| 1. |
- Grahnemo, Louise, et al.
(author)
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Identification of three bacterial species associated with increased appendicular lean mass : the HUNT study.
- 2023
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Journal article (peer-reviewed)abstract
- Appendicular lean mass (ALM) associates with mobility and bone mineral density (BMD). While associations between gut microbiota composition and ALM have been reported, previous studies rely on relatively small sample sizes. Here, we determine the associations between prevalent gut microbes and ALM in large discovery and replication cohorts with information on relevant confounders within the population-based Norwegian HUNT cohort (n = 5196, including women and men). We show that the presence of three bacterial species - Coprococcus comes, Dorea longicatena, and Eubacterium ventriosum - are reproducibly associated with higher ALM. When combined into an anabolic species count, participants with all three anabolic species have 0.80 kg higher ALM than those without any. In an exploratory analysis, the anabolic species count is positively associated with femoral neck and total hip BMD. We conclude that the anabolic species count may be used as a marker of ALM and BMD. The therapeutic potential of these anabolic species to prevent sarcopenia and osteoporosis needs to be determined.
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| 2. |
- Lima, Gustavo M A, et al.
(author)
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FragMAX : the fragment-screening platform at the MAX IV Laboratory
- 2020
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In: Acta Crystallographica Section D: Structural Biology. - 2059-7983. ; 76:Pt 8, s. 771-777
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Journal article (peer-reviewed)abstract
- Advances in synchrotron storage rings and beamline automation have pushed data-collection rates to thousands of data sets per week. With this increase in throughput, massive projects such as in-crystal fragment screening have become accessible to a larger number of research groups. The quality of support offered at large-scale facilities allows medicinal chemistry-focused or biochemistry-focused groups to supplement their research with structural biology. Preparing the experiment, analysing multiple data sets and prospecting for interesting complexes of protein and fragments require, for both newcomers and experienced users, efficient management of the project and extensive computational power for data processing and structure refinement. Here, FragMAX, a new complete platform for fragment screening at the BioMAX beamline of the MAX IV Laboratory, is described. The ways in which users are assisted in X-ray-based fragment screenings and in which the fourth-generation storage ring available at the facility is best exploited are also described.
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| 3. |
- Sjögren, Tove, et al.
(author)
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Protein crystallography in a vapour steam : data collection, reaction initiation and intermediate trapping in naked hydrated protein crystals
- 2002
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In: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 35:1, s. 113-116
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Journal article (peer-reviewed)abstract
- A procedure is presented for experiments on naked unfrozen protein crystals with the crystal mounted in a conventional cryo-loop and surrounded by a stream of a wet gas. The composition and temperature of the vapour stream can be adjusted to keep the crystal without deterioration for many hours. The arrangement allows (i) for rapidly testing crystals for diffraction before freezing, (ii) for data collection between 268-303 K with greatly reduced background, (iii) for the controlled drying or wetting of crystals, (iv) for the anaerobic manipulation of protein crystals, and (v) for the introduction of gaseous or volatile ingredients and reactants into the crystal. The technique offers new experimental possibilities, e.g. in time-resolved structural studies. Reaction initiation in many protein crystals can be achieved by changing the composition of the vapour stream to create a new chemical environment around the crystal and to introduce substrates/reactants either in the gas phase or as microdroplets. Spectral changes during such reactions can be monitored by single-crystal microspectrophotometry, and, once an intermediate has been detected at high concentrations, the crystal can be frozen, e.g. by rapidly switching the warm vapour stream to a cryogenically cooled helium or nitrogen jet. Representative examples are presented in this paper.
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| 4. |
- Sjögren, Tove
(author)
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Structural Plasticity and Function in Cytochrome cd1 Nitrite Reductase
- 2001
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Doctoral thesis (other academic/artistic)abstract
- Cytochrome cd1 nitrite reductase is a bifunctional enzyme, which catalyses the one-electron reduction of nitrite to nitric oxide, and the four-electron reduction of oxygen to water. The latter is a cytochrome oxidase reaction. Both reactions occur on the d1 haem iron of the enzyme.Time resolved crystallographic studies presented here show that the mechanisms of nitrite and oxygen reduction share common elements. This is of interest from an evolutionary point of view since aerobic respiratory enzymes are thought to have evolved from denitrifying enzymes. Despite of similarities, the results also imply different requirements for the timing of electron transfer to the active site in these reactions.Quantum chemical calculations suggest that nitric oxide, the product of nitrite reduction, is not spontaneously released from the haem iron while this is not the case with water. Reduction of the haem while nitric oxide is still bound to it would result in a tight dead-end complex. A mechanism must therefore exist for the selective control of electron transfer during the reaction.Structural studies with a product analogue (carbon monoxide) combined with flash photolysis of the complex in solution revealed an unexpected proton uptake by the active site as the neutral CO molecule left the enzyme. This led to the suggestion that the increased positive potential of the active site triggers preferential electron transfer when the active site is empty.Crystallisation and structure determination of the reduced enzyme revealed extremely large domain rearrangements. These results offer insights into the role of tethered electron shuttle proteins in complex redox systems, and suggests a mechanism for conformational gating in catalysis.
