Nye registreringer

  • DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases 

    Williamson, Adele Kim; Grgic, Miriam; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-07-11)
    DNA ligases join breaks in the phosphodiester backbone of DNA by catalysing the formation of bonds between opposing 5′P and 3′OH ends in an adenylation-dependent manner. Catalysis is accompanied by reorientation of two core domains to provide access to the active site for cofactor utilization and enable substrate binding and product release. The general paradigm is that DNA ligases engage their DNA ...
  • Enzyme mechanism, thermostability, and structural studies of OXA-48 like carbapenemases involved in antibiotic resistance 

    Thomassen, Ane Molden (Master thesis; Mastergradsoppgave, 2018-05-15)
    Antibiotic resistance is being recognized as a world-wide crisis in modern medicine, rapidly outpacing available treatment options. The serine-beta-lactamase OXA-48 was first identified from a carbapenem- and multidrug- resistant Klebsiella pneumoniae isolate in Turkey in 2001, and is now one of the most geographically widespread members of the class D beta-lactamases. OXA-48 like beta-lactamases ...
  • Solvent effect with Multiwavelets 

    Monstad, Rune Sørland (Master thesis; Mastergradsoppgave, 2017-11-15)
    This thesis contains the inclusion of solvent effect in the computational chemistry program MRChem. Water in water systems are of importance.
  • Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives 

    Thode, Sunniva Katharina; Rojek, Ewelina; Kozlowski, Mikolaj; Ahmad, Rafi; Haugen, Peik (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-02-14)
    Siderophores are small molecules synthesized and secreted by bacteria and fungi to scavenge iron. Extracellular ferri-siderohores are recognized by cognate receptors on the cell surface for transport over membranes. Several siderophore systems from <i>Vibrionaceae</i> representatives are known and well understood, e.g., the molecular structure of the siderophore, the biosynthesis gene cluster ...
  • Diagrammatic Coupled Cluster Monte Carlo 

    Scott, Charles J. C.; Di Remigio, Roberto; Crawford, T. Daniel; Thom, Alex J. W. (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-02-09)
    We propose a modified coupled cluster Monte Carlo algorithm that stochastically samples connected terms within the truncated Baker–Campbell–Hausdorff expansion of the similarity-transformed Hamiltonian by construction of coupled cluster diagrams on the fly. Our new approach—diagCCMC—allows propagation to be performed using only the connected components of the similarity-transformed Hamiltonian, ...
  • Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome 

    Jensen, Marianne Slang; Fredriksen, Lasse; Mackenzie, Alasdair; Pope, Phillip; Leiros, Ingar; Chylenski, Piotr; Williamson, Adele Kim; Christopeit, Tony; Østby, Heidi; Vaaje-Kolstad, Gustav; Eijsink, Vincent (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-05-24)
    Enzymatic depolymerization of recalcitrant polysaccharides plays a key role in accessing the renewable energy stored within lignocellulosic biomass, and natural biodiversities may be explored to discover microbial enzymes that have evolved to conquer this task in various environments. Here, a metagenome from a thermophilic microbial community was mined to yield a novel, thermostable cellulase, named ...
  • Species diversity and abundance of shipworms (Mollusca: Bivalvia: Teredinidae) in woody marine debris generated by the Great East Japan Earthquake and Tsunami of 2011 

    Treneman, Nancy C.; Carlton, James T.; Borges, Luisa M. S.; Shipway, Reuben; Raupach, Michael; Altermark, Bjørn (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-02)
    The Tohoku tsunami of March 2011 ejected a vast amount of debris into the Pacific Ocean. Wood boring shipworms (Bivalvia: Teredinidae) were either already present in, or settled on, the wooden fraction of this debris, offering a unique opportunity to study shipworm diversity in rafted wood of a known origin and time of ocean entry. Lumber and other wood began appearing on Central Pacific (Hawaiian ...
  • A molecular phylogeny of wood-borers (Teredinidae) from Japanese Tsunami Marine Debris 

