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  • 1.
    Aster, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström. Univ Geneva, Dept Phys Chem, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland.
    Wang, Shihuai
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Mirmohades, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Esmieu, Charlène
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. CNRS, LCC, 205 Route Narbonne,BP 44099, F-31077 Toulouse 4, France.
    Berggren, Gustav
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Lomoth, Reiner
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Metal vs. ligand protonation and the alleged proton-shuttling role of the azadithiolate ligand in catalytic H-2 formation with FeFe hydrogenase model complexes2019In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 10, no 21, p. 5582-5588Article in journal (Refereed)
    Abstract [en]

    Electron and proton transfer reactions of diiron complexes [Fe(2)adt(CO)(6)] (1) and [Fe(2)adt(CO)(4)(PMe3)(2)] (4), with the biomimetic azadithiolate (adt) bridging ligand, have been investigated by real-time IR- and UV-vis-spectroscopic observation to elucidate the role of the adt-N as a potential proton shuttle in catalytic H-2 formation. Protonation of the one-electron reduced complex, 1(-), occurs on the adt-N yielding 1H and the same species is obtained by one-electron reduction of 1H(+). The preference for ligand vs. metal protonation in the Fe-2(i,0) state is presumably kinetic but no evidence for tautomerization of 1H to the hydride 1Hy was observed. This shows that the adt ligand does not work as a proton relay in the formation of hydride intermediates in the reduced catalyst. A hydride intermediate 1HHy(+) is formed only by protonation of 1H with stronger acid. Adt protonation results in reduction of the catalyst at much less negative potential, but subsequent protonation of the metal centers is not slowed down, as would be expected according to the decrease in basicity. Thus, the adtH(+) complex retains a high turnover frequency at the lowered overpotential. Instead of proton shuttling, we propose that this gain in catalytic performance compared to the propyldithiolate analogue might be rationalized in terms of lower reorganization energy for hydride formation with bulk acid upon adt protonation.

  • 2.
    Ballet, Caroline
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Correia, Mario S. P.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Conway, Louis P.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Locher, Theresa L.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Lehmann, Laura C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Garg, Neeraj
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Chemical Biology for Biomarker Discovery. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vujasinovic, Miroslav
    Karolinska Univ Hosp, Dept Digest Dis, Stockholm, Sweden.
    Deindl, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lohr, J. -Matthias
    Karolinska Inst, Dept Clin Sci Intervent & Technol CLINTEC, Stockholm, Sweden;Karolinska Univ Hosp, Dept Digest Dis, Stockholm, Sweden.
    Globisch, Daniel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Chemical Biology for Biomarker Discovery. Uppsala University, Science for Life Laboratory, SciLifeLab.
    New enzymatic and mass spectrometric methodology for the selective investigation of gut microbiota-derived metabolites2018In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 9, no 29, p. 6233-6239Article in journal (Refereed)
    Abstract [en]

    Gut microbiota significantly impact human physiology through metabolic interaction. Selective investigation of the co-metabolism of bacteria and their human host is a challenging task and methods for their analysis are limited. One class of metabolites associated with this co-metabolism are O-sulfated compounds. Herein, we describe the development of a new enzymatic assay for the selective mass spectrometric investigation of this phase II modification class. Analysis of human urine and fecal samples resulted in the detection of 206 sulfated metabolites, which is three times more than reported in the Human Metabolome Database. We confirmed the chemical structure of 36 sulfated metabolites including unknown and commonly reported microbiota-derived sulfated metabolites using synthesized internal standards and mass spectrometric fragmentation experiments. Our findings demonstrate that enzymatic sample pre-treatment combined with state-of-the-art metabolomics analysis represents a new and efficient strategy for the discovery of unknown microbiota-derived metabolites in human samples. Our described approach can be adapted for the targeted investigation of other metabolite classes as well as the discovery of biomarkers for diseases affected by microbiota.