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| 5. |
- Vassbo, Tove Karin, et al.
(author)
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Effects of a person-centred and thriving-promoting intervention on nursing home staff job satisfaction : A multi-centre, non-equivalent controlled before-after study
- 2020
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In: Nursing Open. - : John Wiley & Sons. - 2054-1058. ; 7, s. 1787-1797
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Journal article (peer-reviewed)abstract
- Aim: To evaluate the effects of a person‐centred and thriving‐promoting intervention in nursing homes on staff job satisfaction, stress of conscience and the person‐centredness of care and of the environment.Design: A multi‐centre, non‐equivalent control group, before–after trial design.Methods: Staff (N = 341) from six nursing homes in Australia, Norway and Sweden were assigned to the intervention or the control group and both groups were evaluated before the intervention, immediately after and by 6 months follow‐up. Staff completed a questionnaire about job satisfaction (primary endpoint), stress of conscience and the person‐centredness of care and of the environment (secondary endpoints). Linear regression models were used to identify the mean scores and to analyse group differences to test the effects of the intervention.Results: The intervention had no statistically significant effects on staff job satisfaction, level of stress of conscience or the perceived person‐centredness of care and of the environment.
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| 6. |
- Wang, Conan, et al.
(author)
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Combined X-ray and NMR analysis of the stability of the cyclotide cystine knot fold that underpins its insecticidal activity and potential use as a drug scaffold
- 2009
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In: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 284:16, s. 10672-10683
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Journal article (peer-reviewed)abstract
- Cyclotides are a family of plant defense proteins that are highly resistant to adverse chemical, thermal, and enzymatic treatment. Here, we present the first crystal structure of a cyclotide, varv F, from the European field pansy, Viola arvensis, determined at a resolution of 1.8 angstrom. The solution state NMR structure was also determined and, combined with measurements of biophysical parameters for several cyclotides, provided an insight into the structural features that account for the remarkable stability of the cyclotide family. The x-ray data confirm the cystine knot topology and the circular backbone, and delineate a conserved network of hydrogen bonds that contribute to the stability of the cyclotide fold. The structural role of a highly conserved Glu residue that has been shown to regulate cyclotide function was also determined, verifying its involvement in a stabilizing hydrogen bond network. We also demonstrate that varv F binds to dodecylphosphocholine micelles, defining the binding orientation and showing that its structure remains unchanged upon binding, further demonstrating that the cyclotide fold is rigid. This study provides a biological insight into the mechanism by which cyclotides maintain their native activity in the unfavorable environment of predator insect guts. It also provides a structural basis for explaining how a cluster of residues important for bioactivity may be involved in self-association interactions in membranes. As well as being important for their bioactivity, the structural rigidity of cyclotides makes them very suitable as a stable template for peptide-based drug design.
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| 7. |
- Wilmot, Carrie M., et al.
(author)
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Defining redox state of X-ray crystal structures by single-crystal ultraviolet visible microspectrophotometry
- 2002
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In: Methods in Enzymology. - 0076-6879 .- 1557-7988. ; 353, s. 301-318
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Journal article (peer-reviewed)abstract
- Exciting results have been emerging from the field of single-crystal X-ray crystallography, giving unprecedented detail of freeze-trapped reaction intermediates from important classes of macromolecules that contain chromophores. These structures have been coupled with single-crystal UV-visible microspectrophotometry. This has defined the distinct catalytic intermediates present in the crystal structures, allowing the correlation of electronic transitions with the observed structural transitions. Of particular note is that many of these structures have been generated “on the fly” during kinetic turnover in the crystal. Most enzymatic reactions proceed through distinct catalytic intermediates that, under favorable conditions, may accumulate transiently in the crystal during turnover. In some cases, the physical constraints of the contacts within crystals may also lead to a significant slowing of the reaction at certain points along the pathway where conformational changes are required. This can lead to a transient build-up of spectrally distinct intermediates in the crystal that can be trapped by flash freezing in liquid nitrogen, allowing a complete single-crystal data set to be collected to the highest possible resolution at a later time. Similar build-up of intermediates may be achieved by altering the pH, temperature, or the solvent environment around the protein in the crystal, or by producing engineered variants that build up an intermediate of interest. The chapter focuses on the technical considerations required to carry out UV-visible microspectroscopy of single crystals.
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