Polyanions and the Proteome

• Published in: Molecular & cellular proteomics Vol. 3; no. 8; pp. 746 - 769
• Main Authors: Jones, LaToya S, Yazzie, Brian, Middaugh, C Russell
• Format: Journal Article
• Language: English
• Published: United States American Society for Biochemistry and Molecular Biology 01-08-2004
• Subjects: Animals; Biological Transport; Humans; Polymers - chemistry; Polymers - metabolism; Polymers - therapeutic use; Protein Array Analysis; Protein Binding; Protein Conformation; Protein Interaction Mapping; Proteins - metabolism; Proteins - physiology; Proteome - metabolism
• ISSN: 1535-9476; 1535-9484
• DOI: 10.1074/mcp.R400008-MCP200

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 that 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.