Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations
Dimerization of the p53 oligomerization domain involves coupled folding and binding of monomers. To examine the dimerization, we have performed molecular dynamics (MD) simulations of dimer folding from the rate-limiting transition state ensemble (TSE). Among 799 putative transition state structures...
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| Veröffentlicht in: | Journal of molecular biology 2005-01, Vol.345 (4), p.869-878 |
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| container_title | Journal of molecular biology |
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| creator | Chong, Lillian T. Snow, Christopher D. Rhee, Young Min Pande, Vijay S. |
| description | Dimerization of the p53 oligomerization domain involves coupled folding and binding of monomers. To examine the dimerization, we have performed molecular dynamics (MD) simulations of dimer folding from the rate-limiting transition state ensemble (TSE). Among 799 putative transition state structures that were selected from a large ensemble of high-temperature unfolding trajectories, 129 were identified as members of the TSE
via calculation of a 50% transmission coefficient from at least 20 room-temperature simulations. This study is the first to examine the refolding of a protein dimer using MD simulations in explicit water, revealing a folding nucleus for dimerization. Our atomistic simulations are consistent with experiment and offer insight that was previously unobtainable. |
| doi_str_mv | 10.1016/j.jmb.2004.10.083 |
| format | Article |
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via calculation of a 50% transmission coefficient from at least 20 room-temperature simulations. This study is the first to examine the refolding of a protein dimer using MD simulations in explicit water, revealing a folding nucleus for dimerization. Our atomistic simulations are consistent with experiment and offer insight that was previously unobtainable.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1016/j.jmb.2004.10.083</identifier><identifier>PMID: 15588832</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Computer Simulation ; Dimerization ; Models, Molecular ; molecular dynamics simulation ; oligomerization ; Protein Folding ; protein interactions ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Reproducibility of Results ; Temperature ; Thermodynamics ; tumor suppressor p53 ; Tumor Suppressor Protein p53 - chemistry ; Tumor Suppressor Protein p53 - metabolism</subject><ispartof>Journal of molecular biology, 2005-01, Vol.345 (4), p.869-878</ispartof><rights>2004 Elsevier Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c383t-253962a16873bcc9206c9aad7e82d38ab5a9e90db9752ec7751625f0b30c37973</citedby><cites>FETCH-LOGICAL-c383t-253962a16873bcc9206c9aad7e82d38ab5a9e90db9752ec7751625f0b30c37973</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0022283604014044$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15588832$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chong, Lillian T.</creatorcontrib><creatorcontrib>Snow, Christopher D.</creatorcontrib><creatorcontrib>Rhee, Young Min</creatorcontrib><creatorcontrib>Pande, Vijay S.</creatorcontrib><title>Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>Dimerization of the p53 oligomerization domain involves coupled folding and binding of monomers. To examine the dimerization, we have performed molecular dynamics (MD) simulations of dimer folding from the rate-limiting transition state ensemble (TSE). Among 799 putative transition state structures that were selected from a large ensemble of high-temperature unfolding trajectories, 129 were identified as members of the TSE
