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Locating the active sites of enzymes using mechanical properties
Author(s) -
SacquinMora Sophie,
Laforet Émilie,
Lavery Richard
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21353
Subject(s) - residue (chemistry) , catalysis , cutoff , amino acid residue , false positive paradox , enzyme , active site , force constant , chemistry , biological system , molecule , computer science , physics , biochemistry , biology , peptide sequence , organic chemistry , artificial intelligence , quantum mechanics , gene
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. Proteins 2007. © 2007 Wiley‐Liss, Inc.