Journal article Open Access
Enright, Matthew B.; Leitner, David M.
<?xml version='1.0' encoding='utf-8'?> <oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"> <dc:creator>Enright, Matthew B.</dc:creator> <dc:creator>Leitner, David M.</dc:creator> <dc:date>2005-01-27</dc:date> <dc:description>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 compact 3- dimensional collapsed polymer. Indeed, we find that on average a protein in its PDB configuration fills about three-quarters of the volume within the protein surface. Protein mass is also found to scale with radius of gyration with an exponent of 2.5 for this set of proteins.</dc:description> <dc:identifier>https://zenodo.org/record/895378</dc:identifier> <dc:identifier>10.1103/physreve.71.011912</dc:identifier> <dc:identifier>oai:zenodo.org:895378</dc:identifier> <dc:rights>info:eu-repo/semantics/openAccess</dc:rights> <dc:title>Mass fractal dimension and the compactness of proteins</dc:title> <dc:type>info:eu-repo/semantics/article</dc:type> <dc:type>publication-article</dc:type> </oai_dc:dc>