Recent additions

  • Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family 

    Isaksen, Geir Villy; Guo, Xiaohu; Söderholm, Annika; Kanchugal P, Sandesh; Warsi, Omar; Eckhard, Ulrich; Silvia, Trigüis; Gogoll, Adolf; Jerlström-Hultqvist, Jon; Åqvist, Johan; Anderson, Dan I; Selmer, Maria (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-02-10)
    The first S-adenosyl methionine (SAM) degrading enzyme (SAMase) was discovered in bacteriophage T3, as a counter-defense against the bacterial restriction-modification system, and annotated as a SAM hydrolase forming 5’ methyl-thioadenosine (MTA) and L-homoserine. From environmental phages, we recently discovered three SAMases with barely detectable sequence similarity to T3 SAMase and without ...
  • Molecular Structure of Copper and μ-Oxodiiron Octafluorocorrole Derivatives: Insights into Ligand Noninnocence 

    Thomas, Kolle E.; Settineri, Nicholas S.; Teat, Simon J.; Steene, Erik (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-04-23)
    Single-crystal X-ray structures were obtained for the copper and μ-oxodiiron complexes of 2,3,7,8,12,13,17,18-octafluoro-5,10,15-triphenylcorrole, hereafter denoted as Cu[F8TPC] and {Fe[F8TPC]}2O. A comparison with the crystal structures of other undecasubstituted Cu corroles, including those with H, Ar, Br, I, and CF3 as β-substituents, showed that the degree of saddling increases in the order: H ...
  • Protonation-Induced Hyperporphyrin Spectra of meso-Aminophenylcorroles 

    Thomassen, Ivar K.; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-04-06)
    UV–vis spectrophotometric titrations have been carried out on <i>meso</i>-tris(<i>o/m/p</i>-aminophenyl)corrole (H<sub>3</sub>[<i>o/m/p</i>-TAPC]) and meso-triphenylcorrole (H<sub>3</sub>[TPC]) in dimethyl sulfoxide with methanesulfonic acid (MSA). Monoprotonation was found to result in hyperporphyrin spectra characterized by new, red-shifted, and intense Q bands. The effect was particularly dramatic ...
  • Facile Supramolecular Engineering of Porphyrin cis Tautomers: The Case of β-Octabromo-meso-tetraarylporphyrins 

    Thomas, Kolle E.; Slebodnick, Carla; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-04-02)
    A porphyrin cis tautomer, where the two central NH protons are on adjacent pyrrole rings, has long been invoked as an intermediate in porphyrin tautomerism. Only recently, however, has such a species been isolated and structurally characterized. Thus, single-crystal X-ray structure determinations of two highly saddled free-base porphyrins, β-heptakis(trifluoromethyl)-meso-tetrakis(p-fluorophenyl)porphyrin, ...
  • Nature of the copper-nitrosyl intermediates of copper nitrite reductases during catalysis 

    Hough, Michael A.; Conradie, Jeanet; Strange, Richard W.; Antonyuk, Svetlana V.; Eady, Robert R.; Ghosh, Abhik; Hasnain, S. Samar (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-10-20)
    The design and synthesis of copper complexes that can reduce nitrite to NO has attracted considerable interest. They have been guided by the structural information on the catalytic Cu centre of the widespread enzymes Cu nitrite reductases but the chemically novel side-on binding of NO observed in all crystallographic studies of these enzymes has been questioned in terms of its functional relevance. ...
  • X-ray absorption spectroscopy of archetypal chromium porphyrin and corrole derivatives 

    Cao, Rui; Thomas, Kolle E.; Ghosh, Abhik; Sarangi, Ritimukta (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-05-29)
    A combination of Cr K-edge XAS and DFT calculations have been performed on archetypal chromium porphyrinoid complexes Cr<sup>IV</sup>[TMP]O (<b>2</b>) and Cr<sup>V</sup>[TPC]O (<b>3</b>), and the results have been compared to the reference compound Cr<sup>III</sup>[TPP]Cl (<b>1</b>), where TPP<sup>2−</sup>, TMP<sup>2−</sup>, and TPC<sup>3−</sup> are the anions of <i>meso</i>-tetraphenylporphyrin, ...
  • The high catalytic rate of the cold-active Vibrio alkaline phosphatase requires a hydrogen bonding network involving a large interface loop 

