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  • 1.
    Ahlford, Katrin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lind, Jesper
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Mäler, Lena
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Rhodium-catalyzed asymmetric transfer hydrogenation of alkyl and aryl ketones in aqueous media2008In: Green Chemistry, ISSN 1463-9262, E-ISSN 1463-9270, Vol. 10, no 8, p. 832-835Article in journal (Refereed)
    Abstract [en]

    A novel lipophilic rhodium catalyst was evaluated in the enantioselective transfer hydrogenation of ketones in water using sodium formate as the hydride donor, and in the presence of sodium docecylsulfonate. Alkyl alkyl ketones were reduced in good yields and in moderate to good enantioselectivities, and the reduction of aryl alkyl ketones proceeded with excellent enantioselectivity (up to 97% ee).

  • 2.
    Li, Xichen
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Chen, Guangju
    Schinzel, Sandra
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    A comparison between artificial and natural water oxidation2011In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 40, no 42, p. 11296-11307Article in journal (Refereed)
    Abstract [en]

    Two artificial water oxidation catalysts, the blue dimer and the Llobet catalyst, have been studied using hybrid DFT methods. The results are compared to those for water oxidation in the natural photosystem II enzyme. Studies on the latter system have now reached a high level of understanding, at present much higher than the one for the artificial systems. A recent high resolution X-ray structural investigation of PSII has confirmed the main features of the structure of the oxygen evolving complex (OEC) suggested by previous DFT cluster studies. The O-O bond formation mechanism suggested is of direct coupling (DC) type between an oxygen radical and a bridging oxo ligand. A similar DC mechanism is found for the Llobet catalyst, while an acid-base (AB) mechanism is preferred for the blue dimer. All of them require at least one oxygen radical. Full energy diagrams, including both redox and chemical steps, have been constructed illustrating similarities and differences to the natural system. Unlike previous DFT studies, the results of the present study suggest that the blue dimer is rate-limited by the initial redox steps, and the Llobet catalyst by O(2) release. The results could be useful for further improvement of the artificial systems.

  • 3.
    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.

  • 4.
    Siegbahn, Per E. M.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Faculty of Science, Department of Physics.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    The quantum chemical clusterapproach for modeling enzymereactions2011In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 1, no 3, p. 323-356Article in journal (Refereed)
    Abstract [en]

    This Overview describes the general concepts behind the quantum chemical clusterapproach formodeling enzyme active sites and reaction mechanisms. First, theunderlying density functional electronic structure method is briefly recapitulated.The cluster methodology is then discussed, including the important observationon the convergence of the solvation effects. The concepts are illustrated usingexamples from recent applications, such as the discrimination between differentreaction mechanisms in phosphotriesterase, the elucidation of origins of regioselectivityin the epoxide-opening reaction of haloalcohol dehalogenase, and finallythe use of the cluster methodology to establish the detailed structure of theoxygen-evolving complex in photosystem II.

  • 5.
    Säwén, Elin
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Massad, Tariq
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Landersjö, Clas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Damberg, Peter
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Population distribution of flexible molecules from maximum entropy analysisusing different priors as background information: application to the phi,psi-conformational space of the a-(1→2)-linked mannose disaccharide presentin N- and O-linked glycoproteins2010In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 8, no 16, p. 3684-3695Article in journal (Refereed)
    Abstract [en]

    The conformational space available to the flexible molecule a-D-Manp-(1→2)-a-D-Manp-OMe, amodel for the a-(1→2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determinedusing experimental data and molecular simulation combined with a maximum entropy approach thatleads to a converged population distribution utilizing different input information. A database survey ofthe Protein Data Bank where structures having the constituent disaccharide were retrieved resulted inan ensemble with >200 structures. Subsequent filtering removed erroneous structures and gave thedatabase (DB) ensemble having three classes of mannose-containing compounds, viz., N- and O-linkedstructures, and ligands to proteins. A molecular dynamics (MD) simulation of the disaccharide revealeda two-state equilibrium with a major and a minor conformational state, i.e., the MD ensemble. Thesetwo different conformation ensembles of the disaccharide were compared to measured experimentalspectroscopic data for the molecule in water solution. However, neither of the two populations werecompatible with experimental data from optical rotation, NMR 1H,1H cross-relaxation rates as well ashomo- and heteronuclear 3J couplings. The conformational distributions were subsequently used asbackground information to generate priors that were used in a maximum entropy analysis. Theresulting posteriors, i.e., the population distributions after the application of the maximum entropyanalysis, still showed notable deviations that were not anticipated based on the prior information.Therefore, reparameterization of homo- and heteronuclear Karplus relationships for the glycosidictorsion angles f and y were carried out in which the importance of electronegative substituents on thecoupling pathway was deemed essential resulting in four derived equations, two 3JCOCC and two 3JCOCHbeing different for the f and y torsions, respectively. These Karplus relationships are denotedJCX/SU09. Reapplication of the maximum entropy analysis gave excellent agreement between theMD- and DB-posteriors. The information entropies show that the current reparametrization of theKarplus relationships constitutes a significant improvement. The fH torsion angle of the disaccharide isgoverned by the exo-anomeric effect and for the dominating conformation fH = -40◦ and yH = 33◦.The minor conformational state has a negative yH torsion angle; the relative populations of the majorand the minor states are ~3 : 1. It is anticipated that application of the methodology will be useful toflexible molecules ranging from small organic molecules to large biomolecules.

  • 6.
    Wagner, Samuel
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Klepsch, Mirjam M.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Schlegel, Susan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Appel, Ansgar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Draheim, Roger
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Tarry, Michael
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Högbom, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    van Wijk, Klaas J.
    Slotboom, Dirk J.
    Persson, Jan O.
    Stockholm University, Faculty of Science, Department of Mathematics.
    de Gier, Jan-Willem
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Tuning Escherichia coli for membrane protein overexpression2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 38, p. 14371-17376Article in journal (Refereed)
    Abstract [en]

    A simple generic method for optimizing membrane protein overexpression in Escherichia coli is still lacking. We have studied the physiological response of the widely used “Walker strains” C41(DE3) and C43(DE3), which are derived from BL21(DE3), to membrane protein overexpression. For unknown reasons, overexpression of many membrane proteins in these strains is hardly toxic, often resulting in high overexpression yields. By using a combination of physiological, proteomic, and genetic techniques we have shown that mutations in the lacUV5 promoter governing expression of T7 RNA polymerase are key to the improved membrane protein overexpression characteristics of the Walker strains. Based on this observation, we have engineered a derivative strain of E. coli BL21(DE3), termed Lemo21(DE3), in which the activity of the T7 RNA polymerase can be precisely controlled by its natural inhibitor T7 lysozyme (T7Lys). Lemo21(DE3) is tunable for membrane protein overexpression and conveniently allows optimizing overexpression of any given membrane protein by using only a single strain rather than a multitude of different strains. The generality and simplicity of our approach make it ideal for high-throughput applications.

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