    Treneman, Nancy C.; Borges, Luisa M. S.; Shipway, Reuben; Raupach, Michael J.; Altermark, Bjørn; Carlton, James T. (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-02)
    The family Teredinidae (shipworms) contains 70-plus species of boring bivalves specialized to live in and digest wood. Traditional means of species identification and taxonomy of this group encounter numerous challenges, often compounded by the diverse and dynamic nature of shipworm ecology and distribution. Modern integrative taxonomic methods are shedding new light on this complex group, from ...
  • Land-allocation and clan-formation in modern residential developments in Oman 

    Heim, Bernhard; Joosten, Marc; Richthofen, Aurel V; Rupp, Florian (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-09-20)
    Abstract Afordable housing with fair and transparent land-allocation measures is a challenge for many countries. The Sultanate of Oman solves this issue by means of land-allocation lotteries in which male and female citizens can participate in order to win a parcel of a new housing area. Besides supporting those in fnancial need the lottery aims to mix the separate tribes of Oman and thus contribute ...
  • The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine 

    Alexeeva, Marina; Åberg, espen; Engh, Richard Alan; Rothweiler, Ulli (Journal article; Tidsskriftartikkel; Peer reviewed, 2015)
    Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a protein kinase associated with neuronal development and brain physiology. The DYRK kinases are very unusual with respect to the sequence of the catalytic loop, in which the otherwise highly conserved arginine of the HRD motif is replaced by a cysteine. This replacement, along with the proximity of a potential disulfide-bridge ...
  • Isocorroles as Homoaromatic NIR-Absorbing Chromophores: A First Quantum Chemical Study 

    Foroutan-Nejad, Cina; Larsen, Simon; Conradie, Jeanet; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-08-10)
    Density functional theory calculations of magnetically induced current densities have revealed high diatropic ring currents in unsubstituted isocorrole consistent with homoaromatic character. An examination of the Kohn-Sham molecular orbitals showed clear evidence of homoconjugative interactions in four occupied π-type molecular orbitals as well as in the LUMO. Remarkably, substituents at the saturated ...
  • PCMSolver: an Open-Source Library for Solvation Modeling 

    Di Remigio, Roberto; Steindal, Arnfinn Hykkerud; Mozgawa, Krzysztof; Weijo, Ville; Cao, Hui; Frediani, Luca (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-11-25)
    PCMSolver is an open‐source library for continuum electrostatic solvation. It can be combined with any quantum chemistry code and requires a minimal interface with the host program, greatly reducing programming effort. As input, PCMSolver needs only the molecular geometry to generate the cavity and the expectation value of the molecular electrostatic potential on the cavity surface. It then returns ...
  • Application of Silicon-Initiated Water Splitting for the Reduction of Organic Substrates 

    Gevorgyan, Ashot; Mkrtchyan, Satenik; Grigoryan, Tatevik; Iaroshenko, Viktor O (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-04-06)
    The use of water as a donor for hydrogen suitable for the reduction of several important classes of organic compounds is described. It is found that the reductive water splitting can be promoted by several metalloids among which silicon shows the best efficiency. The developed methodologies were applied for the reduction of nitro compounds, N‐oxides, sulfoxides, alkenes, alkynes, hydrodehalogenation ...
  • Insight into the fluorescence quenching of Trp214 at HSA by the Dimetridazole ligand from simulation 

    Pomogaev, Valdimir A; Ramazanov, Ruslan R; Ruud, Kenneth; Artyukhov, Victor Ya (Journal article; Tidsskriftartikkel; Peer reviewed, 2017-08-24)
    Spectroscopy is an important tool for detecting drug binding to amino acid sequences. One such important spectroscopic process is the fluorescence quenching due to charge transfer (CT) processes between a drug molecule and the chromophore center of Human Serum Albumin (HSA). We present a theoretical investigation of the CT occurring upon electronic excitation when a dimetridazole (Dmz) molecule ...
  • Iron‐Catalyzed Carbenoid Transfer Reactions of Vinyl Sulfoxonium Ylides: An Experimental and Computational Study 

