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Self-similarity and protein compactness

M. A. Moret1,2,*, M. C. Santana2, G. F. Zebende1,2, and P. G. Pascutti3

  • 1Programa de Modelagem Computacional, SENAI CIMATEC, Salvador, BA, Brazil
  • 2Departamento de Física, UEFS, 44031-460 Feira de Santana, BA, Brazil
  • 3Instituto de Biofísica, UFRJ, 21949-900 Rio de Janeiro, RJ, Brazil

  • *mamoret@gmail.com
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Phys. Rev. E 80, 041908 – Published 6 October, 2009

DOI: https://doi.org/10.1103/PhysRevE.80.041908

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.

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Phys. Rev. E 80, 041908– Published 6 October, 2009
  • Received 13 March 2009

© 2009 American Physical Society

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