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Protein chain packing and percolation threshold

Author

Listed:
  • Moret, M.A.
  • Santana, M.C.
  • Nogueira, E.
  • Zebende, G.F.

Abstract

The major factor that drives a protein chain toward collapse and folding is the hydrophobic effect. Amino acids with apolar side chains join forming a solvent-shielded hydrophobic core. This process pack the structure in the native one. Here we investigate the average packing density of 5526 protein chains deposited in the Brookhaven Protein Data Bank. This analysis is carried out from the scaling analysis of the mass-size exponent and it shows that the exponent is δ=2.47. This fractal dimension of the protein chain is close to the one obtained in the randomly packed spheres near their percolation threshold. The present findings supply a measure of the protein compactness, that tends to a constant protein chain packing. The average packing density tends to ρ=0.86a.u./Å3.

Suggested Citation

  • Moret, M.A. & Santana, M.C. & Nogueira, E. & Zebende, G.F., 2006. "Protein chain packing and percolation threshold," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 361(1), pages 250-254.
    • Handle: RePEc:eee:phsmap:v:361:y:2006:i:1:p:250-254
    DOI: 10.1016/j.physa.2005.08.001
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    References listed on IDEAS

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    1. Zebende, G.F. & Pereira, M.G. & Nogueira Jr., E. & Moret, M.A., 2005. "Universal persistence in astrophysical sources," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 349(3), pages 452-458.
    2. Haslem, John A. & Scheraga, Carl A. & Bedingfield, James P., 1999. "DEA efficiency profiles of U.S. banks operating internationally," International Review of Economics & Finance, Elsevier, vol. 8(2), pages 165-182, June.
    3. Karplus, Martin, 1999. "Protein folding: Insights from simulations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 263(1), pages 389-391.
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    1. Balankin, Alexander S. & Matamoros, Daniel Morales & Pineda León, Ernesto & Rangel, Antonio Horta & Martínez Cruz, Miguel Ángel & Samayoa Ochoa, Didier, 2009. "Topological crossovers in the forced folding of self-avoiding matter," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 388(9), pages 1780-1790.
    2. Ding, Li & Guan, Zhi-Hong, 2008. "Modeling wireless sensor networks using random graph theory," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(12), pages 3008-3016.

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