How Accurately Do Current Force Fields Predict Experimental Peptide Conformations? An Adiabatic Free Energy Dynamics Study
The quality of classical biomolecular simulations is inevitably limited by two problems: the accuracy of the force field used and the comprehensiveness of configuration space sampling. In this work we tackle the sampling problem by carrying out driven adiabatic free energy dynamics to obtain converg...
Gespeichert in:
| Veröffentlicht in: | The journal of physical chemistry. B 2014-06, Vol.118 (24), p.6539-6552 |
|---|---|
| Hauptverfasser: | , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 6552 |
|---|---|
| container_issue | 24 |
| container_start_page | 6539 |
| container_title | The journal of physical chemistry. B |
| container_volume | 118 |
| creator | Tzanov, Alexandar T Cuendet, Michel A Tuckerman, Mark E |
| description | The quality of classical biomolecular simulations is inevitably limited by two problems: the accuracy of the force field used and the comprehensiveness of configuration space sampling. In this work we tackle the sampling problem by carrying out driven adiabatic free energy dynamics to obtain converged free energy surfaces of dipeptides in the gas phase and in solution using selected dihedral angles as collective variables. To calculate populations of conformational macrostates observed in experiment, we introduce a fuzzy clustering algorithm in collective-variable space, which delineates macrostates without prior definition of arbitrary boundaries. With this approach, we calculate the conformational preferences of small peptides with six biomolecular force fields chosen from among the most recent and widely used. We assess the accuracy of each force field against recently published Raman or IR–UV spectroscopy measurements of conformer populations for the dipeptides in solution or in the gas phase. |
| doi_str_mv | 10.1021/jp500193w |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1762055026</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1539470765</sourcerecordid><originalsourceid>FETCH-LOGICAL-a414t-f62b483b3065e88273c9554b295648d03dbccc219b550b40aee07fe0c7d2626d3</originalsourceid><addsrcrecordid>eNqFkU9LxDAQxYMo_j_4BSQXQQ-rk7RJ25Ms664KCy6o55ImU-nSNjVpWddPb2RXT4KHYWaY37zDe4ScMbhmwNnNshMALItWO-SQCQ6jUMnudpYM5AE58n4JwAVP5T454LHkkIE4JJ8PdkXHWg9O9Viv6Z2lk8E5bHs6s04jnVVYG08XDk2lezr96NBVTbirmi6w6yuDdGLb0rpG9ZVt_S0dt3RsKlWEXdOZQ6TTFt1bEF-3qqm0p8_9YNYnZK9UtcfTbT8mr7Ppy-RhNH-6f5yM5yMVs7gflZIXcRoVEUiBacqTSGdCxAXPhIxTA5EptNacZYUQUMSgECEpEXRiuOTSRMfkcqPbOfs-oO_zpvIa61q1aAefsySYEX65_B8VURYnkEgR0KsNqp313mGZd8EX5dY5g_w7lfw3lcCeb2WHokHzS_7EEICLDaC0z5d2cG0w5A-hL4Akkv8</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1539470765</pqid></control><display><type>article</type><title>How Accurately Do Current Force Fields Predict Experimental Peptide Conformations? An Adiabatic Free Energy Dynamics Study</title><source>ACS Publications</source><source>MEDLINE</source><creator>Tzanov, Alexandar T ; Cuendet, Michel A ; Tuckerman, Mark E</creator><creatorcontrib>Tzanov, Alexandar T ; Cuendet, Michel A ; Tuckerman, Mark E</creatorcontrib><description>The quality of classical biomolecular simulations is inevitably limited by two problems: the accuracy of the force field used and the comprehensiveness of configuration space sampling. In this work we tackle the sampling problem by carrying out driven adiabatic free energy dynamics to obtain converged free energy surfaces of dipeptides in the gas phase and in solution using selected dihedral angles as collective variables. To calculate populations of conformational macrostates observed in experiment, we introduce a fuzzy clustering algorithm in collective-variable space, which delineates macrostates without prior definition of arbitrary boundaries. With this approach, we calculate the conformational preferences of small peptides with six biomolecular force fields chosen from among the most recent and widely used. We assess the accuracy of each force field against recently published Raman or IR–UV spectroscopy measurements of conformer populations for the dipeptides in solution or in the gas phase.