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Geometric Structural Aspects Of Proteins And Newcomb–Benford Law

Author

Listed:
  • M. A. MORET

    (Programa de Modelagem Computational — SENAI — Cimatec, Salvador, Bahia, Brazil;
    Departamento de Física — UEFS 44031-460 Feira de Santana, Bahia, Brazil)

  • V. de SENNA

    (Programa de Modelagem Computational — SENAI — Cimatec, Salvador, Bahia, Brazil)

  • M. C. SANTANA

    (Departamento de Física — UEFS 44031-460 Feira de Santana, Bahia, Brazil)

  • G. F. ZEBENDE

    (Programa de Modelagem Computational — SENAI — Cimatec, Salvador, Bahia, Brazil;
    Departamento de Física — UEFS 44031-460 Feira de Santana, Bahia, Brazil)

Abstract

The major factor that drives a protein toward collapse and folding is the hydrophobic effect. At the folding process a hydrophobic core is shielded by the solvent-accessible surface area of the protein. We study the behavior of the numbers in 5526 protein structures present in the Brookhaven Protein Data Bank. The first digit of mass, volume, average radius and solvent-accessible surface area are measured independently and we observe that most of these geometric observables obey the Newcomb–Benford law. That is volume, mass and average radius obey the Newcomb–Benford law. Nevertheless, the digits of the solvent-accessible surface area do not agree with the Newcomb–Benford law. The present findings indicate that the hydrophobic effect is responsible for the anomalous first digit behavior of solvent-accessible surface areas.

Suggested Citation

  • M. A. MORET & V. de SENNA & M. C. SANTANA & G. F. ZEBENDE, 2009. "Geometric Structural Aspects Of Proteins And Newcomb–Benford Law," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 20(12), pages 1981-1988.
    • Handle: RePEc:wsi:ijmpcx:v:20:y:2009:i:12:n:s0129183109014874
    DOI: 10.1142/S0129183109014874
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    Cited by:

    1. Matthew A. Cole & David J. Maddison & Liyun Zhang, 2020. "Testing the emission reduction claims of CDM projects using the Benford’s Law," Climatic Change, Springer, vol. 160(3), pages 407-426, June.
    2. Rocha Filho, T.M. & Mendes, J.F.F. & Lucio, M.L. & Moret, M.A., 2023. "COVID-19 data, mitigation policies and Newcomb–Benford law," Chaos, Solitons & Fractals, Elsevier, vol. 174(C).

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