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1.
  • Chaudhari, Aditya S., et al. (creator_code:aut_t)
  • Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side-chains in EL222
  • 2023
  • record:In_t: Protein Science. - : John Wiley & Sons. - 0961-8368 .- 1469-896X. ; 32:4
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at 45 positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A'α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A'α extension of the LOV domain in controlling EL222 photocycle length.
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2.
  • Zhou, Yu, et al. (creator_code:aut_t)
  • Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth
  • 2023
  • record:In_t: NATURE PLANTS. - : Springer Nature. - 2055-0278. ; 9, s. 978-986
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Improving the carboxylation properties of Rubisco has primarily arisen from unforeseen amino acid substitutions remote from the catalytic site. The unpredictability has frustrated rational design efforts to enhance plant Rubisco towards the prized growth-enhancing carboxylation properties of red algae Griffithsia monilis GmRubisco. To address this, we determined the crystal structure of GmRubisco to 1.7 angstrom. Three structurally divergent domains were identified relative to the red-type bacterial Rhodobacter sphaeroides RsRubisco that, unlike GmRubisco, are expressed in Escherichia coli and plants. Kinetic comparison of 11 RsRubisco chimaeras revealed that incorporating C329A and A332V substitutions from GmRubisco Loop 6 (corresponding to plant residues 328 and 331) into RsRubisco increased the carboxylation rate (kcatc) by 60%, the carboxylation efficiency in air by 22% and the CO2/O-2 specificity (Sc/o) by 7%. Plastome transformation of this RsRubisco Loop 6 mutant into tobacco enhanced photosynthesis and growth up to twofold over tobacco producing wild-type RsRubisco. Our findings demonstrate the utility of RsRubisco for the identification and in planta testing of amino acid grafts from algal Rubisco that can enhance the enzyme's carboxylase potential.
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3.
  • Munke, Anna (creator_code:aut_t)
  • Small Particles with Big Impact : Structural Studies of Viruses and Toxicological Studies of Nanodiamonds
  • 2020
  • swepub:Mat_doctoralthesis_t (swepub:level_scientificother_t)abstract
    • Nanoparticles (NPs) can be found everywhere and their existence has both beneficial and harmful consequences for the environment and living beings. The investigations on which this thesis is based upon have contributed to an increased understanding of some of these particles and to the development of a method that could be used to study their structure.Three different NPs have been studied by different means. In the first study, I describe how single-particle cryo-electron microscopy was used to determine the atomic structure of an algal virus; Chaetoceros tenuissimus RNA virus type II. This virus is taxonomically classified in the order Picornavirales, which includes viruses that infect a wide range of organisms, including humans, plants and insects. By comparing the algal virus structure to structures of related viruses in the order, we could identify a number of traits that were likely acquired or lost among these viruses during the course of evolution. In the second study, rice dwarf virus was utilised as a test sample to develop a new structural biology method, single-particle coherent diffractive imaging (CDI). The method aims to study macromolecules in a single-particle fashion at room temperature with the help of an X-ray free-electron laser, thus enabling studies of fast dynamics without the need to crystallize or freeze the sample. The study was the first of several within a large international collaboration and the first single-particle CDI experiment reported using femtosecond hard X-ray pulses. Despite several advances by the team, many challenges remain for the method to reach its full potential. In the third study, I describe in vitro and in vivo toxicological studies of detonation nanodiamonds (DNDs). I could demonstrate that some DNDs are toxic and that the toxicity is dependent both on the core and surface of the particles. DNDs are suggested for numerous different biomedical applications that alternately utilise their toxic properties or require biocompatibility. The results presented show that these contrasting properties can be exhibited by similar DNDs and that thorough characterisation and close control of the manufacturing process is essential for biomedical applications.This thesis explores how studies of some of nature’s nanoparticles - viruses - can lead to biological insight, how virus NPs can play a role in developing new technologies that may enable an even deeper understanding and explores issues that need to be considered for NPs to reach their potential in biomedical applications.
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4.
