Assignment strategy for fast relaxing signals: complete aminoacid identification in thulium substituted calbindin D 9K.
Identifieur interne : 000620 ( PubMed/Checkpoint ); précédent : 000619; suivant : 000621Assignment strategy for fast relaxing signals: complete aminoacid identification in thulium substituted calbindin D 9K.
Auteurs : Stéphane Balayssac [Italie] ; Beatriz Jiménez ; Mario PiccioliSource :
- Journal of biomolecular NMR [ 0925-2738 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Amino Acids, S100 Calcium Binding Protein G, Thulium.
- methods : Nuclear Magnetic Resonance, Biomolecular.
- Animals, Calbindins, Humans, Protein Structure, Tertiary.
Abstract
Paramagnetic proteins generally contain regions with diverse relaxation properties. Nuclei in regions far from the metal center may behave like those in diamagnetic proteins, but those closer to the metal experience rapid relaxation with accompanying line broadening. We have used a set of NMR experiments optimized to capture data from these various concentric regions in assigning the signals from a paramagnetic Calbindin D 9K derivative in which one of the two calcium ions has been replaced by thulium(III). Normal double- and triple-resonance experiments with 1H detection were used in collecting data from nuclei in the diamagnetic-like region; these approaches identified signals from fewer than 50% of the amino acid residues (those with d > 17.5 A from thulium(III)). Paramagnetism-optimized two-dimensional NMR experiments with 1H detection were used in collecting data from nuclei in the next nearer region (d > 15 A). Standard (d > 14 A) and optimized (d > 9 A) 13C direct-detection experiments were used to capture data from nuclei in the next layer. Finally nuclei closest to the metal were detected by one-dimensional 13C (d > 5 A) and one-dimensional 15N data collection (d > 4.2 A). NMR signals were assigned on the basis of through-bond correlations and, for signals closest to the metal, pseudocontact shifts. The latter were determined from chemical shift differences between assigned signals in thulium(III) and lanthanum(III) derivatives of Calbindin D 9K and they were interpreted on the basis of a structural model for the lanthanide-substituted protein. This approach yielded assignments of at least one resonance per amino acid residue, including those in the thulium(III) coordination sphere.
DOI: 10.1007/s10858-005-5359-z
PubMed: 16518694
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Nuclei in regions far from the metal center may behave like those in diamagnetic proteins, but those closer to the metal experience rapid relaxation with accompanying line broadening. We have used a set of NMR experiments optimized to capture data from these various concentric regions in assigning the signals from a paramagnetic Calbindin D 9K derivative in which one of the two calcium ions has been replaced by thulium(III). Normal double- and triple-resonance experiments with 1H detection were used in collecting data from nuclei in the diamagnetic-like region; these approaches identified signals from fewer than 50% of the amino acid residues (those with d > 17.5 A from thulium(III)). Paramagnetism-optimized two-dimensional NMR experiments with 1H detection were used in collecting data from nuclei in the next nearer region (d > 15 A). Standard (d > 14 A) and optimized (d > 9 A) 13C direct-detection experiments were used to capture data from nuclei in the next layer. Finally nuclei closest to the metal were detected by one-dimensional 13C (d > 5 A) and one-dimensional 15N data collection (d > 4.2 A). NMR signals were assigned on the basis of through-bond correlations and, for signals closest to the metal, pseudocontact shifts. The latter were determined from chemical shift differences between assigned signals in thulium(III) and lanthanum(III) derivatives of Calbindin D 9K and they were interpreted on the basis of a structural model for the lanthanide-substituted protein. This approach yielded assignments of at least one resonance per amino acid residue, including those in the thulium(III) coordination sphere.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">16518694</PMID><DateCreated><Year>2006</Year><Month>03</Month><Day>06</Day></DateCreated><DateCompleted><Year>2006</Year><Month>06</Month><Day>06</Day></DateCompleted><DateRevised><Year>2013</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0925-2738</ISSN><JournalIssue CitedMedium="Print"><Volume>34</Volume><Issue>2</Issue><PubDate><Year>2006</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Journal of biomolecular NMR</Title><ISOAbbreviation>J. Biomol. NMR</ISOAbbreviation></Journal><ArticleTitle>Assignment strategy for fast relaxing signals: complete aminoacid identification in thulium substituted calbindin D 9K.