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PEDS Advance Access published online on September 4, 2007
Protein Engineering Design and Selection, doi:10.1093/protein/gzm041
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

Article

Binding specificities of the GYF domains from two Saccharomyces cerevisiae Paralogs

Alexander Georgiev1, Michael Sjöström2 and Åke Wieslander1,3

1Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, The Arrhenius Laboratories, 106 91 Stockholm, Sweden 2Research Group for Chemometrics, Biological Chemistry, Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden

3 To whom correspondence should be addressed. E-mail: ake{at}dbb.su.se

We have used multivariate statistics and z-scales to represent peptide sequences in a PLS-QSAR model of previously studied binding affinities [ Kofler,M., Motzny,K. and Freund,C. (2005b) Mol. Cell. Proteomics, 4, 1797–1811.] of two GYF domains to an array of immobilized synthetic peptides. As a result, we established structural determinants of the binding specificities of the two proteins. Our model was used to define new sets of yeast proteins potentially interacting with Syh1 (YPL105C) and Smy2 (YBR172C). These sets were subsequently examined for co-occurrence of Gene Ontology terms, leading to suggest a group of likely interacting proteins with a common function in mRNA catabolism. Finally, subcellular localization of a GFP-fused Syh1 and Smy2 reinforced the possibility that these proteins reside in cytoplasmic sites of mRNA degradation, thereby providing experimental confirmation to the predictions from the model.

Keywords: GYF/PLS/QSAR

Received March 9, 2007; revised June 25, 2007; accepted July 5, 2007.


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