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  • 1.
    Berg, Johan
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Block, Stephan
    Hook, Fredrik
    Brzezinski, Peter
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Single Proteoliposomes with E.coli Quinol Oxidase: Proton Pumping without Transmembrane Leaks2017In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 57, no 5, p. 437-445Article in journal (Refereed)
    Abstract [en]

    Respiratory oxidases are transmembrane enzymes that catalyze the reduction of dioxygen to water in the final step of aerobic respiration. This process is linked to proton pumping across the membrane. Here, we developed a method to study the catalytic turnover of the quinol oxidase, cytochromebo(3) from E.coli at single-molecule level. Liposomes with reconstituted cytochromebo(3) were loaded with a pH-sensitive dye and changes in the dye fluorescence, associated with proton transfer and pumping, were monitored as a function of time. The single-molecule approach allowed us to determine the orientation of cytochromebo(3) in the membrane; in approximate to 70% of the protein-containing liposomes protons were released to the outside. Upon addition of substrate we observed the buildup of a pH (in the presence of the K+ ionophore valinomycin), which was stable over at least approximate to 800s. No rapid changes in pH (proton leaks) were observed during steady state proton pumping, which indicates that the free energy stored in the electrochemical gradient in E.coli is not dissipated or regulated through stochastic transmembrane proton leaks, as suggested from an earlier study (Li etal. J. Am. Chem. Soc. (2015) 137, 16055-16063).

  • 2. Larsson, Per
    et al.
    Pouya, Iman
    Lindahl, Erik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
    From Side Chains Rattling on Picoseconds to Ensemble Simulations of Protein Folding2014In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 54, no 8-9, p. 1274-1285Article, review/survey (Refereed)
    Abstract [en]

    Simulations of biological macromolecules have evolved tremendously since the discoveries of the 1970s. The field has moved from simple simulations in vacuo on picosecond scales to milliseconds of accurate sampling of large proteins, and it has become a standard tool in biochemistry and biophysics, rather than a dedicated theoretical one. This is partly due to increasing computational power, but it would not have been possible without huge research efforts invested in new algorithms and software. Here, we illustrate some of this development, both past and future challenges, and in particular, discuss how the recent introduction of modern ensemble methods is breaking the trend of ever-longer simulations to instead focus on throughput and sampling. This has not only helped simulations become much more accurate, but it provides statistical error estimates, which are critical, as simulations are increasingly used to predict properties that have not yet been measured experimentally.

  • 3.
    Marcos, Rocio
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Martín-Matute, Belén
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Combined Enzyme and Transition-Metal Catalysis for Dynamic Kinetic Resolutions2012In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 52, no 7, p. 639-652Article, review/survey (Refereed)
    Abstract [en]

    The preparation of optically pure alcohols, axially chiral allenes, and amine derivatives by using enzymes and transition-metal catalysts through dynamic kinetic resolution (DKR) is reviewed. After a general introduction into enzymatic kinetic resolutions and racemizations catalyzed by transition-metal complexes, selected examples of DKRs are presented, from early work to more recent outstanding contributions, and also applications of this approach.

  • 4. Moberg, Christina
    et al.
    Adolfsson, Hans
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Concepts in asymmetric catalysis2012In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 52, no 7, p. 571-571Article in journal (Other academic)
  • 5.
    Pu, Maoping
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chemistry of Intermolecular Frustrated Lewis Pairs in Motion: Emerging Perspectives and Prospects2015In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 55, no 2, p. 179-195Article, review/survey (Refereed)
    Abstract [en]

    This feature article describes the chemistry in motion of frustrated Lewis pairs (FLPs). With state-of-the-art ab initio molecular dynamics (AIMD) simulations supplemented by minimum energy path (MEP) and potential energy surface (PES) calculations, we examine the binding of CO2 and the heterolytic cleavage of H-2 by a Lewis base (LB), tBu(3)P, and a Lewis acid (LA), B(C6F5)(3). We strive to uncover and understand mechanistic implications of the physical laws that govern the behavior of a LB and a LA when they react with a third species (e.g., CO2 or H-2) at finite temperature. The approximation that we necessarily must make at present is to forgo the quantization of the movement of atoms in favor of the Born-Oppenheimer molecular dynamics (BOMD), which unfold according to the classical (Newton's) laws of motion. However, strict quantum chemical theory is used to compute all of the forces that govern the dynamics of the macromolecular FLP system. Using physical reasoning and innovative computer simulations, we show that multi-scale motion is the predominant mechanistic aspect in reactions of the tBu(3)P/B(C6F5)(3) FLP, as well as, conceivably, those of other similar intermolecular FLPs. Insight achieved thus far leads to a novel activity model for intermolecular FLPs and specific predictions, which could be useful for future experimental and theoretical studies of FLP and other chemistries.

