Locating the active sites of enzymes using mechanical properties.
We have applied the calculation of mechanical properties to a dataset of almost 100 enzymes to determine the extent to which catalytic residues have distinct properties. Specifically, we have calculated force constants describing the ease of moving any given amino acid residue with respect to the other residues in the protein. The results show that catalytic residues are invariably associated with high force constants. Choosing an appropriate cutoff enables the detection of roughly 80% of catalytic residues with only 25% of false positives. It is shown that neither multidomain structures, nor the presence or absence of bound ligands hinder successful detections. It is however noted that active sites near the protein surface are more difficult to detect and that non-catalytic, but structurally key residues may also exhibit high force constants.
Sacquin-Mora
Sophie
S
Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
Laforet
Emilie
E
Lavery
Richard
R
D000595:Amino Acid Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry*; D019563:Mechanics; D008958:Models, Molecular
D004798:Enzymes