  • 3. Bedin, Michele
    et al.
    Karim, Alavi
    Reitti, Marcus
    Carlsson, Anna-Carin C
    Topić, Filip
    Cetina, Mario
    Pan, Fangfang
    Havel, Vaclav
    Al-Ameri, Fatima
    Sindelar, Vladimir
    Rissanen, Kari
    Gräfenstein, Jürgen
    Erdelyi, Mate
    Counterion influence on the N-I-N halogen bond.2015In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 6, no 7, p. 3746-3756Article in journal (Refereed)
    Abstract [en]

    A detailed investigation of the influence of counterions on the [N-I-N]+ halogen bond in solution, in the solid state and in silico is presented. Translational diffusion coefficients indicate close attachment of counterions to the cationic, three-center halogen bond in dichloromethane solution. Isotopic perturbation of equilibrium NMR studies performed on isotopologue mixtures of regioselectively deuterated and nondeuterated analogues of the model system showed that the counterion is incapable of altering the symmetry of the [N-I-N]+ halogen bond. This symmetry remains even in the presence of an unfavorable geometric restraint. A high preference for the symmetric geometry was found also in the solid state by single crystal X-ray crystallography. Molecular systems encompassing weakly coordinating counterions behave similarly to the corresponding silver(i) centered coordination complexes. In contrast, systems possessing moderately or strongly coordinating anions show a distinctly different behavior. Such silver(i) complexes are converted into multi-coordinate geometries with strong Ag-O bonds, whereas the iodine centered systems remain linear and lack direct charge transfer interaction with the counterion, as verified by 15N NMR and DFT computation. This suggests that the [N-I-N]+ halogen bond may not be satisfactorily described in terms of a pure coordination bond typical of transition metal complexes, but as a secondary bond with a substantial charge-transfer character.

  • 4.
    Calixto, Ana Rita
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry. Univ Porto, Dept Quim & Bioquim, UCIBIO REQUIMTE, Fac Ciencias, Rua Campo Alegre S-N, P-4169007 Porto, Portugal.
    Ramos, Maria Joao
    Univ Porto, Dept Quim & Bioquim, UCIBIO REQUIMTE, Fac Ciencias, Rua Campo Alegre S-N, P-4169007 Porto, Portugal.
    Fernandes, Pedro Alexandrino
    Univ Porto, Dept Quim & Bioquim, UCIBIO REQUIMTE, Fac Ciencias, Rua Campo Alegre S-N, P-4169007 Porto, Portugal.
    Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway2019In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 10, no 30, p. 7212-7221Article in journal (Refereed)
    Abstract [en]

    The role of conformational diversity in enzyme catalysis has been a matter of analysis in recent studies. Pre-organization of the active site has been pointed out as the major source for enzymes' catalytic power. Following this line of thought, it is becoming clear that specific, instantaneous, non-rare enzyme conformations that make the active site perfectly pre-organized for the reaction lead to the lowest activation barriers that mostly contribute to the macroscopically observed reaction rate. The present work is focused on exploring the relationship between structure and catalysis in HIV-1 protease (PR) with an adiabatic mapping method, starting from different initial structures, collected from a classical MD simulation. The first, rate-limiting step of the HIV-1 PR catalytic mechanism was studied with the ONIOM QM/MM methodology (B3LYP/6-31G(d):ff99SB), with activation and reaction energies calculated at the M06-2X/6-311++G(2d,2p):ff99SB level of theory, in 19 different enzyme:substrate conformations. The results showed that the instantaneous enzyme conformations have two independent consequences on the enzyme's chemistry: they influence the barrier height, something also observed in the past in other enzymes, and they also influence the specific reaction pathway, which is something unusual and unexpected, challenging the "one enzyme-one substrate-one reaction mechanism" paradigm. Two different reaction mechanisms, with similar reactant probabilities and barrier heights, lead to the same gem-diol intermediate. Subtle nanosecond-timescale rearrangements in the active site hydrogen bonding network were shown to determine which reaction the enzyme follows. We named this phenomenon chemical disorder. The results make us realize the unexpected mechanistic consequences of conformational diversity in enzymatic reactivity.

  • 5.
    D'Amario, Luca
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Föhlinger, Jens
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Boschloo, Gerrit
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Unveiling hole trapping and surface dynamics of NiO nanoparticles2018In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 9, no 1, p. 223-230Article in journal (Refereed)
    Abstract [en]

    The research effort in mesoporous p-type semiconductors is increasing due to their potential application in photoelectrochemical energy conversion devices. In this paper an electron-hole pair is created by band-gap excitation of NiO nanoparticles and the dynamics of the electron and the hole is followed until their recombination. By spectroscopic characterization it was found that surface Ni3+ states work as traps for both electrons and holes. The trapped electron was assigned to a N2+ state and the trapped hole to a Ni4+ state. The recombination kinetics of these traps was studied and related with the concept of hole relaxation suggested before.The timescale of the hole relaxation was foundto be in the order of tens of ns. Finally the spectrosc opic evidence of this relaxation is presented in a sensitized film.