  • Andersson, Britt-Inger (creator_code:aut_t)
  • Förstudie Del A Underlag till en FoU-strategi : inspel till myndighetens strategiska plan 2021-2023
  • 2019
  • swepub:Mat_report_t (swepub:level_scientificother_t)abstract
    • Syftet med förstudien är att ta fram ett underlag till en FoU-strategi för myndigheten. Den ska användas som inspel till myndighetens kommande strategiska plan 2021– 2023. Myndigheten saknar en FoU-strategi som omfattar hela verksamheten. Idag utförs en liten del egen forskningsverksamhet främst runforskning och en större del annan FoU-verksamhet. I stort sett all FoU utförs i samarbete och/eller samverkan med externa parter exempelvis museer, universitet och högskolor. I rapporten har sex kategorier av FoU-verksamhet identifierats. De flesta avdelningar utför FoU-verksamhet främst Kulturvårdsavdelningen, men även Arkiv och bibliotek samt Informationsavdelningen. Kulturmiljöavdelningen arbetar främst operativt med FoU-anslaget och det tillhörande externa FoU-programmet. Staben arbetar strategiskt med FoU-frågor i Sverige och inom EU samt ansvarar strategiskt för det externa FoU-programmet.
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5.
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6.
  • Bielecki, Johan, 1982, et al. (creator_code:aut_t)
  • Electrospray sample injection for single-particle imaging with x-ray lasers
  • 2019
  • record:In_t: Science advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 5:5
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The possibility of imaging single proteins constitutes an exciting challenge for x-ray lasers. Despite encouraging results on large particles, imaging small particles has proven to be difficult for two reasons: not quite high enough pulse intensity from currently available x-ray lasers and, as we demonstrate here, contamination of the aerosolized molecules by nonvolatile contaminants in the solution. The amount of contamination on the sample depends on the initial droplet size during aerosolization. Here, we show that, with our electrospray injector, we can decrease the size of aerosol droplets and demonstrate virtually contaminant-free sample delivery of organelles, small virions, and proteins. The results presented here, together with the increased performance of next-generation x-ray lasers, constitute an important stepping stone toward the ultimate goal of protein structure determination from imaging at room temperature and high temporal resolution.
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7.
  • Hasse, Dirk, et al. (creator_code:aut_t)
  • Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus
  • 2019
  • record:In_t: Acta Crystallographica Section D. - : INT UNION CRYSTALLOGRAPHY. - 2059-7983. ; 75, s. 1107-1118
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The core of beta-lactam antibiotics originates from amino acids of primary metabolism in certain microorganisms. beta-Lactam-producing bacteria, including Streptomyces clavuligerus, synthesize the precursor of the amino acid alpha-aminoadipic acid by the catabolism of lysine in two steps. The second reaction, the oxidation of piperideine-6-carboxylate (or its open-chain form alpha-aminoadipate semialdehyde) to alpha-aminoadipic acid, is catalysed by the NAD(+)-dependent enzyme piperideine-6-carboxylate dehydrogenase (P6CDH). This structural study, focused on ligand binding and catalysis, presents structures of P6CDH from S. clavuligerus in its apo form and in complexes with the cofactor NAD(+), the product alpha-aminoadipic acid and a substrate analogue, picolinic acid. P6CDH adopts the common aldehyde dehydrogenase fold, consisting of NAD-binding, catalytic and oligomerization domains. The product binds in the oxyanion hole, close to the catalytic residue Cys299. Clear density is observed for the entire cofactor, including the nicotinamide riboside, in the binary complex. NAD(+) binds in an extended conformation with its nicotinamide ring overlapping with the binding site of the carboxylate group of the product, implying that the conformation of the cofactor may change during catalysis. The binding site of the substrate analogue overlaps with that of the product, suggesting that the cyclic form of the substrate, piperideine-6-carboxylate, may be accepted as a substrate by the enzyme. The catalytic mechanism and the roles of individual residues are discussed in light of these results.
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8.
