InforLorV4, Hal, Checkpoint, bibRecord, 000575

A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions

Identifieur interne : 000575 ( Hal/Checkpoint ); précédent : 000574; suivant : 000576

A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions

Auteurs : Anisah Ghoorah [France] ; Marie-Dominique Devignes [France] ; Seyed Alborzi [France] ; Malika Smaïl-Tabbone [France] ; David Ritchie [France]

Source :

RBID : Hal:hal-01216748

English descriptors

mix :
- domain-domain interactions, interaction promiscuity, protein binding sites, protein domain, protein secondary structure, protein-protein interactions.

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.

Url:

https://hal.inria.fr/hal-01216748

DOI: 10.3390/biology4020327

Links toward previous steps (curation, corpus...)

to stream Hal, to step Corpus: 000495
to stream Hal, to step Curation: 000495

Links to Exploration step

Hal:hal-01216748

Le document en format XML

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<profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>domain-domain interactions</term>
<term>interaction promiscuity</term>
<term>protein binding sites</term>
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<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>
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<hal api="V3"><titleStmt><title xml:lang="en">A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions</title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions</title>
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<surname>Ghoorah</surname>
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<author role="aut"><persName><forename type="first">Marie-Dominique</forename>
<surname>Devignes</surname>
</persName>
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<surname>Alborzi</surname>
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<email>seyed-ziaeddin.alborzi@inria.fr</email>
<idno type="halAuthorId">1234130</idno>
<affiliation ref="#struct-420402"></affiliation>
</author>
<author role="aut"><persName><forename type="first">Malika</forename>
<surname>Smaïl-Tabbone</surname>
</persName>
<email>malika@loria.fr</email>
<idno type="idHal">malika-smail-tabbone</idno>
<idno type="halAuthorId">62326</idno>
<affiliation ref="#struct-205125"></affiliation>
</author>
<author role="aut"><persName><forename type="first">David</forename>
<surname>Ritchie</surname>
</persName>
<email>Dave.Ritchie@loria.fr</email>
<idno type="idHal">david-ritchie</idno>
<idno type="halAuthorId">448588</idno>
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<title level="j">Biology</title>
<imprint><publisher>MDPI</publisher>
<biblScope unit="volume">4</biblScope>
<biblScope unit="issue">2</biblScope>
<biblScope unit="pp">327-343</biblScope>
<date type="datePub">2015-04-09</date>
<date type="dateEpub">2015-04-09</date>
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<idno type="doi">10.3390/biology4020327</idno>
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<textClass><keywords scheme="author"><term xml:lang="en">protein secondary structure</term>
<term xml:lang="en">protein domain</term>
<term xml:lang="en">protein binding sites</term>
<term xml:lang="en">protein-protein interactions</term>
<term xml:lang="en">domain-domain interactions</term>
<term xml:lang="en">interaction promiscuity</term>
</keywords>
<classCode scheme="halDomain" n="info.info-bi">Computer Science [cs]/Bioinformatics [q-bio.QM]</classCode>
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<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.</abstract>
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A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions

A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions

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