Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack
The coiled‐coil stability and rigidity may be of importance for molecular electronics (electronically bistable molecules). The coiled‐coil binding free energy has been calculated using molecular dynamics (MD). The energy has been computed as a difference of the appropriate free energies; derived for...
Gespeichert in:
| Veröffentlicht in: | Journal of computational chemistry 2002-01, Vol.23 (1), p.106-110 |
|---|---|
| Hauptverfasser: | , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 110 |
|---|---|
| container_issue | 1 |
| container_start_page | 106 |
| container_title | Journal of computational chemistry |
| container_volume | 23 |
| creator | Orzechowski, Marek Cieplak, Piotr Piela, Lucjan |
| description | The coiled‐coil stability and rigidity may be of importance for molecular electronics (electronically bistable molecules). The coiled‐coil binding free energy has been calculated using molecular dynamics (MD). The energy has been computed as a difference of the appropriate free energies; derived for the coiled‐coil and isolated α‐helices separately. All MD simulations have been performed using an explicit model of the solvent, whereas the continuum solvent approach has been applied to analyze the MD trajectories. The computed stability of the coiled‐coil is of the order of −87 kcal/mol, i.e., about −1.2 kcal/mol per amino acid residue, and arises mainly from the electrostatic interactions and hydrophobic effect. The entropy term has been roughly estimated to be of the order of −22 kcal/mol. This assures that coiled‐coil polypeptides may be used as a stable molecular scaffolding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 106–110, 2002 |
| doi_str_mv | 10.1002/jcc.10020 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_71542156</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>71542156</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3940-3608bd8b528d7dc8bc974f20c1b14bd7f8d448acca522ad55b914c1b7baf39093</originalsourceid><addsrcrecordid>eNp1kE1PxCAURYnR6Pix8A8YViYuqlBKKUvT6KgxfiQa3RGgNKLMdAQanX8vtaOuXJD3Es49ebkA7GN0jBHKT161_l7QGphgxMuMV-x5HUwQ5nlWlRRvge0QXhFChJbFJtjCmGNCGJ2A-PBiOm-i1dLB9HTvZLTdHHYtjC8G6s4602TDgCFKZZ2NS2jn8ENG44dlpObRfMYhZGOAiy4Eq5yBfTBQBijhrHNmUHvopX7bBRutdMHsreYOeDw_e6gvsuvb6WV9ep1pwguUkRJVqqkUzauGNbpSmrOizZHGCheqYW3VFEUltZY0z2VDqeK4SJ9MyZZwxMkOOBy9C9-99yZEMbNBG-fk3HR9EAzTIse0TODRCGqfTvemFQtvZ9IvBUZiaFakir8XlNiDlbRXM9P8katOE3AyAh-puuX_JnFV1z_KbEzYkGr8TUj_JkqWlOLpZirYHZnW9_e1YOQLmDeVyA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>71542156</pqid></control><display><type>article</type><title>Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack</title><source>MEDLINE</source><source>Wiley Online Library Journals Frontfile Complete</source><creator>Orzechowski, Marek ; Cieplak, Piotr ; Piela, Lucjan</creator><creatorcontrib>Orzechowski, Marek ; Cieplak, Piotr ; Piela, Lucjan</creatorcontrib><description>The coiled‐coil stability and rigidity may be of importance for molecular electronics (electronically bistable molecules). The coiled‐coil binding free energy has been calculated using molecular dynamics (MD). The energy has been computed as a difference of the appropriate free energies; derived for the coiled‐coil and isolated α‐helices separately. All MD simulations have been performed using an explicit model of the solvent, whereas the continuum solvent approach has been applied to analyze the MD trajectories. The computed stability of the coiled‐coil is of the order of −87 kcal/mol, i.e., about −1.2 kcal/mol per amino acid residue, and arises mainly from the electrostatic interactions and hydrophobic effect. The entropy term has been roughly estimated to be of the order of −22 kcal/mol. This assures that coiled‐coil polypeptides may be used as a stable molecular scaffolding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 106–110, 2002</description><identifier>ISSN: 0192-8651</identifier><identifier>EISSN: 1096-987X</identifier><identifier>DOI: 