Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight?
Identifieur interne : 001029 ( Main/Exploration ); précédent : 001028; suivant : 001030Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight?
Auteurs : J S Fetrow [États-Unis] ; N. Siew ; J A Di Gennaro ; M. Martinez-Yamout ; H J Dyson ; J. SkolnickSource :
- Protein science : a publication of the Protein Society [ 0961-8368 ] ; 2001.
Descripteurs français
- KwdFr :
- Algorithmes (MeSH), Animaux (MeSH), Bases de données comme sujet (MeSH), Biologie informatique (méthodes), Caenorhabditis elegans (enzymologie), Caenorhabditis elegans (génétique), Conformation des protéines (MeSH), Dichroïsme circulaire (MeSH), Génome fongique (MeSH), Humains (MeSH), Modèles moléculaires (MeSH), Motifs d'acides aminés (MeSH), Oxidoreductases (composition chimique), Oxidoreductases (génétique), Oxidoreductases (métabolisme), Relation quantitative structure-activité (MeSH), Reproductibilité des résultats (MeSH), Saccharomyces cerevisiae (enzymologie), Saccharomyces cerevisiae (génétique), Similitude de séquences d'acides aminés (MeSH), Sites de fixation (MeSH), Sous-unités de protéines (MeSH), Spectroscopie par résonance magnétique (MeSH).
- MESH :
- composition chimique : Oxidoreductases.
- enzymologie : Caenorhabditis elegans, Saccharomyces cerevisiae.
- génétique : Caenorhabditis elegans, Oxidoreductases, Saccharomyces cerevisiae.
- métabolisme : Oxidoreductases.
- méthodes : Biologie informatique.
- Algorithmes, Animaux, Bases de données comme sujet, Conformation des protéines, Dichroïsme circulaire, Génome fongique, Humains, Modèles moléculaires, Motifs d'acides aminés, Relation quantitative structure-activité, Reproductibilité des résultats, Similitude de séquences d'acides aminés, Sites de fixation, Sous-unités de protéines, Spectroscopie par résonance magnétique.
English descriptors
- KwdEn :
- Algorithms (MeSH), Amino Acid Motifs (MeSH), Animals (MeSH), Binding Sites (MeSH), Caenorhabditis elegans (enzymology), Caenorhabditis elegans (genetics), Circular Dichroism (MeSH), Computational Biology (methods), Databases as Topic (MeSH), Genome, Fungal (MeSH), Humans (MeSH), Magnetic Resonance Spectroscopy (MeSH), Models, Molecular (MeSH), Oxidoreductases (chemistry), Oxidoreductases (genetics), Oxidoreductases (metabolism), Protein Conformation (MeSH), Protein Subunits (MeSH), Quantitative Structure-Activity Relationship (MeSH), Reproducibility of Results (MeSH), Saccharomyces cerevisiae (enzymology), Saccharomyces cerevisiae (genetics), Sequence Homology, Amino Acid (MeSH).
- MESH :
- chemical , chemistry : Oxidoreductases.
- enzymology : Caenorhabditis elegans, Saccharomyces cerevisiae.
- genetics : Caenorhabditis elegans, Oxidoreductases, Saccharomyces cerevisiae.
- chemical , metabolism : Oxidoreductases.
- methods : Computational Biology.
- Algorithms, Amino Acid Motifs, Animals, Binding Sites, Circular Dichroism, Databases as Topic, Genome, Fungal, Humans, Magnetic Resonance Spectroscopy, Models, Molecular, Protein Conformation, Protein Subunits, Quantitative Structure-Activity Relationship, Reproducibility of Results, Sequence Homology, Amino Acid.
Abstract
A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone.
DOI: 10.1110/ps.49201
PubMed: 11316881
PubMed Central: PMC2374196
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">11316881</PMID><DateCompleted><Year>2001</Year><Month>06</Month><Day>07</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0961-8368</ISSN><JournalIssue CitedMedium="Print"><Volume>10</Volume><Issue>5</Issue><PubDate><Year>2001</Year><Month>May</Month></PubDate></JournalIssue><Title>Protein science : a publication of the Protein Society</Title><ISOAbbreviation>Protein Sci</ISOAbbreviation></Journal><ArticleTitle>Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight?</ArticleTitle><Pagination><MedlinePgn>1005-14</MedlinePgn></Pagination><Abstract><AbstractText>A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fetrow</LastName><ForeName>J S</ForeName><Initials>JS</Initials><AffiliationInfo><Affiliation>Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Siew</LastName><ForeName>N</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Di Gennaro</LastName><ForeName>J A</ForeName><Initials>JA</Initials></Author><Author ValidYN="Y"><LastName>Martinez-Yamout</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Dyson</LastName><ForeName>H J</ForeName><Initials>HJ</Initials></Author><Author ValidYN="Y"><LastName>Skolnick</LastName><ForeName>J</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 GM048835</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>GM48835</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Protein Sci</MedlineTA><NlmUniqueID>9211750</NlmUniqueID><ISSNLinking>0961-8368</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D021122">Protein 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UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011487" MajorTopicYN="N">Protein Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D021122" MajorTopicYN="N">Protein Subunits</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D021281" MajorTopicYN="Y">Quantitative Structure-Activity Relationship</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012441" MajorTopicYN="N">Saccharomyces cerevisiae</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017386" MajorTopicYN="N">Sequence Homology, Amino Acid</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate 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Martinez-Yamout</name><name sortKey="Siew, N" sort="Siew, N" uniqKey="Siew N" first="N" last="Siew">N. Siew</name><name sortKey="Skolnick, J" sort="Skolnick, J" uniqKey="Skolnick J" first="J" last="Skolnick">J. Skolnick</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Fetrow, J S" sort="Fetrow, J S" uniqKey="Fetrow J" first="J S" last="Fetrow">J S Fetrow</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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