A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta
ABSTRACT Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology‐based methods, protein–protein interfaces are challenging to determine de novo using conventional...
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| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2015-02, Vol.83 (2), p.309-317 |
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| creator | Rossi, Paolo Shi, Lei Liu, Gaohua Barbieri, Christopher M. Lee, Hsiau-Wei Grant, Thomas D. Luft, Joseph R. Xiao, Rong Acton, Thomas B. Snell, Edward H. Montelione, Gaetano T. Baker, David Lange, Oliver F. Sgourakis, Nikolaos G. |
| description | ABSTRACT
Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology‐based methods, protein–protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet‐V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1. Unlike conventional methods relying on a dense network of experimental restraints, the sparse data are used to limit conformational search during optimization of a physically realistic energy function. This work highlights a new approach for studying minor conformational changes due to structural plasticity within a single dimeric interface in solution. Proteins 2015; 83:309–317. © 2014 Wiley Periodicals, Inc. |
| doi_str_mv | 10.1002/prot.24719 |
| format | Article |
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Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology‐based methods, protein–protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet‐V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1. Unlike conventional methods relying on a dense network of experimental restraints, the sparse data are used to limit conformational search during optimization of a physically realistic energy function. This work highlights a new approach for studying minor conformational changes due to structural plasticity within a single dimeric interface in solution. Proteins 2015; 83:309–317. © 2014 Wiley Periodicals, Inc.</description><identifier>ISSN: 0887-3585</identifier><identifier>EISSN: 1097-0134</identifier><identifier>DOI: 10.1002/prot.24719</identifier><identifier>PMID: 25388768</identifier><language>eng</language><publisher>United States: Blackwell Publishing Ltd</publisher><subject>Alteromonadaceae - chemistry ; Bacterial Proteins - chemistry ; Colwellia ; CS-Rosetta modeling ; Models, Molecular ; nuclear magnetic resonance spectroscopy ; Nuclear Magnetic Resonance, Biomolecular ; protein complex ; Protein Structure, Secondary ; Protein Structure, Tertiary ; residual dipolar coupling ; Scattering, Small Angle ; small-angle X-ray scattering ; Solutions ; X-Ray Diffraction</subject><ispartof>Proteins, structure, function, and bioinformatics, 2015-02, Vol.83 (2), p.309-317</ispartof><rights>2014 Wiley Periodicals, Inc.</rights><rights>2015 Wiley Periodicals, Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fprot.24719$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fprot.24719$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,780,784,885,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25388768$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Rossi, Paolo</creatorcontrib><creatorcontrib>Shi, Lei</creatorcontrib><creatorcontrib>Liu, Gaohua</creatorcontrib><creatorcontrib>Barbieri, Christopher M.</creatorcontrib><creatorcontrib>Lee, Hsiau-Wei</creatorcontrib><creatorcontrib>Grant, Thomas D.</creatorcontrib><creatorcontrib>Luft, Joseph R.</creatorcontrib><creatorcontrib>Xiao, Rong</creatorcontrib><creatorcontrib>Acton, Thomas B.</creatorcontrib><creatorcontrib>Snell, Edward H.</creatorcontrib><creatorcontrib>Montelione, Gaetano T.</creatorcontrib><creatorcontrib>Baker, David</creatorcontrib><creatorcontrib>Lange, Oliver F.</creatorcontrib><creatorcontrib>Sgourakis, Nikolaos G.</creatorcontrib><title>A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta</title><title>Proteins, structure, function, and bioinformatics</title><addtitle>Proteins</addtitle><description>ABSTRACT
Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology‐based methods, protein–protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet‐V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1. Unlike conventional methods relying on a dense network of experimental restraints, the sparse data are used to limit conformational search during optimization of a physically realistic energy function. This work highlights a new approach for studying minor conformational changes due to structural plasticity within a single dimeric interface in solution. Proteins 2015; 83:309–317. © 2014 Wiley Periodicals, Inc.