10.1002/jcc.10020</identifier><identifier>PMID: 11913375</identifier><language>eng</language><publisher>New York: Wiley Periodicals, Inc</publisher><subject>Amino Acid Sequence ; Amino Acids - chemistry ; charge transfer ; coiled-coil ; Crystallography, X-Ray ; electron acceptor ; electron donor ; Entropy ; free energy of binding ; free energy of solvation ; mnemon ; Models, Theoretical ; Protein Conformation ; Protein Structure, Secondary ; Proteins - chemistry ; stability ; Static Electricity ; Water - chemistry</subject><ispartof>Journal of computational chemistry, 2002-01, Vol.23 (1), p.106-110</ispartof><rights>Copyright © 2002 Wiley Periodicals, Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3940-3608bd8b528d7dc8bc974f20c1b14bd7f8d448acca522ad55b914c1b7baf39093</citedby><cites>FETCH-LOGICAL-c3940-3608bd8b528d7dc8bc974f20c1b14bd7f8d448acca522ad55b914c1b7baf39093</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fjcc.10020$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjcc.10020$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,777,781,1412,27905,27906,45555,45556</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11913375$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Orzechowski, Marek</creatorcontrib><creatorcontrib>Cieplak, Piotr</creatorcontrib><creatorcontrib>Piela, Lucjan</creatorcontrib><title>Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack</title><title>Journal of computational chemistry</title><addtitle>J. Comput. Chem</addtitle><description>The coiled‐coil stability and rigidity may be of importance for molecular electronics (electronically bistable molecules). The coiled‐coil binding free energy has been calculated using molecular dynamics (MD). The energy has been computed as a difference of the appropriate free energies; derived for the coiled‐coil and isolated α‐helices separately. All MD simulations have been performed using an explicit model of the solvent, whereas the continuum solvent approach has been applied to analyze the MD trajectories. The computed stability of the coiled‐coil is of the order of −87 kcal/mol, i.e., about −1.2 kcal/mol per amino acid residue, and arises mainly from the electrostatic interactions and hydrophobic effect. The entropy term has been roughly estimated to be of the order of −22 kcal/mol. This assures that coiled‐coil polypeptides may be used as a stable molecular scaffolding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 106–110, 2002</description><subject>Amino Acid Sequence</subject><subject>Amino Acids - chemistry</subject><subject>charge transfer</subject><subject>coiled-coil</subject><subject>Crystallography, X-Ray</subject><subject>electron acceptor</subject><subject>electron donor</subject><subject>Entropy</subject><subject>free energy of binding</subject><subject>free energy of solvation</subject><subject>mnemon</subject><subject>Models, Theoretical</subject><subject>Protein Conformation</subject><subject>Protein Structure, Secondary</subject><subject>Proteins - chemistry</subject><subject>stability</subject><subject>Static Electricity</subject><subject>Water - chemistry</subject><issn>0192-8651</issn><issn>1096-987X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2002</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kE1PxCAURYnR6Pix8A8YViYuqlBKKUvT6KgxfiQa3RGgNKLMdAQanX8vtaOuXJD3Es49ebkA7GN0jBHKT161_l7QGphgxMuMV-x5HUwQ5nlWlRRvge0QXhFChJbFJtjCmGNCGJ2A-PBiOm-i1dLB9HTvZLTdHHYtjC8G6s4602TDgCFKZZ2NS2jn8ENG44dlpObRfMYhZGOAiy4Eq5yBfTBQBijhrHNmUHvopX7bBRutdMHsreYOeDw_e6gvsuvb6WV9ep1pwguUkRJVqqkUzauGNbpSmrOizZHGCheqYW3VFEUltZY0z2VDqeK4SJ9MyZZwxMkOOBy9C9-99yZEMbNBG-fk3HR9EAzTIse0TODRCGqfTvemFQtvZ9IvBUZiaFakir8XlNiDlbRXM9P8katOE3AyAh-puuX_JnFV1z_KbEzYkGr8TUj_JkqWlOLpZirYHZnW9_e1YOQLmDeVyA</recordid><startdate>20020115</startdate><enddate>20020115</enddate><creator>Orzechowski, Marek</creator><creator>Cieplak, Piotr</creator><creator>Piela, Lucjan</creator><general>Wiley