On the asymmetry of the residue compositions of the binding sites on protein surfaces.
By screening all the ligand binding sites in the Protein Data Bank, we have found that while it is geometrically possible that a loop, formed from a protein chain with residues ZYX, would "impersonate" another chain-loop with residues XYZ by a simple twisting of either the loop or the bound ligand, it almost never happens. This fact is rather surprising, and implies a notable asymmetry, since (i) loops in the folded proteins sometimes can be flexible enough to be twisted, but (ii) ligands are almost always extremely mobile before binding to the protein, therefore they can turn around and bind to residue-sequence ZYX as well. Data availability: The supplementary Table 3 lists the appearances of the residue-sequences and their inverses in the binding sites of the whole PDB, and is available at http://www.worldscient.com/jbcb/.
Iván
Gábor
G
Eötvös University, Budapest, Hungary.
Szabadka
Zoltán
Z
Grolmusz
Vince
V
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D001665:Binding Sites; D003628:Database Management Systems; D030562:Databases, Protein; D008969:Molecular Sequence Data; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*
D000596:Amino Acids; D011506:Proteins