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To be folded or to be unfolded?

Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia

(RECEIVED May 25, 2004; FINAL REVISION July 17, 2004; ACCEPTED July 17, 2004)

The lack of ordered structure in "natively unfolded" proteins raises a general question: Are there intrinsic properties of amino acid residues that are responsible for the absence of fixed structure at physiological conditions? In this article, we demonstrate that the competence of a protein to be folded or to be unfolded may be determined by the property of amino acid residues to form a sufficient number of contacts in a globular state. The expected average number of contacts per residue calculated from the amino acid sequence alone (using the average number of contacts for 20 amino acid residues in globular proteins) can be used as one of the simple indicators of natively unfolded proteins. The prediction accuracy for the sets of 80 folded and 90 natively unfolded proteins reaches 89% if the expected average number of contacts is used as a parameter and 83% in the case of hydrophobicity. An optimal set of artificial parameters for 20 amino acid residues obtained by Monte Carlo algorithm to maximally separate the sets of 90 natively unfolded and 80 folded proteins demonstrates the upper limit for prediction accuracy, which is 95%.

Keywords: number of contacts per residue; natively unfolded protein; globular protein; Monte Carlo simulation

Reprint requests to: Oxana V. Galzitskaya, Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia; e-mail: ogalzit{at}vega.protres.ru; fax: +7-095-924-0493.

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