Periodicals, Inc</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>20020115</creationdate><title>Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack</title><author>Orzechowski, Marek ; Cieplak, Piotr ; Piela, Lucjan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3940-3608bd8b528d7dc8bc974f20c1b14bd7f8d448acca522ad55b914c1b7baf39093</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2002</creationdate><topic>Amino Acid Sequence</topic><topic>Amino Acids - chemistry</topic><topic>charge transfer</topic><topic>coiled-coil</topic><topic>Crystallography, X-Ray</topic><topic>electron acceptor</topic><topic>electron donor</topic><topic>Entropy</topic><topic>free energy of binding</topic><topic>free energy of solvation</topic><topic>mnemon</topic><topic>Models, Theoretical</topic><topic>Protein Conformation</topic><topic>Protein Structure, Secondary</topic><topic>Proteins - chemistry</topic><topic>stability</topic><topic>Static Electricity</topic><topic>Water - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Orzechowski, Marek</creatorcontrib><creatorcontrib>Cieplak, Piotr</creatorcontrib><creatorcontrib>Piela, Lucjan</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>Journal of computational chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Orzechowski, Marek</au><au>Cieplak, Piotr</au><au>Piela, Lucjan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack</atitle><jtitle>Journal of computational chemistry</jtitle><addtitle>J. Comput. Chem</addtitle><date>2002-01-15</date><risdate>2002</risdate><volume>23</volume><issue>1</issue><spage>106</spage><epage>110</epage><pages>106-110</pages><issn>0192-8651</issn><eissn>1096-987X</eissn><abstract>The coiled‐coil stability and rigidity may be of importance for molecular electronics (electronically bistable molecules). The coiled‐coil binding free energy has been calculated using molecular dynamics (MD). The energy has been computed as a difference of the appropriate free energies; derived for the coiled‐coil and isolated α‐helices separately. All MD simulations have been performed using an explicit model of the solvent, whereas the continuum solvent approach has been applied to analyze the MD trajectories. The computed stability of the coiled‐coil is of the order of −87 kcal/mol, i.e., about −1.2 kcal/mol per amino acid residue, and arises mainly from the electrostatic interactions and hydrophobic effect. The entropy term has been roughly estimated to be of the order of −22 kcal/mol. This assures that coiled‐coil polypeptides may be used as a stable molecular scaffolding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 106–110, 2002</abstract><cop>New York</cop><pub>Wiley Periodicals, Inc</pub><pmid>11913375</pmid><doi>10.1002/jcc.10020</doi><tpages>5</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0192-8651 |
| ispartof | Journal of computational chemistry, 2002-01, Vol.23 (1), p.106-110 |
| issn | 0192-8651 1096-987X |
| language | eng |
| recordid | cdi_proquest_miscellaneous_71542156 |
| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Amino Acid Sequence Amino Acids - chemistry charge transfer coiled-coil Crystallography, X-Ray electron acceptor electron donor Entropy free energy of binding free energy of solvation mnemon Models, Theoretical Protein Conformation Protein Structure, Secondary Proteins - chemistry stability Static Electricity Water - chemistry |
| title | Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-20T03%3A55%3A02IST&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=Theoretical%20calculation%20of%20the%20coiled-coil%20stability%20in%20water%20in%20the%20context%20of%20its%20possible%20use%20as%20a%20molecular%20rack&rft.jtitle=Journal%20of%20computational%20chemistry&rft.au=Orzechowski,%20Marek&rft.date=2002-01-15&rft.volume=23&rft.issue=1&rft.spage=106&rft.epage=110&rft.pages=106-110&rft.issn=0192-8651&rft.eissn=1096-987X&rft_id=info:doi/10.1002/jcc.10020&rft_dat=%3Cproquest_cross%3E71542156%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=71542156&rft_id=info:pmid/11913375&rfr_iscdi=true |