    Hjörleifsson, Jens Guðmundur; Helland, Ronny; Magnusdottir, Manuela; Ásgeirsson, Bjarni (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-11-16)
    The role of surface loops in mediating communication through residue networks is still a relatively poorly understood part in the study of cold adaptation of enzymes, especially in terms of their quaternary interactions. Alkaline phosphatase (AP) from the psychrophilic marine bacterium <i>Vibrio splendidus</i> (VAP) is characterized by an analogous large surface loop in each monomer, referred to as ...
  • 1H, 13C, 15N resonance assignment of the apo form of the small, chitin-active lytic polysaccharide monooxygenase JdLPMO10A from Jonesia denitrificans 

    Christensen, Idd Andrea; Eijsink, Vincent; Aachmann, Finn Lillelund; Courtade, Gaston (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-11-19)
    The lytic polysaccharide monooxygenase <i>Jd</i>LPMO10A is the N-terminal domain of the multimodular protein Jd1381. The isolated <i>Jd</i>LPMO10A domain is one of the smallest chitin-active lytic polysaccharide monooxygenases known to date with a size of only 15.5 kDa. <i>Jd</i>LPMO10A is a copper-dependent oxidative enzyme that depolymerizes chitin by hydroxylating the C1 carbon in the glycosidic ...
  • nsroot: Minimalist process isolation tool implemented with Linux namespaces 

    Raknes, Inge Alexander; Fjukstad, Bjørn; Bongo, Lars Ailo Aslaksen (Journal article; Tidsskriftartikkel, 2017-11-26)
    Data analyses in the life sciences are moving from tools run on a personal computer to services run on large computing platforms. This creates a need to package tools and dependencies for easy installation, configuration and deployment on distributed platforms. In addition, for secure execution there is a need for process isolation on a shared platform. Existing virtual machine and container ...
  • Synthesis and molecular structure of perhalogenated rhenium-oxo corroles 

    Alemayehu, Abraham B.; Einrem, Rune F.; McCormick‑McPherson, Laura J.; Settineri, Nicholas S.; Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-11-12)
    As part of our efforts to develop rhenium-oxo corroles as photosensitizers for oxygen sensing and photodynamic therapy, we investigated the potential <i>β</i>-perhalogenation of five ReO <i>meso</i>-tris(<i>para</i>-X-phenyl)corroles, Re[T<i>p</i>XPC](O) (X = CF<sub>3</sub>, H, F, CH<sub>3</sub>, and OCH<sub>3</sub>), with elemental chlorine and bromine. With Cl<sub>2</sub>, <i>β</i>-octachlorinated ...
  • Iridium corroles exhibit weak near-infrared phosphorescence but efficiently sensitize singlet oxygen formation 

    Ghosh, Abhik (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-05-05)
    Six-coordinate iridium(III) triarylcorrole derivatives, Ir[T<i>p</i>XPC)]L<sub>2</sub>, where T<i>p</i>XPC = tris(para-X-phenyl)corrole (X = CF<sub>3</sub>, H, Me, and OCH<sub>3</sub>) and L = pyridine (py), trimethylamine (tma), isoquinoline (isoq), 4-dimethylaminopyridine (dmap), and 4-picolinic acid (4pa), have been examined, with a view to identifying axial ligands most conducive to near-infrared ...
  • Description of the uEMEP_v5 downscaling approach for the EMEP MSC-W chemistry transport model 

    Denby, Bruce; Gauss, Michael; Wind, Peter; Mu, Qing; Wærsted, Eivind Grøtting; Fagerli, Hilde; Valdebenito Bustamante, Alvaro Moises; Klein, Heiko (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-12-11)
    A description of the new air quality downscaling model – the urban EMEP (uEMEP) and its combination with the EMEP MSC-W model (European Monitoring and Evaluation Programme Meteorological Synthesising Centre West) – is presented. uEMEP is based on well-known Gaussian modelling principles. The uniqueness of the system is in its combination with the EMEP MSC-W model and the “local fraction” calculation ...
  • Unequivocal structure confirmation of a breitfussin analog by anisotropic NMR measurements 

    Ndukwe, Ikenna E.; Lam, Yu-hong; Pandey, Sunil Kumar; Haug, Bengt Erik; Bayer, Annette; Sherer, Edward C.; Blinov, Kirill A.; Williamson, R. Thomas; Isaksson, Johan; Reibarkh, Mikhail; Liu, Yizhou; Martin, Gary E. (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-09-21)
    Structural features of proton-deficient heteroaromatic natural products, such as the breitfussins, can severely complicate their characterization by NMR spectroscopy. For the breitfussins in particular, the constitution of the five-membered oxazole central ring cannot be unequivocally established via conventional NMR methods when the 4′-position is halogenated. The level of difficulty is exacerbated ...
  • X-ray crystal structure of Vibrio alkaline phosphatase with the non-competitive inhibitor cyclohexylamine 

    Ásgeirsson, Bjarni; Markússon, Sigurbjörn; Hlynsdóttir, Sigríður S.; Helland, Ronny; Hjörleifsson, Jens G. (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-10-15)
    <i>Background</i> - <i>Para</i>-nitrophenyl phosphate, the common substrate for alkaline phosphatase (AP), is available as a cyclohexylamine salt. Here, we report that cyclohexylamine is a non-competitive inhibitor of APs.<br><br> <i>Methods</i> - Cyclohexylamine inhibited four different APs. Co-crystallization with the cold-active <i>Vibrio</i> AP (VAP) was performed and the structure solved.<br><br> ...
  • Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds 

    Williamson, Adele Kim; Leiros, Hanna-Kirsti S. (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-05-04)
    DNA ligases are diverse enzymes with essential functions in replication and repair of DNA; here we review recent advances in their structure and distribution and discuss how this contributes to understanding their biological roles and technological potential. Recent high-resolution crystal structures of DNA ligases from different organisms, including DNA-bound states and reaction intermediates, have ...
  • A scalable and green one-minute synthesis of substituted phenols 

    Elumalai, Vijayaragavan; Hansen, Jørn H (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-11-07)
    A mild, green and highly efficient protocol was developed for the synthesis of substituted phenols via <i>ipso</i>-hydroxylation of arylboronic acids in ethanol. The method utilizes the combination of aqueous hydrogen peroxide as the oxidant and H<sub>2</sub>O<sub>2</sub>/HBr as the reagent under unprecedentedly simple and convenient conditions. A wide range of arylboronic acids were smoothly ...
  • Methanotroph populations and CH 4 oxidation potentials in High Arctic peat are altered by herbivory induced vegetation change 

    Rainer, Edda Marie; Seppey, Victor William Christophe; Tveit, Alexander Tøsdal; Svenning, Mette Marianne (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-07-08)
    Methane oxidizing bacteria (methanotrophs) within the genus <i>Methylobacter</i> constitute the biological filter for methane (CH<sub>4</sub>) in many Arctic soils. Multiple <i>Methylobacter</i> strains have been identified in these environments but we seldom know the ecological significance of the different strains. High-Arctic peatlands in Svalbard are heavily influenced by herbivory, leading to ...
  • First-Principles Calculation of 1H NMR Chemical Shifts of Complex Metal Polyhydrides: The Essential Inclusion of Relativity and Dynamics 

    Castro, Abril C; Balcells, David; Repisky, Michal; Helgaker, Trygve; Cascella, Michele (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-11-23)
    <sup>1</sup>H NMR spectroscopy has become an important technique for the characterization of transition-metal hydride complexes, whose metal-bound hydrides are often difficult to locate by X-ray diffraction. In this regard, the accurate prediction of <sup>1</sup>H NMR chemical shifts provides a useful, but challenging, strategy to help in the interpretation of the experimental spectra. In this work, ...
  • Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae 

    Mazurkewich, Scott; Helland, Ronny; Mackenzie, Alasdair; Eijsink, Vincent; Pope, Phillip Byron; Brändén, Gisela; Larsbrink, Johan (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-08-13)
    Chitin is one of the most abundant renewable organic materials found on earth. The chitin utilization locus in <i>Flavobacterium johnsoniae</i>, which encodes necessary proteins for complete enzymatic depolymerization of crystalline chitin, has recently been characterized but no detailed structural information on the enzymes was provided. Here we present protein structures of the <i>F. johnsoniae</i> ...
  • Centre for Digital Life Norway - Annual report 2017 

    Unknown author (Research report; Forskningsrapport, 2018)
    Centre for Digital Life Norway (DLN) is a virtual centre, institutionally anchored at NTNU, UiO and UiB. It is funded by the Research Council of Norway under the Digital Life (DL) initiative and receives in kind support from the host universities. The centre is built around the 12 research projects are currently funded through the research council’s Digital Life initiative. DLNs mission is ...

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