</ArticleTitle><Pagination><MedlinePgn>63-73</MedlinePgn></Pagination><Abstract><AbstractText>Paramagnetic proteins generally contain regions with diverse relaxation properties. Nuclei in regions far from the metal center may behave like those in diamagnetic proteins, but those closer to the metal experience rapid relaxation with accompanying line broadening. We have used a set of NMR experiments optimized to capture data from these various concentric regions in assigning the signals from a paramagnetic Calbindin D 9K derivative in which one of the two calcium ions has been replaced by thulium(III). Normal double- and triple-resonance experiments with 1H detection were used in collecting data from nuclei in the diamagnetic-like region; these approaches identified signals from fewer than 50% of the amino acid residues (those with d > 17.5 A from thulium(III)). Paramagnetism-optimized two-dimensional NMR experiments with 1H detection were used in collecting data from nuclei in the next nearer region (d > 15 A). Standard (d > 14 A) and optimized (d > 9 A) 13C direct-detection experiments were used to capture data from nuclei in the next layer. Finally nuclei closest to the metal were detected by one-dimensional 13C (d > 5 A) and one-dimensional 15N data collection (d > 4.2 A). NMR signals were assigned on the basis of through-bond correlations and, for signals closest to the metal, pseudocontact shifts. The latter were determined from chemical shift differences between assigned signals in thulium(III) and lanthanum(III) derivatives of Calbindin D 9K and they were interpreted on the basis of a structural model for the lanthanide-substituted protein. This approach yielded assignments of at least one resonance per amino acid residue, including those in the thulium(III) coordination sphere.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Balayssac</LastName><ForeName>Stéphane</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiménez</LastName><ForeName>Beatriz</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Piccioli</LastName><ForeName>Mario</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Biomol NMR</MedlineTA><NlmUniqueID>9110829</NlmUniqueID><ISSNLinking>0925-2738</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000596">Amino Acids</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D064026">Calbindins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D064030">S100 Calcium Binding Protein G</NameOfSubstance></Chemical><Chemical><RegistryNumber>8RKC5ATI4P</RegistryNumber><NameOfSubstance UI="D013932">Thulium</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName MajorTopicYN="N" UI="D000596">Amino Acids</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000737">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D000818">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D064026">Calbindins</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D006801">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="Y" UI="D019906">Nuclear Magnetic Resonance, Biomolecular</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000379">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D017434">Protein Structure, Tertiary</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D064030">S100 Calcium Binding Protein G</DescriptorName><QualifierName MajorTopicYN="Y" UI="Q000737">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D013932">Thulium</DescriptorName><QualifierName MajorTopicYN="Y" UI="Q000737">chemistry</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2005</Year><Month>6</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2005</Year><Month>11</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>3</Month><Day>7</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>6</Month><Day>7</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>3</Month><Day>7</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="doi">10.1007/s10858-005-5359-z</ArticleId><ArticleId IdType="pubmed">16518694</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Italie</li></country></list><tree><noCountry><name sortKey="Jimenez, Beatriz" sort="Jimenez, Beatriz" uniqKey="Jimenez B" first="Beatriz" last="Jiménez">Beatriz Jiménez</name><name sortKey="Piccioli, Mario" sort="Piccioli, Mario" uniqKey="Piccioli M" first="Mario" last="Piccioli">Mario Piccioli</name></noCountry><country name="Italie"><noRegion><name sortKey="Balayssac, Stephane" sort="Balayssac, Stephane" uniqKey="Balayssac S" first="Stéphane" last="Balayssac">Stéphane Balayssac</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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