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Binding specificities of the GYF domains from two Saccharomyces cerevisiae paralogs.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2007 (English)In: Protein Eng Des Sel, ISSN 1741-0126, Vol. 20, no 9, 443-52 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2007. Vol. 20, no 9, 443-52 p.
Keyword [en]
Algorithms, Cytoplasm/metabolism, Fungal Proteins/chemistry/metabolism, Green Fluorescent Proteins/metabolism, Least-Squares Analysis, Models; Theoretical, Peptides/chemistry, Protein Binding, Protein Structure; Tertiary, RNA; Messenger/metabolism, Reproducibility of Results, Saccharomyces cerevisiae/*metabolism, Software, Structure-Activity Relationship
URN: urn:nbn:se:su:diva-12054ISI: 000250685400004PubMedID: 17804396OAI: diva2:178574
Available from: 2008-01-15 Created: 2008-01-15 Last updated: 2011-01-11Bibliographically approved

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Georgiev, AlexanderWieslander, Åke
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