Net charge center as the simplest model of a protein identifies up to 100% of active/binding site residues.

BACKGROUND: Electrostatic steering of ligands into active/binding sites is important for enzymatic catalysis and enhancing the affinity of metal-binding proteins. The net charge center of a protein, which describes the distribution of the charged residues in the protein subunit, has a specific location. As active sites in biological molecules are also located specifically, the biological implications of the model were examined by analyzing the relative locations of the net charge centers and the active/binding sites. MATERIAL/METHODS: Spatial structures from a set of 11 proteins with experimentally defined electrostatic steering residues and definitely known active site residues were analyzed. RESULTS: In 9 of 11 proteins, 70-100% of the active site residues belong to the residue cluster around the net charge center. On average, the charge center cluster identifies 78% of the active sites and 80% of the steering residues with few false positives. In several cases, comparison of proteins from different sources has shown that the differences in association rates correlate quantitatively with the relative locations of the net charge centers. CONCLUSIONS: In most of the proteins studied the net charge center is located close to the active site. Therefore, the active site in a novel enzyme or the binding site in a protein can be predicted solely from the three-dimensional structure of the protein. The residues forming clusters around the net charge center are often organized into continuous hydrophilic sequences, important for rapid and correct formation of the active site region during protein folding.