With homology- modeling techniques, molecular mechanics and molecular dynamics methods, a 3D structure model of the human inosine triphosphatase(ITPase; EC 3. 6. 1. 19) is created and refined. This model is further assessed by Profile- 3D and ProStat, which confirm that the refined model is reliable. With this model, a flexible docking study is performed, and the results indicate that Arg178, Lys19 and Glu44 are three important determinant residues in substrate binding because they have prominent interaction energies with ITP and form strong hydrogen bonds with ITP. In addition, we further find that the P32T substitution alters the α- helices of ITPase but the β- sheets are almost not changed, and the mutation induces the interaction energy between ITPase and ITP to increase, which are consistent with the conclusion predicted by Sumi et al. 8 The results from the mutagenesis imply that Pro32 is vital for the catalytic activity.

With homology modeling techniques, molecular mechanics, and molecular dynamics methods, a 3D structure model of Ndx1 is created and refined. This model is further assessed by Profile- 3D and ProStat, which confirm that the refined model is reliable. With this model, a flexible docking study is performed and the result indicates that Glu46, Arg88, and Glu90 are three important determinant residues in binding, as they have strong hydrogen bonding interactions and electrostatic interactions with Ap6A. In addition, we further find that three residues, Ser38, Leu39 and Glu46, coordinate enzyme- bound Mg2+ ions in complex N- A. The Glu46 is consistent with the experimental results by Iwai et al., and the other four residues mentioned above may also play vital roles in catalysis of Ndx1.

In order to understand the mechanisms of ligand binding and the interaction between the ligand and the bovine phenol sulfotransferase,(bSULTlAl, EC 2. 8. 2. 1) a three- dimensional(3D) model of the bSULTlAl is generated based on the crystal structure of the estrogen sulfotransferase(PDB code lAQU) by using the InsightII/ Homology module. With the aid of the molecular mechanics and molecular dynamics methods, the final refined model is obtained and is further assessed by Profile- 3D and ProStat, which show that the refined model is reliable. With this model, a flexible docking study is performed and the results indicate that 3'- phosphoadenosine- 5'- phosphosulfate(PAPS) is a more preferred ligand than coenzyme A(CoA), and that His108 forms hydrogen bond with PAPS, which is in good agreement with the experimental results. From these docking studies, we also suggest that Phe255, Phe24 and Tyr169 in bSULTlAl are three important determinant residues in binding as they have strong van- der- Waals contacts with the ligand. The hydrogen- bonding interactions also play an important role for the stability of the complex. Our results may be helpful for further experimental investigations.

The three- dimensional(3D) model of the 3- hydroxykynurenine transaminase(3- HKT) is constructed based on the crystal structure of the alanine- glyoxylate aminotransferase(EC 2. 6. 1. 44, PDB code 1VJO) by using InsightII/ Homology module. With the aid of the molecular mechanics and molecular dynamics methods, the last refined model is obtained and further assessed by Profile- 3D and ProStat, which confirm that the refined model is reliable. With this model, a fiexible docking study is performed and the result indicates that Trp104 and Gln204 are important residues as they have strong hydrogen bonding interactions with 3- HK respectively and they will act as a vital role in catalysis of 3- HKT. The Trp104 is in good agreement with the experimental result by Li et al. From the docking studies, we also suggest that the residues of Lys205 and Pro211 in 3- HKT are two important determinant residues in binding as they have strong van der Waals contacts with the 3- HK. Our results may be helpful for further experimental investigations.

The substrate specificities of glutathione peroxidase(GPX) mimic, 6, 6'- ditellurobis(6- deoxy- β- cyclodextrin)(6- TeCD), for three hydroperoxides(ROOH), H2O2, tertbutyl hydroperoxide(t- BuOOH) and cumene hydroperoxide(CuOOH), are investigated through molecular dynamics(MD) simulations. The most stable conformations and the total interaction energies of complex of 6- TeCD with ROOH are used to evaluate the substrate specificity of 6- TeCD. The steady- state kinetics of 6- TeCD is studied and the Michaelis- Menten constant(Km) and second- order rate constant kmax/ KROOH show that 6- TeCD displays different affinity and specificity to ROOH. These results of experiments are well consistent with ones obtained by MD simulations, indicating that MD simulations could be applied to evaluation substrate specificity of small- molecule enzyme mimics.