A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions
Identifieur interne : 000772 ( Main/Exploration ); précédent : 000771; suivant : 000773A 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.
English descriptors
- mix :
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 (“
Url:
DOI: 10.3390/biology4020327
PubMed: 25860777
PubMed Central: 4498303
Affiliations:
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Ghoorah</name><affiliation><nlm:aff id="af1-biology-04-00327">Department of Computer Science and Engineering, University of Mauritius, 80837 Reduit, Mauritius; E-Mail:<email>a.ghoorah@uom.ac.mu</email></nlm:aff></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:aff id="af2-biology-04-00327">CNRS, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France; E-Mail:<email>devignes@loria.fr</email></nlm:aff></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:aff id="af3-biology-04-00327">Inria Nancy—Grand Est, 54600 Villers-lès-Nancy, France; E-Mail:<email>seyed-ziaeddin.alborzi@inria.fr</email></nlm:aff></affiliation><affiliation><nlm:aff id="af4-biology-04-00327">University of Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France; E-Mail:<email>malika.smail@loria.fr</email></nlm:aff></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:aff id="af4-biology-04-00327">University of Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France; E-Mail:<email>malika.smail@loria.fr</email></nlm:aff></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:aff id="af3-biology-04-00327">Inria Nancy—Grand Est, 54600 Villers-lès-Nancy, France; E-Mail:<email>seyed-ziaeddin.alborzi@inria.fr</email></nlm:aff></affiliation></author></analytic><series><title level="j">Biology</title><idno type="eISSN">2079-7737</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>domain-domain interactions</term><term>interaction promiscuity</term><term>protein binding sites</term><term>protein domain</term><term>protein secondary structure</term><term>protein-protein interactions</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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 (“<italic>α</italic>” for helices, “<italic>β</italic>” for strands, and “<italic>γ</italic>” for irregular structure) and we have analysed how frequently these classes occur in DDIs. Our results show that <italic>β</italic> elements are not highly represented in DFBSs compared to <italic>α</italic> and <italic>γ</italic> elements. At the DDI level, all classes of binding sites tend to preferentially bind to the same class of binding sites and <italic>α</italic>/<italic>β</italic> 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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ezkurdia, I" uniqKey="Ezkurdia I">I. Ezkurdia</name></author><author><name sortKey="Bartoli, L" uniqKey="Bartoli L">L. Bartoli</name></author><author><name sortKey="Fariselli, P" uniqKey="Fariselli P">P. Fariselli</name></author><author><name sortKey="Casadio, R" uniqKey="Casadio R">R. Casadio</name></author><author><name sortKey="Valencia, A" uniqKey="Valencia A">A. Valencia</name></author><author><name sortKey="Tress, M L" uniqKey="Tress M">M.L. Tress</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Berman, H M" uniqKey="Berman H">H.M. 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Berman</name></author><author><name sortKey="Battistuz, T" uniqKey="Battistuz T">T. Battistuz</name></author><author><name sortKey="Bhat, T N" uniqKey="Bhat T">T.N. Bhat</name></author><author><name sortKey="Bluhm, W F" uniqKey="Bluhm W">W.F. Bluhm</name></author><author><name sortKey="Bourne, P E" uniqKey="Bourne P">P.E. Bourne</name></author><author><name sortKey="Burkhardt, K" uniqKey="Burkhardt K">K. Burkhardt</name></author><author><name sortKey="Iype, L" uniqKey="Iype L">L. Iype</name></author><author><name sortKey="Jain, S" uniqKey="Jain S">S. Jain</name></author><author><name sortKey="Fagan, P" uniqKey="Fagan P">P. Fagan</name></author><author><name sortKey="Marvin, J" uniqKey="Marvin J">J. Marvin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Holm, L" uniqKey="Holm L">L. Holm</name></author><author><name sortKey="Sander, C" uniqKey="Sander C">C. Sander</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Alborzi, Seyed Ziaeddin" sort="Alborzi, Seyed Ziaeddin" uniqKey="Alborzi S" first="Seyed Ziaeddin" last="Alborzi">Seyed Ziaeddin Alborzi</name><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name><name sortKey="Ghoorah, Anisah W" sort="Ghoorah, Anisah W" uniqKey="Ghoorah A" first="Anisah W." last="Ghoorah">Anisah W. Ghoorah</name><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W." last="Ritchie">David W. Ritchie</name><name sortKey="Smail Tabbone, Malika" sort="Smail Tabbone, Malika" uniqKey="Smail Tabbone M" first="Malika" last="Smaïl-Tabbone">Malika Smaïl-Tabbone</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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