Determination of the Internal Return Mechanism Catalyzed by Enzyme VldE: Molecular Dynamics Analysis
Doctor of Philosophy (PhD)
We examined the nitrogen bond formation between cyclitols to form pseudo-polysaccharides, which are the natural glycosyl transferase inhibitors with potentials of natural antibiotics or diabetic therapeutics. The molecular basis of attachment of valienol to validamine 7-phosphate (Va7P) via a C-N glycosidic bond formation was studied, performing molecular dynamic simulation (MDS) of the apo protein, the substrate complex, and the product complex. Analysis of the mainchain root-mean-square deviation (RMSD), (Rg), and solvent accessible surface area (SASA), consistently revealed a protein global conformational change and its relevance to the bindings of substrates or products. The apo protein was shown to be in an equilibrium between the ‘open’ and ‘closed’ conformations and the equilibrium shifted to the ‘closed’ conformation upon bindings of substrates or products, suggesting an ‘induced fit’.
To relate the conformational change to the VldE catalytic mechanism, the conformational shift was further validated by principal component analysis (PCA) of Ca atoms and analysis of the mainchain atom root mean square fluctuations (RMSF) and changes in the secondary structural components. It was shown that the ‘open’ and ‘closed’ is ultimately related to the N-terminal domain (residues 1-256) movement relative to the C-terminal domain (257-497). In addition, the interatomic interaction analysis between ligands revealed that the N-terminal domain movement by the conformational shift positions the valienol moiety of the donor substrate aplanar to the acceptor such that the C-N bond can be formed with the internal SNi substitution of the GDP moiety and the acceptor via a front side nucleophilic attack of the acceptor.
Bratcher, Derek Rodney, "Determination of the Internal Return Mechanism Catalyzed by Enzyme VldE: Molecular Dynamics Analysis" (2023). LSU Doctoral Dissertations. 6151.
Available for download on Monday, May 13, 2030