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Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Oct;80(4 Pt 1):041908. Epub 2009 Oct 6.

Self-similarity and protein compactness.

Author information

1
Programa de Modelagem Computacional, SENAI CIMATEC, Salvador, BA, Brazil. mamoret@gmail.com

Abstract

The hydrophobic effect is the major factor that drives a protein toward collapse and folding. As a consequence of the folding process a hydrophobic core is shielded by the solvent-accessible surface area of the protein. We analyze the solvent-accessible surface area of 1825 nonhomolog protein chains deposited in the Brookhaven Protein Data Bank. This solvent-accessible surface area presents an intrinsic self-similarity behavior. The comparison between the accessible surface area as function of the number of amino acids and the accessible surface area as function of gyration radius supplies a measure of the scaling exponent close to the one observed by volume as function of radius of gyration or by mass-size exponent. The present finding indicates that the fractal analysis describes the protein compactness as an object packing between random spheres in percolation threshold and crumpled wires.

PMID:
19905343
DOI:
10.1103/PhysRevE.80.041908
[Indexed for MEDLINE]
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