  • 6.
    Gilbert Gatty, Mélina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Pullen, Sonja
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Sheibani, E.
    Royal Inst Technol, Dept Chem Chem Sci & Engn, KTH, Organ Chem, S-10044 Stockholm, Sweden;Univ Ishafan, Dept Chem, Ishafan 8174673441, Iran.
    Tian, Haining
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Ott, Sascha
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Hammarström, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Direct evidence of catalyst reduction on dye and catalyst co-sensitized NiO photocathodes by mid-infrared transient absorption spectroscopy2018In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 9, no 22, p. 4983-4991Article in journal (Refereed)
    Abstract [en]

    Co-sensitization of molecular dyes and catalysts on semiconductor surfaces is a promising strategy to build photoelectrodes for solar fuel production. In such a photoelectrode, understanding the charge transfer reactions between the molecular dye, catalyst and semiconductor material is key to guide further improvement of their photocatalytic performance. Herein, femtosecond mid-infrared transient absorption spectroscopy is used, for the first time, to probe charge transfer reactions leading to catalyst reduction on co-sensitized nickel oxide (NiO) photocathodes. The NiO films were co-sensitized with a molecular dye and a proton reducing catalyst from the family of [FeFe](bdt)(CO)(6) (bdt = benzene-1,2-dithiolate) complexes. Two dyes were used: an organic push-pull dye denoted E2 with a triarylamine-oligothiophene-dicyanovinyl structure and a coumarin 343 dye. Upon photo-excitation of the dye, a clear spectroscopic signature of the reduced catalyst is observed a few picoseconds after excitation in all co-sensitized NiO films. However, kinetic analysis of the transient absorption signals of the dye and reduced catalyst reveal important mechanistic differences in the first reduction of the catalyst depending on the co-sensitized molecular dye (E2 or C343). While catalyst reduction is preceded by hole injection in NiO in C343-sensitized NiO films, the singly reduced catalyst is formed by direct electron transfer from the excited dye E2* to the catalyst in E2-sensitized NiO films. This change in mechanism also impacts the lifetime of the reduced catalyst, which is only ca. 50 ps in E2-sensitized NiO films but is >5 ns in C343-sensitized NiO films. Finally, the implication of this mechanistic study for the development of better co-sensitized photocathodes is discussed.

  • 7.
    Goronzy, I. N.
    et al.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA..
    Rawle, R. J.
    Univ Virginia, Dept Mol Physiol & Biomed Engn, Box 800886, Charlottesville, VA 22908 USA..
    Boxer, S. G.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA..
    Kasson, Peter M.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology. Univ Virginia, Dept Mol Physiol & Biomed Engn, Box 800886, Charlottesville, VA 22908 USA..
    Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering2018In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 9, no 8, p. 2340-2347Article in journal (Refereed)
    Abstract [en]

    Influenza virus infects cells by binding to sialylated glycans on the cell surface. While the chemical structure of these glycans determines hemagglutinin-glycan binding affinity, bimolecular affinities are weak, so binding is avidity-dominated and driven by multivalent interactions. Here, we show that membrane spatial organization can control viral binding. Using single-virus fluorescence microscopy, we demonstrate that the sterol composition of the target membrane enhances viral binding avidity in a dose-dependent manner. Binding shows a cooperative dependence on concentration of receptors for influenza virus, as would be expected for a multivalent interaction. Surprisingly, the ability of sterols to promote viral binding is independent of their ability to support liquid-liquid phase separation in model systems. We develop a molecular explanation for this observation via molecular dynamics simulations, where we find that cholesterol promotes small-scale clusters of glycosphingolipid receptors. We propose a model whereby cholesterol orders the monomeric state of glycosphingolipid receptors, reducing the entropic penalty of receptor association and thus favoring multimeric complexes without phase separation. This model explains how cholesterol and other sterols control the spatial organization of membrane receptors for influenza and increase viral binding avidity. A natural consequence of this finding is that local cholesterol concentration in the plasma membrane of cells may alter the binding avidity of influenza virions. Furthermore, our results demonstrate a form of cholesterol-dependent membrane organization that does not involve lipid rafts, suggesting that cholesterol's effect on cell membrane heterogeneity is likely the interplay of several different factors.

