Rapid Free Energy Calculation of Peptide Self-Assembly by REMD Umbrella Sampling
We extend umbrella sampling with replica exchange steps to calculate free energies that are important in the self-assembly of peptides. This leads to a more than 10-fold speed up over conventional umbrella sampling, thereby providing a practical method to calculate these free-energy differences. Thi...
Gespeichert in:
| Veröffentlicht in: | The journal of physical chemistry. B 2008-10, Vol.112 (43), p.13493-13498 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 13498 |
|---|---|
| container_issue | 43 |
| container_start_page | 13493 |
| container_title | The journal of physical chemistry. B |
| container_volume | 112 |
| creator | Wolf, Maarten G Jongejan, Jaap A Laman, Jon D de Leeuw, Simon W |
| description | We extend umbrella sampling with replica exchange steps to calculate free energies that are important in the self-assembly of peptides. This leads to a more than 10-fold speed up over conventional umbrella sampling, thereby providing a practical method to calculate these free-energy differences. This approach can also observe first-order phase transitions and pinpoint the location of the concomitant boundary. When conformational changes are involved, this method can handle peptides up to ∼7 residues, providing a rapid and accurate assessment of the thermodynamic properties of model systems, and can thus be used to answer fundamental questions about peptide self-assembly. When no major conformational changes are involved, we expect the size limit to be equal to that of standard molecular dynamics. |
| doi_str_mv | 10.1021/jp804285e |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_69703604</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>69703604</sourcerecordid><originalsourceid>FETCH-LOGICAL-a351t-98c340911de5c6dff4abb2874f9303e88c6c08f57a24be7b4609ea520f4fc4ea3</originalsourceid><addsrcrecordid>eNptkM1OwzAQhC0EoqVw4AWQLyBxCNiJ7TjHUlpAAlHR9mw5zhql5A87kcjbE9QKLhxGu9J-mt0dhM4puaEkpLfbRhIWSg4HaEx5SIJB8eG-F5SIETrxfktIyEMpjtGISskGRWO0fNNNnuGFA8DzCtx7j2e6MF2h27yucG3xEpo2zwCvoLDB1Hso06LHaY_f5i_3eFOmDopC45UumyKv3k_RkdWFh7N9naDNYr6ePQbPrw9Ps-lzoCNO2yCRJmIkoTQDbkRmLdNpGsqY2SQiEUhphCHS8liHLIU4ZYIkoId_LLOGgY4m6Grn27j6swPfqjL35ueUCurOK5HEJBKEDeD1DjSu9t6BVY3LS-16RYn6iU_9xjewF3vTLi0h-yP3eQ1AsANy38LX71y7DyXiKOZqvVwpfic5EYQrOfCXO14br7Z156ohk38WfwMW2IQv</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>69703604</pqid></control><display><type>article</type><title>Rapid Free Energy Calculation of Peptide Self-Assembly by REMD Umbrella Sampling</title><source>MEDLINE</source><source>ACS Publications</source><creator>Wolf, Maarten G ; Jongejan, Jaap A ; Laman, Jon D ; de Leeuw, Simon W</creator><creatorcontrib>Wolf, Maarten G ; Jongejan, Jaap A ; Laman, Jon D ; de Leeuw, Simon W</creatorcontrib><description>We extend umbrella sampling with replica exchange steps to calculate free energies that are important in the self-assembly of peptides. This leads to a more than 10-fold speed up over conventional umbrella sampling, thereby providing a practical method to calculate these free-energy differences. This approach can also observe first-order phase transitions and pinpoint the location of the concomitant boundary. When conformational changes are involved, this method can handle peptides up to ∼7 residues, providing a rapid and accurate assessment of the thermodynamic properties of model systems, and can thus be used to answer fundamental questions about peptide self-assembly. When no major conformational changes are involved, we expect the size limit to be equal to that of standard molecular dynamics.</description><identifier>ISSN: 1520-6106</identifier><identifier>EISSN: 1520-5207</identifier><identifier>DOI: 10.1021/jp804285e</identifier><identifier>PMID: 18841883</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Algorithms ; B: Macromolecules, Soft Matter ; Biopolymers - chemistry ; Computer Simulation ; Energy Transfer ; Models, Statistical ; Peptides - chemical synthesis ; Peptides - chemistry ; Protein Conformation ; Software</subject><ispartof>The journal of physical chemistry. B, 2008-10, Vol.112 (43), p.13493-13498</ispartof><rights>Copyright © 2008 American Chemical Society</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a351t-98c340911de5c6dff4abb2874f9303e88c6c08f57a24be7b4609ea520f4fc4ea3</citedby><cites>FETCH-LOGICAL-a351t-98c340911de5c6dff4abb2874f9303e88c6c08f57a24be7b4609ea520f4fc4ea3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/jp804285e$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/jp804285e$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,780,784,2765,27076,27924,27925,56738,56788</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18841883$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wolf, Maarten G</creatorcontrib><creatorcontrib>Jongejan, Jaap A</creatorcontrib><creatorcontrib>Laman, Jon D</creatorcontrib><creatorcontrib>de Leeuw, Simon W</creatorcontrib><title>Rapid Free Energy Calculation of Peptide Self-Assembly by REMD Umbrella Sampling</title><title>The journal of physical chemistry. B</title><addtitle>J. Phys. Chem. B</addtitle><description>We extend umbrella sampling with replica exchange steps to calculate free energies that are important in the self-assembly of peptides. This leads to a more than 10-fold speed up over conventional umbrella sampling, thereby providing a practical method to calculate these free-energy differences. This approach can also observe first-order phase transitions and pinpoint the location of the concomitant boundary. When conformational changes are involved, this method can handle peptides up to ∼7 residues, providing a rapid and accurate assessment of the thermodynamic properties of model systems, and can thus be used to answer fundamental questions about peptide self-assembly. When no major conformational changes are involved, we expect the size limit to be equal to that of standard molecular dynamics.