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Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions

Nature Precedings

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Title Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions
 
Date 2007-01-19T11:36:08Z
 
Creator Pedro Beltrao
Luis Serrano
 
Subject Ecology
Bioinformatics
Evolutionary Biology
 
Description Protein interaction networks are an important part of the post-genomic effort to integrate a part-list view of the cell into system-level understanding. Using a set of 11 yeast genomes we show that combining comparative genomics and secondary structure information greatly increases consensus-based prediction of SH3 targets. Benchmarking of our method against positive and negative standards gave 83% accuracy with 26% coverage. The concept of an optimal divergence time for effective comparative genomics studies was analyzed, demonstrating that genomes of species that diverged very recently from _Saccharomyces cerevisiae_ (_S. mikatae_, _S. bayanus_, and _S. paradoxus_), or a long time ago (_Neurospora crassa_ and _Schizosaccharomyces pombe_), contain less information for accurate prediction of SH3 targets than species within the optimal divergence time proposed. We also show here that intrinsically disordered SH3 domain targets are more probable sites of interaction than equivalent sites within ordered regions. Our findings highlight several novel S. cerevisiae SH3 protein interactions, the value of selection of optimal divergence times in comparative genomics studies, and the importance of intrinsic disorder for protein interactions. Based on our results we propose novel roles for the _S. cerevisiae_ proteins Abp1p in endocytosis and Hse1p in endosome protein sorting.
 
Identifier http://precedings.nature.com/documents/16/version/1
oai:nature.com:10.1038/npre.2007.16.1
http://dx.doi.org/10.1038/npre.2007.16.1
 
Source Nature Precedings
 
Type Presentation
 
Rights Creative Commons Attribution 3.0 License