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# Mass fractal dimension and the compactness of proteins

Enright, Matthew B.; Leitner, David M.

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{
"description": "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.",
"creator": [
{
"@type": "Person",
"name": "Enright, Matthew B."
},
{
"@type": "Person",
"name": "Leitner, David M."
}
],
"headline": "Mass fractal dimension and the compactness of proteins",
"datePublished": "2005-01-27",
"url": "https://zenodo.org/record/895378",
"@context": "https://schema.org/",
"identifier": "https://doi.org/10.1103/physreve.71.011912",
"@id": "https://doi.org/10.1103/physreve.71.011912",
"@type": "ScholarlyArticle",
"name": "Mass fractal dimension and the compactness of proteins"
}
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