Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions
Correspondence: (Login to view email address)
- EMBL-Heidelberg
- EMBL-CRG Barcelona
- Document Type:
- Presentation
- Date:
- Received 19 January 2007 11:36 UTC; Posted 19 January 2007
- Subjects:
- Ecology, Bioinformatics, Evolutionary Biology
- Abstract:
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.
- Presented at:
- FEBS workshop “MODULAR PROTEIN DOMAINS, 10 September 2005
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Additional information
- License:
- This document is licensed to the public under the Creative Commons Attribution 2.5 License
- How to cite this document:
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Beltrao, Pedro and Serrano, Luis. Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2007.16.1> (2007)
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