A structure-based classification and analysis of protein domain family binding sites and their interactions.
Identifieur interne : 000058 ( PubMed/Corpus ); précédent : 000057; suivant : 000059A structure-based classification and analysis of protein domain family binding sites and their interactions.
Auteurs : Anisah W. Ghoorah ; Marie-Dominique Devignes ; Seyed Ziaeddin Alborzi ; Malika Smaïl-Tabbone ; David W. RitchieSource :
- Biology [ 2079-7737 ] ; 2015.
Abstract
While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive non-redundant set of domain family binding sites (DFBSs) and hetero domain-domain interactions (DDIs) extracted from our updated KBDOCK resource. We have partitioned 4001 DFBSs into five classes using their propensities for three types of secondary structural elements ("α" for helices, "β" for strands, and "γ" for irregular structure) and we have analysed how frequently these classes occur in DDIs. Our results show that β elements are not highly represented in DFBSs compared to α and γ elements. At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and α/β contacts are significantly disfavored. Very few DFBSs are promiscuous: 80% of them interact with just one Pfam domain. About 50% of our Pfam domains bear only one single-partner DFBS and are therefore monogamous in their interactions with other domains. Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein.
DOI: 10.3390/biology4020327
PubMed: 25860777
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A structure-based classification and analysis of protein domain family binding sites and their interactions.</title><author><name sortKey="Ghoorah, Anisah W" sort="Ghoorah, Anisah W" uniqKey="Ghoorah A" first="Anisah W" last="Ghoorah">Anisah W. Ghoorah</name><affiliation><nlm:affiliation>Department of Computer Science and Engineering, University of Mauritius, 80837 Reduit, Mauritius. a.ghoorah@uom.ac.mu.</nlm:affiliation></affiliation></author><author><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name><affiliation><nlm:affiliation>CNRS, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France. devignes@loria.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Alborzi, Seyed Ziaeddin" sort="Alborzi, Seyed Ziaeddin" uniqKey="Alborzi S" first="Seyed Ziaeddin" last="Alborzi">Seyed Ziaeddin Alborzi</name><affiliation><nlm:affiliation>Inria Nancy-Grand Est, 54600 Villers-lès-Nancy, France. malika.smail@loria.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Smail Tabbone, Malika" sort="Smail Tabbone, Malika" uniqKey="Smail Tabbone M" first="Malika" last="Smaïl-Tabbone">Malika Smaïl-Tabbone</name><affiliation><nlm:affiliation>University of Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France. malika.smail@loria.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W" last="Ritchie">David W. Ritchie</name><affiliation><nlm:affiliation>Inria Nancy-Grand Est, 54600 Villers-lès-Nancy, France. Dave.Ritchie@inria.fr.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="doi">10.3390/biology4020327</idno><idno type="RBID">pubmed:25860777</idno><idno type="pmid">25860777</idno><idno type="wicri:Area/PubMed/Corpus">000058</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000058</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A structure-based classification and analysis of protein domain family binding sites and their interactions.</title><author><name sortKey="Ghoorah, Anisah W" sort="Ghoorah, Anisah W" uniqKey="Ghoorah A" first="Anisah W" last="Ghoorah">Anisah W. Ghoorah</name><affiliation><nlm:affiliation>Department of Computer Science and Engineering, University of Mauritius, 80837 Reduit, Mauritius. a.ghoorah@uom.ac.mu.</nlm:affiliation></affiliation></author><author><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name><affiliation><nlm:affiliation>CNRS, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France. devignes@loria.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Alborzi, Seyed Ziaeddin" sort="Alborzi, Seyed Ziaeddin" uniqKey="Alborzi S" first="Seyed Ziaeddin" last="Alborzi">Seyed Ziaeddin Alborzi</name><affiliation><nlm:affiliation>Inria Nancy-Grand Est, 54600 Villers-lès-Nancy, France. malika.smail@loria.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Smail Tabbone, Malika" sort="Smail Tabbone, Malika" uniqKey="Smail Tabbone M" first="Malika" last="Smaïl-Tabbone">Malika Smaïl-Tabbone</name><affiliation><nlm:affiliation>University of Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France. malika.smail@loria.fr.</nlm:affiliation></affiliation></author><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W" last="Ritchie">David W. Ritchie</name><affiliation><nlm:affiliation>Inria Nancy-Grand Est, 54600 Villers-lès-Nancy, France. Dave.Ritchie@inria.fr.