Theoretical Studies On Molecular Dynamics Simulation And Reaction Mechanism For Several Proteins

In recent years, along with the development of homology, molecule mechanics, dynamics, and quantum mechanics theories, and the process of calculator technique, molecule simulations have already become a main research method in the fields of biology science to analyze the interaction between receptor and ligand and to describe the catalytic mechanism.In our thesis, homology modeling, molecule mechanics, dynamics, and quantum mechanics methods were used to theoretically study on the potency and selectivity ligands of the proteins, the reaction mechanism ofα-Phosphomannomutase1 in both protonated and deprotonated state, and improving the GPX activity of the human single-chain Fv antibody. The main results are summarized as follows:1. Homology modeling and Molecular dynamics study on N-acetylneuraminate lyaseN-acetyl-neuraminic acid (sialic acid) is an interesting high carbon sugar with important pharmaceutical implications. It plays a prominent role in numerous biological functions, including virus infections.In this investigation, the 3D structure of hNAL was built by homology modeling, which was based on the known crystal structure of N-acetylneuraminate lyase from E.coli. And then energy minimization and molecular dynamics were used to refine the structure. With this model, a flexible docking study was performed and the docking results indicate that the AcHN group in sialic acid can stabilize the position and orientation in active site of hNAL. Thr51 and Tyr143 may be the key amino acids residues interacting with the substrates, and Asp176 and Ser218 may help sialic acid interact with hNAL steady. 2. Theoretical Studies on Interaction Mode Between human 2-Amino 3-carboxymuconate 6-semialdehyde Decarboxylase and Substrate and Inhibitor2-amino 3-carboxymuconate 6-semialdehyde Decarboxylase (hACMSD) occupies a key positition at the branching point of ACMS metabolic pathways and control the final fate of the metabolites in both pathway.The three dimensional structure of hACMSD was modeled and refined by using Homology modeling and Molecular dynamics. The complex structures of the substrate or inhibitor with hACMSD were obtained and investigated through ligand-receptor docking studies by means of Affinity. The binding pattern predicted by the affinity module reveals Arg47, Val48 and the catalytic Zn2+ interacted with substrate or inhibitor. By contrasting the results of the ACMS and QA, ACMS interacts more easy with ACMSD than QA.3. Molecular Simulation on Interaction between Glutathione S-transferase M5 and Substrate or InhibitorsThe three dimensional structure of glutathione S-transferase (GSTM5) was modeled and refined by using Homology modeling and Molecular dynamics. The complex structures of the substrate and inhibitor, ethacrynic acid and pentahydroxyflavone, with GSTM5 were obtained and investigated through ligand-receptor docking studies by means of Affinity. The complex of GSTM5 and ligands predicted by the affinity module reveals Tyr7,Trp8,Leu13,His108,Val112 interacted with substrate or inhibitors. And the inhibition of pentahydroxyflavone is more than ethacrynic acid.4. 3D Structure and Catalytic Mechanism Potency Study on AspartoacylaseDeficiency in aspartoacylase (ASPA) is the established cause of Canavan disease (CD), a fatal progressive leukodystrophy affecting young children.The 3D model of the aspartoacylase-2 from human is constructed based on the crystal structure of the aspartoacylase-1. With this model, a flexible docking study is performed and the results indicate that Asp68, Asn70, Asp168, Glu178, Tyr288 and zinc ion play major roles in catalysis of hASPA-2. By contrasting the result, aspartoacylase-1 are performed the same operation. Quantum chemistry calculations show after the water coordinated to the zinc ion, the interactions between the NAA and hASPA become stronger. 5. DFT Investigation on the Reaction Mechanism Catalyzed byα-Phosphomannomutase1 in Protonated/Deprotonated stateCongenital disorder of glycosylation type 1a (CDG-1a) which is a congenital disease, is caused by mutations inα-Phosphomannomutase1 (α-PMM1).The reaction mechanism of theα-PMM1 enzyme has been investigated by means of density functional theory using the hydrid functional B3LYP.α-PMM1 catalyzes the interconversion of theα-D-mannose 1-phosphate to D-mannose 6-phosphate via a mannose-1, 6-(bis) phosphate intermediate. The quantum chemical models, which were chosen in protonated/deprotonated states models, were built on the basis of the docking result. The process of the phosphoryl group transfer from Asp19 to the mannose 6-phosphate is in different steps in the two states, but are both coupled with the protons transfer. In addition, our results support the hypothesis that the Asp19 as a nucleophile plays an important role in theα-PMM1 biology function, indicate Gln62 helps to stabilize the phosphoryl group and the structure of the substrate, and the deprotonated states is more suitable for product release.6. Improving GPX activity of selenium-containing human single-chain Fv antibody by site-directed mutation based on the structural analysisGPX is a well-known antioxidant selenoenzyme which can catalyze the reduction of a variety of hydroperoxides and consequently protect cells and other biological tissues against oxidative damage.In this investigation, the 3D structure of ScFv-B3 was built by homology modeling. And then energy minimization and molecular dynamics were used to refine the structure. With this model, two active sites were obtained and the Affinity was performed to obtain the complexes of the substrate GSH. Through interaction analysis, it was determined that the total interaction energy in Site 1 is more negative than that in Site 2, thus Site1 is the more likely binding site. Ala180 in Site 1 and Ala44 in Site 2 were the optimal choices for the candidate according to the principles above to improve the GPX activity. Our calculation results are good agreement with the experiment results made by the experimental cooperate team.