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  • 1.
    Aguilar, Ximena
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Weise, Christoph
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wolf-Watz, Magnus
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wittung-Stafshede, Pernilla
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Macromolecular crowding extended to a heptameric system: the co-chaperonin protein 102011In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 50, no 14, p. 3034-3044Article in journal (Refereed)
    Abstract [en]

    Experiments on monomeric proteins have shown that macromolecular crowding can stabilize toward heat perturbation and also modulate native-state structure. To assess the effects of macromolecular crowding on unfolding of an oligomeric protein, we here tested the effects of the synthetic crowding agent Ficoll 70 on human cpn10 (GroES in E. coli), a heptameric protein consisting of seven identical β-barrel subunits assembling into a ring. Using far-UV circular dichroism (CD), tyrosine fluorescence, nuclear magnetic resonance (NMR), and cross-linking experiments, we investigated thermal and chemical stability, as well as the heptamer-monomer dissociation constant, without and with crowding agent. We find that crowding shifts the heptamer-monomer equilibrium constant in the direction of the heptamer. The cpn10 heptamer is both thermally and thermodynamically stabilized in 300 mg/mL Ficoll 70 as compared to regular buffer conditions. Kinetic unfolding experiments show that the increased stability in crowded conditions, in part, is explained by slower unfolding rates. A thermodynamic cycle reveals that in presence of 300 mg/mL Ficoll the thermodynamic stability of each cpn10 monomer increases by over 30%, whereas the interfaces are stabilized by less than 10%. We also introduce a new approach to analyze the spectroscopic data that makes use of multiple wavelengths: this provides robust error estimates of thermodynamic parameters.

  • 2. Borgström, Johan
    et al.
    Egermayer, Monica
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Chemistry.
    Quist, Per-Ola
    Piculell, Lennart
    Liquid crystallinity versus gelation of kappa-carrageenan in mixed salts: effects of molecular weight, salt composition, and ionic strength1998In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 14, no 17, p. 4935-44Article in journal (Refereed)
    Abstract [en]

    The recently discovered isotropic/nematic phase transition in kappa-carrageenan was further examined by macroscopic observations and by NMR. A state diagram, which is the equivalent of a phase diagram but including also nonequilibrium states (in our case a gel), was established in the mixed salt solutions of NaI/CsI where the competition between phase separation and gelation could be studied. The phase boundaries of the nematic phase depended on molecular weight and ionic strength qualitatively as expected for a charged rigid polymer. From these data the persistence length of the kappa-carrageenan helix was estimated as 60-90 nm. The volume fraction of the nematic phase depended sensitively on the overall helical content. In coexisting phases, the helical content was larger in the nematic than in the isotropic phase.

  • 3.
    Bui, Nhat Thi Hong
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jiang, Wen
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Irgum, Knut
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Synthesis of poly(N-[tris(hydroxymethyl)methyl]acrylamide) functionalized porous silica for application in hydrophilic interaction chromatography2012In: Journal of Separation Science, ISSN 1615-9306, E-ISSN 1615-9314, Vol. 35, no 23, p. 3257-3269Article in journal (Refereed)
    Abstract [en]

    Porous silica coated by a highly hydrophilic and nonionic tentacle-type polymeric layer was synthesized by free radical "grafting from" polymerization of N-[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]-2-propenamide (TRIS-acrylamide) in partly aqueous solutions. The radical initiator sites were incorporated on the silica surfaces via a two-step reaction comprising thionyl chloride activation and subsequent reaction with tert-butyl hydroperoxide. The surface-bound tert-butylperoxy groups were then used as thermally triggered initiators for graft polymerization of TRIS-acrylamide. The synthesized materials were characterized by diffusive reflectance Fourier transform infrared specotroscopy, X-ray photoelectron spectroscopy, and CHN elemental analysis. Photon correlation spectroscopy was used to determine changes in ζ-potentials resulting from grafting, (29) Si magic angle spinning nuclear magnetic resonance spectroscopy (MAS-NMR) spectroscopy was used to assess the ratio of silanol to siloxane groups in the substrate and the grafted material, and the changes in surface area and mesopore distribution were determined by nitrogen cryosorption. Chromatographic evaluation in hydrophilic interaction chromatography (HILIC) mode showed that the materials were suitable for use as stationary phases, featuring good separation efficiency, a comparatively high retention, and a selectivity that differed from most commercially available HILIC phases. A comparison of this neutral phase with a previously reported N-(2-hydroxypropyl)-linked TRIS-type hydrophilic tentacle phase with weak anion exchange functionality revealed substantial differences in retention patterns.

  • 4.
    Clifton, Luke A.
    et al.
    ISIS Neutron and Muon Source, Science and Technology Facilities Council, Didcot, United Kingdom.
    Ul Mushtaq, Ameeq
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ådén, Jörgen
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wacklin-Knecht, Hanna
    European Spallation Source, European Research Infrastructure Consortium, Lund, Sweden.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Insight into Bcl-2 proteins' functioning at mitochondrial membrane level2023In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 122, no 3S1, p. 232a-232a, article id 1130-PosArticle in journal (Refereed)
    Abstract [en]

    Programmed cell death (apoptosis) is essential in life. In its intrinsic apoptotic pathway opposing members of the B-cell lymphoma 2 (Bcl-2) protein family control the permeability of the mitochondrial outer membrane (MOM) and the release of apoptotic factors such as cytochrome c. Any misregulation of this process can cause disorders most prominently cancer, where often upregulation of cell protecting (anti-apoptotic) Bcl-2 members such as the Bcl-2 membrane protein itself plays a notorious role by blocking MOM perforation by - often drug induced - apoptotic proteins such as Bax which would cause cancer cell death normally. Here, we apply neutron reflectometry (NR) on supported lipid bilayers which mimic MOM environment and solid state/liquid state NMR spectroscopy to unravel the molecular basis driving opposing proteins to interact with each other at the MOM; a mechanism which is not really understood yet due to lack of high-resolution structural insight. Based on our central hypothesis that Bcl-2 drives its cell-protecting function at a membrane-embedded location as revealed by NR (1), we focus i) to determine the structure of human Bcl-2 protein in its membrane setting by combining solution and solid-state NMR; ii) use NR to study the kinetics and lipid/protein pore assemblied upon binding of Bax to mitochondrial membranes and its membrane destroying activities there; and iii) unravel the nature of direct interaction between Bcl-2 and Bax to neutralize each other. Knowledge generated here, will be indispensable in understanding the regulative function of the Bcl-2 family at mitochondrial membranes.

  • 5.
    Clifton, Luke A.
    et al.
    SIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK.
    Wacklin-Knecht, Hanna P.
    European Spallation Source ERIC, ESS, Lund, Sweden; Department of Chemistry, Division of Physical Chemistry, Lund University, Lund, Sweden.
    Ådén, Jörgen
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ul Mushtaq, Ameeq
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Creation of distinctive Bax-lipid complexes at mitochondrial membrane surfaces drives pore formation to initiate apoptosis2023In: Science Advances, E-ISSN 2375-2548, Vol. 9, no 22, article id eadg7940Article in journal (Refereed)
    Abstract [en]

    Apotosis is an essential process tightly regulated by the Bcl-2 protein family where proapoptotic Bax triggers cell death by perforating the mitochondrial outer membrane. Although intensively studied, the molecular mechanism by which these proteins create apoptotic pores remains elusive. Here, we show that Bax creates pores by extracting lipids from outer mitochondrial membrane mimics by formation of Bax/lipid clusters that are deposited on the membrane surface. Time-resolved neutron reflectometry and Fourier transform infrared spectroscopy revealed two kinetically distinct phases in the pore formation process, both of which were critically dependent on cardiolipin levels. The initially fast adsorption of Bax on the mitochondrial membrane surface is followed by a slower formation of pores and Bax-lipid clusters on the membrane surface. Our findings provide a robust molecular understanding of mitochondrial membrane perforation by cell-killing Bax protein and illuminate the initial phases of programmed cellular death. Bax initiates apoptosis by perforating mitochondrial membranes via formation of pores and extramembranous Bax-lipid complexes.

  • 6.
    De Oliveira, Danilo Hirabae
    et al.
    Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden; Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden.
    Gowda, Vasantha
    Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gustafsson, Linnea
    Spiber Technologies AB, Stockholm, Sweden.
    Sanches Pires, Rodrigo
    Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden.
    Riekel, Christian
    European Synchrotron Radiation Facility, Grenoble Cedex, France.
    Barth, Andreas
    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
    Lendel, Christofer
    Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden.
    Hedhammar, My
    Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden.
    Structural conversion of the spidroin C-terminal domain during assembly of spider silk fibers2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 4670Article in journal (Refereed)
    Abstract [en]

    The major ampullate Spidroin 1 (MaSp1) is the main protein of the dragline spider silk. The C-terminal (CT) domain of MaSp1 is crucial for the self-assembly into fibers but the details of how it contributes to the fiber formation remain unsolved. Here we exploit the fact that the CT domain can form silk-like fibers by itself to gain knowledge about this transition. Structural investigations of fibers from recombinantly produced CT domain from E. australis MaSp1 reveal an α-helix to β-sheet transition upon fiber formation and highlight the helix No4 segment as most likely to initiate the structural conversion. This prediction is corroborated by the finding that a peptide corresponding to helix No4 has the ability of pH-induced conversion into β-sheets and self-assembly into nanofibrils. Our results provide structural information about the CT domain in fiber form and clues about its role in triggering the structural conversion of spidroins during fiber assembly.

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  • 7.
    Dingeldein, Artur P. G.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lidman, Martin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dynamical and Structural Alterations withing Lipid-Protein Assemblies Control Apoptotic Pore Formation - A Solid State NMR Study2016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, no 3, p. 59A-60AArticle in journal (Other academic)
  • 8.
    Dingeldein, Artur P. G.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Oxidatively stressed mitochondria-mimicking membranes: a molecular insight into their organization during apoptosis2018In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1860, no 12, p. 2644-2654Article in journal (Refereed)
    Abstract [en]

    Mitochondria are crucially involved in the removal of eukaryotic cells by the intrinsic pathway of programmed cell death (apoptosis). The mitochondrion's outer membrane (MOM) is the platform where this pathway takes place. Upon oxidative stress triggering apoptotic action, the MOM undergoes permeabilization and release of cytochrome c, ultimately causing cell death. This membrane perforation is regulated not only by opposing members of the Bcl-2 protein family meeting at the MOM but also actively the membrane itself. Upon oxidative damage, the membrane undergoes severe reorganization causing an increase in cell death-causing apoptotic Bcl-2 proteins. To understand the active role of MOM, we provided a detailed molecular view of its structural and dynamic reorganization upon oxidative stress by solid-state C-13 MAS NMR (magic angle spinning nuclear magnetic resonance) accompanied by calorimetric studies. By focusing on MOM-like vesicles doped with oxidized lipid species, direct polarization C-13 MAS NMR provided a quantitative overview and identification of all lipid moieties across the membrane. H-1-C-1(3) cross polarization and insensitive nuclei enhanced by polarization transfer MAS NMR generated a dynamic - mobile versus restricted - membrane profile. Oxidized phospholipids significantly perturb the structural membrane organization and increase membrane dynamics. These perturbations are not uniformly distributed as the hydrophobic core is reflecting the melting of lipid chains and increase in molecular disorder directly, whereas the interface and headgroup region undergo complex dynamical changes, reflecting increased intra-molecular flexibility of these moieties. These changes are potentially crucial in augmenting pro-apoptotic action of proteins like Bax.

  • 9.
    Dingeldein, Artur P. G.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ådén, Jörgen
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wacklin, Hanna P.
    Clifton, Luke A.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mitochondrial Membrane Organization under Oxidative Stress: Insight by Solid-State NMR and Neutron Reflectometry2019In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 116, no 3, p. 508A-508AArticle in journal (Other academic)
  • 10.
    Dingeldein, Artur Peter Günther
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pokorna, Sarka
    Lidman, Martin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sachl, Radek
    Hof, Martin
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Apoptotic Bax at Oxidatively Stressed Mitochondrial Membranes: Lipid Dynamics and Permeabilization2017In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 10, p. 2147-2158Article in journal (Refereed)
    Abstract [en]

    Mitochondria are crucial compartments of eukaryotic cells because they function as the cellular power plant and play a central role in the early stages of programmed cell death (apoptosis). To avoid undesired cell death, this apoptotic pathway is tightly regulated by members of the Bcl-2 protein family, which interact on the external surface of the mitochondria, i.e., the mitochondrial outer membrane (MOM), and modulate its permeability to apoptotic factors, controlling their release into the cytosol. A growing body of evidence suggests that the MOM lipids play active roles in this permeabilization process. In particular, oxidized phospholipids (OxPls) formed under intracellular stress seem to directly induce apoptotic activity at the MOM. Here we show that the process of MOM pore formation is sensitive to the type of OxPls species that are generated. We created MOM-mimicking liposome systems, which resemble the cellular situation before apoptosis and upon triggering of oxidative stress conditions. These vesicles were studied using P-31 solid-state magic-angle-spinning nuclear magnetic resonance spectroscopy and differential scanning calorimetry, together with dye leakage assays. Direct polarization and cross-polarization nuclear magnetic resonance experiments enabled us to probe the heterogeneity of these membranes and their associated molecular dynamics. The addition of apoptotic Bax protein to OxPls-containing vesicles drastically changed the membranes' dynamic behavior, almost completely negating the previously observed effect of temperature on the lipids' molecular dynamics and inducing an ordering effect that led to more cooperative membrane melting. Our results support the hypothesis that the mitochondrion-specific lipid cardiolipin functions as a first contact site for Bax during its translocation to the MOM in the onset of apoptosis. In addition, dye leakage assays revealed that different OxPls species in the MOM-mimicking vesicles can have opposing effects on Bax pore formation.

  • 11.
    Dingeldein, Artur Peter Günther
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Åden, Jörgen
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wacklin, Hanna
    Sachl, Radek
    Pokorná, Sárka
    Hof, Martin
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Oxidatively Stressed Mitochondrial Membranes: Insight into their Organization and Function during Apoptosis2018Conference paper (Refereed)
  • 12.
    Dinh, Van Minh
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Khokarale, Santosh Govind
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ojeda-May, Pedro
    Umeå University, Faculty of Science and Technology, High Performance Computing Center North (HPC2N).
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Irgum, Knut
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Industrial Chemistry & Reaction Engineering, Department of Chemical Engineering, Process Chemistry Centre, Åbo Akademi University, ÅboTurku, Finland.
    Ionic liquid strategy for chitosan production from chitin and molecular insights2024In: RSC Sustainability, E-ISSN 2753-8125, Vol. 2, no 4, p. 1154-1164Article in journal (Refereed)
    Abstract [en]

    To produce chitosan is an interesting research. Chitosan is an important polysaccharide in terms of its various applications in industries and is produced from chitin, an abundant biopolymer in crustacean shell biomass wastes. Traditional processes for chitosan manufacture are commonly based on highly concentrated alkaline or acid solutions which are, however, severely eroding and harmful to the environment. In this study, we have described a ‘greener’ method using 1-ethyl-3-methylimidazolium acetate, [Emim][OAc] ionic liquid (IL), for decrystallization of shrimp crystalline chitin flakes followed by a microwave-mediated NaOH or tetrabutylammonium hydroxide, [TBA][OH], solution-based deacetylation for chitosan production. The decrease in crystallinity in IL pre-treated chitin was confirmed by XRD and SEM analysis which subsequently benefited chitosan production with up to 85% degree of deacetylation (%DDA) in shorter time periods (1-2 hours) and lower alkaline concentrations (20-40%). The %DDA in chitin/chitosan was estimated via FT-IR and NMR analysis. Notably, we could regenerate the ionic liquids: in case of [Emim][OAc] 97 wt.% and in case of [TBA][OH] 83 wt.% could be reused. Roles of ionic liquids in the process were discussed. Molecular dynamics (MD) simulations showed the roles of [TBA]+ cations in the molecular driving forces of [TBA][OH]-induced deacetylation mechanism. The strategy promises a sustainable and milder reaction approach to the existing highly corrosive alkaline- or acid-involved processes for chitosan production.

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  • 13.
    Driver, Gordon W.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Huang, Yang
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Laaksonen, Aatto
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wang, Yonglei
    Westlund, Per-Olof
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Correlated/non-correlated ion dynamics of charge-neutral ion couples: the origin of ionicity in ionic liquids2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 7, p. 4975-4988Article in journal (Refereed)
    Abstract [en]

    Proton/Fluoride spin-lattice ($T_1$) nuclear magnetic relaxation dispersion (NMRD) measurements of 1-butyl-3-methyl-$1H$-imidazolium hexa-fluorophosphate, [$C_4mim][PF_6]$, have been carried out using high field spectrometers and fast-field-cycling instrument at proton Larmor frequencies ranging from 10kHz to 40 MHz, at different temperatures. The NMRD profiles are interpreted by means of a simple relaxation model based on the inter- and intra-ionic dipole-dipole relaxation mechanism. Using an atomic molecular-ion dynamic simulation at 323 K the relevant spin dipole-dipole(DD) correlation functions are calculated. The results indicate the NMRD profiles can be rationalized using intra- and inter-ionic spin DD interactions, however, both are mainly modulated by ionic reorientation because of temporary correlations with cations, where modulation by translational diffusion plays a minor role. Reorientational dynamics of charge-neutral ion couples (i.e. $[C_4mim]^{...}[PF_6]$) and $[C_4mim]^{+}$ ions are in the nano-second (ns) time range whereas the reorientation of $[PF_6]{^-}$ is characterized by a reorientational correlation time in the pico-second (ps) regime. Based on the NMRD profiles we conclude the main relaxation mechanism for $[PF_6]{^-}$ is, due to fast internal reorientational motion, a partially averaged F-F intra and a F-H inter-ionic DD coupling as the anion resides in close proximity to its temporary oppositely charged cation partner. The F-$T_1$- NMRD data display a ns dispersions which is interpreted as being due to correlated reorientational modulations resultant from H-containing charge-neutral ion couple $[C_4mim]^{...}[PF_6]$. The analysis of ionicity is based on the free anion fraction, $f$ and it increase with temperature with $f$ $\rightarrow$ 1 at the highest temperatures investigated. The fraction is obtained from the H-F NMRD profiles as correlated-non-correlated dynamics of the ions. The analysis of $T_1$ relaxation rates of C, H, F and P at high fields cannot generally give the fraction of ion but are consistent with the interpretation based on the NMRD profiles with relaxation contributions due to DD-intra and -inter, CSA-intra (and -inter for C), including spin rotation for P. The investigation has led to a description of the mechanics governing ion transport in the title ionic liquid via identification of transient correlated/non-correlated ion dynamics.

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  • 14. Drotz, Stina Harrysson
    et al.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Nilsson, Mats B
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Öquist, Mats G
    Both catabolic and anabolic heterotrophic microbial activity proceed in frozen soils2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 49, p. 21046-21051Article in journal (Refereed)
    Abstract [en]

    A large proportion of the global soil carbon pool is stored in soils of high-latitude ecosystems in which microbial processes and production of greenhouse gases proceed during the winter months. It has been suggested that microorganisms have limited ability to sequester substrates at temperatures around and below 0 °C and that a metabolic shift to dominance of catabolic processes occurs around these temperatures. However, there are contrary indications that anabolic processes can proceed, because microbial growth has been observed at far lower temperatures. Therefore, we investigated the utilization of the microbial substrate under unfrozen and frozen conditions in a boreal forest soil across a temperature range from -9 °C to +9 °C, by using gas chromatography-isotopic ratio mass spectrometry and (13)C magic-angle spinning NMR spectroscopy to determine microbial turnover and incorporation of (13)C-labeled glucose. Our results conclusively demonstrate that the soil microorganisms maintain both catabolic (CO(2) production) and anabolic (biomass synthesis) processes under frozen conditions and that no significant differences in carbon allocation from [(13)C]glucose into [(13)C]CO(2) and cell organic (13)C-compounds occurred between +9 °C and -4 °C. The only significant metabolic changes detected were increased fluidity of the cell membranes synthesized at frozen conditions and increased production of glycerol in the frozen samples. The finding that the processes in frozen soil are similar to those in unfrozen soil has important implications for our general understanding and conceptualization of soil carbon dynamics in high-latitude ecosystems.

  • 15.
    Drotz, Stina Harrysson
    et al.
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences. Umeå.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Nilsson, Mats
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences. Umeå.
    Öquist, Mats G
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences. Umeå.
    Effects of soil organic matter composition on unfrozen water content and heterotrophic CO2 production of frozen soils2010In: Geochimica et Cosmochimica Acta, ISSN 0016-7037, E-ISSN 1872-9533, Vol. 74, no 8, p. 2281-90Article in journal (Refereed)
    Abstract [en]

    Several recent studies have highlighted the importance of soil organic matter (SOM) mineralization at high latitudes during winter for ecosystem carbon (C) balances, and the ability of the soil to retain unfrozen water at sub-zero temperatures has been shown to be a major determinant of C mineralization rates. Further, SOM is believed to strongly influence the liquid water contents in frozen surface layers of boreal forest soils and tundra, but the mechanisms and specific factors involved are currently unknown. Here we evaluate the effects of the chemical composition of SUM on the amount of unfrozen water, the pore size equivalents in which unfrozen water can exist, and the microbial heterotrophic activity at sub-zero temperatures in boreal forest soils. To do this, we have characterized the chemical composition of SUM in forest soil samples (surface O-horizons) using solid state CP-MAS (cross polarization magic angle spinning) NMR spectroscopy. The acquired information was then used to elucidate the extent to which different fractions of SUM can explain the observed variations in unfrozen water content, pore size equivalents, and biogenic CO2 production rates in the examined soil samples under frozen conditions (-4 degrees C). The data evaluation was done by the use of principal component analysis (PCA) and projections to latent structures by means of partial least square (PLS). We conclude that aromatic, O-aromatic, methoxy/N-alkyl and alkyl C are the major SOM components affecting frozen boreal forest soil's ability to retain unfrozen water and sustain heterotrophic activity (95% confidence level). Our results reveal that solid carbohydrates have a significant negative impact (95% confidence level) on CO2 production in frozen boreal spruce forest soils, in contrast to the positive effects of carbohydrate polymers during unfrozen conditions. We conclude that the hierarchy of environmental factors controlling SOM mineralization changes as soils freeze. The effect of SUM composition on pore size distribution and unfrozen water content has a superior influence on SUM mineralization and hence on heterotrophic CO2 production of frozen soils. (C) 2010 Elsevier Ltd. All rights reserved.

  • 16.
    Erhagen, Björn
    et al.
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Öquist, Mats
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Haei, Mahsa
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Ilstedt, Ulrik
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Nilsson, Mats B
    Department of Forest Ecology & Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Temperature response of litter and soil organic matter decomposition is determined by chemical composition of organic material2013In: Global Change Biology, ISSN 1354-1013, E-ISSN 1365-2486, Vol. 19, no 12, p. 3858-3871Article in journal (Refereed)
    Abstract [en]

    The global soil carbon pool is approximately three times larger than the contemporary atmospheric pool, therefore even minor changes to its integrity may have major implications for atmospheric CO2 concentrations. While theory predicts that the chemical composition of organic matter should constitute a master control on the temperature response of its decomposition, this relationship has not yet been fully demonstrated. We used laboratory incubations of forest soil organic matter (SOM) and fresh litter material together with NMR spectroscopy to make this connection between organic chemical composition and temperature sensitivity of decomposition. Temperature response of decomposition in both fresh litter and SOM was directly related to the chemical composition of the constituent organic matter, explaining 90% and 70% of the variance in Q10 in litter and SOM respectively. The Q10 of litter decreased with increasing proportions of aromatic and O-aromatic compounds, and increased with increased contents of alkyl- and O-alkyl carbons. In contrast, in SOM, decomposition was affected only by carbonyl compounds. To reveal why a certain group of organic chemical compounds affected the temperature sensitivity of organic matter decomposition in litter and SOM, a more detailed characterisation of the (13) C aromatic region using Heteronuclear Single Quantum Coherence (HSQC) was conducted. The results revealed considerable differences in the aromatic region between litter and SOM. This suggests that the correlation between chemical composition of organic matter and the temperature response of decomposition differed between litter and SOM. The temperature response of soil decomposition processes can thus be described by the chemical composition of its constituent organic matter, this paves the way for improved ecosystem modelling of biosphere feedbacks under a changing climate.

  • 17. Filippov, Andrey
    et al.
    Munavirov, Bulat
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ishmuhametova, Valentina
    Rudakova, Maya
    Shriram, Prashant
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Pharmacology.
    Tavelin, Staffan
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Pharmacology.
    Interaction of a poly(acrylic acid) oligomer with dimyristoylphosphatidylcholine bilayers2011In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 27, no 7, p. 3754-3761Article in journal (Refereed)
    Abstract [en]

    We studied the influence of 5 kDa poly(acrylic acid) (PAA) on the phase state, thermal properties, and lateral diffusion in bilayered systems of dimyristoylphosphatidylcholine (DMPC) using (31)P NMR spectroscopy, differential scanning calorimetry (DSC), (1)H NMR with a pulsed field gradient, and (1)H nuclear Overhauser enhancement spectroscopy (NOESY). The presence of PAA does not change the lamellar structure of the system. (1)H MAS NOESY cross-peaks observed for the interaction between lipid headgroups and polyion protons demonstrated only surface PAA-biomembrane interaction. Small concentrations of PAA (up to ∼4 mol %) lead to the appearance of a new lateral phase with a higher main transition temperature, a lower cooperativity, and a lower enthalpy of transition. Higher concentrations lead to the disappearance of measurable thermal effects. The lateral diffusion coefficient of DMPC and the apparent activation energy of diffusion gradually decreased at PAA concentrations up to around 4 mol %. The observed effects were explained by the formation of at least two types of PAA-DMPC lateral complexes as has been described earlier (Fujiwara, M.; Grubbs, R. H.; Baldeschwieler, J. D. J. Colloid Interface Sci., 1997, 185, 210). The first one is characterized by a stoichiometry of around 28 lipids per polymer, which corresponds to the adsorption of the entire PAA molecule onto the membrane. Lipid molecules of the complex are exchanged with the "pure" lipid bilayer, with the lifetime of the complex being less than 0.1 s. The second type of DMPC-PAA complex is characterized by a stoichiometry of 6 to 7 lipids per polymer and contains PAA molecules that are only partially adsorbed onto the membrane. A decrease in the DMPC diffusion coefficient and activation energy for diffusion in the presence of PAA was explained by the formation of a new cooperative unit for diffusion, which contains the PAA molecule and several molecules of lipids.

  • 18. Harrysson Drotz, Stina
    et al.
    Tilston, Emma L
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Contributions of matric and osmotic potentials to the unfrozen water content of frozen soils2009In: Geoderma, ISSN 0016-7061, E-ISSN 1872-6259, Vol. 148, no 3-4, p. 392-8Article in journal (Refereed)
    Abstract [en]

    Recent reports show that biogeochemical processes continue when the soil is frozen, but are limited by water availability. However, there is little knowledge about the interactive effects of soil and environmental variables on amounts of unfrozen water in frozen soils. The aims of this study were to determine the contributions of matric and osmotic potentials to the unfrozen water content of frozen soil. We determined the effects of matric and osmotic potential on unfrozen water contents of frozen mineral soil fractions (ranging from coarse sand to fine silt) at − 7 °C, and estimated the contributions of these potentials to liquid water contents in samples from organic surface layers of boreal soils frozen at − 4 °C. In the mineral soil fractions the unfrozen water contents appeared to be governed solely by the osmotic potential, but in the humus layers of the sampled boreal soils both the osmotic and matric potentials control unfrozen water content, with osmotic potential contributing 20 to 69% of the total water potential. We also determined pore size equivalents, where unfrozen water resides at − 4 °C, and found a strong correlation between these equivalents and microbial CO2 production. The larger the pores in which the unfrozen water is found the larger the microbial activity that can be sustained. The osmotic potential may therefore be a key determinant of unfrozen water and carbon dynamics in frozen soil.

  • 19.
    Hasegawa, Shun
    et al.
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Marshall, John
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Näsholm, Torgny
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Decadal nitrogen addition alters chemical composition of soil organic matter in a boreal forest2021In: Geoderma, ISSN 0016-7061, E-ISSN 1872-6259, Vol. 386, article id 114906Article in journal (Refereed)
    Abstract [en]

    Boreal forests store approximately 470 Pg of carbon (C) in the soil, and rates of soil C accumulation are significantly enhanced by long-term nitrogen (N) enrichment. Dissecting the compositional profile of soils could help better understand the potential mechanisms driving changes in C cycling under enriched N conditions.

    We examined the impacts of long-term N addition on the chemical composition of soil organic matter (SOM) in a mature boreal forest. Two large experimental plots (15 ha each) were established: a control and a fertilised plot. The latter received NH4NO3 fertilizer at an average rate of 75 kg N ha−1 year−1 for 12 years. While the centre of this plot received the prescribed amounts of fertilizer, the year-to-year variation in distribution of fertilizer around the designated edges of the plot created a gradient in N-loading. Along this gradient, a compositional shift in SOM in the organic horizon was assessed using two methods: pyrolysis-gas chromatography/mass spectrometry (GC/MS) and solid-state 13C nuclear magnetic resonance spectroscopy (13C NMR).

    Both of these methods revealed that the chemical composition of SOM changed with increasing N loading, with an increased fraction of lignin derivatives (i.e., aromatic, methoxy/N-alkyl C) relative to that of carbohydrate (i.e., O-alkyl C), accompanied by increased soil C mass (kg m−2) at the fertilised plot. Also, the relative abundance of N compounds in the pyrolysis products increased with the N loading, mainly due to increased methyl N-acetyl-α-D-glucosaminide in the F/H horizon, plausibly of microbial origin. Microbial N processing likely contributed to soil accumulation of fertilizer-derived N.

    Our results corroborate the hypothesis that addition of inorganic N suppresses enzymatic white-rot decomposition relative to non-enzymatic brown-rot oxidation. Taken together, our study suggests that N enrichment leads to a selective accumulation of lignin-derived compounds and points to a key role of such compounds for N-induced SOM accumulation.

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  • 20.
    Huang, Yang
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wang, Young-lei
    Laaksonen, Aatto
    Arrhenius Laboratory, Stockholm University, Sweden .
    Westlund, Per-Olof
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Analysis of proton/fluoride spin-lattice NMR dispersion experiment of an ionic liquid, BMIM[PF6] by using molecular dynamics simulations and relaxation theory2015Manuscript (preprint) (Other academic)
    Abstract [en]

    Proton/Fluoride spin-lattice nuclear magnetic relaxation dispersion(NMRD) measurements of 1-Butyl-3-methylimidazolium-hexa fluorophosphate (BMIM[PF6])have been carried out using a 1T Stelar FFC2000 fast-field-cycling instrument at proton Larmor frequencies ranging from 10 kHz to 40 MHz and at different temperatures. The NMRD profiles are interpreted by means of a simple relaxation modelbased on the inter- and intra-molecular dipole dipole relaxation mechanims. Using an atomic and a coarse-grained (CG)Molecular Dynamics (MD) simulations at temperature 323 K the relevant dipole-dipole correlation functions are calculated. The result indicate that the NMRD profiles can be rationalized using a combination of intra and inter molecular dipole-dipole couplings. However, both are mainly modulated by molecular reorientation whereas translation diffusion plays a minor role. The molecular reorientation dynamics  of BMIM[PF6] ,BMIM+ ion are in the nano secondtime regime whereas the reorientation of  [PF6]- is much faster and loses its correlation in the ps regime. The relaxation mechanism for  [PF6]- is H-F inter-molecular dipole-dipole coupling which is modulated by the reorientation of  the H-containing molecule.

  • 21.
    Huynh, Chau Minh
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mavliutova, Liliia
    Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, Malmö, Sweden.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sellergren, Börje
    Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, Malmö, Sweden.
    Irgum, Knut
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Elucidation of the binding orientation in α2,3- and α2,6-linked neu5ac-gal epitopes toward a hydrophilic molecularly imprinted monolith2023In: ACS Omega, E-ISSN 2470-1343, Vol. 8, no 46, p. 44238-44249Article in journal (Refereed)
    Abstract [en]

    N-Acetylneuraminic acid and its α2,3/α2,6-glycosidic linkages with galactose (Neu5Ac-Gal) are major carbohydrate antigen epitopes expressed in various pathological processes, such as cancer, influenza, and SARS-CoV-2. We here report a strategy for the synthesis and binding investigation of molecularly imprinted polymers (MIPs) toward α2,3 and α2,6 conformations of Neu5Ac-Gal antigens. Hydrophilic imprinted monoliths were synthesized from melamine monomer in the presence of four different templates, namely, N-acetylneuraminic acid (Neu5Ac), N-acetylneuraminic acid methyl ester (Neu5Ac-M), 3′-sialyllactose (3SL), and 6′-sialyllactose (6SL), in a tertiary solvent mixture at temperatures varying from −20 to +80 °C. The MIPs prepared at cryotemperatures showed a preferential affinity for the α2,6 linkage sequence of 6SL, with an imprinting factor of 2.21, whereas the α2,3 linkage sequence of 3SL resulted in nonspecific binding to the polymer scaffold. The preferable affinity for the α2,6 conformation of Neu5Ac-Gal was evident also when challenged by a mixture of other mono- and disaccharides in an aqueous test mixture. The use of saturation transfer difference nuclear magnetic resonance (STD-NMR) on suspensions of crushed monoliths allowed for directional interactions between the α2,3/α2,6 linkage sequences on their corresponding MIPs to be revealed. The Neu5Ac epitope, containing acetyl and polyalcohol moieties, was the major contributor to the sequence recognition for Neu5Ac(α2,6)Gal(β1,4)Glc, whereas contributions from the Gal and Glc segments were substantially lower.

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  • 22. Jonsson, Hanna
    et al.
    Blume-Werry, Gesche
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wackett, Adrian
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Olofsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Emelia, Arvidsson
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Klaminder, Jonatan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Invasive earthworms alter carbon sequestration in sub-arctic tundra ecosystemsManuscript (preprint) (Other academic)
  • 23. Lendel, Christofer
    et al.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mayzel, Maxim
    Andersson, C. Evalena
    Karlsson, Göran
    Härd, Torleif
    Combined Solution- and Magic Angle Spinning NMR Reveals Regions of Distinct Dynamics in Amyloid β Protofibrils2016In: ChemistrySelect, E-ISSN 2365-6549, Vol. 1, no 18, p. 5850-5853Article in journal (Refereed)
    Abstract [en]

    Solid-state magic angle spinning (MAS) NMR has emerged as an important tool for investigations of protein aggregates and amyloid fibrils, which are not accessible for solution NMR experiments. We recently presented a structural model for amyloid β (Aβ) protofibrils based on MAS-NMR data. The absence of resonances for the N-terminus of Aβ in this dataset suggested that it might be disordered and more dynamic than the structural core. We here provide evidence for a distinct dynamic regime in the N-terminal part of the peptide and show that the structural characteristics of this region can be elucidated using 13C-detected solution NMR. The results shed more light on the structural properties of pre-fibrillar Aβ species and demonstrate the potential of combining MAS and solution NMR experiments for the characterization of structure and dynamics of complex protein assemblies.

  • 24.
    Lidman, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dingeldein, Artur
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pokorná, Šárka
    Šachl, Radek
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hof, Martin
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The Role of Lipids in Regulation of Programmed Cell Death2016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, no 3, p. 473A-473AArticle in journal (Refereed)
  • 25.
    Lidman, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pokorná, Šárka
    Dingeldein, Artur P. G.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wallgren, Marcus
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Šachl, Radek
    Hof, Martin
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The oxidized phospholipid PazePC promotes permeabilization of mitochondrial membranes by Bax2016In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1858, no 6, p. 1288-1297Article in journal (Refereed)
    Abstract [en]

    Mitochondria play a crucial role in programmed cell death via the intrinsic apoptotic pathway, which is tightly regulated by the B-cell CLL/lymphoma-2 (Bcl-2) protein family. Intracellular oxidative stress causes the translocation of Bax, a pro-apoptotic family member, to the mitochondrial outer membrane (MOM) where it induces membrane permeabilization. Oxidized phospholipids (OxPls) generated in the MOM during oxidative stress directly affect the onset and progression of mitochondria-mediated apoptosis. Here we use MOM-mimicking lipid vesicles doped with varying concentrations of 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC), an OxPl species known to significantly enhance Bax-membrane association, to investigate three key aspects of Bax's action at the MOM: 1) induction of Bax pores in membranes without additional mediator proteins, 2) existence of a threshold OxPl concentration required for Bax-membrane action and 3) mechanism by which PazePC disturbs membrane organization to facilitate Bax penetration. Fluorescence leakage studies revealed that Bax-induced leakage, especially its rate, increased with the vesicles' PazePC content without any detectable threshold neither for OxPl nor Bax. Moreover, the leakage rate correlated with the Bax to lipid ratio and the PazePC content. Solid state NMR studies and calorimetric experiments on the lipid vesicles confirmed that OxPl incorporation disrupted the membrane's organization, enabling Bax to penetrate into the membrane. In addition, 15N cross polarization (CP) and insensitive nuclei enhanced by polarization transfer (INEPT) MAS NMR experiments using uniformly 15N-labeled Bax revealed dynamically restricted helical segments of Bax embedded in the membrane, while highly flexible protein segments were located outside or at the membrane surface.

  • 26. Liebau, Jobst
    et al.
    Tersa, Montse
    Trastoy, Beatriz
    Patrick, Joan
    Rodrigo-Unzueta, Ane
    Corzana, Francisco
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Guerin, Marcelo E.
    Mäler, Lena
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
    Unveiling the activation dynamics of a fold-switch bacterial glycosyltransferase by19F NMR2020In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 295, no 29, p. 9868-9878Article in journal (Refereed)
    Abstract [en]

    Fold-switch pathways remodel the secondary structure topology of proteins in response to the cellular environment. It is a major challenge to understand the dynamics of these folding processes. Here, we conducted an in-depth analysis of the α-helix–to–β-strand and β-strand–to–α-helix transitions and domain motions displayed by the essential mannosyltransferase PimA from mycobacteria. Using 19F NMR, we identified four functionally relevant states of PimA that coexist in dynamic equilibria on millisecond-to-second timescales in solution. We discovered that fold-switching is a slow process, on the order of seconds, whereas domain motions occur simultaneously but are substantially faster, on the order of milliseconds. Strikingly, the addition of substrate accelerated the fold-switching dynamics of PimA. We propose a model in which the fold-switching dynamics constitute a mechanism for PimA activation.

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  • 27.
    Lindgren, Matteus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Westlund, Per-Olof
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    A combined molecular dynamic simulation and Urea 14N NMR relaxation study of the Urea - lysozyme system2010In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 75, no 3, p. 953-9Article in journal (Refereed)
    Abstract [en]

    Urea in the lysozyme solvation shell has been studied by utilizing a combination of urea , water NMR relaxation experiments and a molecular dynamics simulation of the urea–lysozyme system. Samples with lysozyme in the native fold in water as well as in 3 M urea have been studied, as well as denatured lysozyme in a 8.5 M urea solvent. The spin relaxation rates of the samples with folded protein show a clear field dependence, which is consistent with a few urea molecules having long residence times on the protein surface and preferentially located in pockets and grooves on the protein. By combining the 3 M urea NMR relaxation data and data from the MD simulation, a full parameter set of the relaxation model is found which can successfully predict the experimental relaxation rates of the 3 M urea sample. However, in the parameter fitting it is evident that the rotational dynamics of urea in the MD simulation is slightly too fast to be consistent with the NMR relaxation rates, perhaps a result of the fast dynamics of the TIP3P water model. The relaxation rates of urea in the proximity of the unfolded lysozyme lack field dependence, which can be interpreted as a loss of pockets and grooves on the denatured protein. The extracted model parameters from the 3 M sample are adjusted and tested on a simple model of the unfolded protein sample and are seen to be in agreement with the relaxation rates. It is shown that the combination of NMR relaxation and MD simulations can be used to create a microscopic picture of the solvent at the protein interface, which can be used for example in the study of chemical denaturation.

  • 28.
    Lindström, Fredrick
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Bokvist, Marcus
    Umeå University, Faculty of Science and Technology, Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Chemistry.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Chemistry.
    Association of amyloid-β peptide with membrane surfaces monitored by solid state NMR2002In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 4, no 22, p. 5524-5530Article in journal (Refereed)
    Abstract [en]

    Amyloid-β peptide (Aβ), a key substance in Alzheimers disease (AD), is characterized by its abnormal folding into neurotoxic aggregates. Since Aβ comprises an extracellular and transmembrane domain, some of its neurotoxic actions might be exerted via interactions with neuronal membranes. Wideline and magic angle spinning 14N and 31P NMR have been used in combination with differential scanning calorimetry and circular dichroism spectroscopy to investigate the association between Aβ1–40 peptide and membranes with different electrostatic surface potentials. Calorimetric measurements showed that all membrane systems were in the liquid crystalline state at 308 K. Binding of Aβ1–40 at a 30 1 lipid/peptide ratio to membranes composed of neutral dimyristoyl-phosphatidylcholine (DMPC) and negatively charged dimyristoylphosphatidylglycerol (DMPG) at a 4 : 1 molar ratio is mainly driven electrostatically, reflected in characteristic changes of the isotropic 31P chemical shift values for both lipids. In addition, the average orientation of the choline headgroup of DMPC, with its electric P–N+(CH3)3 dipole, changed directly in response to the reduced negative membrane surface potential. The deviation in tilt angle of the PN vector relative to the membrane surface is manifested in the observed 14N NMR quadrupole splitting and can therefore be described semiquantitatively. Adding Aβ1–40 to membranes with nominal neutral surface charge, but composed of a ternary mixture of DMPC with DMPG and the cationic amphiphile didodecyldimethyl–ammonium bromide (DDAB) at a 3 : 1 : 1 molar ratio revealed surprisingly electrostatic interactions visible in the NMR spectra. Since Aβ1–40 does not bind to neutral DMPC bilayers a model is proposed, in which on a molecular level the charged residues of Aβ1–40 peptide can interact independently with lipid headgroups of various charges in these microscopically heterogeneous systems.

  • 29. Maljanen, M
    et al.
    Virkajärvi, P
    Hytönen, J
    Öquist, M
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Chemistry.
    Martikainen, P J
    Nitrous oxide production in boreal soils with variable organic matter content at low temperature – snow manipulation experiment2009In: Biogeosciences, ISSN 1726-4170, E-ISSN 1726-4189, Vol. 6, no 11, p. 2461-73Article in journal (Refereed)
    Abstract [en]

    Agricultural soils are the most important sources for the greenhouse gas nitrous oxide (N2O), which is produced and emitted from soils also at low temperatures. The processes behind emissions at low temperatures are still poorly known. Snow is a good insulator and it keeps soil temperature rather constant. To simulate the effects of a reduction in snow depth on N2O emission in warming climate, snow pack was removed from experimental plots on three different agricultural soils (sand, mull, peat). Removal of snow lowered soil temperature and increased the extent and duration of soil frost in sand and mull soils. This led to enhanced N2O emissions during freezing and thawing events. The cumulative emissions during the first year when snow was removed over the whole winter were 0.25, 0.66 and 3.0 g N2O-N m−2 yr−1 in control plots of sand, mull and peat soils, respectively. In the treatment plots, without snow cover, the respective cumulative emissions were 0.37, 1.3 and 3.3 g N2O-N m−2 yr−1. Shorter snow manipulation during the second year did not increase the annual emissions. Only 20% of the N2O emission occurred during the growing season. Thus, these results highlight the importance of the winter season for this exchange and that the year-round measurements of annual N2O emissions from boreal soils are integral for estimating their N2O source strength. N2O accumulated in the frozen soil during winter and the soil N2O concentration correlated with the depth of frost but not with the winter N2O emission rates per se. Also laboratory incubations of soil samples showed high production rates of N2O at temperatures below 0°C, especially in the sand and peat soils.

  • 30.
    Nguyen, Anh Mai
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dinh, Ngoc Phuoc
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Cam, Quach Minh
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Irgum, Knut
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Preparation and characterization of sizable macroporous epoxy resin-based monolithic supports for flow-through systems2009In: Journal of Separation Science, ISSN 1615-9306, E-ISSN 1615-9314, Vol. 32, no 15-16, p. 2608-2618Article in journal (Refereed)
    Abstract [en]

    This paper presents further results from our efforts to prepare sizable macroporous monolithic materials from epoxy resins and polyamines by emulsion polymerization. For their uses as supports in flow systems, the study aimed at developing materials possessing maximum fluid permeability, high mechanical stability, and a controlled porosity and surface area. Characterization of the materials has been carried out using different techniques, focusing on morphological and mechanical features, and on the surface chemistry. Morphology and porosity were studied with SEM, nitrogen adsorption/desorption, mercury intrusion porosimetry (MIP), and (2)H NMR cryoporosimetry. The chemical composition of the bulk structures and their surfaces was studied by means of bulk elemental analysis and X-ray photoelectron spectroscopy, and potentiometric titration was used to assess the relative amounts of amines and epoxy groups. Essentially, the morphological features were a high fluid permeability, but rather low specific surface area. Convective flow was facilitated by large, interconnected, and evenly spaced macropores which were formed by nonporous skeletons of the connected-rod type. Despite the interfacial nature of the polymerization, the bulk and the surface of the fully cured materials showed similar elemental compositions. All materials were found to have a high surface density of hydroxyl groups, which facilitates functionalization reactions.

  • 31. Pawar, Prashant Mohan-Anupama
    et al.
    Derba-Maceluch, Marta
    Chong, Sun-Li
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Bashar, Shamrat Shafiul
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ahvenainen, Patrik
    Hedenström, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ozparpucu, Merve
    Ruggeberg, Markus
    Serimaa, Ritva
    Lawoko, Martin
    Tenkanen, Maija
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mellerowicz, Ewa J.
    In muro deacetylation of xylan affects lignin properties and improves saccharification of aspen wood2017In: Biotechnology for Biofuels, E-ISSN 1754-6834, Vol. 10, article id 98Article in journal (Refereed)
    Abstract [en]

    Background: Lignocellulose from fast growing hardwood species is a preferred source of polysaccharides for advanced biofuels and “green” chemicals. However, the extensive acetylation of hardwood xylan hinders lignocellulose saccharification by obstructing enzymatic xylan hydrolysis and causing inhibitory acetic acid concentrations during microbial sugar fermentation. To optimize lignocellulose for cost-effective saccharification and biofuel production, an acetyl xylan esterase AnAXE1 from Aspergillus niger was introduced into aspen and targeted to cell walls.

    Results: AnAXE1-expressing plants exhibited reduced xylan acetylation and grew normally. Without pretreatment, their lignocellulose yielded over 25% more glucose per unit mass of wood (dry weight) than wild-type plants. Glucose yields were less improved (+7%) after acid pretreatment, which hydrolyses xylan. The results indicate that AnAXE1 expression also reduced the molecular weight of xylan, and xylan–lignin complexes and/or lignin co-extracted with xylan, increased cellulose crystallinity, altered the lignin composition, reducing its syringyl to guaiacyl ratio, and increased lignin solubility in dioxane and hot water. Lignin-associated carbohydrates became enriched in xylose residues, indicating a higher content of xylo-oligosaccharides.

    Conclusions: This work revealed several changes in plant cell walls caused by deacetylation of xylan. We propose that deacetylated xylan is partially hydrolyzed in the cell walls, liberating xylo-oligosaccharides and their associated lignin oligomers from the cell wall network. Deacetylating xylan thus not only increases its susceptibility to hydrolytic enzymes during saccharification but also changes the cell wall architecture, increasing the extractability of lignin and xylan and facilitating saccharification.

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  • 32. Pawar, Prashant Mohan-Anupama
    et al.
    Ratke, Christine
    Balasubramanian, Vimal K.
    Chong, Sun-Li
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Adriasola, Mathilda
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenstrom, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Szwaj, Klaudia
    Derba-Maceluch, Marta
    Gaertner, Cyril
    Mouille, Gregory
    Ezcurra, Ines
    Tenkanen, Maija
    Jonsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mellerowicz, Ewa J.
    Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, p. 1491-1505Article in journal (Refereed)
    Abstract [en]

    High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21. Histochemical analysis of promoter:: GUS lines in hybrid aspen (Populus tremula x tremuloides) showed activation of RWA-A and -B promoters in the secondary wall formation zone, while RWA-C and -D promoter activity was diffuse. Ectopic downregulation of either clade reduced wood xylan and xyloglucan acetylation. Suppressing both clades simultaneously using the wood-specific promoter reduced wood acetylation by 25% and decreased acetylation at position 2 of Xylp in the dimethyl sulfoxide-extracted xylan. This did not affect plant growth but decreased xylose and increased glucose contents in the noncellulosic monosaccharide fraction, and increased glucose and xylose yields of wood enzymatic hydrolysis without pretreatment. Both RWA clades regulate wood xylan acetylation in aspen and are promising targets to improve wood saccharification.

  • 33.
    Rogne, Per
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Anugwom, Ikenna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Laboratory of Industrial Chemistry and Reaction Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Wolf-Watz, Magnus
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Real-time 31P NMR investigation on the catalytic behavior of the enzyme Adenylate kinase in the matrix of a switchable ionic liquid2015In: ChemSusChem, ISSN 1864-5631, E-ISSN 1864-564X, Vol. 8, no 2, p. 3764-3768Article in journal (Refereed)
    Abstract [en]

    The integration of highly efficient enzymatic catalysis with the solvation properties of ionic liquids for an environmentally friendly and efficient use of raw materials such as wood requires fundamental knowledge about the influence of relevant ionic liquids on enzymes. Switchable ionic liquids (SIL) are promising candidates for implementation of enzymatic treatments of raw materials. One industrially interesting SIL is constituted by monoethanol amine (MEA) and 1,8-diazabicyclo-[5.4.0]-undec-7-ene (DBU) formed with sulfur dioxide (SO2) as the coupling media (DBU-SO2-MEASIL). It has the ability to solubilize the matrix of lignocellulosic biomass while leaving the cellulose backbone intact. Using a novel 31P  NMR-based real-time assay we show that this SIL is compatible with enzymatic catalysis because a model enzyme, adenylate kinase, retains its activity in up to at least 25 wt % of DBU-SO2-MEASIL. Thus this SIL appears suitable for, for example, enzymatic degradation of hemicellulose.

  • 34. Rowat, Amy C.
    et al.
    Brask, Jesper
    Sparrman, Tobias
    Umeå University, Faculty of Medicine, Medical Biochemistry and Biophsyics.
    Jensen, Knud J.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Lindblom, Göran
    Umeå University, Faculty of Science and Technology, Chemistry.
    Ipsen, John H.
    Commentary: Farnesylated peptides in model membranes: a biophysical investigation (vol 33, pg 300, 2003)2004In: European Biophysics Journal, Vol. 33, no 6, p. 562-3Article in journal (Refereed)
  • 35. Rowat, Amy C.
    et al.
    Brask, Jesper
    Sparrman, Tobias
    Umeå University, Faculty of Medicine, Medical Biochemistry and Biophsyics.
    Jensen, Knud J.
    Lindblom, Göran
    Faculty of Science and Technology, Chemistry.
    Ipsen, John H.
    Farnesylated peptides in model membranes: a biophysical investigation2004In: European Biophysics Journal, ISSN 0175-7571 (Print) 1432-1017 (Online), Vol. 33, no 4, p. 300-9Article in journal (Refereed)
    Abstract [en]

    Protein prenylation plays an important role in signal transduction, protein–protein interactions, and the localization and association of proteins with membranes. Using three different techniques, this study physically characterizes the interactions between model dimyristoylphosphatidylcholine membranes and a series of farnesylated peptides. Magic angle spinning nuclear Overhauser enhancement spectroscopy and differential scanning calorimetry reveal that both charged [Ac-Asn-Lys-Asn-Cys-(farnesyl)-OMe and Ac-Asn-Lys-Asn-Cys-(farnesyl)-NH2] and uncharged [Ac-Cys-(farnesyl)-OMe and farnesol] species partition into dimyristoylphosphatidylcholine bilayers. Calorimetry and vesicle fluctuation analysis of giant unilamellar vesicles show that the charged peptides modestly decrease the main gel–fluid phase transition and markedly increase the bending rigidity of large unilamellar vesicles. Uncharged species, on the other hand, dramatically decrease the main phase transition and modestly decrease the bending rigidity. No difference with carboxyl methylation is detected.

  • 36.
    Rundqvist, Louise
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ådén, Jörgen
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wallgren, Marcus
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Olsson, Ulrika
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wolf-Watz, Magnus
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Noncooperative folding of subdomains in Adenylate Kinase2009In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 48, no 9, p. 1911-1927Article in journal (Refereed)
    Abstract [en]

    Conformational change is regulating the biological activity of a large number of proteins and enzymes. Efforts in structural biology have provided molecular descriptions of the interactions that stabilize the stable ground states on the reaction trajectories during conformational change. Less is known about equilibrium thermodynamic stabilities of the polypeptide segments that participate in structural changes and whether the stabilities are relevant for the reaction pathway. Adenylate kinase (Adk) is composed of three subdomains: CORE, ATPlid, and AMPbd. ATPlid and AMPbd are flexible nucleotide binding subdomains where large-scale conformational changes are directly coupled to catalytic activity. In this report, the equilibrium thermodynamic stabilities of Adk from both mesophilic and hyperthermophilic bacteria were investigated using solution state NMR spectroscopy together with protein engineering experiments. Equilibrium hydrogen to deuterium exchange experiments indicate that the flexible subdomains are of significantly lower thermodynamic stability compared to the CORE subdomain. Using site-directed mutagenesis, parts of ATPlid and AMPbd could be selectively unfolded as a result of perturbation of hydrophobic clusters located in these respective subdomains. Analysis of the perturbed Adk variants using NMR spin relaxation and Cα chemical shifts shows that the CORE subdomain can fold independently of ATPlid and AMPbd; consequently, folding of the two flexible subdomains occurs independently of each other. Based on the experimental results it is apparent that the flexible subdomains fold into their native structure in a noncooperative manner with respect to the CORE subdomain. These results are discussed in light of the catalytically relevant conformational change of ATPlid and AMPbd.

  • 37. Sar, Suchandra
    et al.
    Öqvist, Lena Sundqvist
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Engström, Fredrik
    Samuelsson, Caisa
    Characterization of Double Leached Waelz Oxide for Identification of Fluoride Mineral2019In: Metals, ISSN 2075-4701, Vol. 9, no 3, article id 361Article in journal (Refereed)
    Abstract [en]

    Double leached Waelz oxide (DLWO), with 76% zinc, is a secondary zinc containing raw materials obtained by the treatment of electric arc furnace dust. The content of fluoride in DLWO is still too high for direct leaching, as fluoride has a detrimental effect on electrowinning for zinc production. Knowledge of the characteristics of DLWO, and especially on how a fluoride mineral might exist, can contribute to further improvement of the selective leaching for the removal of fluoride. In this study, DLWO was characterized using analytical techniques, such as inductively coupled plasma-optical emission spectroscopy (ICP-OES), F-19 liquid-state nuclear magnetic resonance (F-19 LS NMR), X-ray powder diffraction analysis (XRD), scanning electron microscopy coupled with energy dispersive spectroscopy (SEM-EDS) and F-19 solid-state nuclear magnetic resonance (F-19 SS NMR). This study showed that DLWO mainly consisted of zincite (ZnO), cerussite (PbCO3) and a spinel containing zinc, iron and manganese. The fluoride mineral identified was calcium fluoride (CaF2). In SEM analysis, fluorine was found in larger grains together with calcium and oxygen, which was possibly calcium carbonate.

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  • 38. Segura, Javier H.
    et al.
    Nilsson, Mats B.
    Haei, Mahsa
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mikkola, Jyri-Pekka
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Industrial Chemistry & Reaction Engineering, Process Chemistry Centre, Åbo.
    Gräsvik, John
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Öquist, Mats G.
    Microbial mineralization of cellulose in frozen soils2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, no 1, article id 1154Article in journal (Refereed)
    Abstract [en]

    High-latitude soils store ~40% of the global soil carbon and experience winters of up to 6 months or more. The winter soil CO2 efflux importantly contributes to the annual CO2 budget. Microorganisms can metabolize short chain carbon compounds in frozen soils. However, soil organic matter (SOM) is dominated by biopolymers, requiring exoenzymatic hydrolysis prior to mineralization. For winter SOM decomposition to have a substantial influence on soil carbon balances it is crucial whether or not biopolymers can be metabolized in frozen soils. We added 13C-labeled cellulose to frozen (−4 °C) mesocosms of boreal forest soil and followed its decomposition. Here we show that cellulose biopolymers are hydrolyzed under frozen conditions sustaining both CO2 production and microbial growth contributing to slow, but persistent, SOM mineralization. Given the long periods with frozen soils at high latitudes these findings are essential for understanding the contribution from winter to the global carbon balance.

  • 39. Segura, Javier H.
    et al.
    Nilsson, Mats B.
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Haei, Mahsa
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Székely, Anna
    Bertilsson, Stefan
    Öquist, Mats G.
    Microbial utilization of simple carbon substrates in boreal peat soils at low temperatures2019In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 135, p. 438-448Article in journal (Refereed)
    Abstract [en]

    Boreal peatlands are key high-latitude ecosystem types and act as a carbon (C) sink storing an estimated 25% of the world's soil C. These environments are currently seeing the most substantial changing climate, especially during the winter. CO2 emissions during the winter can correspond to 80% of the growing season's net CO2 assimilation. Yet, our conceptual understanding of the controls on microbial metabolic activity in peat soils at temperatures ≤0 °C is poor. We used stable isotope probing of peat samples and tracked the fate of 13C-glucose using 13C-NMR. We show that microorganisms in frozen boreal peat soils utilize monomeric C-substrates to sustain both catabolic and anabolic metabolism at temperatures down to −5 °C. The 13C-substrate was transformed into 13C–CO2, different metabolites, and incorporated into membrane phospholipid fatty acids. The 16S rRNA-based community analyses revealed the activity at −3 °C changes the composition of the bacterial community over relevant timescales. Below 0 °C, small temperature changes have strong effects on process rates and small differences in winter soil temperature may affect C dynamics of northern peatlands. Understanding biological processes at low and below zero temperatures are central for the overall functioning of these systems representing one of the world's major soil C pools.

  • 40. Segura, Javier H.
    et al.
    Nilsson, Mats B.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Serk, Henrik
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Schleucher, Juergen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Tolu, Julie
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Öquist, Mats G.
    Boreal tree species affect soil organic matter composition and saprotrophic mineralization rates2019In: Plant and Soil, ISSN 0032-079X, E-ISSN 1573-5036, Vol. 441, no 1-2, p. 173-190Article in journal (Refereed)
    Abstract [en]

    Aims: To investigate how different tree species affect the composition of SOM and its mineralization in boreal forest ecosystems.

    Methods: We used pyrolysis GC-MS for molecular-level characterization of the SOM formed under five common boreal tree species at a replicated field experiment similar to 50years after plantation. We incubated soil samples at 4, 9, 14 and 19 degrees C and measured inherent CO2 production and substrate-induced respiration. We then evaluated if the saprotrophic microbial activity and its temperature sensitivity was controlled by the SOM composition.

    Results: The molecular composition of the SOM emerged as key factor influencing SOM properties in plots with different tree species. Most of the variance in the SOM content was explained by the organo-chemical composition of the SOM. More importantly, the fraction of the microbial community able to utilize the native SOM was largely controlled by the SOM organo-chemical composition. Temperature sensitivity of CO2 production (Q(10)) was not explained by SOM composition. However, the microbial access to different SOM pools varied with temperature.

    Conclusions: These results bridge the gap between the paradigms of short-term litter and long-term SOM decomposition showing that, on an intermediate timescale (similar to 50 years), boreal tree species affect SOM molecular composition and saprotrophic mineralization rates.

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  • 41.
    Shamshir, Adel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dinh, Ngoc Phuoc
    Jonsson, Tobias
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ashiq, Muhammad Jamshaid
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Irgum, Knut
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Interaction of toluene with polar stationary phases under conditions typical of hydrophilic interaction chromatography probed by saturation transfer difference nuclear magnetic resonance spectroscopy2019In: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1588, p. 58-67Article in journal (Refereed)
    Abstract [en]

    Toluene has been used as void volume (zero retention) marker since the inception of hydrophilic interaction chromatography (HILIC), based on the assumption that its hydrophobicity should prevent it from interacting with stationary phases envisioned to be covered by relatively thick layers of water. Recent work has shown that the void volumes of partly water-swollen HILIC phases are not identical to the volumes probed by toluene, yet the compound is still ubiquitously used as void volume marker. As part of our investigations of the retention mechanisms in HILIC, we probed the extent to which toluene is capable of penetrating into the water-enriched layer and to interact with the functional groups of three commercially available hydrophilic and polar stationary phases with different charge properties and water-retaining abilities, using saturation transfer difference 1H nuclear magnetic resonance (STD-NMR) spectroscopy at high resolution magic angle spinning (HR-MAS) conditions. The test solutions were 1000 ppm of toluene in deuterated acetonitrile and water mixtures, with and without addition of ammonium acetate, in order to mimic a set of conditions typically encountered in HILIC separations. Interactions between toluene and the functional groups on the stationary phases were probed by equilibrating the phases with these eluent mimics and measuring the transfer of magnetization from stationary phase protons to the protons of toluene. Our results show that toluene is indeed capable of traversing the water-enriched layers of all the three tested phases and of interacting with protons that are tightly associated with the stationary phases.

  • 42.
    Shamshir, Adel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Diduco AB, Umeå, Sweden.
    Dinh, Ngoc Phuoc
    Diduco AB.
    Jonsson, Tobias
    Diduco AB.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Irgum, Knut
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Probing the retention mechanism of small hydrophilic molecules in hydrophilic interaction chromatography using saturation transfer difference nuclear magnetic resonance spectroscopy2020In: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1623, article id 461130Article in journal (Refereed)
    Abstract [en]

    The interactions and dynamic behavior of a select set of polar probe solutes have been investigated on three hydrophilic and polar commercial stationary phases using saturation transfer difference 1 H nuclear magnetic resonance (STD-NMR) spectroscopy under magic angle spinning conditions. The stationary phases were equilibrated with a select set of polar solutes expected to show different interaction patterns in mixtures of deuterated acetonitrile and deuterium oxide, with ammonium acetate added to a total concentration that mimics typical eluent conditions for hydrophilic interaction chromatography (HILIC). The methylene groups of the stationary phases were selectively irradiated to saturate the ligand protons, at frequencies that minimized the overlaps with reporting protons in the test probes. During and after this radiation, the saturation rapidly spreads to all protons in the stationary phase by spin diffusion, and from those to probe protons in contact with the stationary phase. Probe protons that have been in close contact with the stationary phase and subsequently been released to the solution phase will have been more saturated due to a more efficient transfer of spin polarization by the nuclear Overhauser effect. They will therefore show a higher signal after processing of the data. Saturation transfers to protons in neutral and charged solutes could in some instances show clear orientation patterns of these solutes towards the stationary phases. The saturation profile of formamide and its N-methylated counterparts showed patterns that could be interpreted as oriented hydrogen bond interaction. From these studies, it is evident that the functional groups on the phase surface have a strong contribution to the selectivity in HILIC, and that the retention mechanism has a significant contribution from oriented interactions.

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  • 43.
    Shamshir, Adel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University.
    Dinh, Ngoc Phuoc
    Diduco AB.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jonsson, Tobias
    Diduco AB.
    Irgum, Knut
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Retention and Selectivity of Nucleobases and Nucleosides in Hydrophilic Interaction Chromatography Investigated by Saturation Transfer Difference Nuclear Magnetic Resonance SpectroscopyManuscript (preprint) (Other academic)
  • 44.
    Shamshir, Adel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Westlund, Per-Olof
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Analysis of the behaviour of confined molecules using 2H T1 nuclear magnetic relaxation dispersion2020In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 118, no 6, article id e1645367Article in journal (Refereed)
    Abstract [en]

    A four-site exchange model is developed in order to explain deuterium -nuclear magnetic relaxation dispersion (NMRD) profiles of acetonitrile in silica pore systems. The four-site exchange model comprises a bulk, surface and two types of burried or cavity sites. It is found that the residence time of acetonitrile- at a flat Si-surface is less than 100 ps. No bilayer-like ordering of acetonitrile is formed at the Si-surface because no quadrupole splitting was observed. The dispersion in the deuterium T1-NMRD profiles are due to relatively few so-called beta-sites with molecular residence time in the range 0.2-2 micro seconds. This deuterium T-NMR dispersion experiment suggest that the retention time of different analysts can be studied in terms of their residence time in beta sites.

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  • 45.
    Shimizu, Kenichi
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, UK.
    Driver, Gordon W.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lucas, Marie
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Shchukarev, Andrey
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Boily, Jean-Francois
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Bifluoride ([HF2](-)) formation at the fluoridated aluminium hydroxide/water interface2016In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 45, no 22, p. 9045-9050Article in journal (Refereed)
    Abstract [en]

    This study uncovers bifluoride-type (difluorohydrogenate(I); [HF2](-)) species formed at mineral/water interfaces. Bifluoride forms at equivalent to Al-F surface sites resulting from the partial fluoridation of gibbsite (gamma-Al(OH3)) and bayerite (alpha-Al(OH3)) particles exposed to aqueous solutions of 50 mM NaF. Fluoride removal from these solutions is proton-promoted and results in a strongly self-buffered suspensions at circumneutral pH, proceeds at a F : H consumption ratio of 2 : 1, and with recorded losses of up to 17 mM fluoride (58 F nm(-2)). These loadings exceed crystallographic site densities by a factor of 3-4, yet the reactions have no resolvable impact on particle size, shape and mineralogy. X-ray photoelectron spectroscopy (XPS) of frozen (-155 degrees C) wet mineral pastes revealed coexisting surface F- and HF0 species. Electron energy loss features pointed to multilayer distribution of these species at the mineral/water interface. XPS also uncovered a distinct form of Na+ involved in binding fluoride-bearing species. XPS and solid state magic angle spinning F-19 nuclear magnetic resonance measurements showed that these fluoride species were highly comparable to a sodium-bifluoride (NaHF2) reference. First layer surface species are represented as =Al-F-H-F-Al= and =Al-F-Na-F-Al=, and may form multi-layered species into the mineral/water interface. These results consequently point to a potentially overlooked inorganic fluorine species in a technologically relevant mineral/water interfacial systems.

  • 46. Song, Yu
    et al.
    Jiang, Tao
    Liem-Nguyen, Van
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Björn, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Skyllberg, Ulf
    Thermodynamics of Hg(II) bonding to thiol groups in Suwannee River natural organic matter resolved by competitive ligand exchange, Hg L-III-Edge EXAFS and H-1 NMR spectroscopy2018In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 52, no 15, p. 8292-8301Article in journal (Refereed)
    Abstract [en]

    A molecular level understanding of the thermodynamics and kinetics of the chemical bonding between mercury, Hg(II), and natural organic matter (NOM) associated thiol functional groups (NOM-RSH) is required if bioavailability and transformation processes of Hg in the environment are to be fully understood. This study provides the thermodynamic stability of the Hg(NOM-RS)(2) structure using a robust method in which cysteine (Cys) served as a competing ligand to NOM (Suwannee River 2R101N sample) associated RSH groups. The concentration of the latter was quantified to be 7.5 +/- 0.4 mu mol g(-1) NOM by Hg L-III-edge EXAFS spectroscopy. The Hg(Cys)(2) molecule concentration in chemical equilibrium with the Hg(II)-NOM complexes was directly determined by HPLC-ICPMS and losses of free Cys due to secondary reactions with NOM was accounted for in experiments using H-1 NMR spectroscopy and C-13 isotope labeled Cys. The log K +/- SD for the formation of the Hg(NOM-RS)(2) molecular structure, Hg2+ + 2NOM-RS- = Hg(NOM-RS)(2), and for the Hg(Cys)(NOM-RS) mixed complex, Hg2+ + Cys(-) + NOM-RS- = Hg(Cys)(NOM-RS), were determined to be 40.0 +/- 0.2 and 38.5 +/- 0.2, respectively, at pH 3.0. The magnitude of these constants was further confirmed by H-1 NMR spectroscopy and the Hg(NOM-RS)(2) structure was verified by Hg L-III-edge EXAFS spectroscopy. An important finding is that the thermodynamic stabilities of the complexes Hg(NOM-RS)(2), Hg(Cys)(NOM-RS) and Hg(Cys)(2) are very similar in magnitude at pH values <7, when all thiol groups are protonated. Together with data on 15 low molecular mass (LMM) thiols, as determined by the same method (Liem-Ngyuen et al. Thermodynamic stability of mercury(II) complexes formed with environmentally relevant low-molecular-mass thiols studied by competing ligand exchange and density functional theory. Environ. Chem. 2017, 14, (4), 243-253.), the constants for Hg(NOM-RS)(2) and Hg(Cys)(NOM-RS) represent an internally consistent thermodynamic data set that we recommend is used in studies where the chemical speciation of Hg(II) is determined in the presence of NOM and LMM thiols.

  • 47.
    Sparrman, Tobias
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Svenningsson, Leo
    Sahlin-Sjovold, Karin
    Nordstierna, Lars
    Westman, Gunnar
    Bernin, Diana
    A revised solid-state NMR method to assess the crystallinity of cellulose2019In: Cellulose, ISSN 0969-0239, E-ISSN 1572-882X, Vol. 26, no 17, p. 8993-9003Article in journal (Refereed)
    Abstract [en]

    The crystallinity of cellulose has a strong impact on various material properties. Over the years, many methods have become available to estimate the crystallinity. The purpose of this work was to revise existing NMR-based methods and to introduce a complementary NMR method related to the C-13 T-1 relaxation time. The C-13 T-1 differs by an order of magnitude for amorphous and crystalline polymers among them cellulose. We have utilized the signal boost of H-1-C-13 cross polarization and the difference in C-13 T-1 as a filter to calculate the degree of crystallinity. The evaluation of the method is based on the difference in peak integrals, which is fed into a simple equation. The method was applied to five cellulosic samples of different nature and compared the obtained degree of crystallinity with the degree estimated from deconvoluted X-ray scattering patterns. Furthermore, an attempt has been made to give a basic understanding on the origin of CP enhancement in order to validate various proposed NMR methods. With the recent progress of NMR equipment, the presented method can be automatized and applied to a series of samples using a sample changer.

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  • 48.
    Sparrman, Tobias
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Westlund, Per-Olof
    Umeå University, Faculty of Science and Technology, Chemistry.
    An NMR line shape and relaxation analysis of heavy water powder spectra of the L, L and P phases in the DPPC/water system2003In: Physical Chemistry Chemical Physics, Vol. 5, p. 2114-21Article in journal (Refereed)
    Abstract [en]

    The 2H2O NMR powder line shapes and relaxation times, T1 and T2, of the liquid crystal L, the intermediate P and the gel L phases of dipalmitoylphosphatidylcholine (DPPC)/2H2O-system are analysed. The water structure and dynamics of the lipid/water interfaces of DPPC in the hydration regime, where all water molecules are associated to the interface, are described in terms of orientational order parameters and correlation times. The line shape of the ripple phase (P) is analysed assuming model parameters of the gel or liquid crystalline phase. The narrow line shape of the ripple phase is partly due to an extra average of the quadrupole interaction because of lateral diffusion along the curved surface, reducing the splitting with a factor 0.5–0.2 depending on the nature of the curved ripple surface. However, more importantly, an extra reduction of the quadrupole splitting may be due to the same reorganization of water, among bound sites with different signs of the order parameter, which also explains the increase in the quadrupole splitting with temperature observed in the liquid crystalline phase. The linewidths in 14N MAS NMR spectra clearly indicate slow dynamics of the polar headgroup in the ripple phase. The results indicate that the headgroup hydrations of the ripple and liquid crystalline phases are similar, while the acyl chains are still in their gel state in the ripple phase. The increased headgroup area introduces a stress, as confirmed by the slow headgroup dynamics, which causes the bilayer to curve in the ripple phase.

  • 49.
    Sparrman, Tobias
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Westlund, Per-Olof
    Umeå University, Faculty of Science and Technology, Chemistry.
    H-2 NMR relaxation and line shape analysis of water in a lamellar liquid crystalline phase formed by dodecyldimethylamineoxide (DDAO) and (H2O)-H-22001In: JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, Vol. 105, no 50, p. 12524-8Article in journal (Refereed)
    Abstract [en]

    Present study combines NMR relaxation and line shape analysis for heavy water in the lamellar liquid crystalline phase of DDAO/(2)-H2O, NMR spin-lattice, spin-spin relaxation times and the quadrupole splitting are measured at two temperatures and three different water contents in the hydration regime. A molecular picture of water hydration of the DDAO/(2)-H2O interface is extracted, which indicates a much more rapid water translational diffusion along the detergent interface, as compared to phospholipid interfaces. The local order and dynamics of the bound water are, however, not changing much between the two interfaces. This indicates, that local interactions of water with the headgroup are not much dependent on the actual phase or detergent system. This work also presents clear experimental evidence for a dip at the magic angle of the H-2 powder spectrum, as theoretically predicted. Raising the temperature removes this observed dip at the isotropic frequency. This corresponds to an increase in the correlation time tau (c) from 8.5 ns at 25 degreesC to 20 ns at 55 degreesC, where tau (c) is related to translational dynamics of water along the detergent/water interface. However, this counter-intuitive increase in tau (c) with temperature may be interpreted as a reorganization of water at the interface, as is further supported by increasing quadrupolar splittings with increasing temperature.

  • 50. Sparrman, Tobias
    et al.
    Öquist, M
    Klemedtsson, L
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Nilsson, M
    Quantifying unfrozen water in frozen soil by high-field 2H NMR2004In: Environmental Science & Technology, Vol. 38, no 20, p. 5420-5Article in journal (Refereed)
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