  • 8.
    Hua, Yong
    et al.
    KTH Royal Inst Technol, Sch Chem Sci & Engn, Dept Chem, Organ Chem,Ctr Mol Devices, Teknikringen 30, SE-10044 Stockholm, Sweden..
    Xu, Bo
    KTH Royal Inst Technol, Sch Chem Sci & Engn, Dept Chem, Organ Chem,Ctr Mol Devices, Teknikringen 30, SE-10044 Stockholm, Sweden..
    Liu, Peng
    KTH Royal Inst Technol, Sch Chem Sci & Engn, Dept Chem, Appl Phys Chem, Teknikringen 30, SE-10044 Stockholm, Sweden..
    Chen, Hong
    KTH Royal Inst Technol, Sch Chem Sci & Engn, Dept Chem, Organ Chem,Ctr Mol Devices, Teknikringen 30, SE-10044 Stockholm, Sweden..
    Tian, Haining
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Cheng, Ming
    KTH Royal Inst Technol, Sch Chem Sci & Engn, Dept Chem, Organ Chem,Ctr Mol Devices, Teknikringen 30, SE-10044 Stockholm, Sweden..
    Kloo, Lars
    KTH Royal Inst Technol, Sch Chem Sci & Engn, Dept Chem, Appl Phys Chem, Teknikringen 30, SE-10044 Stockholm, Sweden..
    Sun, Licheng
    KTH Royal Inst Technol, Sch Chem Sci & Engn, Dept Chem, Organ Chem,Ctr Mol Devices, Teknikringen 30, SE-10044 Stockholm, Sweden.;Dalian Univ Technol, DUT KTH Joint Res Ctr Mol Devices, State Key Lab Fine Chem, Dalian 116024, Peoples R China..
    High conductivity Ag-based metal organic complexes as dopant-free hole-transport materials for perovskite solar cells with high fill factors2016In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 7, no 4, p. 2633-2638Article in journal (Refereed)
    Abstract [en]

    Hole-transport materials (HTMs) play an important role as hole scavenger materials in the most efficient perovskite solar cells (PSCs). Here, for the first time, two Ag-based metal organic complexes (HA1 and HA2) are employed as a new class of dopant-free hole-transport material for application in PSCs. These HTMs show excellent conductivity and hole-transport mobility. Consequently, the devices based on these two HTMs exhibit unusually high fill factors of 0.76 for HA1 and 0.78 for HA2, which are significantly higher than that obtained using spiro-OMeTAD (0.69). The cell based on HA1-HTM in its pristine form achieved a high power conversion efficiency of 11.98% under air conditions, which is comparable to the PCE of the cell employing the well-known doped spiro-MeOTAD (12.27%) under the same conditions. More importantly, their facile synthesis and purification without using column chromatography makes these new silver-based HTMs highly promising for future commercial applications of PSCs. These results provide a new way to develop more low-cost and high conductivity metal-complex based HTMs for efficient PSCs.

  • 9.
    Jorner, Kjell
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Jahn, Burkhard O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. SciClus GmbH & Co. KG, Moritz-von-Rohr-Str. 1a, 07745 Jena, Germany .
    Bultinck, Patrick
    SciClus GmbH & Co. KG, Moritz-von-Rohr-Str. 1a, 07745 Jena, Germany.
    Ottosson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Triplet state homoaromaticity: concept, computational validation and experimental relevance2018In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 9, no 12, p. 3165-3176Article in journal (Refereed)
    Abstract [en]

    Cyclic conjugation that occurs through-space and leads to aromatic properties is called homoaromaticity. Here we formulate the homoaromaticity concept for the triplet excited state (T1) based on Baird's 4n rule and validate it through extensive quantum-chemical calculations on a range of different species (neutral, cationic and anionic). By comparison to well-known ground state homoaromatic molecules we reveal that five of the investigated compounds show strong T1 homoaromaticity, four show weak homoaromaticity and two are non-aromatic. Two of the compounds have previously been identified as excited state intermediates in photochemical reactions and our calculations indicate that they are also homoaromatic in the first singlet excited state. Homoaromaticity should therefore have broad implications in photochemistry. We further demonstrate this by computational design of a photomechanical “lever” that is powered by relief of homoantiaromatic destabilization in the first singlet excited state.

  • 10.
    Kalepu, Jagadeesh
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Gandeepan, Parthasarathy
    Georg August Univ Gottingen, Inst Organ & Biomol Chem, Tammannstr 2, D-37077 Gottingen, Germany.
    Ackermann, Lutz
    Georg August Univ Gottingen, Inst Organ & Biomol Chem, Tammannstr 2, D-37077 Gottingen, Germany.
    Pilarski, Lukasz T.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    C4-H indole functionalisation: precedent and prospects2018In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 9, no 18, p. 4203-4216Article in journal (Refereed)
    Abstract [en]

    C4-decorated indoles feature in a plethora of bioactive and functional compounds of importance to natural product synthesis, material sciences, as well as crop protection and pharmaceutical industries. Traditionally, their syntheses largely involved harsh stoichiometric metalations and radical reactions. However, transition metal catalysed C-H activation has recently evolved into a powerful strategy for the late-stage diversification of indoles at the C4-H position. Modern photoredox, enzymatic and precious transition metal catalysis represent the key stimuli for developing challenging C-C and C-Het bond forming transformations under mild reaction conditions. Herein, we discuss the evolution and application of these methods for the step-economical transformations of otherwise inert C4-H bonds up to December 2017.