  • 6. Spekreijse, Jurjen
    et al.
    Inge, Andrew Kentaro
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Öhrström, Lars
    Lignin Based Molecular Materials - a Zinc Vanillate with a Hydrogen Bonded 4-and 8-connected Net with a New Topology2018In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 58, no 9-10, p. 1127-1130Article in journal (Refereed)
    Abstract [en]

    Vanillic acid, C8H8O4, is a possible product from a future biorefinery with lignin as raw material. Two coordination compounds with this ligand in two different protonation states were prepared: 1 [Zn(C8H7O4)(2)(H2O)(2)] and 2 [Co-2(C8H6O4)(2)(H2O)(6)] 2H(2)O. Both compounds form extended 3D structures with strong hydrogen bonds. A high symmetry 8- and 4-connected network topology, jus, is found in 1. The dinuclear coordination entity in 2 hints at a potentially useful SBU for MOF synthesis from lignin based bridging ligands.

  • 7.
    von Ballmoos, Christoph
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. University of Bern, Switzerland.
    Smirnova, Irina
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Poiana, Federica
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gonska, Nathalie
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Chang, Hsin-Yang
    Gennis, Robert B.
    Brzezinski, Peter
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ädelroth, Pia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Dynamics of the K-B Proton Pathway in Cytochrome ba(3) from Thermus thermophilus2017In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 57, no 5, p. 424-436Article in journal (Refereed)
    Abstract [en]

    The ba(3) cytochrome c oxidase from Thermus thermophilus is a B-type oxygen-reducing heme-copper oxidase and a proton pump. It uses only one proton pathway for transfer of protons to the catalytic site, the K-B pathway. It was previously shown that the ba(3) oxidase has an overall similar reaction sequence to that in mitochondrial-like A-type oxidases. However, the timing of loading the pump site, and formation and decay of catalytic intermediates is different in the two types of oxidases. In the present study, we have investigated variants in which two amino acids of the K-B proton pathway leading to the catalytic site were exchanged; Tyr-248 (located approximate to 23 angstrom below the active site towards the cytoplasm) in subunit I (Y248T) and Glu-15 (approximate to 26 angstrom below the active site, approximate to 16 angstrom from Tyr-248) in subunit II (E15(II)Q). Even though the overall catalytic turnover in these two variants is similar and very low (<1% of wildtype), the substitutions had distinctly different effects on the kinetics of proton transfer to the catalytic site. The results indicate that the Glu-15(II) is the only essentially crucial residue of the K-B pathway, but that the Tyr-248 also plays a distinct role in defining an internal proton donor and controlling the dynamics of proton transfer to the pump site and the catalytic site.

  • 8.
    Wallin, Cecilia
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Luo, Jinghui
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. University of Oxford, UK.
    Jarvet, Jüri
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. The National Institute of Chemical Physics and Biophysics, Estonia.
    Wärmländer, Sebastian K. T. S.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gräslund, Astrid
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    The Amyloid-beta Peptide in Amyloid Formation Processes: Interactions with Blood Proteins and Naturally Occurring Metal Ions2017In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 57, no 7-8, p. 674-685Article, review/survey (Refereed)
    Abstract [en]

    This review describes interactions between the amyloid- peptide (A) involved in Alzheimer's disease (AD) and endogenous metal ions and proteins, with an emphasis on future potential drug therapies and targets. AD is characterised by loss of neurons, memory, and cognitive functions, and by formation of cerebral senile plaque deposits. These plaques consist mainly of aggregated A peptides. AD pathology includes a) on the molecular level imbalanced concentrations of A peptides and metal ions, and formation of amyloid structures, and b) on the physiological level a combination of inflammatory responses and oxidative stress effects causing neuronal death. Interestingly, certain blood proteins and metal ions can affect the A amyloid aggregation process. These interactions are the topics of the present review. A deeper understanding of these interactions could facilitate new therapeutic strategies against AD. Previous therapeutic approaches and trials are also briefly described.

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