Theoretical Studies Of Non-Heme Enzyme And Intermolecular Force Field

The researches mainly includes two aspects, one is about the structural and catalytic properties of the mononuclear non-heme enzyme. The mononuclear non-heme enzyme is a kind of iron dependent oxygenases, which is important in biological, environmental and medical applications. A common structural motif of these non-heme enzymes is the2-His-1-carboxylate facial triad binding the divalent iron. Molecular dynamic simulations and QM/MM methods were used to study the catalytic reaction mechanism of Hydroxyethylphosphonate dioxygenase (HEPD) enzyme. The conditions that may ailed the enzymatic reaction were analyzed and the tunability of the reaction pathway was discussed Intermolecular interactions(such as halogen bonds and cation-π et al) and the coordinated interactions are usually highly directional, which cannot properly be described in classic force field. We designed a polarizable ellipsoidal force field (PEff) to improve the description of intermolecular interactions in classic force fields. And the PEff model has been attempted to study the halogen bonding in biomolecules. The PEff model is also useful to derive the force field of coordinated interactions (such as zinc and iron enzymes).The conclusions are summarized in the following section:1. Hydroxyethylphosphonate dioxygenase (HEPD) is a typical mononuclear non-heme enzyme, which catalyzes a critical step in phosphinothricin (PT) biosynthetic pathway. HEPD activates O2by the divalent iron and catalyzes the conversion of2-HEP to HMP. By employing ab initio quantum mechanical/molecular mechanical (QM/MM) and molecular dynamics simulations(MD), we have provided further evidence against the previously proposed hydroperoxylation or hydroxylation mechanism of hydroxyethylphosphonate dioxygenase (HEPD). HEPD employs an interesting catalytic cycle based on concatenated bifurcations. This enzymatic reaction occurs in four major steps on the basis of our QM/MM calculations. The first step is the abstraction of hydrogen atom from the substrate, which leads to a distal or proximal hydroperoxo species (Fe(Ⅲ)-OOH). The second step is the cleavage of the O-O bond, and in the third step, the carbon-carbon bond is broken subsequently. Finally,2-HEP is converted to HMP The residue Glu176could take part in the catalytic reaction via a proton assisted mechanism. The reaction directions seem to be tunable and show significant environment dependence. These conclusions may provide insight to the development of biochemistry and material sciences.2. The experimental studies suggest that water molecules play an important role in the catalytic reaction process of HEPD. Molecular dynamic (MD) simulations also point out that the trapped water at the active site is important in the active site.This work proposes a water involved reaction mechanism, where water molecules serve as an oxygen source in the generation of mononuclear non-heme iron oxo complexes. Meanwhile, water molecules seem to be responsible for converting the reactive hydroxyl radical group (’OH) to the ferric hydroxide (Fe(Ⅲ)-OH) in a specific way. This converting reaction may prevent the enzyme from damages caused by the hydroxyl radical groups. This work could provide a better interpretation on how the intermediates interact with water molecules and a quantitatively understanding on the018label experimental evidences in which only a relatively smaller ratio of oxygen atoms in water molecules (about40%) are incorporated into the final product HMP.3. The current research reports a polarizable ellipsoidal force field (PEff) for the directional intermolecular interactions. Since widely applications of halogen bonds and the difficulty of modeling them in classical force fields, the PEff model was used to study the halogen bonds. The anisotropic effects and short-range quantum effects are two essential characters in the formation of halogen bonds. The anisotropic charge distribution was represented with the combination of a negative charged sphere and a positively charged ellipsoid. The polarization energy was incorporated by the induced dipole model. The resulting force field is "physically motivated", which includes separate, explicit terms to account for the electrostatic, repulsion/dispersion and polarization interaction. 4.The PF.ff modelis largelycompatible with existing,standard simulation packages The fitted parameters are transferable and compatible with the general AMBER force field (GAFF). This PEff model could correctly reproduces the potential energy surface of halogen bonds at MP2level. Finally, the prediction of the halogen bond properties of human Cathcpsin L (hcatL) has been found to be in excellent qualitative agreement with the co-crystal structures. Judging from the notably improved accuracy in comparison with the fixed charge models, the PEff model is expected to form the foundation for developing high quality force field of coordinated complex.