  • 11.
    Land, Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Ceccaldi, Pierre
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Meszaros, Livia S.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Lorenzi, Marco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Redman, Holly J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Senger, Moritz
    Free Univ Berlin, Inst Expt Phys, Expt Mol Biophys, Arnimallee 14, DE-14195 Berlin, Germany.
    Stripp, Sven T.
    Free Univ Berlin, Inst Expt Phys, Expt Mol Biophys, Arnimallee 14, DE-14195 Berlin, Germany.
    Berggren, Gustav
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Discovery of novel [FeFe]-hydrogenases for biocatalytic H-2-production2019In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 10, no 43, p. 9941-9948Article in journal (Refereed)
    Abstract [en]

    A new screening method for [FeFe]-hydrogenases is described, circumventing the need for specialized expression conditions as well as protein purification for initial characterization. [FeFe]-hydrogenases catalyze the formation and oxidation of molecular hydrogen at rates exceeding 10(3) s(-1), making them highly promising for biotechnological applications. However, the discovery of novel [FeFe]-hydrogenases is slow due to their oxygen sensitivity and dependency on a structurally unique cofactor, complicating protein expression and purification. Consequently, only a very limited number have been characterized, hampering their implementation. With the purpose of increasing the throughput of [FeFe]-hydrogenase discovery, we have developed a screening method that allows for rapid identification of novel [FeFe]-hydrogenases as well as their characterization with regards to activity (activity assays and protein film electrochemistry) and spectroscopic properties (electron paramagnetic resonance and Fourier transform infrared spectroscopy). The method is based on in vivo artificial maturation of [FeFe]-hydrogenases in Escherichia coli and all procedures are performed on either whole cells or non-purified cell lysates, thereby circumventing extensive protein purification. The screening was applied on eight putative [FeFe]-hydrogenases originating from different structural sub-classes and resulted in the discovery of two new active [FeFe]-hydrogenases. The [FeFe]-hydrogenase from Solobacterium moorei shows high H-2-gas production activity, while the enzyme from Thermoanaerobacter mathranii represents a hitherto uncharacterized [FeFe]-hydrogenase sub-class. This latter enzyme is a putative sensory hydrogenase and our in vivo spectroscopy study reveals distinct differences compared to the well established H-2 producing HydA1 hydrogenase from Chlamydomonas reinhardtii.

  • 12.
    Latallo, M. J.
    et al.
    Univ Virginia, Dept Mol Physiol..
    Cortina, G. A.
    Department of Molecular Physiology, University of Virginia; Department of Biomedical Engineering, University of Virginia.
    Faham, S.
    Univ Virginia, Dept Mol Physiol..
    Nakamoto, R. K.
    Univ Virginia, Dept Mol Physiol..
    Kasson, P. M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Virginia, Department of Molecular Physiology; Department of Biomedical Engineering, University of Virginia,.
    Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme2017In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 8, no 9, p. 6484-6492Article in journal (Refereed)
    Abstract [en]

    The CTX-M family of beta lactamases mediate broad-spectrum antibiotic resistance and are present in the majority of drug-resistant Gram-negative bacterial infections worldwide. Allosteric mutations that increase catalytic rates of these drug resistance enzymes have been identified in clinical isolates but are challenging to predict prospectively. We have used molecular dynamics simulations to predict allosteric mutants increasing CTX-M9 drug resistance, experimentally testing top mutants using multiple antibiotics. Purified enzymes show an increase in catalytic rate and efficiency, while mutant crystal structures show no detectable changes from wild-type CTX-M9. We hypothesize that increased drug resistance results from changes in the conformational ensemble of an acyl intermediate in hydrolysis. Machine-learning analyses on the three top mutants identify changes to the binding-pocket conformational ensemble by which these allosteric mutations transmit their effect. These findings show how molecular simulation can predict how allosteric mutations alter active-site conformational equilibria to increase catalytic rates and thus resistance against common clinically used antibiotics.

