NMR trial models: experiences with the colicin immunity protein Im7 and the p85alpha C-terminal SH2-peptide complex
Two cases of successful molecular replacement using NMR trial models are presented. One is the crystal structure of the Escherichia coli colicin immunity protein Im7; the other is a heretofore unreported crystal structure of a specific PDGF receptor-derived peptide complex of the carboxy-terminal SH...
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| Veröffentlicht in: | Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2001-10, Vol.57 (Pt 10), p.1397-1404 |
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| container_issue | Pt 10 |
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| container_title | Acta crystallographica. Section D, Biological crystallography. |
| container_volume | 57 |
| creator | Pauptit, R A Dennis, C A Derbyshire, D J Breeze, A L Weston, S A Rowsell, S Murshudov, G N |
| description | Two cases of successful molecular replacement using NMR trial models are presented. One is the crystal structure of the Escherichia coli colicin immunity protein Im7; the other is a heretofore unreported crystal structure of a specific PDGF receptor-derived peptide complex of the carboxy-terminal SH2 domain from the p85alpha subunit of human phosphatidylinositol 3-OH kinase. In both cases, molecular replacement was non-trivial. Success was achieved using trial models that consisted of an ensemble of NMR structures from which the more flexible portions had been excised. Use of maximum-likelihood refinement proved critical to be able to refine the poor starting models. The challenges typical of the use of NMR trial models in molecular replacement are discussed. |
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One is the crystal structure of the Escherichia coli colicin immunity protein Im7; the other is a heretofore unreported crystal structure of a specific PDGF receptor-derived peptide complex of the carboxy-terminal SH2 domain from the p85alpha subunit of human phosphatidylinositol 3-OH kinase. In both cases, molecular replacement was non-trivial. Success was achieved using trial models that consisted of an ensemble of NMR structures from which the more flexible portions had been excised. Use of maximum-likelihood refinement proved critical to be able to refine the poor starting models. 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Section D, Biological crystallography.</title><addtitle>Acta Crystallogr D Biol Crystallogr</addtitle><description>Two cases of successful molecular replacement using NMR trial models are presented. One is the crystal structure of the Escherichia coli colicin immunity protein Im7; the other is a heretofore unreported crystal structure of a specific PDGF receptor-derived peptide complex of the carboxy-terminal SH2 domain from the p85alpha subunit of human phosphatidylinositol 3-OH kinase. In both cases, molecular replacement was non-trivial. Success was achieved using trial models that consisted of an ensemble of NMR structures from which the more flexible portions had been excised. Use of maximum-likelihood refinement proved critical to be able to refine the poor starting models. The challenges typical of the use of NMR trial models in molecular replacement are discussed.</description><subject>Bacterial Proteins - chemistry</subject><subject>Colicins</subject><subject>Crystallography, X-Ray</subject><subject>Humans</subject><subject>Magnetic Resonance Spectroscopy</subject><subject>Models, Molecular</subject><subject>Peptide Fragments - chemistry</subject><subject>Peptide Fragments - metabolism</subject><subject>Phosphatidylinositol 3-Kinases - chemistry</subject><subject>Phosphatidylinositol 3-Kinases - metabolism</subject><subject>Protein Conformation</subject><subject>Receptors, Platelet-Derived Growth Factor - chemistry</subject><subject>src Homology Domains</subject><issn>0907-4449</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2001</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNo1kMFLwzAchXNQ3Jz-C5KTt0KSJkvqTYa6wVTQ3Uua_MoiSRubFLf_3qrz9ODx8fF4Z2hOKiILznk1Q5cpfRBCGCvlBZpRKpaSCjpH6eX5DefBaY9Db8GnOwyHCIODzkDCXy7vcd4DNr13xnXYhTB2Lh9xHPoMU7EJEuvO_kJRCe3jXuNVkWEIrpus72tWRIjZ2R9JiB4OV-i81T7B9SkXaPf4sFuti-3r02Z1vy2i4LTQrRVGcFNyVgompuFMKK4kWy6rtiVAZcmpabWyvGxkBdpWioG0BIyxttHlAt3-aaepnyOkXAeXDHivO-jHVEvKiFBKTeDNCRybALaOgwt6ONb_L5XfJAFi9A</recordid><startdate>200110</startdate><enddate>200110</enddate><creator>Pauptit, R A</creator><creator>Dennis, C A</creator><creator>Derbyshire, D J</creator><creator>Breeze, A L</creator><creator>Weston, S A</creator><creator>Rowsell, S</creator><creator>Murshudov, G N</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7X8</scope></search><sort><creationdate>200110</creationdate><title>NMR trial models: experiences with the colicin immunity protein Im7 and the p85alpha C-terminal SH2-peptide complex</title><author>Pauptit, R A ; Dennis, C A ; Derbyshire, D J ; Breeze, A L ; Weston, S A ; Rowsell, S ; Murshudov, G N</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p541-afd5c54c34235252372584872669ff0e17341cfa8d43b79ead982e7d0eccddba3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2001</creationdate><topic>Bacterial Proteins - chemistry</topic><topic>Colicins</topic><topic>Crystallography, X-Ray</topic><topic>Humans</topic><topic>Magnetic Resonance Spectroscopy</topic><topic>Models, Molecular</topic><topic>Peptide Fragments - chemistry</topic><topic>Peptide Fragments - metabolism</topic><topic>Phosphatidylinositol 3-Kinases - chemistry</topic><topic>Phosphatidylinositol 3-Kinases - metabolism</topic><topic>Protein Conformation</topic><topic>Receptors, Platelet-Derived Growth Factor - chemistry</topic><topic>src Homology Domains</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pauptit, R A</creatorcontrib><creatorcontrib>Dennis, C A</creatorcontrib><creatorcontrib>Derbyshire, D J</creatorcontrib><creatorcontrib>Breeze, A L</creatorcontrib><creatorcontrib>Weston, S A</creatorcontrib><creatorcontrib>Rowsell, S</creatorcontrib><creatorcontrib>Murshudov, G N</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>MEDLINE - Academic</collection><jtitle>Acta crystallographica. 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One is the crystal structure of the Escherichia coli colicin immunity protein Im7; the other is a heretofore unreported crystal structure of a specific PDGF receptor-derived peptide complex of the carboxy-terminal SH2 domain from the p85alpha subunit of human phosphatidylinositol 3-OH kinase. In both cases, molecular replacement was non-trivial. Success was achieved using trial models that consisted of an ensemble of NMR structures from which the more flexible portions had been excised. Use of maximum-likelihood refinement proved critical to be able to refine the poor starting models. The challenges typical of the use of NMR trial models in molecular replacement are discussed.</abstract><cop>United States</cop><pmid>11567151</pmid><tpages>8</tpages></addata></record> |
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| ispartof | Acta crystallographica. Section D, Biological crystallography., 2001-10, Vol.57 (Pt 10), p.1397-1404 |
| issn | 0907-4449 |
| language | eng |
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| source | MEDLINE; Crystallography Journals Online; Wiley Online Library Journals Frontfile Complete; Alma/SFX Local Collection |
| subjects | Bacterial Proteins - chemistry Colicins Crystallography, X-Ray Humans Magnetic Resonance Spectroscopy Models, Molecular Peptide Fragments - chemistry Peptide Fragments - metabolism Phosphatidylinositol 3-Kinases - chemistry Phosphatidylinositol 3-Kinases - metabolism Protein Conformation Receptors, Platelet-Derived Growth Factor - chemistry src Homology Domains |
| title | NMR trial models: experiences with the colicin immunity protein Im7 and the p85alpha C-terminal SH2-peptide complex |
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