  • Carlsson, Gunilla H., et al. (creator_code:aut_t)
  • The elusive ligand complexes of the DWARF14 strigolactone receptor
  • 2018
  • record:In_t: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 69:9, s. 2345-2354
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Strigolactones, a group of terpenoid lactones, control many aspects of plant growth and development, but the active forms of these plant hormones and their mode of action at the molecular level are still unknown. The strigolactone protein receptor is unusual because it has been shown to cleave the hormone and supposedly forms a covalent bond with the cleaved hormone fragment. This interaction is suggested to induce a conformational change in the receptor that primes it for subsequent interaction with partners in the signalling pathway. Substantial efforts have been invested into describing the interaction of synthetic strigolactone analogues with the receptor, resulting in a number of crystal structures. This investigation combines a re-evaluation of models in the Protein Data Bank with a search for new conditions that may permit the capture of a receptor-ligand complex. While weak difference density is frequently observed in the binding cavity, possibly due to a low-occupancy compound, the models often contain features not supported by the X-ray data. Thus, at this stage, we do not believe that any detailed deductions about the nature, conformation, or binding mode of the ligand can be made with any confidence.
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9.
  • Locmelis, Roland, 1984- (creator_code:aut_t)
  • Structural biology studies of thylakoid lumen proteins required for photosystem II assembly and function
  • 2018
  • swepub:Mat_doctoralthesis_t (swepub:level_scientificother_t)abstract
    • Little is known about the structures and functions of thylakoid lumen proteins. However, some of these proteins have an essential role in photosynthesis. Photosystem II (PSII) complexes are embedded in the thylakoid membrane of oxygenic photosynthetic organisms and one of the central subunits, the D1 protein, is damaged by light during the light driven water – splitting reaction and must be replaced frequently. One of the thylakoid lumen proteins that is essential for assembly and renewal of PSII complexes is the High Chlorophyll Fluorescence 136 (HCF136) protein. Another important protein for the PSII complex assembly is the Low PSII Accumulation Protein 19 (LPA19). Both proteins, HCF136 and LPA19, were shown to bind to the core subunits of the PSII complex from the lumenal side and LPA19 has been shown to explicitly interact with the soluble C-terminus of the D1 protein, one of the core PSII complex proteins. Prior to the replacement of the damaged D1 protein, the PSII complex needs to be disassembled, which is done with the help of the Maintenance of Photosystem II under High light 2 (MPH2) protein. MPH2, also called TL16, is required during the repair cycle of the PSII complex particularly under increased and fluctuating light conditions.In this work I have determined the three-dimensional X-ray structures of the HCF136 protein at 1.6 Å resolution and the LPA19 protein at 1.2 Å resolution and have also biochemically analyzed possible interactions of HCF136 with the C-termini of D1 protein. In addition, we have determined the NMR structure of the MPH2 protein.The protein structures of HCF136, LPA19, and MPH2 determined from A. thaliana provide us with a starting point for further studies to improve our understanding of their functional roles in the assembly, maintenance, disassembly and renewal of the PSII complex. The structures are revealing the molecular details that are particularly important during the design of mutations to study protein-protein interactions and the binding of co-factors.Furthermore, I have contributed to the characterization of AnPrx6, the 1-Cyx peroxiredoxin from Anabaena sp. 7120. Peroxiredoxins are important caretakers of reactive oxygen species and a homolog PrxQ in A.thaliana is found in the thylakoid lumen. The dimeric AnPrx6 protein revealed different active site residues conformations in each of the dimers, which is probably coupled to its enzymatic activity. Unexpectedly, the protein acted also as a chaperone and showed chaperone activity in its dimeric state, which is a novelty for Prx proteins.
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10.
  • Munke, Anna, et al. (creator_code:aut_t)
  • Coherent diffraction of single Rice Dwarf Virus particles using soft X-rays at the Linac Coherent Light Source
  • 2018
  • record:In_t: Nature Scientific Data.
  • swepub:Mat_article_t (swepub:level_scientificother_t)abstract
    • Single particle imaging using X-ray Free Electron Lasers has recently made major advancements that have facilitated experiments on smaller samples compared to the earliest reported works on giant viruses and cells. Here, the technique was used to image the 70 nm Rice dwarf virus, for which the generated dataset is described here. The virus particles were aerosolized and injected into the X-ray beam of the Linac Coherent Light Source. A total number of 36534 diffraction patterns were recorded, of which approximately 10 % were classified as ‘single hits’ by the RedFlamingo software. With the anticipation to advance method development, the dataset along with usage instructions are deposited in the Coherent X-ray imaging data bank, free to access and analyze.
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