  • 13.
    Ma, Huan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Szeler, Klaudia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Kamerlin, Shina Caroline Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Widersten, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA)2016In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 7, p. 1415-1421Article in journal (Refereed)
    Abstract [en]

    DERA, 2-deoxyribose-5-phosphate aldolase, catalyzes the retro-aldol cleavage of 2-deoxy-ribose-5-phosphate (dR5P) into glyceraldehyde-3-phosphate (G3P) and acetaldehyde in a branch of the pentose phosphate pathway. In addition to the physiological reaction, DERA also catalyzes the reverse addition reaction and, hence, is an interesting candidate for biocatalysis of carboligation reactions, which are central to synthetic chemistry. An obstacle to overcome for this enzyme to become a truly useful biocatalyst, however, is to relax the very strict dependency of this enzyme on phoshorylated substrates. We have studied herein the role of the non-canonical phosphate-binding site of this enzyme, consisting of Ser238 and Ser239, by site-directed and site-saturation mutagenesis, coupled to kinetic analysis of mutants. In addition, we have performed molecular dynamics simulations on the wild-type and four mutant enzymes, to analyse how mutations at this phosphate-binding site may affect the protein structure and dynamics. Further examination of the S239P mutant revealed that this variant increases the enthalpy change at the transition state, relative to the wild-type enzyme, but concomitant loss in entropy causes an overall relative loss in the TS free energy change. This entropy loss, as measured by the temperature dependence of catalysed rates, was mirrored in both a drastic loss in dynamics of the enzyme, which contributes to phosphate binding, as well as an overall loss in anti-correlated motions distributed over the entire protein. Our combined data suggests that the degree of anticorrelated motions within the DERA structure is coupled to catalytic efficiency in the DERA-catalyzed retro-aldol cleavage reaction, and can be manipulated for engineering purposes.

  • 14.
    Nishimura, Naoyuki
    et al.
    Univ Cambridge, Cavendish Lab, JJ Thomson Ave, Cambridge CB3 0HE, England;Asahi Kasei Corp, Corp Res & Dev, 2-1 Samejima, Fuji, Shizuoka 4168501, Japan.
    Allardice, Jesse R.
    Univ Cambridge, Cavendish Lab, JJ Thomson Ave, Cambridge CB3 0HE, England.
    Xiao, James
    Univ Cambridge, Cavendish Lab, JJ Thomson Ave, Cambridge CB3 0HE, England.
    Gu, Qifei
    Univ Cambridge, Cavendish Lab, JJ Thomson Ave, Cambridge CB3 0HE, England.
    Gray, Victor
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Univ Cambridge, Cavendish Lab, JJ Thomson Ave, Cambridge CB3 0HE, England.
    Rao, Akshay
    Univ Cambridge, Cavendish Lab, JJ Thomson Ave, Cambridge CB3 0HE, England.
    Photon upconversion utilizing energy beyond the band gap of crystalline silicon with a hybrid TES-ADT/PbS quantum dots system2019In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 10, no 18, p. 4750-4760Article in journal (Refereed)
    Abstract [en]

    The recent introduction of inorganic semiconductor quantum dots (QDs) as triplet sensitizers for molecular semiconductors has led to significant interest in harvesting low energy photons, which can then be used for photon upconversion (PUC), via triplet-triplet annihilation (TTA). A key goal is the harvesting of photons from below the bandgap of crystalline silicon 1.12 eV (approximate to 1100 nm) and their upconversion into the visible region. In practice, the systems demonstrated so far have been limited to harvesting photons with energies above 1.2 eV (approximate to 1 mu m), due to two reasons: firstly the need to use transmitter ligands which allow efficient energy harvesting from the QD but introduce an energy loss of larger than 200 meV in transmission from the QD to the annihilator, and secondly due to the use of molecules such as tetracene which cannot accept smaller energy than 1.2 eV. Here, we introduce a new strategy to overcome these difficulties by using a low energy triplet annihilator that also harvests excitations efficiently from QDs. Specifically, we show that 5,11-bis(triethylsilylethynyl) anthradithiophene (TES-ADT, triplet energy of 1.08 eV: ca. 1150 nm) functions as a triplet annihilator (20% TTA efficiency) while also rapidly extracting triplet excitons from lead sulfide (PbS) QDs with a rate constant of k = ca. 2 x 10(-8) s(-1) with an excitation at 1064 nm. This rate is consistent with an orbital overlap between TES-ADT and PbS QDs, which we propose is due to the thiophene group of TES-ADT, which enables a close association with the PbS surface, allowing this system to function both as annihilator and transmitter. Our results pave the way for the design of triplet annihilators that can closely associate with the QD surface and harvest low energy excitons with minute losses in energy during the TET process, with the ultimate goal of efficiently utilizing photon energy beyond the bandgap of crystalline silicon.