</description><identifier>ISSN: 1520-6106</identifier><identifier>EISSN: 1520-5207</identifier><identifier>DOI: 10.1021/jp500193w</identifier><identifier>PMID: 24620905</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Adiabatic flow ; Algorithms ; Dipeptides - chemistry ; Dipeptides - metabolism ; Dynamics ; Free energy ; Gas phases ; Gases - chemistry ; Mathematical analysis ; Molecular Dynamics Simulation ; Peptides ; Populations ; Protein Conformation ; Sampling ; Solutions - chemistry ; Thermodynamics</subject><ispartof>The journal of physical chemistry. B, 2014-06, Vol.118 (24), p.6539-6552</ispartof><rights>Copyright © 2014 American Chemical Society</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a414t-f62b483b3065e88273c9554b295648d03dbccc219b550b40aee07fe0c7d2626d3</citedby><cites>FETCH-LOGICAL-a414t-f62b483b3065e88273c9554b295648d03dbccc219b550b40aee07fe0c7d2626d3</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/jp500193w$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/jp500193w$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,776,780,2752,27053,27901,27902,56713,56763</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24620905$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tzanov, Alexandar T</creatorcontrib><creatorcontrib>Cuendet, Michel A</creatorcontrib><creatorcontrib>Tuckerman, Mark E</creatorcontrib><title>How Accurately Do Current Force Fields Predict Experimental Peptide Conformations? An Adiabatic Free Energy Dynamics Study</title><title>The journal of physical chemistry. B</title><addtitle>J. Phys. Chem. B</addtitle><description>The quality of classical biomolecular simulations is inevitably limited by two problems: the accuracy of the force field used and the comprehensiveness of configuration space sampling. In this work we tackle the sampling problem by carrying out driven adiabatic free energy dynamics to obtain converged free energy surfaces of dipeptides in the gas phase and in solution using selected dihedral angles as collective variables. To calculate populations of conformational macrostates observed in experiment, we introduce a fuzzy clustering algorithm in collective-variable space, which delineates macrostates without prior definition of arbitrary boundaries. With this approach, we calculate the conformational preferences of small peptides with six biomolecular force fields chosen from among the most recent and widely used. We assess the accuracy of each force field against recently published Raman or IR–UV spectroscopy measurements of conformer populations for the dipeptides in solution or in the gas phase.</description><subject>Adiabatic flow</subject><subject>Algorithms</subject><subject>Dipeptides - chemistry</subject><subject>Dipeptides - metabolism</subject><subject>Dynamics</subject><subject>Free energy</subject><subject>Gas phases</subject><subject>Gases - chemistry</subject><subject>Mathematical analysis</subject><subject>Molecular Dynamics Simulation</subject><subject>Peptides</subject><subject>Populations</subject><subject>Protein Conformation</subject><subject>Sampling</subject><subject>Solutions - chemistry</subject><subject>Thermodynamics</subject><issn>1520-6106</issn><issn>1520-5207</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU9LxDAQxYMo_j_4BSQXQQ-rk7RJ25Ms664KCy6o55ImU-nSNjVpWddPb2RXT4KHYWaY37zDe4ScMbhmwNnNshMALItWO-SQCQ6jUMnudpYM5AE58n4JwAVP5T454LHkkIE4JJ8PdkXHWg9O9Viv6Z2lk8E5bHs6s04jnVVYG08XDk2lezr96NBVTbirmi6w6yuDdGLb0rpG9ZVt_S0dt3RsKlWEXdOZQ6TTFt1bEF-3qqm0p8_9YNYnZK9UtcfTbT8mr7Ppy-RhNH-6f5yM5yMVs7gflZIXcRoVEUiBacqTSGdCxAXPhIxTA5EptNacZYUQUMSgECEpEXRiuOTSRMfkcqPbOfs-oO_zpvIa61q1aAefsySYEX65_B8VURYnkEgR0KsNqp313mGZd8EX5dY5g_w7lfw3lcCeb2WHokHzS_7EEICLDaC0z5d2cG0w5A-hL4Akkv8</recordid><startdate>20140619</startdate><enddate>20140619</enddate><creator>Tzanov, Alexandar T</creator><creator>Cuendet, Michel A</creator><creator>Tuckerman, Mark E</creator><general>American Chemical Society</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>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>L7M</scope></search><sort><creationdate>20140619</creationdate><title>How Accurately Do Current Force Fields Predict Experimental Peptide Conformations? An Adiabatic Free