Journal article Open Access

Mass fractal dimension and the compactness of proteins

Enright, Matthew B.; Leitner, David M.

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  <identifier identifierType="URL"></identifier>
      <creatorName>Enright, Matthew B.</creatorName>
      <givenName>Matthew B.</givenName>
      <creatorName>Leitner, David M.</creatorName>
      <givenName>David M.</givenName>
    <title>Mass fractal dimension and the compactness of proteins</title>
    <date dateType="Issued">2005-01-27</date>
  <resourceType resourceTypeGeneral="Text">Journal article</resourceType>
    <alternateIdentifier alternateIdentifierType="url"></alternateIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1103/physreve.71.011912</relatedIdentifier>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
    <description descriptionType="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 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
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