  • 15.
    Retegan, Marius
    et al.
    Max Planck Inst Chem Energy Convers, D-45470 Mulheim, Germany..
    Krewald, Vera
    Max Planck Inst Chem Energy Convers, D-45470 Mulheim, Germany..
    Mamedov, Fikret
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Neese, Frank
    Max Planck Inst Chem Energy Convers, D-45470 Mulheim, Germany..
    Lubitz, Wolfgang
    Max Planck Inst Chem Energy Convers, D-45470 Mulheim, Germany..
    Cox, Nicholas
    Max Planck Inst Chem Energy Convers, D-45470 Mulheim, Germany..
    Pantazis, Dimitrios A.
    Max Planck Inst Chem Energy Convers, D-45470 Mulheim, Germany..
    A five-coordinate Mn(IV) intermediate in biological water oxidation: spectroscopic signature and a pivot mechanism for water binding2016In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 7, no 1, p. 72-84Article in journal (Refereed)
    Abstract [en]

    Among the four photo-driven transitions of the water-oxidizing tetramanganese-calcium cofactor of biological photosynthesis, the second-last step of the catalytic cycle, that is the S-2 to S-3 state transition, is the crucial step that poises the catalyst for the final O-O bond formation. This transition, whose intermediates are not yet fully understood, is a multi-step process that involves the redox-active tyrosine residue and includes oxidation and deprotonation of the catalytic cluster, as well as the binding of a water molecule. Spectroscopic data has the potential to shed light on the sequence of events that comprise this catalytic step, which still lacks a structural interpretation. In this work the S-2-S-3 state transition is studied and a key intermediate species is characterized: it contains a Mn3O4Ca cubane subunit linked to a five-coordinate Mn(IV) ion that adopts an approximately trigonal bipyramidal ligand field. It is shown using high-level density functional and multireference wave function calculations that this species accounts for the near-infrared absorption and electron paramagnetic resonance observations on metastable S-2-S-3 intermediates. The results confirm that deprotonation and Mn oxidation of the cofactor must precede the coordination of a water molecule, and lead to identification of a novel low-energy water binding mode that has important implications for the identity of the substrates in the mechanism of biological water oxidation.

  • 16.
    Soetbeer, Janne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Dongare, Prateek
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Hammarstrom, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Marcus-type driving force correlations reveal the mechanism of proton-coupled electron transfer for phenols and [Ru(bpy)(3)](3+) in water at low pH2016In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 7, no 7, p. 4607-4612Article in journal (Refereed)
    Abstract [en]

    Proton-coupled electron transfer (PCET) from tyrosine and other phenol derivatives in water is an important elementary reaction in chemistry and biology. We examined PCET between a series of phenol derivatives and photogenerated [Ru(bpy)3](3+) in low pH (<= 4) water using the laser flash-quench technique. From an analysis of the kinetic data using a Marcus-type free energy relationship, we propose that our model system follows a stepwise electron transfer-proton transfer (ETPT) pathway with a pH independent rate constant at low pH in water. This is in contrast to the concerted or proton-first (PTET) mechanisms that often dominate at higher pH and/or with buffers as primary proton acceptors. The stepwise mechanism remains competitive despite a significant change in the pK(a) and redox potential of the phenols which leads to a span of rate constants from 1 x 10(5) to 2 x 10(9) M (1) s (1). These results support our previous studies which revealed separate mechanistic regions for PCET reactions and also assigned phenol oxidation by [Ru(bpy)(3)](3+) at low pH to a stepwise PCET mechanism.

