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Submitted on March 29, 2004
Revised on May 3, 2004
Accepted on May 13, 2004
Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047
Corresponding Author: middaugh{at}ku.edu
The behavior of the proteome reflects spatial and temporal organization both within and without cells. We propose that various macromolecular entities possessing polyanionic character such as proteoglycans, lipid bilayer surfaces, microtubules, microfilaments and polynucleotides may provide a functional network which mediates a variety of cellular phenomena. The interaction of proteins with this array of polyanions is characterized by a lower degree of specificity than seen with most commonly recognized macromolecular interactions. In this commentary, potential roles for this polyanion network in diverse functions such as protein/protein interactions, protein folding and stabilization, macromolecular transport and various disease processes are all considered as well as the use of polyanions as therapeutic agents. The role of small polyanions in the regulation of protein/polyanion interactions is also postulated. We provide preliminary experimental analysis of the extent to which proteins interact with polyanions inside cells using a combination of two-dimensional chromatographic and electrophoretic methods and antibody arrays. We conclude that many hundreds to thousands of such interactions are present in cells and argue that future understanding of the proteome will require that the “polyanion world” be taken into account.
This article has been cited by other articles:
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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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 N. R. Deleault, B. T. Harris, J. R. Rees, and S. Supattapone From the Cover: Formation of native prions from minimal components in vitro PNAS, June 5, 2007; 104(23): 9741 - 9746. [Abstract] [Full Text] [PDF]
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 T. J. Kamerzell, S. B. Joshi, D. McClean, L. Peplinskie, K. Toney, D. Papac, M. Li, and C. R. Middaugh Parathyroid hormone is a heparin/polyanion binding protein: Binding energetics and structure modification Protein Sci., June 1, 2007; 16(6): 1193 - 1203. [Abstract] [Full Text] [PDF]
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 N. Salamat-Miller, J. Fang, C. W. Seidel, Y. Assenov, M. Albrecht, and C. R. Middaugh A Network-based Analysis of Polyanion-binding Proteins Utilizing Human Protein Arrays J. Biol. Chem., April 6, 2007; 282(14): 10153 - 10163. [Abstract] [Full Text] [PDF]
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C. W. Kim, K. S. Han, K.-S. Ryu, B. H. Kim, K.-H. Kim, S. I. Choi, and B. L. Seong N-terminal domains of native multidomain proteins have the potential to assist de novo folding of their downstream domains in vivo by acting as solubility enhancers Protein Sci., April 1, 2007; 16(4): 635 - 643. [Abstract] [Full Text] [PDF]
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 N. Salamat-Miller, J. Fang, C. W. Seidel, A. M. Smalter, Y. Assenov, M. Albrecht, and C. R. Middaugh A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays Mol. Cell. Proteomics, December 1, 2006; 5(12): 2263 - 2278. [Abstract] [Full Text] [PDF]
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