via calculation of a 50% transmission coefficient from at least 20 room-temperature simulations. This study is the first to examine the refolding of a protein dimer using MD simulations in explicit water, revealing a folding nucleus for dimerization. Our atomistic simulations are consistent with experiment and offer insight that was previously unobtainable.</description><subject>Computer Simulation</subject><subject>Dimerization</subject><subject>Models, Molecular</subject><subject>molecular dynamics simulation</subject><subject>oligomerization</subject><subject>Protein Folding</subject><subject>protein interactions</subject><subject>Protein Structure, Quaternary</subject><subject>Protein Structure, Tertiary</subject><subject>Reproducibility of Results</subject><subject>Temperature</subject><subject>Thermodynamics</subject><subject>tumor suppressor p53</subject><subject>Tumor Suppressor Protein p53 - chemistry</subject><subject>Tumor Suppressor Protein p53 - metabolism</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kcFu1DAURS0EosOUD-gGeQWrDLbf2LHLqupQWqm0C2BtOc5L61ESD3aCNHw9iWZEu-rGlp_PvYt3CDnjbMUZV5-3q21XrQRj6-m9YhpekQVn2hRagX5NFowJUQgN6oS8y3nLGJOw1m_JCZdSaw1iQcZN6DCFv24IsaexocMj0p0Eet-Gh_jsaxM7F_pzelNjP4Qm-P8JR69iW4f-gd6NvsUx02pPv8cW_di6RDf73nXBZ_ojdNNgTuVT8qZxbcb3x3tJfl19_Xl5Xdzef7u5vLgtPGgYCiHBKOG40iVU3hvBlDfO1SVqUYN2lXQGDasrU0qBviwlV0I2rALmoTQlLMmnQ-8uxd8j5sF2IXtsW9djHLPVYKThaz2TH18kVQmg1tOxJPwA-hRzTtjYXQqdS3vLmZ2t2K2drNjZyjyarEyZD8fyseqwfkocNUzAlwOA0zL-BEw2-4C9xzok9IOtY3ih_h_55J18</recordid><startdate>20050128</startdate><enddate>20050128</enddate><creator>Chong, Lillian T.</creator><creator>Snow, Christopher D.</creator><creator>Rhee, Young Min</creator><creator>Pande, Vijay S.</creator><general>Elsevier Ltd</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>7X8</scope><scope>7TO</scope><scope>H94</scope></search><sort><creationdate>20050128</creationdate><title>Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations</title><author>Chong, Lillian T. ; Snow, Christopher D. ; Rhee, Young Min ; Pande, Vijay S.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c383t-253962a16873bcc9206c9aad7e82d38ab5a9e90db9752ec7751625f0b30c37973</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Computer Simulation</topic><topic>Dimerization</topic><topic>Models, Molecular</topic><topic>molecular dynamics simulation</topic><topic>oligomerization</topic><topic>Protein Folding</topic><topic>protein interactions</topic><topic>Protein Structure, Quaternary</topic><topic>Protein Structure, Tertiary</topic><topic>Reproducibility of Results</topic><topic>Temperature</topic><topic>Thermodynamics</topic><topic>tumor suppressor p53</topic><topic>Tumor Suppressor Protein p53 - chemistry</topic><topic>Tumor Suppressor Protein p53 - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chong, Lillian T.</creatorcontrib><creatorcontrib>Snow, Christopher D.</creatorcontrib><creatorcontrib>Rhee, Young Min</creatorcontrib><creatorcontrib>Pande, Vijay S.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chong, Lillian T.</au><au>Snow, Christopher D.</au><au>Rhee, Young Min</au><au>Pande, Vijay S.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>2005-01-28</date><risdate>2005</risdate><volume>345</volume><issue>4</issue><spage>869</spage><epage>878</epage><pages>869-878</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>Dimerization of the p53 oligomerization domain involves coupled folding and binding of monomers. To examine the dimerization, we have performed molecular dynamics (MD) simulations of dimer folding from the rate-limiting transition state ensemble (TSE). Among 799 putative transition state structures that were selected from a large ensemble of high-temperature unfolding trajectories, 129 were identified as members of the TSE
via calculation of a 50% transmission coefficient from at least 20 room-temperature simulations. This study is the first to examine the refolding of a protein dimer using MD simulations in explicit water, revealing a folding nucleus for dimerization. Our atomistic simulations are consistent with experiment and offer insight that was previously unobtainable.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>15588832</pmid><doi>10.1016/j.jmb.2004.10.083</doi><tpages>10</tpages></addata></record> |
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| language | eng |
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| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | Computer Simulation Dimerization Models, Molecular molecular dynamics simulation oligomerization Protein Folding protein interactions Protein Structure, Quaternary Protein Structure, Tertiary Reproducibility of Results Temperature Thermodynamics tumor suppressor p53 Tumor Suppressor Protein p53 - chemistry Tumor Suppressor Protein p53 - metabolism |
| title | Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations |
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