  • 17.
    Warzok, Ulrike
    et al.
    Free Univ Berlin, Inst Chem & Biochem, Takustr 3, D-14195 Berlin, Germany.
    Marianski, Mateusz
    Max Planck Gesell, Fritz Haber Inst, Faradayweg 4-6, D-14195 Berlin, Germany;CUNY, Hunter Coll, New York, NY 10021 USA.
    Hoffmann, Waldemar
    Free Univ Berlin, Inst Chem & Biochem, Takustr 3, D-14195 Berlin, Germany;Max Planck Gesell, Fritz Haber Inst, Faradayweg 4-6, D-14195 Berlin, Germany.
    Turunen, Jaakko
    Univ Jyvaskyla, NanoSci Ctr, Dept Chem, POB 35, Jyvaskyla 40014, Finland.
    Rissanen, Kari
    Univ Jyvaskyla, NanoSci Ctr, Dept Chem, POB 35, Jyvaskyla 40014, Finland.
    Pagel, Kevin
    Free Univ Berlin, Inst Chem & Biochem, Takustr 3, D-14195 Berlin, Germany;Max Planck Gesell, Fritz Haber Inst, Faradayweg 4-6, D-14195 Berlin, Germany.
    Schalley, Christoph A.
    Free Univ Berlin, Inst Chem & Biochem, Takustr 3, D-14195 Berlin, Germany;Northwestern Polytech Univ, Sch Life Sci, 127 Youyi Xilu, Xian 710072, Shaanxi, Peoples R China.
    Surprising solvent-induced structural rearrangements in large [N center dot center dot center dot I+center dot center dot center dot N] halogen-bonded supramolecular capsules: an ion mobility-mass spectrometry study2018In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 9, no 44, p. 8343-8351Article in journal (Refereed)
    Abstract [en]

    Coordinative halogen bonds have recently gained interest for the assembly of supramolecular capsules. Ion mobility-mass spectrometry and theoretical calculations now reveal the well-defined gas-phase structures of dimeric and hexameric [NI+N] halogen-bonded capsules with counterions located inside their cavities as guests. The solution reactivity of the large hexameric capsule shows the intriguing solvent-dependent equilibrium between the hexamer and an unprecedented pentameric [NI+N] halogen-bonded capsule, when the solvent is changed from chloroform to dichloromethane. The intrinsic flexibility of the cavitands enables this novel structure to adopt a pseudo-trigonal bipyramidal geometry with nine [NI+N] bonds along the edges and two pyridine binding sites uncomplexed.

  • 18.
    Zyubko, Tatyana
    et al.
    Skolkovo Inst Sci & Technol, Ctr Life Sci, Moscow, Russia; Peter Great St Petersburg Polytech Univ, St Petersburg, Russia.
    Serebryakova, Marina
    Skolkovo Inst Sci & Technol, Ctr Life Sci, Moscow, Russia; Lomonosov Moscow State Univ, AN Belozersky Inst Physicochem Biol, Moscow Russia; Russian Acad Sci, Inst Gene Biol, Moscow, Russia.
    Andreeva, Julia
    Skolkovo Inst Sci & Technol, Moscow, Russia; Russian Acad Sci, Moscow, Russia.
    Metelev, Mikhail
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Skolkovo Inst Sci & Technol, Moscow, Russia; Peter Great St Petersburg Polytech Univ, St Petersburg, Russia; Russian Acad Sci, Inst Gene Biol, Moscow Russia.
    Lippens, Guy
    Ups, INSA, INRA, TBI, CNRS, Toulouse, France.
    Dubiley, Svetlana
    Skolkovo Inst Sci & Technol, Moscow, Russia; Russian Acad Sci, Inst Gene Biol, Moscow, Russia.
    Severinov, Konstantin
    Skolkovo Inst Sci & Technol, Moscow, Russia; Waksman Inst Microbiol, Piscataway, NJ USA.
    Efficient in vivo synthesis of lasso peptide pseudomycoidin proceeds in the absence of both the leader and the leader peptidase2019In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 10, no 42, p. 9699-9707Article in journal (Refereed)
    Abstract [en]

    Bacterial lasso peptides are made from linear ribosomally synthesized precursors by specific cleavage at the leader-core junction site of the precursor by a dedicated protease recognizing the leader, followed by cyclisation of the newly formed N-terminus of the core part with a side chain of the internal aspartic or glutamic residue catalyzed by a macrolactam synthetase. The resulting structure has a tail that is threaded and fixed inside the cycle formed. Here, we characterize a new lasso peptide, pseudomycoidin, encoded by Bacillus pseudomycoides DSM 12442. The most surprising and unique feature of pseudomycoidin is that it can be produced in vivo from the ribosomally synthesized core part by a macrolactam synthetase, in the absence of the leader protease. The minimalism of the pseudomycoidin synthesis system makes it a powerful model to generate pseudomycoidin-based lasso-peptide libraries and to study the poorly understood process of lasso formation. We detected two additional pseudomycoidin modifications: phosphorylation of a terminal residue that was previously observed in another lasso peptide, followed by glycosylation, which was not observed heretofore. We speculate that these bulky C-terminal modifications may help maintain the threaded lasso topology of the compound synthesized by the macrolactam synthetase.

1 - 18 of 18
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