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

Anisah Ghoorah 1 Marie-Dominique Devignes 2 Seyed Ziaeddin Alborzi 2 Malika Smaïl-Tabbone 3 David Ritchie 2 
2 CAPSID - Computational Algorithms for Protein Structures and Interactions
Inria Nancy - Grand Est, LORIA - AIS - Department of Complex Systems, Artificial Intelligence & Robotics
3 ORPAILLEUR - Knowledge representation, reasonning
Inria Nancy - Grand Est, LORIA - NLPKD - Department of Natural Language Processing & Knowledge Discovery
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.
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Submitted on : Friday, October 16, 2015 - 7:35:57 PM
Last modification on : Thursday, August 4, 2022 - 5:18:45 PM

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Anisah Ghoorah, Marie-Dominique Devignes, Seyed Ziaeddin Alborzi, Malika Smaïl-Tabbone, David Ritchie. A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions. Biology, 2015, 4 (2), pp.327-343. ⟨10.3390/biology4020327⟩. ⟨hal-01216748⟩



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