Theoretical Studies On Structure Prediction, Docking Study For Several Enzymes

With the development of computer technology, medicine chemistry, molecular biology and computational chemistry,computer aided molecular modeling has become a very important and active research field. In this thesis, molecular mechanics and molecular dynamics methods are used to build three dimensional models for three enzymes and study their structures properties in detail. Some creative results were obtained from the methods mentioned above. The main results are outlined as follows:1. The structures and function research of human CYP2C9 and CYP2C9*13 variant. CYP2C9*13 is a new allele of human CYP2C9 characterized by mutation encoding Leu90Pro substitution. The three-dimensional structure models of the substrate-free CYP2C9*1 and its variant CYP2C9*13 were constructed by molecular dynamics simulations. The trans configuration of the bond between Pro90 and Asp89 in CYP2C9*13 is firstly identified. The structure change caused by Leu90Pro replacement was revealed and used to explain the dramatic decrease of the enzymatic activity. Consequent docking study is consistent with the results of the kinetic experiments.The 3D structures of variants, L90I, L90G, L90R, L90Q and L90W were constructed by molecular dynamics for further research. The results suggest that the changes in catalysis activity by the substitution at residue 90 are due to changes in size of entrance, interaction between substrates and the proteins, and stability. Thus the residue 90 of CYP2C9 would have an important role on the enzyme.2. Homology modeling and docking studies of homoserine transsuccinylase from Escherichia coli. The three dimensional structure of homoserine transsuccinylase from Escherichia coli (EcHTS) was modeled by using homology and molecular dynamics methods. On the basis of the modeling, the components of active site in EcHTS were analyzed. The structure analysis shows that Cys142 but not Lys47 is the main residue for the nucleophile during the catalytic reaction. The docking of succinyl-CoA with EcHTS has also been performed, and the important residues for binding were identified.3. Homology modeling and docking studies of novelα/βhydrolase fold proteins W14 and W15. The three dimensional structure of novelα/βhydrolase fold proteins W14 and W15 were modeled by using homology and molecular dynamics methods. On the basis of the modeling, the components and the structures of active sites in W14 and W15 were analyzed and compared. The docking of 1-naphtyl acetate with the two proteins have also been performed and compared. Gly82 and Val13 were key residues to form the oxyanion-hole and stabilized the negatively charged transition state that occurs during hydrolysis. Other important residues for binding were also identified.