Journal article Open Access
Enright, Matthew B.; Leitner, David M.
<?xml version='1.0' encoding='UTF-8'?> <record xmlns="http://www.loc.gov/MARC21/slim"> <leader>00000nam##2200000uu#4500</leader> <datafield tag="540" ind1=" " ind2=" "> <subfield code="a">Other (Open)</subfield> </datafield> <datafield tag="260" ind1=" " ind2=" "> <subfield code="c">2005-01-27</subfield> </datafield> <controlfield tag="005">20200120174238.0</controlfield> <controlfield tag="001">895378</controlfield> <datafield tag="909" ind1="C" ind2="O"> <subfield code="p">openaire</subfield> <subfield code="o">oai:zenodo.org:895378</subfield> </datafield> <datafield tag="520" ind1=" " ind2=" "> <subfield code="a">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.</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="a">Leitner, David M.</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">557135</subfield> <subfield code="z">md5:35830e479f707465aae61ae2f603cf45</subfield> <subfield code="u">https://zenodo.org/record/895378/files/article.pdf</subfield> </datafield> <datafield tag="542" ind1=" " ind2=" "> <subfield code="l">open</subfield> </datafield> <datafield tag="980" ind1=" " ind2=" "> <subfield code="a">publication</subfield> <subfield code="b">article</subfield> </datafield> <datafield tag="100" ind1=" " ind2=" "> <subfield code="a">Enright, Matthew B.</subfield> </datafield> <datafield tag="024" ind1=" " ind2=" "> <subfield code="a">10.1103/physreve.71.011912</subfield> <subfield code="2">doi</subfield> </datafield> <datafield tag="245" ind1=" " ind2=" "> <subfield code="a">Mass fractal dimension and the compactness of proteins</subfield> </datafield> <datafield tag="650" ind1="1" ind2="7"> <subfield code="a">cc-by</subfield> <subfield code="2">opendefinition.org</subfield> </datafield> </record>
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