Self-similarity and protein compactness.
The hydrophobic effect is the major factor that drives a protein toward collapse and folding. As a consequence of the folding process a hydrophobic core is shielded by the solvent-accessible surface area of the protein. We analyze the solvent-accessible surface area of 1825 nonhomolog protein chains deposited in the Brookhaven Protein Data Bank. This solvent-accessible surface area presents an intrinsic self-similarity behavior. The comparison between the accessible surface area as function of the number of amino acids and the accessible surface area as function of gyration radius supplies a measure of the scaling exponent close to the one observed by volume as function of radius of gyration or by mass-size exponent. The present finding indicates that the fractal analysis describes the protein compactness as an object packing between random spheres in percolation threshold and crumpled wires.
Moret
M A
MA
Programa de Modelagem Computacional, SENAI CIMATEC, Salvador, BA, Brazil. mamoret@gmail.com
Santana
M C
MC
Zebende
G F
GF
Pascutti
P G
PG
D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D014867:Water / Q000737:chemistry
D011506:Proteins; D012997:Solvents; D014867:Water