publication . Article . Other literature type . 2005

Mass fractal dimension and the compactness of proteins.

Enright, Matthew B.; Leitner, David M.;
Open Access
  • Published: 27 Jan 2005 Journal: Physical Review E, volume 71 (issn: 1539-3755, eissn: 1550-2376, Copyright policy)
  • Publisher: American Physical Society (APS)
Abstract
Vibrational dynamics and energy flow in a protein are related by Alexander-Orbach theory to the protein's mass fractal dimension, D, and spectral dimension, d . Burioni et al. [Proteins: Struct., Funct. and Bioinformatics 55, 529 (2004)] recently proposed a relation between d and protein size based on their computational analysis of a set of proteins ranging from about 100 to several thousand amino acids. We report here values for D computed for 200 proteins from the Protein Data Bank (PDB) ranging from about 100 to over 10,000 amino acids and examine variation of D with protein size. The average D is found to be 2.5, significantly smaller than a completely comp...
Subjects
free text keywords: Classical mechanics, Compact space, Fractal, Physics, Fractal dimension, Geometry, Mathematical analysis, Fractal dimension on networks
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