A server and database for dipole moments of proteins.
An Internet server at http://bip.weizmann.ac.il/dipol calculates the net charge, dipole moment and mean radius of any 3D protein structure or its constituent peptide chains, and displays the dipole vector superimposed on a ribbon backbone of the protein. The server can also display the angle between the dipole and a selected list of amino acid residues in the protein. When the net charges and dipole moments of approximately 12 000 non-homologous PDB biological units (PISCES set), and their unique chains of length 50 residues or longer, were examined, the great majority of both charges and dipoles fell into a very narrow range of values, with long extended tails containing a few extreme outliers. In general, there is no obvious relation between a protein's charge or dipole moment and its structure or function, so that its electrostatic properties are highly specific to the particular protein, except that the majority of chains with very large positive charges or dipoles bind to ribosomes or interact with nucleic acids.
Felder
Clifford E
CE
Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.
Prilusky
Jaime
J
Silman
Israel
I
Sussman
Joel L
JL
D001703:Biophysics / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016206:Databases, Bibliographic; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry*; D005656:Fungal Proteins / Q000737:chemistry; D008433:Mathematics; D008958:Models, Molecular; D015233:Models, Statistical; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
D004798:Enzymes; D005656:Fungal Proteins; D011506:Proteins