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  • 1.
    Lind, Maria E. S.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemical Modeling of Enantioconvergency in Soluble Epoxide HydrolaseManuscript (preprint) (Other academic)
  • 2.
    Lind, Maria E. S.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemistry as a Tool in Asymmetric Biocatalysis: Limonene Epoxide Hydrolase Test Case2013In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 52, no 17, p. 4563-4567Article in journal (Refereed)
  • 3.
    Lind, Maria E. S.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical Study of Reaction Mechanism and Stereoselectivity of Arylmalonate Decarboxylase2014In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 4, no 11, p. 4153-4160Article in journal (Refereed)
    Abstract [en]

    The reaction mechanism of arylmalonate decarboxylase is investigated using density functional theory calculations. This enzyme catalyzes the asymmetric decarboxylation of prochiral disubstituted malonic acids to yield the corresponding enantiopure carboxylic acids. The quantum chemical cluster approach is employed, and two different models of the active site are designed: a small one to study the mechanism and characterize the stationary points and a large one to study the enantioselectivity. The reactions of both α-methyl-α-phenylmalonate and α-methyl-α-vinylmalonate are considered, and different substrate binding modes are assessed. The calculations overall give strong support to the suggested mechanism in which decarboxylation of the substrate first takes place, followed by a stereoselective protonation by a cysteine residue. The enediolate intermediate and the transition states are stabilized by a number of hydrogen bonds that make up the dioxyanion hole, resulting in feasible energy barriers. It is further demonstrated that the enantioselectivity in the case of α-methyl-α-phenylmalonate substrate is dictated already in the substrate binding, because only one binding mode is energetically accessible, whereas in the case of the smaller α-methyl-α-vinylmalonate substrate, both the binding and the following transition states contribute to the enantioselectivity.

  • 4.
    Lind, Maria E.S.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemical Modeling of Asymmetric Enzymatic Reactions: Applications to Limonene Epoxide Hydrolase and Arylmalonate Decarboxylase2013Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, density functional theory has been employed to study the reactionmechanisms of two enzymes with possible applications in asymmetric biocatalysis.To reproduce and rationalize the stereoselectivity of the enzymes, quite large cluster models that account for the chiral environment of the active site have been used.

    In the first study, the enantioselectivity of the wild-type limonene epoxidehydrolase and two groups of mutants thereof, that show either (R,R)- or (S,S)-selectivity, were investigated. Using the cluster approach, the enantioselectivity for each variant of the enzyme was calculated and the results are in good agreement with the experimental data. It was found that the enantioselectivity of the enzyme variants is controlled by the steric hindrance introduced or relieved bythe different mutations.

    The second study concerns the reaction mechanism and stereoselectivity of arylmalonate decarboxylase. The calculations support the proposed two-step mechanism, in which decarboxylation and protonation of the substrate occur separately. The stereoselectivity of the enzyme is governed by repulsive steric interactions between the substrate and the residues that deffine a large and a small cavity in the active site. Depending on the size of the substrate, the selectivity was found to be determined already at the binding of the substrate or in the subsequent transition state.

    The results presented in this thesis demonstrate that the quantum chemical cluster approach for modeling enzymes is indeed a very valuable tool in the study of asymmetric biocatalysis.

  • 5.
    Popović-Bijelić, Ana
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Kowol, Christian R.
    Lind, Maria E. S.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Luo, Jinghui
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Enyedy, Éva A.
    Arion, Vladimir B.
    Gräslund, Astrid
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ribonucleotide reductase inhibition by metal complexes of Triapine (3-aminopyridine-2-carboxaldehyde thiosemicarbazone): A combined experimental and theoretical study2011In: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-1948, Vol. 105, no 11, p. 1422-1431Article in journal (Refereed)
    Abstract [en]

    Triapine (3-aminopyridine-2-carboxaldehyde thiosemicarbazone, 3-AP) is currently the most promising chemotherapeutic compound among the class of α-N-heterocyclic thiosemicarbazones. Here we report further insights into the mechanism(s) of anticancer drug activity and inhibition of mouse ribonucleotide reductase (RNR) by Triapine. In addition to the metal-free ligand, its iron(III), gallium(III), zinc(II) and copper(II) complexes were studied, aiming to correlate their cytotoxic activities with their effects on the diferric/tyrosyl radical center of the RNR enzyme in vitro. In this study we propose for the first time a potential specific binding pocket for Triapine on the surface of the mouse R2 RNR protein. In our mechanistic model, interaction with Triapine results in the labilization of the diferric center in the R2 protein. Subsequently the Triapine molecules act as iron chelators. In the absence of external reductants, and in presence of the mouse R2 RNR protein, catalytic amounts of the iron(III)–Triapine are reduced to the iron(II)–Triapine complex. In the presence of an external reductant (dithiothreitol), stoichiometric amounts of the potently reactive iron(II)–Triapine complex are formed. Formation of the iron(II)–Triapine complex, as the essential part of the reaction outcome, promotes further reactions with molecular oxygen, which give rise to reactive oxygen species (ROS) and thereby damage the RNR enzyme. Triapine affects the diferric center of the mouse R2 protein and, unlike hydroxyurea, is not a potent reductant, not likely to act directly on the tyrosyl radical.

  • 6.
    Sheng, Xiang
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lind, Maria E. S.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical study of the reaction mechanism of phenolic acid decarboxylase2015In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 282, no 24, p. 4703-4713Article in journal (Refereed)
    Abstract [en]

    The cofactor-free phenolic acid decarboxylases (PADs) catalyze the non-oxidative decarboxylation of phenolic acids to their corresponding p-vinyl derivatives. Phenolic acids are toxic to some organisms, and a number of them have evolved the ability to transform these compounds, including PAD-catalyzed reactions. Since the vinyl derivative products can be used as polymer precursors and are also of interest in the food-processing industry, PADs might have potential applications as biocatalysts. We have investigated the detailed reaction mechanism of PAD from Bacillus subtilis using quantum chemical methodology. A number of different mechanistic scenarios have been considered and evaluated on the basis of their energy profiles. The calculations support a mechanism in which a quinone methide intermediate is formed by protonation of the substrate double bond, followed by C-C bond cleavage. A different substrate orientation in the active site is suggested compared to the literature proposal. This suggestion is analogous to other enzymes with p-hydroxylated aromatic compounds as substrates, such as hydroxycinnamoyl-CoA hydratase-lyase and vanillyl alcohol oxidase. Furthermore, on the basis of the calculations, a different active site residue compared to previous proposals is suggested to act as the general acid in the reaction. The mechanism put forward here is consistent with the available mutagenesis experiments and the calculated energy barrier is in agreement with measured rate constants. The detailed mechanistic understanding developed here might be extended to other members of the family of PAD-type enzymes. It could also be useful to rationalize the recently developed alternative promiscuous reactivities of these enzymes.

  • 7.
    Sheng, Xiang
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lind, Maria E. S.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical Study of the Reaction Mechanism of Phenolic Acid DecarboxylaseManuscript (preprint) (Other academic)
1 - 7 of 7
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