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Träfflista för sökning "WFRF:(Ryde Ulf) ;pers:(Van Severen Marie Céline)"

Sökning: WFRF:(Ryde Ulf) > Van Severen Marie Céline

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1.
  • Caldararu, Octav, et al. (författare)
  • QM/MM study of the reaction mechanism of sulfite oxidase
  • 2018
  • Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Sulfite oxidase is a mononuclear molybdenum enzyme that oxidises sulfite to sulfate in many organisms, including man. Three different reaction mechanisms have been suggested, based on experimental and computational studies. Here, we study all three with combined quantum mechanical (QM) and molecular mechanical (QM/MM) methods, including calculations with large basis sets, very large QM regions (803 atoms) and QM/MM free-energy perturbations. Our results show that the enzyme is set up to follow a mechanism in which the sulfur atom of the sulfite substrate reacts directly with the equatorial oxo ligand of the Mo ion, forming a Mo-bound sulfate product, which dissociates in the second step. The first step is rate limiting, with a barrier of 39-49 kJ/mol. The low barrier is obtained by an intricate hydrogen-bond network around the substrate, which is preserved during the reaction. This network favours the deprotonated substrate and disfavours the other two reaction mechanisms. We have studied the reaction with both an oxidised and a reduced form of the molybdopterin ligand and quantum-refinement calculations indicate that it is in the normal reduced tetrahydro form in this protein.
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2.
  • Van Severen, Marie-Céline, et al. (författare)
  • A quantum-mechanical study of the reaction mechanism of sulfite oxidase.
  • 2014
  • Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 1432-1327 .- 0949-8257. ; 19:7, s. 1165-1179
  • Tidskriftsartikel (refereegranskat)abstract
    • The oxidation of sulfite to sulfate by two different models of the active site of sulfite oxidase has been studied. Both protonated and deprotonated substrates were tested. Geometries were optimized with density functional theory (TPSS/def2-SV(P)) and energies were calculated either with hybrid functionals and large basis sets (B3LYP/def2-TZVPD) including corrections for dispersion, solvation, and entropy, or with coupled-cluster theory (LCCSD(T0)) extrapolated toward a complete basis set. Three suggested reaction mechanisms have been compared and the results show that the lowest barriers are obtained for a mechanism where the substrate attacks a Mo-bound oxo ligand, directly forming a Mo-bound sulfate complex, which then dissociates into the products. Such a mechanism is more favorable than mechanisms involving a Mo-sulfite complex with the substrate coordinating either by the S or O atom. The activation energy is dominated by the Coulomb repulsion between the Mo complex and the substrate, which both have a negative charge of -1 or -2.
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3.
  • Van Severen, Marie-Celine, et al. (författare)
  • Understanding the Chemistry of Lead at a Molecular Level : The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins
  • 2013
  • Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:5, s. 2416-2424
  • Tidskriftsartikel (refereegranskat)abstract
    • Pb2+ complexes can attain several different topologies, depending of the shape of the Pb 6s6p lone pair. In this paper, we study structures with a bisdirected Pb lone pair with quantum mechanics (DFT) and QM/MM calculations. We study small symmetric Pb2+ models to see what factors are needed to get a bisdirected lone pair. Two important mechanisms have been found: First, the repulsion of the lone pair of Pb2+ with other lone pairs in the equatorial plane leads to a bisdirected structure. Second, a bisdirected lone pair can also arise due to interactions with double bonds, lone pairs, or hydrogen atoms. Moreover, we have analyzed Pb2+ sites in proteins and to see if a bisdirected lone pair can exist in an asymmetrical environment. Several instances of bisdirected lone pairs were discovered.
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