</description><subject>Algorithms</subject><subject>B: Macromolecules, Soft Matter</subject><subject>Biopolymers - chemistry</subject><subject>Computer Simulation</subject><subject>Energy Transfer</subject><subject>Models, Statistical</subject><subject>Peptides - chemical synthesis</subject><subject>Peptides - chemistry</subject><subject>Protein Conformation</subject><subject>Software</subject><issn>1520-6106</issn><issn>1520-5207</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNptkM1OwzAQhC0EoqVw4AWQLyBxCNiJ7TjHUlpAAlHR9mw5zhql5A87kcjbE9QKLhxGu9J-mt0dhM4puaEkpLfbRhIWSg4HaEx5SIJB8eG-F5SIETrxfktIyEMpjtGISskGRWO0fNNNnuGFA8DzCtx7j2e6MF2h27yucG3xEpo2zwCvoLDB1Hso06LHaY_f5i_3eFOmDopC45UumyKv3k_RkdWFh7N9naDNYr6ePQbPrw9Ps-lzoCNO2yCRJmIkoTQDbkRmLdNpGsqY2SQiEUhphCHS8liHLIU4ZYIkoId_LLOGgY4m6Grn27j6swPfqjL35ueUCurOK5HEJBKEDeD1DjSu9t6BVY3LS-16RYn6iU_9xjewF3vTLi0h-yP3eQ1AsANy38LX71y7DyXiKOZqvVwpfic5EYQrOfCXO14br7Z156ohk38WfwMW2IQv</recordid><startdate>20081030</startdate><enddate>20081030</enddate><creator>Wolf, Maarten G</creator><creator>Jongejan, Jaap A</creator><creator>Laman, Jon D</creator><creator>de Leeuw, Simon W</creator><general>American Chemical Society</general><scope>BSCLL</scope><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></search><sort><creationdate>20081030</creationdate><title>Rapid Free Energy Calculation of Peptide Self-Assembly by REMD Umbrella Sampling</title><author>Wolf, Maarten G ; Jongejan, Jaap A ; Laman, Jon D ; de Leeuw, Simon W</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a351t-98c340911de5c6dff4abb2874f9303e88c6c08f57a24be7b4609ea520f4fc4ea3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Algorithms</topic><topic>B: Macromolecules, Soft Matter</topic><topic>Biopolymers - chemistry</topic><topic>Computer Simulation</topic><topic>Energy Transfer</topic><topic>Models, Statistical</topic><topic>Peptides - chemical synthesis</topic><topic>Peptides - chemistry</topic><topic>Protein Conformation</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wolf, Maarten G</creatorcontrib><creatorcontrib>Jongejan, Jaap A</creatorcontrib><creatorcontrib>Laman, Jon D</creatorcontrib><creatorcontrib>de Leeuw, Simon W</creatorcontrib><collection>Istex</collection><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><jtitle>The journal of physical chemistry. B</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wolf, Maarten G</au><au>Jongejan, Jaap A</au><au>Laman, Jon D</au><au>de Leeuw, Simon W</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Rapid Free Energy Calculation of Peptide Self-Assembly by REMD Umbrella Sampling</atitle><jtitle>The journal of physical chemistry. B</jtitle><addtitle>J. Phys. Chem. B</addtitle><date>2008-10-30</date><risdate>2008</risdate><volume>112</volume><issue>43</issue><spage>13493</spage><epage>13498</epage><pages>13493-13498</pages><issn>1520-6106</issn><eissn>1520-5207</eissn><abstract>We extend umbrella sampling with replica exchange steps to calculate free energies that are important in the self-assembly of peptides. This leads to a more than 10-fold speed up over conventional umbrella sampling, thereby providing a practical method to calculate these free-energy differences. This approach can also observe first-order phase transitions and pinpoint the location of the concomitant boundary. When conformational changes are involved, this method can handle peptides up to ∼7 residues, providing a rapid and accurate assessment of the thermodynamic properties of model systems, and can thus be used to answer fundamental questions about peptide self-assembly. When no major conformational changes are involved, we expect the size limit to be equal to that of standard molecular dynamics.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>18841883</pmid><doi>10.1021/jp804285e</doi><tpages>6</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1520-6106 |
| ispartof | The journal of physical chemistry. B, 2008-10, Vol.112 (43), p.13493-13498 |
| issn | 1520-6106 1520-5207 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_69703604 |
| source | MEDLINE; ACS Publications |
| subjects | Algorithms B: Macromolecules, Soft Matter Biopolymers - chemistry Computer Simulation Energy Transfer Models, Statistical Peptides - chemical synthesis Peptides - chemistry Protein Conformation Software |
| title | Rapid Free Energy Calculation of Peptide Self-Assembly by REMD Umbrella Sampling |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-06T16%3A38%3A01IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Rapid%20Free%20Energy%20Calculation%20of%20Peptide%20Self-Assembly%20by%20REMD%20Umbrella%20Sampling&rft.jtitle=The%20journal%20of%20physical%20chemistry.%20B&rft.au=Wolf,%20Maarten%20G&rft.date=2008-10-30&rft.volume=112&rft.issue=43&rft.spage=13493&rft.epage=13498&rft.pages=13493-13498&rft.issn=1520-6106&rft.eissn=1520-5207&rft_id=info:doi/10.1021/jp804285e&rft_dat=%3Cproquest_cross%3E69703604%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=69703604&rft_id=info:pmid/18841883&rfr_iscdi=true |