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Describing some characters of serine proteinase using fractal analysis

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  • Peng, Xin
  • Qi, Wei
  • Su, Rongxin
  • He, Zhimin

Abstract

In this paper we calculated the fractal dimensions of four proteins, chymotrypsin, elastase, trypsin and subtilisin, which are made up of about 220–275 amino acids and belong to the family of serine proteinase by using three definitions of fractal dimension i.e. the chain fractal dimension (DL), the mass fractal dimension (Dm) and the correlation fractal dimension (Dc). We also analyzed the relationship between fractal dimension and space structure or secondary structure contents of proteins. The results showed that the values of fractal dimensions are almost same for the global mammalian enzymes (chymotrypsin, elastase and trypsin), but different for the global subtilisin. This demonstrated that the more similar structures, the more equal fractal dimensions, and if the fractal dimensions of proteins are different from each other, the three dimensional structures should not be similar. On the other hand, the detailed structures and fractal dimensions of the active sites of four enzymes are extraordinarily similar. Therefore, the fractal method can be applied to the elucidation of the proteins evolution.

Suggested Citation

  • Peng, Xin & Qi, Wei & Su, Rongxin & He, Zhimin, 2012. "Describing some characters of serine proteinase using fractal analysis," Chaos, Solitons & Fractals, Elsevier, vol. 45(7), pages 1017-1023.
    • Handle: RePEc:eee:chsofr:v:45:y:2012:i:7:p:1017-1023
    DOI: 10.1016/j.chaos.2012.04.002
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    References listed on IDEAS

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    1. Lee, Chang-Yong, 2008. "Self-similarity of biopolymer backbones in the ribosome," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(19), pages 4871-4880.
    2. Isvoran, Adriana & Pitulice, Laura & Craescu, Constantin T. & Chiriac, Adrian, 2008. "Fractal aspects of calcium binding protein structures," Chaos, Solitons & Fractals, Elsevier, vol. 35(5), pages 960-966.
    3. Tejera, E. & Machado, A. & Rebelo, I. & Nieto-Villar, J., 2009. "Fractal protein structure revisited: Topological, kinetic and thermodynamic relationships," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 388(21), pages 4600-4608.
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