</description><subject>Alteromonadaceae - chemistry</subject><subject>Bacterial Proteins - chemistry</subject><subject>Colwellia</subject><subject>CS-Rosetta modeling</subject><subject>Models, Molecular</subject><subject>nuclear magnetic resonance spectroscopy</subject><subject>Nuclear Magnetic Resonance, Biomolecular</subject><subject>protein complex</subject><subject>Protein Structure, Secondary</subject><subject>Protein Structure, Tertiary</subject><subject>residual dipolar coupling</subject><subject>Scattering, Small Angle</subject><subject>small-angle X-ray scattering</subject><subject>Solutions</subject><subject>X-Ray Diffraction</subject><issn>0887-3585</issn><issn>1097-0134</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkU9PFDEYxhujkQW8-AFMEy9eBtrp_4vJQhRMEGTZBG9Np9PZLc5O13YG3W9vh4WNePL0Nnl_z9OnfQB4i9ERRqg8XsfQH5VUYPUCTDBSokCY0JdggqQUBWGS7YH9lO4QQlwR_hrslYzkFZcToKdwuamir-Hl19nxzfT7TVGZ5Gpo1tnW2CVsQoS1Tzb6le9M77sFDK1fhJWL3sLxbuc76LvexcZYl-CQRmYWkut7cwheNaZN7s3jPADzz5_mp-fFxdXZl9PpReEpJaqobV1ZxSpGmaNG2YYIycoaW6eEqDlxDWJ5WqIMahBhllTGMotESZSkiByAj1vb9VCtXG1d10fT6nUObeJGB-P1803nl3oR7jVDHFOGs8GHR4MYfg4u9XqV3-za1nQuDEljzigXTKLyf9AxlcAso-__Qe_CELv8EZminEjMJM3Uu7_D71I_tZQBvAV--dZtdnuM9Ni_HjvQD_3rb7Or-cMpa4qtxqfe_d5pTPyhuSCC6dvLM42v5yfknM_0LfkD0WezFw</recordid><startdate>201502</startdate><enddate>201502</enddate><creator>Rossi, Paolo</creator><creator>Shi, Lei</creator><creator>Liu, Gaohua</creator><creator>Barbieri, Christopher M.</creator><creator>Lee, Hsiau-Wei</creator><creator>Grant, Thomas D.</creator><creator>Luft, Joseph R.</creator><creator>Xiao, Rong</creator><creator>Acton, Thomas B.</creator><creator>Snell, Edward H.</creator><creator>Montelione, Gaetano T.</creator><creator>Baker, David</creator><creator>Lange, Oliver F.</creator><creator>Sgourakis, Nikolaos G.</creator><general>Blackwell Publishing Ltd</general><general>Wiley Subscription Services, Inc</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>201502</creationdate><title>A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta</title><author>Rossi, Paolo ; Shi, Lei ; Liu, Gaohua ; Barbieri, Christopher M. ; Lee, Hsiau-Wei ; Grant, Thomas D. ; Luft, Joseph R. ; Xiao, Rong ; Acton, Thomas B. ; Snell, Edward H. ; Montelione, Gaetano T. ; Baker, David ; Lange, Oliver F. ; Sgourakis, Nikolaos G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-i4439-dcdbc95b545e4a9cf37852d1ce977d63ef057d6c39a0f035c3bac5c072398403</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Alteromonadaceae - chemistry</topic><topic>Bacterial Proteins - chemistry</topic><topic>Colwellia</topic><topic>CS-Rosetta modeling</topic><topic>Models, Molecular</topic><topic>nuclear magnetic resonance spectroscopy</topic><topic>Nuclear Magnetic Resonance, Biomolecular</topic><topic>protein complex</topic><topic>Protein Structure, Secondary</topic><topic>Protein Structure, Tertiary</topic><topic>residual dipolar coupling</topic><topic>Scattering, Small Angle</topic><topic>small-angle X-ray scattering</topic><topic>Solutions</topic><topic>X-Ray Diffraction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Rossi, Paolo</creatorcontrib><creatorcontrib>Shi, Lei</creatorcontrib><creatorcontrib>Liu, Gaohua</creatorcontrib><creatorcontrib>Barbieri, Christopher M.</creatorcontrib><creatorcontrib>Lee, Hsiau-Wei</creatorcontrib><creatorcontrib>Grant, Thomas D.</creatorcontrib><creatorcontrib>Luft, Joseph R.</creatorcontrib><creatorcontrib>Xiao, Rong</creatorcontrib><creatorcontrib>Acton, Thomas B.</creatorcontrib><creatorcontrib>Snell, Edward H.</creatorcontrib><creatorcontrib>Montelione, Gaetano T.</creatorcontrib><creatorcontrib>Baker, David</creatorcontrib><creatorcontrib>Lange, Oliver F.</creatorcontrib><creatorcontrib>Sgourakis, Nikolaos G.</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Proteins, structure, function, and bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Rossi, Paolo</au><au>Shi, Lei</au><au>Liu, Gaohua</au><au>Barbieri, Christopher M.</au><au>Lee, Hsiau-Wei</au><au>Grant, Thomas D.</au><au>Luft, Joseph R.</au><au>Xiao, Rong</au><au>Acton, Thomas B.</au><au>Snell, Edward H.</au><au>Montelione, Gaetano T.</au><au>Baker, David</au><au>Lange, Oliver F.</au><au>Sgourakis, Nikolaos G.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta</atitle><jtitle>Proteins, structure, function, and bioinformatics</jtitle><addtitle>Proteins</addtitle><date>2015-02</date><risdate>2015</risdate><volume>83</volume><issue>2</issue><spage>309</spage><epage>317</epage><pages>309-317</pages><issn>0887-3585</issn><eissn>1097-0134</eissn><abstract>ABSTRACT
Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology‐based methods, protein–protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet‐V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1. Unlike conventional methods relying on a dense network of experimental restraints, the sparse data are used to limit conformational search during optimization of a physically realistic energy function. This work highlights a new approach for studying minor conformational changes due to structural plasticity within a single dimeric interface in solution. Proteins 2015; 83:309–317. © 2014 Wiley Periodicals, Inc.</abstract><cop>United States</cop><pub>Blackwell Publishing Ltd</pub><pmid>25388768</pmid><doi>10.1002/prot.24719</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Proteins, structure, function, and bioinformatics, 2015-02, Vol.83 (2), p.309-317 |
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| source | MEDLINE; Wiley Online Library All Journals |
| subjects | Alteromonadaceae - chemistry Bacterial Proteins - chemistry Colwellia CS-Rosetta modeling Models, Molecular nuclear magnetic resonance spectroscopy Nuclear Magnetic Resonance, Biomolecular protein complex Protein Structure, Secondary Protein Structure, Tertiary residual dipolar coupling Scattering, Small Angle small-angle X-ray scattering Solutions X-Ray Diffraction |
| title | A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta |
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