Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/14256
Title: Interactome-Wide Prediction of Protein-Protein Binding Sites Reveals Effects of Protein Sequence Variation in Arabidopsis thaliana
Authors: Leal Valentim, Felipe
NEVEN, Frank 
BOYEN, Peter 
van Dijk, Aalt D. J.
Issue Date: 2012
Source: PLoS One, 7(10), ( ART N° e47022)
Abstract: The specificity of protein-protein interactions is encoded in those parts of the sequence that compose the binding interface. Therefore, understanding how changes in protein sequence influence interaction specificity, and possibly the phenotype requires knowing the location of binding sites in those sequences. However, large-scale detection of protein interfaces remains a challenge. Here, we present a sequence- and interactome-based approach to mine interaction motifs from the recently published Arabidopsis thaliana interactome. The resultant proteome-wide predictions are available via www.ab.wur.nl/sliderbio and set the stage for further investigations of protein-protein binding sites. To assess our method, we first show that, by using a priori information calculated from protein sequences, such as evolutionary conservation and residue surface accessibility, we improve the performance of interface prediction compared to using only interactome data. Next, we present evidence for the functional importance of the predicted sites, which are under stronger selective pressure than the rest of protein sequence. We also observe a tendency for compensatory mutations in the binding sites of interacting proteins. Subsequently, we interrogated the interactome data to formulate testable hypotheses for the molecular mechanisms underlying effects of protein sequence mutations. Examples include proteins relevant for various developmental processes. Finally, we observed, by analysing pairs of paralogs, a correlation between functional divergence and sequence divergence in interaction sites. This analysis suggests that large-scale predction of binding sites can cast light on evolutionary processes that shape protein-protein interaction.
Document URI: http://hdl.handle.net/1942/14256
ISSN: 1932-6203
e-ISSN: 1932-6203
DOI: 10.1371/journal.pone.0047022
ISI #: 000309995100051
Category: A1
Type: Journal Contribution
Validations: ecoom 2013
Appears in Collections:Research publications

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