| Summary: | 碩士 === 國立臺北科技大學 === 化學工程系碩士班 === 91 === In this study, molecular dynamics simulations were performed to investigate 1) the effects of various metal ions on the binding of substrate to human alcohol dehydrogenase β2β2; 2) the effects of solvent and temperature on the structural integrity of monomeric melittin; and 3) the chelating mechanisms of various metal ions to the His-tag motifs. For alcohol dehydrogenase, both structural and catalytic zinc ions, Zns and Zna, respectively, were shown to influence the structural integrity of the substrate binding pocket of the human alcohol dehydrogenase 22. By manual docking, the results indicated that the replacement of catalytic zinc ion or both catalytic and structural zinc ions with Cu2+ results in better substrate binding affinity (ethanol) than the wild type enzyme. Furthermore, the width of the bottleneck formed by L116 and V294 in the substrate binding pocket plays an important role for substrate entrance. For melittin, 200 ps molecular dynamics simulations were performed with temperature jump technique. The results demonstrated that the -helix content and melting temperature of melittin increased with increasing the aliphatic chain length of the alcohol and decreased with increasing simulation temperature. The weaker dielectric constant of longer aliphatic chain length of alcohol possibly reduces the hydrogen bonding between amide protons and surrounding solvent molecules, therefore stabilizes the secondary structure of melittin. For the chelating mechanisms of His-tag motifs, our simulations demonstrated that the chelation mostly involved the i and i+2 His residues for Ni2+, Zn2+, Cu2+, and Co2+, while the cooperation of 3 His residues was necessary when Fe3+ was involved in chelation with His-tags having more than 4 His residues. In addition, His-tag6 was found to have little effect on the structural integrity while the target protein contains more than 68 amino acid residues. We also detected that Ni2+ interacted with the imidazole nitrogen of His3 in the beginning of chelation and then entered into the pocket formed by His3 and His5 at 4 ns during the 10 ns molecular dynamics simulations.
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