title: Mass fractal dimension and the compactness of proteins.
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 . Proteins: Struct., Funct. Bioinf. 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 three-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.
authors.affiliation: Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Enright
authors.forename: David M
authors.initials: DM
authors.lastname: Leitner
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D017709:Fractals; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D008970:Molecular Weight; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure*; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins