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Biology 2015, 4(2), 327-343; doi:10.3390/biology4020327

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

1
Department of Computer Science and Engineering, University of Mauritius, 80837 Reduit, Mauritius
2
CNRS, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France
3
Inria Nancy—Grand Est, 54600 Villers-lès-Nancy, France
4
University of Lorraine, LORIA, Campus Scientifique, BP 239, 54506 Vandoeuvre-lès-Nancy, France
*
Author to whom correspondence should be addressed.
Received: 16 January 2015 / Revised: 24 March 2015 / Accepted: 31 March 2015 / Published: 9 April 2015
(This article belongs to the Special Issue Protein-Protein Interactions)
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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. View Full-Text
Keywords: protein secondary structure; protein domain; protein binding sites; protein-protein interactions; domain-domain interactions; interaction promiscuity protein secondary structure; protein domain; protein binding sites; protein-protein interactions; domain-domain interactions; interaction promiscuity
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Ghoorah, A.W.; Devignes, M.-D.; Alborzi, S.Z.; Smaïl-Tabbone, M.; Ritchie, D.W. A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions. Biology 2015, 4, 327-343.

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