Residue network in protein native structure belongs to the universality class of a three-dimensional critical percolation cluster.
Single protein molecules are regarded as contact networks of amino-acid residues. Relationships between the shortest path lengths and the numbers of residues within single molecules in the native structures are examined for various sized proteins. A universal scaling among proteins is obtained, which shows that the residue networks are fractal networks. This universal fractal network is characterized with three kinds of dimensions: the network topological dimension D{c} approximately 1.9 , the fractal dimension D{f} approximately 2.5 , and the spectral dimension D{s} approximately 1.3 . These values are in surprisingly good coincidence with those of the three-dimensional critical percolation cluster. Hence the residue contact networks in the protein native structures belong to the universality class of the three-dimensional percolation cluster. The criticality is relevant to the ambivalence in the protein native structures, the coexistence of stability and instability, both of which are necessary for protein functions.
Morita
Hidetoshi
H
Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan. Hidetoshi.Morita@inln.cnrs.fr
Takano
Mitsunori
M
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins