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First-Principles Calculation of 1H NMR Chemical Shifts of Complex Metal Polyhydrides: The Essential Inclusion of Relativity and Dynamics
(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, ... -
Novel Synthesis of Lipoxine A4 Analogues. Towards Allostric Modulators for Human Cannabinoid Receptor Type 1
(Master thesis; Mastergradsoppgave, 2015-11-15)The synthesis of the benzoid-based lipoxine A4 (LXA4) is the focus of this study specifically, the para substituted benzoid system. LXA4 is an endogenous agonist binding with high affinity to (ALXR) receptor that initiate it to display anti-inflammatory and antioxidant activities. Arachidonic acid is the cascade of LXA4 and its derivatives. These compounds belong to the biological active eicosanoids, ... -
Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae
(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
(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 ... -
Computational Studies of Selected Mutants of Shrimp Alkaline Phosphatase
(Master thesis; Mastergradsoppgave, 2020-06-01)Drug discovery and refinement for use in the industry is an important and lucrative field within chemistry. In this regard, computational chemistry has shown to be a valuable tool in assisting drug discovery. A set of intriguing proteins used in drug discovery are cold-adapted enzymes. These enzymes have a lower activation point which makes them of interest in industrial use. In this study, the ... -
Total Synthesis of Phorbazole B
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-10-21)Phorbazoles are polychlorinated heterocyclic secondary metabolites isolated from a marine sponge and several of these natural products have shown inhibitory activity against cancer cells. In this work, a synthesis of the trichlorinated phorbazole B using late stage electrophilic chlorination was developed. The synthesis relied on the use of an oxazole precursor, which was protected with an iodine ... -
Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-10-06)<i>Background</i> - The genome of <i>Vibrionaceae</i> bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (<i>ori1</i>). This is believed to be a growth optimization strategy to satisfy ... -
The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-02-21)Chromatin post‐translational modifications are thought to be important for epigenetic effects on gene expression. Methylation of histone N‐terminal tail lysine residues constitutes one of many such modifications, executed by families of histone lysine methyltransferase (HKMTase). One such protein is ASHH2 from the flowering plant <i>Arabidopsis thaliana</i>, equipped with the interaction domain, CW, ... -
Iridium Corroles Exhibit Weak Near-Infrared Phosphorescence but Efficiently Sensitize Singlet Oxygen Formation
(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(<i>para</i>-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 ... -
Protonation-Induced Hyperporphyrin Spectra of meso-Aminophenylcorroles
(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 <i>meso-</i>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 ... -
Predicting liquid loss of frozen and thawed cod from hyperspectral imaging
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-08-20)As the ability to appraise the quality of every fish in a delivery in a consistent, objective, and rapid manner has numerous advantages for both sellers and buyers, there has been much research into methods to achieve this. One possible proxy for quality assessment is liquid loss, which correlates with undesirable sensory attributes. This study evaluated whether hyperspectral imaging could predict ... -
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-09-11)Infectious pancreatic necrosis virus (IPNV) infection has been a major problem in salmonid aquaculture. Marker-assisted selection of individuals with resistant genotype at the major IPN quantitative trait locus (IPN-QTL) has significantly reduced mortality in recent years. We have identified host miRNAs that respond to IPNV challenge in salmon fry that were either homozygous resistant (RR) or ... -
Structural insights into the enhanced carbapenemase efficiency of OXA-655 compared to OXA-10
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-07-19)Carbapenemases are the main cause of carbapenem resistance in Gram‐negative bacteria. How β‐lactamases with weak carbapenemase activity, such as the OXA‐10‐type class D β‐lactamases, contribute to anti‐bacterial drug resistance is unclear. OXA‐655 is a T26M and V117L OXA‐10 variant, recently identified from hospital wastewater. Despite exhibiting stronger carbapenemase activity towards ertapenem ... -
Structural and biochemical characterization of the environmental MBLs MYO-1, ECV-1 and SHD-1
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-05-28)<i>Background</i> - MBLs form a large and heterogeneous group of bacterial enzymes conferring resistance to β-lactam antibiotics, including carbapenems. A large environmental reservoir of MBLs has been identified, which can act as a source for transfer into human pathogens. Therefore, structural investigation of environmental and clinically rare MBLs can give new insights into structure–activity ... -
Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds
(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 ... -
Sequence analysis of nonulosonic acid biosynthetic gene clusters in Vibrionaceae and Moritella viscosa
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-07-20)Nonulosonic acid (NulO) biosynthesis in bacteria is directed by <i>nab</i> gene clusters that can lead to neuraminic, legionaminic or pseudaminic acids. Analysis of the gene content from a set mainly composed of <i>Aliivibrio salmonicida</i> and <i>Moritella viscosa</i> strains reveals the existence of several unique nab clusters, for which the NulO products were predicted. This prediction method ... -
Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable QM/MM
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-06-12)Multi-photon absorption properties, particularly two-photon absorption (2PA), of fluorescent proteins (FPs) have made them attractive tools in deep-tissue clinical imaging. Although the diversity of photophysical properties for FPs is wide, there are some caveats predominant among the existing FP variants that need to be overcome, such as low quantum yields and small 2PA cross-sections. From a ... -
MiMiC: Multiscale Modeling in Computational Chemistry
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-03-20)Hybrid quantum mechanics/molecular mechanics (QM/MM) approaches are commonly used methods for investigating a plethora of chemical, biochemical, and biophysical processes that require explicit treatment of the electronic degrees of freedom when the system is too big to be entirely treated by QM methods alone (Warshel and Levitt, 1976; Senn and Thiel, 2009; Adhireksan et al., 2014; Campomanes et al., ... -
Static polarizabilities at the basis set limit: A benchmark of 124 species
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-06-16)Benchmarking molecular properties with Gaussian-type orbital (GTO) basis sets can be challenging, because one has to assume that the computed property is at the complete basis set (CBS) limit, without a robust measure of the error. Multiwavelet (MW) bases can be systematically improved with a controllable error, which eliminates the need for such assumptions. In this work, we have used MWs within ... -
Structural studies of triazole inhibitors with promising inhibitor effects against antibiotic resistance metallo-β-lactamases
(Journal article; Tidsskriftartikkel; Peer reviewed, 2020-06-18)Metallo-β-lactamases (MBLs) are an emerging cause of bacterial antibiotic resistance by hydrolysing all classes of β-lactams except monobactams, and the MBLs are not inhibited by clinically available serine-β-lactamase inhibitors. Two of the most commonly encountered MBLs in clinical isolates worldwide – the New Delhi metallo-β-lactamase (NDM-1) and the Verona integron-encoded metallo-β-lactamase ...
