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This article is part of the supplement: IEEE 7th International Conference on Bioinformatics and Bioengineering at Hardvard Medical School

Open Access Research

Protein intrinsic disorder toolbox for comparative analysis of viral proteins

Gerard Kian-Meng Goh1*, A Keith Dunker1 and Vladimir N Uversky123*

Author Affiliations

1 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA

2 Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA

3 Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia

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BMC Genomics 2008, 9(Suppl 2):S4  doi:10.1186/1471-2164-9-S2-S4

Published: 16 September 2008

Abstract

To examine the usefulness of protein disorder predictions as a tool for the comparative analysis of viral proteins, a relational database has been constructed. The database includes proteins from influenza A and HIV-related viruses. Annotations include viral protein sequence, disorder prediction, structure, and function. Location of each protein within a virion, if known, is also denoted. Our analysis reveals a clear relationship between proximity to the RNA core and the percentage of predicted disordered residues for a set of influenza A virus proteins.

Neuraminidases (NA) and hemagglutinin (HA) of major influenza A pandemics tend to pair in such a way that both proteins tend to be either ordered-ordered or disordered-disordered by prediction. This may be the result of these proteins evolving from being lipid-associated. High abundance of intrinsic disorder in envelope and matrix proteins from HIV-related viruses likely represents a mechanism where HIV virions can escape immune response despite the availability of antibodies for the HIV-related proteins. This exercise provides an example showing how the combined use of intrinsic disorder predictions and relational databases provides an improved understanding of the functional and structural behaviour of viral proteins.