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Molecular & Cellular Proteomics 5:2263-2278, 2006.
© 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays^*,S

Nazila Salamat-Miller, Jianwen Fang, Christopher W. Seidel^¶, Aaron M. Smalter, Yassen Assenov^||, Mario Albrecht^|| and C. Russell Middaugh^,**

From the Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, Bioinformatics Core Facility, University of Kansas, Lawrence, Kansas 66045, ^¶ Stowers Institute for Medical Research, Kansas City, Missouri 64110, and ^|| Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany

The high affinity of certain cellular polyanions for many proteins (polyanion-binding proteins (PABPs)) has been demonstrated previously. It has been hypothesized that such polyanions may be involved in protein structure stabilization, stimulation of folding through chaperone-like activity, and intra- and extracellular protein transport as well as intracellular organization. The purpose of the proteomics studies reported here was to seek evidence for the idea that the nonspecific but high affinity interactions of PABPs with polyanions have a functional role in intracellular processes. Utilizing yeast protein arrays and five biotinylated cellular polyanion probes (actin, tubulin, heparin, heparan sulfate, and DNA), we identified proteins that interact with these probes and analyzed their structural and amino acid sequence requirements as well as their predicted functions in the yeast proteome. We also provide evidence for the existence of a network-like system for PABPs and their potential roles as critical hubs in intracellular behavior. This investigation takes a first step toward achieving a better understanding of the nature of polyanion-protein interactions within cells and introduces an alternative way of thinking about intracellular organization.

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				J. Fang, Y. Dong, N. Salamat-Miller, and C. Russell Middaugh DB-PABP: a database of polyanion-binding proteins Nucleic Acids Res., January 11, 2008; 36(suppl_1): D303 - D306. [Abstract] [Full Text] [PDF]

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