Continuum mechanical parameterisation of cytoplasmic dynein from atomistic simulation
•MD simulations of cytoplasmic dynein show stalk angular fluctuations are significant.•The measured dynamics can be well represented at a coarse-grained level using FFEA.•Continuum parameterisation captures the higher flexibility of the ATP-bound motor. Cytoplasmic dynein is responsible for intra-ce...
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| Veröffentlicht in: | Methods (San Diego, Calif.) Calif.), 2021-01, Vol.185, p.39-48 |
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| container_title | Methods (San Diego, Calif.) |
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| creator | Hanson, Benjamin S. Iida, Shinji Read, Daniel J. Harlen, Oliver G. Kurisu, Genji Nakamura, Haruki Harris, Sarah A. |
| description | •MD simulations of cytoplasmic dynein show stalk angular fluctuations are significant.•The measured dynamics can be well represented at a coarse-grained level using FFEA.•Continuum parameterisation captures the higher flexibility of the ATP-bound motor.
Cytoplasmic dynein is responsible for intra-cellular transport in eukaryotic cells. Using Fluctuating Finite Element Analysis (FFEA), a novel algorithm that represents proteins as continuum viscoelastic solids subject to thermal noise, we are building computational tools to study the mechanics of these molecular machines. Here we present a methodology for obtaining the material parameters required to represent the flexibility of cytoplasmic dynein within FFEA from atomistic molecular dynamics (MD) simulations, and show that this continuum representation is sufficient to capture the principal dynamic properties of the motor. |
| doi_str_mv | 10.1016/j.ymeth.2020.01.021 |
| format | Article |
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Cytoplasmic dynein is responsible for intra-cellular transport in eukaryotic cells. Using Fluctuating Finite Element Analysis (FFEA), a novel algorithm that represents proteins as continuum viscoelastic solids subject to thermal noise, we are building computational tools to study the mechanics of these molecular machines. Here we present a methodology for obtaining the material parameters required to represent the flexibility of cytoplasmic dynein within FFEA from atomistic molecular dynamics (MD) simulations, and show that this continuum representation is sufficient to capture the principal dynamic properties of the motor.</description><identifier>ISSN: 1046-2023</identifier><identifier>EISSN: 1095-9130</identifier><identifier>DOI: 10.1016/j.ymeth.2020.01.021</identifier><identifier>PMID: 32007556</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Dynein ; Fluctuating finite element analysis ; Hierarchical biomechanics ; Molecular dynamics ; Multiscale simulation ; Principal component analysis</subject><ispartof>Methods (San Diego, Calif.), 2021-01, Vol.185, p.39-48</ispartof><rights>2020 Elsevier Inc.</rights><rights>Copyright © 2020 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c470t-89d421b07cfd6579e55b5a051eb1f291378872d0412a6743ad0ffcc27b355ae3</citedby><cites>FETCH-LOGICAL-c470t-89d421b07cfd6579e55b5a051eb1f291378872d0412a6743ad0ffcc27b355ae3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S1046202319302440$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65534</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32007556$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hanson, Benjamin S.</creatorcontrib><creatorcontrib>Iida, Shinji</creatorcontrib><creatorcontrib>Read, Daniel J.</creatorcontrib><creatorcontrib>Harlen, Oliver G.</creatorcontrib><creatorcontrib>Kurisu, Genji</creatorcontrib><creatorcontrib>Nakamura, Haruki</creatorcontrib><creatorcontrib>Harris, Sarah A.</creatorcontrib><title>Continuum mechanical parameterisation of cytoplasmic dynein from atomistic simulation</title><title>Methods (San Diego, Calif.)</title><addtitle>Methods</addtitle><description>•MD simulations of cytoplasmic dynein show stalk angular fluctuations are significant.•The measured dynamics can be well represented at a coarse-grained level using FFEA.•Continuum parameterisation captures the higher flexibility of the ATP-bound motor.
