Journal article Open Access

Mass fractal dimension and the compactness of proteins

Enright, Matthew B.; Leitner, David M.


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{
  "DOI": "10.1103/physreve.71.011912", 
  "author": [
    {
      "family": "Enright, Matthew B."
    }, 
    {
      "family": "Leitner, David M."
    }
  ], 
  "issued": {
    "date-parts": [
      [
        2005, 
        1, 
        27
      ]
    ]
  }, 
  "abstract": "Vibrational dynamics and energy flow in a protein are related by Alexander-Orbach\ntheory to the protein's mass fractal dimension, D, and spectral dimension, d . Burioni et\nal. [Proteins: Struct., Funct. and Bioinformatics 55, 529 (2004)] recently proposed a\nrelation between d and protein size based on their computational analysis of a set of\nproteins ranging from about 100 to several thousand amino acids. We report here values\nfor D computed for 200 proteins from the Protein Data Bank (PDB) ranging from about\n100 to over 10,000 amino acids and examine variation of D with protein size. The\naverage D is found to be 2.5, significantly smaller than a completely compact 3-\ndimensional collapsed polymer. Indeed, we find that on average a protein in its PDB\nconfiguration fills about three-quarters of the volume within the protein surface. Protein\nmass is also found to scale with radius of gyration with an exponent of 2.5 for this set of\nproteins.", 
  "title": "Mass fractal dimension and the compactness of proteins", 
  "type": "article-journal", 
  "id": "895378"
}
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