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Biology</title><idno type="eISSN">2079-7737</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive non-redundant set of domain family binding sites (DFBSs) and hetero domain-domain interactions (DDIs) extracted from our updated KBDOCK resource. We have partitioned 4001 DFBSs into five classes using their propensities for three types of secondary structural elements ("α" for helices, "β" for strands, and "γ" for irregular structure) and we have analysed how frequently these classes occur in DDIs. Our results show that β elements are not highly represented in DFBSs compared to α and γ elements. At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and α/β contacts are significantly disfavored. Very few DFBSs are promiscuous: 80% of them interact with just one Pfam domain. About 50% of our Pfam domains bear only one single-partner DFBS and are therefore monogamous in their interactions with other domains. Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="PubMed-not-MEDLINE"><PMID Version="1">25860777</PMID><DateCreated><Year>2015</Year><Month>04</Month><Day>11</Day></DateCreated><DateCompleted><Year>2015</Year><Month>04</Month><Day>11</Day></DateCompleted><DateRevised><Year>2015</Year><Month>07</Month><Day>11</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2079-7737</ISSN><JournalIssue CitedMedium="Print"><Volume>4</Volume><Issue>2</Issue><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>Biology</Title><ISOAbbreviation>Biology (Basel)</ISOAbbreviation></Journal><ArticleTitle>A structure-based classification and analysis of protein domain family binding sites and their interactions.</ArticleTitle><Pagination><MedlinePgn>327-43</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3390/biology4020327</ELocationID><Abstract><AbstractText>While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive non-redundant set of domain family binding sites (DFBSs) and hetero domain-domain interactions (DDIs) extracted from our updated KBDOCK resource. We have partitioned 4001 DFBSs into five classes using their propensities for three types of secondary structural elements ("α" for helices, "β" for strands, and "γ" for irregular structure) and we have analysed how frequently these classes occur in DDIs. Our results show that β elements are not highly represented in DFBSs compared to α and γ elements. At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and α/β contacts are significantly disfavored. Very few DFBSs are promiscuous: 80% of them interact with just one Pfam domain. About 50% of our Pfam domains bear only one single-partner DFBS and are therefore monogamous in their interactions with other domains. Conversely, promiscuous Pfam domains bear several DFBSs among which one or two are promiscuous, thereby multiplying the promiscuity of the concerned protein.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ghoorah</LastName><ForeName>Anisah W</ForeName><Initials>AW</Initials><AffiliationInfo><Affiliation>Department of Computer Science and Engineering, University of Mauritius, 80837 Reduit, Mauritius. a.ghoorah@uom.ac.mu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Devignes</LastName><ForeName>Marie-Dominique</ForeName><Initials>MD</Initials><AffiliationInfo><Affiliation>CNRS, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France. devignes@loria.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alborzi</LastName><ForeName>Seyed Ziaeddin</ForeName><Initials>SZ</Initials><AffiliationInfo><Affiliation>Inria Nancy-Grand Est, 54600 Villers-lès-Nancy, France. malika.smail@loria.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>University of Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France. malika.smail@loria.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Smaïl-Tabbone</LastName><ForeName>Malika</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>University of Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France. malika.smail@loria.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ritchie</LastName><ForeName>David W</ForeName><Initials>DW</Initials><AffiliationInfo><Affiliation>Inria Nancy-Grand Est, 54600 Villers-lès-Nancy, France. Dave.Ritchie@inria.fr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>04</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Biology (Basel)</MedlineTA><NlmUniqueID>101587988</NlmUniqueID><ISSNLinking>2079-7737</ISSNLinking></MedlineJournalInfo><OtherID Source="NLM">PMC4498303</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>1</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2015</Year><Month>3</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>3</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>4</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>4</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>4</Month><Day>11</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pii">biology4020327</ArticleId><ArticleId IdType="doi">10.3390/biology4020327</ArticleId><ArticleId IdType="pubmed">25860777</ArticleId><ArticleId IdType="pmc">PMC4498303</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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