Mass fractal dimension and the compactness of proteins.
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.
Enright
Matthew B
MB
Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA.
Leitner
David M
DM
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
D011506:Proteins