    Vaitla, Janakiram; Bayer, Annette; Hopmann, Kathrin Helen (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-10-15)
    A method for the generation of unprecedented vinyl carbenoids from sulfoxonium ylides has been developed and applied in the synthesis of a diverse array of heterocycles such as indolizines, pyrroles, 3‐pyrrolin‐2‐ones, and furans. The reactions proceed by FeBr<sub>2</sub> catalysis under mild reaction conditions with a broad substrate scope. A reaction pathway involving iron carbenoids is proposed ...
  • Rhodium-Catalyzed Hydrocarboxylation: Mechanistic Analysis Reveals Unusual Transition State for Carbon–Carbon Bond Formation 

    Pavlovic, Ljiljana; Vaitla, Janakiram; Bayer, Annette; Hopmann, Kathrin Helen (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-03-12)
    The mechanism of rhodium-COD-catalyzed hydrocarboxylation of styrene derivatives and α,β-unsaturated carbonyl compounds with CO<sub>2</sub> has been investigated using density functional theory (PBE-D2/IEFPCM). The calculations support a catalytic cycle as originally proposed by Mikami and co-workers including β-hydride elimination, insertion of the unsaturated substrate into a rhodium–hydride bond, ...
  • Mutational analysis of the pro-peptide of a marine intracellular subtilisin protease supports its role in inhibition 

    Bjerga, Gro Elin Kjæreng; Larsen, Øivind; ARSIN, Hasan; Williamson, Adele Kim; Garcia-Moyano, Antonio; Leiros, Ingar; Puntervoll, Pål (Journal article; Tidsskriftartikkel; Preprint; Manuskript, 2018-06-16)
    Intracellular subtilisin proteases (ISPs) have important roles in protein processing during the stationary phase in bacteria. Their unregulated protein degrading activity may have adverse effects inside a cell, but little is known about their regulatory mechanism. Until now, ISPs have mostly been described from <i>Bacillus</i> species, with structural data from a single homolog. Here, we study a ...
  • Biochemical characterization of ParI, an orphan C5-DNA methyltransferase from Psychrobacter arcticus 273-4 

    Grgic, Miriam; Williamson, Adele Kim; Bjerga, Gro Elin Kjæreng; Altermark, Bjørn; Leiros, Ingar (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-05-25)
    <p>Cytosine-specific DNA methyltransferases are important enzymes in most living organisms. In prokaryotes, most DNA methyltransferases are members of the type II restriction-modification system where they methylate host DNA, thereby protecting it from digestion by the accompanying restriction endonucleases. DNA methyltransferases can also act as solitary enzymes having important roles in controlling ...
  • An efficient pseudo-spectral method for the description of atomic electronic wave functions – Application to the hydrogen atom in a uniform magnetic field 

    Woywod, Clemens; Roy, Susmita; Maiti, Kiran; Ruud, Kenneth (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-09-27)
    <p>The mapping of an electronic state on a real-space support lattice may offer advantages over a basis set ansatz in cases where there are linear dependences due to basis set overcompleteness or when strong internal or external fields are present. Such discretization methods are also of interest because they allow for the convenient numerical integration of matrix elements of local operators. We ...
  • Unraveling the Microscopic Origin of Triplet Lasing from Organic Solids 

    Paul, Lopa; Banerjee, Ambar; Paul, Ankan; Ruud, Kenneth; Chakrabarti, Swapan (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-07-16)
    We present a heuristic mechanism for the origin of the unusual triplet lasing from (E)-3-(((4-nitrophenyl)imino)methyl)-2H-thiochroman-4-olate·BF<sub>2</sub>. We demonstrate that whereas the moderate lifetime (1.03 μs) of the first triplet state (T<sub>1</sub>) prohibits triplet–triplet annihilation, the relatively faster S<sub>1</sub> → T<sub>1</sub> intersystem crossing and the 10<sup>4</sup> times ...

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