Active site prediction for comparative model structures with thematics.
THEMATICS (Theoretical Microscopic Titration Curves) is a simple, reliable computational predictor of the active sites of enzymes from structure. Our method, based on well-established Finite Difference Poisson-Boltzmann techniques, identifies the ionisable residues with anomalous predicted titration behavior. A cluster of two or more such perturbed residues is a very reliable predictor of the active site. The protein does not have to bear any resemblance in sequence or structure to any previously characterized protein, but the method does require the three-dimensional structure. We now present evidence that THEMATICS can also locate the active site in structures built by comparative modeling from similar structures. Results are given for a total of 21 sets of proteins, including 21 templates and 83 comparative model structures. Detailed results are presented for three sets of orthologous proteins (Triosephosphate isomerase, 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase, and Aspartate aminotransferase) and for one set of human homologues of Aldose reductase with different functions. THEMATICS correctly locates the active site in the model structures. This suggests that the method can be applicable to a much larger set of proteins for which an experimentally determined structure is unavailable. With a few exceptions, the predicted active sites in the comparative model structures are similar to that of the corresponding template structure.
Shehadi
Ihsan A
IA
Department of Chemistry, United Arab Emirates University, Al-Ain, United Arab Emirates. I.Shehadi@uaeu.ac.ae
Abyzov
Alexej
A
Uzun
Alper
A
Wei
Ying
Y
Murga
Leonel F
LF
Ilyin
Valentin
V
Ondrechen
Mary Jo
MJ
D000465:Algorithms; D001665:Binding Sites; D004789:Enzyme Activation; D004798:Enzymes / Q000032:analysis / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D013329:Structure-Activity Relationship; D017186:Titrimetry / Q000379:methods*
D004798:Enzymes