdRbK1-AQ-So5fE3WR3Z_ciFGltoaBgvQlhk0zalfwzm6j99qZYRU8Dvzfz3mMIuWQ0YJTJm8QFpcUgpIwPIKCSHZExEwJ80EodkzGlIH2pQI_ImXOvlIagNDslo1BAKLmEMXlZVh1uWtPZauOVdYFpX5jWy3aVKW3qPGfLAXS2rpz3Ybutl25xEEzhNW2d7I_ws8HWllh1zuvdnjwtpo8zf75cn5OT3BQOLw5zQp7ns_Xdwl893C_vpis_jYTufCN4kggqojzUOsy44YpzzKgxOodEaaRapECjRCPwkEMe8ZwpaWQicqORRRNy--3b9EmJWTp0aU0RN0Mt0-7i2tj4v1LZbbyp32MOAFLDYHB9MGjrtx5dF5fWpVgUpsK6dzGTkvIIBFPD6tXfrN-Qn5dGX_m8fBc</recordid><startdate>2015</startdate><enddate>2015</enddate><creator>Kirmizialtin, Serdal</creator><creator>Hennelly, Scott P</creator><creator>Schug, Alexander</creator><creator>Onuchic, Jose N</creator><creator>Sanbonmatsu, Karissa Y</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>2015</creationdate><title>Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT</title><author>Kirmizialtin, Serdal ; Hennelly, Scott P ; Schug, Alexander ; Onuchic, Jose N ; Sanbonmatsu, Karissa Y</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c359t-a54bb5053f2992d4a4844ed0aa9f7b89e095c703b9e74247f34f186a6b5fa9e13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Acylation</topic><topic>Computational Biology - methods</topic><topic>Hydroxyl Radical - chemistry</topic><topic>Ligands</topic><topic>Models, Molecular</topic><topic>Molecular Dynamics Simulation</topic><topic>Nucleic Acid Conformation</topic><topic>RNA - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kirmizialtin, Serdal</creatorcontrib><creatorcontrib>Hennelly, Scott P</creatorcontrib><creatorcontrib>Schug, Alexander</creatorcontrib><creatorcontrib>Onuchic, Jose N</creatorcontrib><creatorcontrib>Sanbonmatsu, Karissa Y</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Methods in enzymology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kirmizialtin, Serdal</au><au>Hennelly, Scott P</au><au>Schug, Alexander</au><au>Onuchic, Jose N</au><au>Sanbonmatsu, Karissa Y</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT</atitle><jtitle>Methods in enzymology</jtitle><addtitle>Methods Enzymol</addtitle><date>2015</date><risdate>2015</risdate><volume>553</volume><spage>215</spage><epage>234</epage><pages>215-234</pages><issn>0076-6879</issn><eissn>1557-7988</eissn><abstract>Integration and calibration of molecular dynamics simulations with experimental data remain a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2'-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the force field according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations.</abstract><cop>United States</cop><pmid>25726467</pmid><doi>10.1016/bs.mie.2014.10.061</doi><tpages>20</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | Acylation Computational Biology - methods Hydroxyl Radical - chemistry Ligands Models, Molecular Molecular Dynamics Simulation Nucleic Acid Conformation RNA - chemistry |
| title | Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT |
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