Journal article Open Access
Enright, Matthew B.; Leitner, David M.
<?xml version='1.0' encoding='utf-8'?> <resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd"> <identifier identifierType="URL">https://zenodo.org/record/895378</identifier> <creators> <creator> <creatorName>Enright, Matthew B.</creatorName> <givenName>Matthew B.</givenName> <familyName>Enright</familyName> </creator> <creator> <creatorName>Leitner, David M.</creatorName> <givenName>David M.</givenName> <familyName>Leitner</familyName> </creator> </creators> <titles> <title>Mass fractal dimension and the compactness of proteins</title> </titles> <publisher>Zenodo</publisher> <publicationYear>2005</publicationYear> <dates> <date dateType="Issued">2005-01-27</date> </dates> <resourceType resourceTypeGeneral="JournalArticle"/> <alternateIdentifiers> <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/895378</alternateIdentifier> </alternateIdentifiers> <relatedIdentifiers> <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1103/physreve.71.011912</relatedIdentifier> </relatedIdentifiers> <rightsList> <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights> </rightsList> <descriptions> <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 proteins.</description> </descriptions> </resource>
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