Energy Dynamics Study</title><author>Tzanov, Alexandar T ; Cuendet, Michel A ; Tuckerman, Mark E</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a414t-f62b483b3065e88273c9554b295648d03dbccc219b550b40aee07fe0c7d2626d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Adiabatic flow</topic><topic>Algorithms</topic><topic>Dipeptides - chemistry</topic><topic>Dipeptides - metabolism</topic><topic>Dynamics</topic><topic>Free energy</topic><topic>Gas phases</topic><topic>Gases - chemistry</topic><topic>Mathematical analysis</topic><topic>Molecular Dynamics Simulation</topic><topic>Peptides</topic><topic>Populations</topic><topic>Protein Conformation</topic><topic>Sampling</topic><topic>Solutions - chemistry</topic><topic>Thermodynamics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tzanov, Alexandar T</creatorcontrib><creatorcontrib>Cuendet, Michel A</creatorcontrib><creatorcontrib>Tuckerman, Mark E</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>Engineered Materials Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><jtitle>The journal of physical chemistry. B</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tzanov, Alexandar T</au><au>Cuendet, Michel A</au><au>Tuckerman, Mark E</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>How Accurately Do Current Force Fields Predict Experimental Peptide Conformations? An Adiabatic Free Energy Dynamics Study</atitle><jtitle>The journal of physical chemistry. B</jtitle><addtitle>J. Phys. Chem. B</addtitle><date>2014-06-19</date><risdate>2014</risdate><volume>118</volume><issue>24</issue><spage>6539</spage><epage>6552</epage><pages>6539-6552</pages><issn>1520-6106</issn><eissn>1520-5207</eissn><abstract>The quality of classical biomolecular simulations is inevitably limited by two problems: the accuracy of the force field used and the comprehensiveness of configuration space sampling. In this work we tackle the sampling problem by carrying out driven adiabatic free energy dynamics to obtain converged free energy surfaces of dipeptides in the gas phase and in solution using selected dihedral angles as collective variables. To calculate populations of conformational macrostates observed in experiment, we introduce a fuzzy clustering algorithm in collective-variable space, which delineates macrostates without prior definition of arbitrary boundaries. With this approach, we calculate the conformational preferences of small peptides with six biomolecular force fields chosen from among the most recent and widely used. We assess the accuracy of each force field against recently published Raman or IR–UV spectroscopy measurements of conformer populations for the dipeptides in solution or in the gas phase.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>24620905</pmid><doi>10.1021/jp500193w</doi><tpages>14</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1520-6106 |
| ispartof | The journal of physical chemistry. B, 2014-06, Vol.118 (24), p.6539-6552 |
| issn | 1520-6106 1520-5207 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1762055026 |
| source | ACS Publications; MEDLINE |
| subjects | Adiabatic flow Algorithms Dipeptides - chemistry Dipeptides - metabolism Dynamics Free energy Gas phases Gases - chemistry Mathematical analysis Molecular Dynamics Simulation Peptides Populations Protein Conformation Sampling Solutions - chemistry Thermodynamics |
| title | How Accurately Do Current Force Fields Predict Experimental Peptide Conformations? An Adiabatic Free Energy Dynamics Study |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-20T03%3A44%3A59IST&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=How%20Accurately%20Do%20Current%20Force%20Fields%20Predict%20Experimental%20Peptide%20Conformations?%20An%20Adiabatic%20Free%20Energy%20Dynamics%20Study&rft.jtitle=The%20journal%20of%20physical%20chemistry.%20B&rft.au=Tzanov,%20Alexandar%20T&rft.date=2014-06-19&rft.volume=118&rft.issue=24&rft.spage=6539&rft.epage=6552&rft.pages=6539-6552&rft.issn=1520-6106&rft.eissn=1520-5207&rft_id=info:doi/10.1021/jp500193w&rft_dat=%3Cproquest_cross%3E1539470765%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=1539470765&rft_id=info:pmid/24620905&rfr_iscdi=true |