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Bioinformatics Advance Access originally published online on June 4, 2004
Bioinformatics 2004 20(17):2904-2910; doi:10.1093/bioinformatics/bth344
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Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.

Discovery Note

Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins

Neeraj Pandey {dagger}, Mythily Ganapathi {dagger}, Kaushal Kumar , Dipayan Dasgupta , Sushanta Kumar Das Sutar and Debasis Dash *

Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Mall Road, Delhi 110 007, India

Received on February 24, 2004; revised on April 22, 2004; accepted on May 13, 2004
Advance Access Publication June 4, 2004

Summary: Absence of any regular structure is increasingly being observed in structural studies of proteins. These disordered regions or random coils, which have been observed under physiological conditions, are indicators of protein plasticity. The wide variety of interactions possible due to the flexibility of these ‘natively disordered’ regions confers functional advantage to the protein and the organism in general. This concept is underscored by the increasing proportion of intrinsically unstructured proteins seen with the ascension in the complexity of the organisms.

The ‘natively unfolded/disordered’ state of the protein can be predicted utilizing Uversky's or Dunker's algorithm. We utilized Uversky's prediction scheme and based on the unique position of a protein in the charge–hydrophobicity plot, a derived net score was used to predict the overall disorder of the human housekeeping and non-housekeeping proteins. Substantial numbers of proteins in both the classes were predicted to be unfolded. However, comparative genomic analysis of predicted unfolded Homo sapiens proteins with homologues in Caenorhabditis elegans, Drosophila melanogaster and Mus musculus revealed significant increase in unfoldedness in non-housekeeping proteins in comparison with housekeeping proteins. Our analysis in the evolutionary context suggests addition or substitution of amino acid residues which favour unfoldedness in non-housekeeping proteins compared to housekeeping proteins.

Supplementary information: http://www.igib.res.in/data/pda/proteindisorderanalysis.html

Contact: ddash{at}igib.res.in

* To whom correspondence should be addressed.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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