Cytoplasmic dynein is responsible for intra-cellular transport in eukaryotic cells. Using Fluctuating Finite Element Analysis (FFEA), a novel algorithm that represents proteins as continuum viscoelastic solids subject to thermal noise, we are building computational tools to study the mechanics of these molecular machines. Here we present a methodology for obtaining the material parameters required to represent the flexibility of cytoplasmic dynein within FFEA from atomistic molecular dynamics (MD) simulations, and show that this continuum representation is sufficient to capture the principal dynamic properties of the motor.</description><subject>Dynein</subject><subject>Fluctuating finite element analysis</subject><subject>Hierarchical biomechanics</subject><subject>Molecular dynamics</subject><subject>Multiscale simulation</subject><subject>Principal component analysis</subject><issn>1046-2023</issn><issn>1095-9130</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp9kEtLxDAQgIMovn-BID16aZ0kTbM9eJDFFwhe9BzSdIpZmmZNUmH_vVlXPXrKkPnm9RFyQaGiQJvrVbVxmN4rBgwqoBUwukeOKbSibCmH_W1cN2VO8yNyEuMKACiTi0NyxBmAFKI5Jm9LPyU7zbMrHJp3PVmjx2Ktg869Mdiok_VT4YfCbJJfjzo6a4p-M6GdiiF4V-jknY0p_0br5vGbPyMHgx4jnv-8p-T1_u51-Vg-vzw8LW-fS1NLSOWi7WtGO5Bm6BshWxSiExoExY4OLB8hFwvJeqgp042sue5hGIxhsuNCaOSn5GrXdh38x4wxqbyJwXHUE_o5KsYFcN5CQzPKd6gJPsaAg1oH63TYKApqq1Ot1LdOtdWpgKqsM1dd_gyYO4f9X82vvwzc7ADMV35aDCoai5PB3gY0SfXe_jvgC25UiJY</recordid><startdate>202101</startdate><enddate>202101</enddate><creator>Hanson, Benjamin S.</creator><creator>Iida, Shinji</creator><creator>Read, Daniel J.</creator><creator>Harlen, Oliver G.</creator><creator>Kurisu, Genji</creator><creator>Nakamura, Haruki</creator><creator>Harris, Sarah A.</creator><general>Elsevier Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>202101</creationdate><title>Continuum mechanical parameterisation of cytoplasmic dynein from atomistic simulation</title><author>Hanson, Benjamin S. ; Iida, Shinji ; Read, Daniel J. ; Harlen, Oliver G. ; Kurisu, Genji ; Nakamura, Haruki ; Harris, Sarah A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c470t-89d421b07cfd6579e55b5a051eb1f291378872d0412a6743ad0ffcc27b355ae3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Dynein</topic><topic>Fluctuating finite element analysis</topic><topic>Hierarchical biomechanics</topic><topic>Molecular dynamics</topic><topic>Multiscale simulation</topic><topic>Principal component analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hanson, Benjamin S.</creatorcontrib><creatorcontrib>Iida, Shinji</creatorcontrib><creatorcontrib>Read, Daniel J.</creatorcontrib><creatorcontrib>Harlen, Oliver G.</creatorcontrib><creatorcontrib>Kurisu, Genji</creatorcontrib><creatorcontrib>Nakamura, Haruki</creatorcontrib><creatorcontrib>Harris, Sarah A.</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Methods (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hanson, Benjamin S.</au><au>Iida, Shinji</au><au>Read, Daniel J.</au><au>Harlen, Oliver G.</au><au>Kurisu, Genji</au><au>Nakamura, Haruki</au><au>Harris, Sarah A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Continuum mechanical parameterisation of cytoplasmic dynein from atomistic simulation</atitle><jtitle>Methods (San Diego, Calif.)</jtitle><addtitle>Methods</addtitle><date>2021-01</date><risdate>2021</risdate><volume>185</volume><spage>39</spage><epage>48</epage><pages>39-48</pages><issn>1046-2023</issn><eissn>1095-9130</eissn><abstract>•MD simulations of cytoplasmic dynein show stalk angular fluctuations are significant.•The measured dynamics can be well represented at a coarse-grained level using FFEA.•Continuum parameterisation captures the higher flexibility of the ATP-bound motor.
Cytoplasmic dynein is responsible for intra-cellular transport in eukaryotic cells. Using Fluctuating Finite Element Analysis (FFEA), a novel algorithm that represents proteins as continuum viscoelastic solids subject to thermal noise, we are building computational tools to study the mechanics of these molecular machines. Here we present a methodology for obtaining the material parameters required to represent the flexibility of cytoplasmic dynein within FFEA from atomistic molecular dynamics (MD) simulations, and show that this continuum representation is sufficient to capture the principal dynamic properties of the motor.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>32007556</pmid><doi>10.1016/j.ymeth.2020.01.021</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Methods (San Diego, Calif.), 2021-01, Vol.185, p.39-48 |
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| language | eng |
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| source | Elsevier ScienceDirect Journals Complete |
| subjects | Dynein Fluctuating finite element analysis Hierarchical biomechanics Molecular dynamics Multiscale simulation Principal component analysis |
| title | Continuum mechanical parameterisation of cytoplasmic dynein from atomistic simulation |
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