The absence of S. cerevisiae binding sites in the distantly related species could be the result of a more complex model whereby one binding site is substituted for another site bound by a different transcription factor.
Ala290 at the interface of ThMA dimer in the vicinity of the substrate-binding site was substituted with isoleucine, which may cause a structural change due to its bulky side chain.
Data for "Sorachi Chubu Koiki Rengo", which includes study site, is substituted for the study site.
ESE sites were substituted at a mean rate of 5.4% as compared to 5.9% for non-ESE sites.
To investigate the role of selected amino acids on substrate preference, three amino acids in the GOOX-VN substrate binding site were previously substituted to corresponding residues in chito-oligosaccharide oxidase (ChitO) from Fusarium graminearum[ 15] or carbohydrate oxidase from Microdochium nivale[ 17], which show 45%and42%2% sequence identity to GOOX-VN, respectively [ 7].
The substituted benzene moieties of 6 and 7, which were oriented towards the opposite site of the mPGES-1 binding site, were predicted to be embedded in a hydrophobic site formed by mainly aromatic or hydrophobic amino acids (e.g., Tyr28, Tyr130, Thr131, Ala31, and Ile32).
Otherwise, this binding site is regarded as an incorrectly predicted binding site.
Furthermore, in a work by Kong et al that analyzed antibodies of HCV, the major antibody binding sites were found to be conserved, and the residues that were substituted in those sites showed similar hydrophobicity [ 36].
Mutagenesis was performed using a QuikChange Site-Directed Mutagenesis Kit (Stratagene, La Jolla, CA, USA), and all the adenines of miRNA-binding sequences were substituted with thymines.
Potential binding sites were elucidated by docking.
