An improved model of the <i>Trypanosoma brucei</i> CTP synthetase glutaminase domain-acivicin complex

The natural product acivicin inhibits the glutaminase activity of CTP synthetase and is a potent lead compound for drug discovery in the area of neglected tropical diseases, specifically trypanosomaisis. A 2.1 Å resolution crystal structure of the acivicin adduct with the glutaminase domain from Trypanosoma brucei CTP synthetase has been deposited in the Protein Data Bank and provides a template for structure-based approaches to design new inhibitors. However, our assessment of that data identified deficiencies in the model. We now report an improved and corrected inhibitor structure with changes to the chirality at one position, the orientation and covalent structure of the isoxazoline moiety and the location of a chloride in an oxyanion binding site that is exploited during catalysis. The model is now in agreement with established chemical principles and allows an accurate description of molecular recognition of the ligand and the mode of binding in a potentially valuable drug target.</p

Secondary Structure Prediction of Protein Constructs Using Random Incremental Truncation and Vacuum-Ultraviolet CD Spectroscopy

A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE is excepted to provide key information on the description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. Towards this long-term aim, the random library ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine constructs of UDE were chosen to decipher structural and functional relationships. Vacuum ultraviolet circular dichroism (VUVCD) spectroscopy was performed to define the secondary structure content and location within UDE and its truncated variants. The quantitative analysis demonstrated exclusive alpha-helical content for the full-length protein, which is preserved in the truncated constructs. Arrangement of alpha-helical bundles within the truncated protein segments suggested new domain boundaries which differ from the conserved motifs determined by sequence-based alignment of UDE homologues. Here we demonstrate that the combination of ESPRIT and VUVCD spectroscopy provides a new structural description of UDE and confirms that the truncated constructs are useful for further detailed functional studies

Recycling and reusing of waste concrete fines as granulated aggregates

Abstract In recent years, a large amount of construction and demolition waste has been generated by many demolition and construction projects because of fast urbanization. There is therefore a growing need for the sustainable management of construction waste and its recycling. The fine fraction of construction waste is especially challenging to reuse, and the problem is that it is yet to be fully utilized. Current options for the recycling of recycled concrete fines are limited, and there is a lack of research related to this. Today, recycled concrete fines are typically dumped in landfill, which requires large areas and may cause environmental contamination through water and soil pollution. The recycling and utilization of recycled concrete fines could make a significant contribution to sustainable development and the environment. This thesis, examined the possibility of the utilization of the recycled concrete fines. The general aim was to produce artificial aggregates from different recycled concrete fines by granulation. The results of this thesis show that with suitable co-binders and curing methods, it is possible to produce artificial aggregates from recycled concrete fines that have comparable engineering properties as commercial lightweight aggregates. Most of the produced artificial aggregates can be classified as lightweight aggregates according to the EN 13055-1 standard. It was observed that the strength of the produced aggregates was highly dependent on their reactivity, particle size, and the different co-binders and curing methods used. The lightweight concrete produced from these artificial aggregates showed almost similar strength to lightweight concrete produced from commercial lightweight aggregate. Original papers Kursula, K., Perumal, P., Ohenoja, K., &amp; Illikainen, M. (2022). Production of artificial aggregates by granulation and carbonation of recycled concrete fines. Journal of Material Cycles and Waste Management, 24(6), 2141&ndash;2150. https://doi.org/10.1007/s10163-022-01457-y https://doi.org/10.1007/s10163-022-01457-y Self-archived version Moukannaa, S., Kursula, K., Perumal, P., Ohenoja, K., &amp; Illikainen, M. (2022). Recycling of precast concrete waste sludge with paper mill and biomass ashes for lightweight granulated aggregate production. Frontiers in Materials, 9, 877160. https://doi.org/10.3389/fmats.2022.877160 https://doi.org/10.3389/fmats.2022.877160 Self-archived version Kursula, K., Illikainen, M., &amp; Perumal, P. (2023). Recycling alkali activated slag into artificial aggregate: Influence of particle size distribution of the starting material on granulation. Low-Carbon Materials and Green Construction, 1(1), 28. https://doi.org/10.1007/s44242-023-00031-5 https://doi.org/10.1007/s44242-023-00031-5 Self-archived version Kursula, K., Mistri, A., Illikainen, M., &amp; Perumal, P. (2024). Utilization of fine concrete waste as a lightweight aggregate via granulation: Technical and environmental assessment. Journal of Cleaner Production, 434, 139938. https://doi.org/10.1016/j.jclepro.2023.139938 https://doi.org/10.1016/j.jclepro.2023.139938 Self-archived version Tiivistelmä Kaupungistuminen on johtanut viime vuosina moniin rakennus- ja purkuprojekteihin, joka on tuottanut valtavan määrän erilaista rakennus- ja purkujätettä. Näin ollen rakennus- ja purkujätteen kierrättämiselle ja ympäristöystävälliselle uudelleenkäytölle on kasvavaa kysyntää. Erityisesti betonijätteestä syntyvä hienoaines on haastavaa kierrättää ja ongelmana on, ettei sitä pystytä täysin hyödyntämään. Nykyiset vaihtoehdot jätebetonijauheen kierrättämiselle ovat vähäiset ja tutkimusta sen hyödyntämisestä on tehty vähän. Yleensä jätebetonin hienoaine on viety kaatopaikalle, mikä vaatii suuria maapinta-aloja ja on ympäristölle haitallista sillä se saattaa saastuttaa maaperää ja luonnonvesiä. Näin ollen jätebetonijauheen hyödyntämisellä olisi suuria etuja kestävän kehityksen ja ympäristön kannalta. Tässä väitöskirjassa tarkoituksena on tutkia jätebetonin hienoaineksen hyödyntämismahdollisuuksia. Erityinen tavoite oli tuottaa aggregaatteja erilaisista jätebetonijauheista rakeistusprosessin avulla. Väitöskirjan tulokset osoittavat, että sopivien sideaineiden ja kovetusmenetelmien avulla on mahdollista tuottaa jätebetonijauheesta aggregaatteja, joilla on vertailukelpoiset ominaisuudet kaupallisen kevytsoran kanssa. Suurin osa tuotetuista aggregaateista voidaan luokitella kevytsoraksi standardin EN 13055-1 mukaan. Tutkimuksessa havaittiin, että tuotettujen aggregaattien lujuus riippui suuresti käytetyn betonijauheen reaktiivisuudesta ja partikkelikoosta, sekä käytetystä sideaineesta ja kovetusmenetelmästä. Näillä aggregaateilla valmistettujen kevytbetonien lujuus oli vertailukelpoinen kaupallisella kevytsoralla valmistettuun betoniin. Osajulkaisut Kursula, K., Perumal, P., Ohenoja, K., &amp; Illikainen, M. (2022). Production of artificial aggregates by granulation and carbonation of recycled concrete fines. Journal of Material Cycles and Waste Management, 24(6), 2141&ndash;2150. https://doi.org/10.1007/s10163-022-01457-y https://doi.org/10.1007/s10163-022-01457-y Rinnakkaistallennettu versio Moukannaa, S., Kursula, K., Perumal, P., Ohenoja, K., &amp; Illikainen, M. (2022). Recycling of precast concrete waste sludge with paper mill and biomass ashes for lightweight granulated aggregate production. Frontiers in Materials, 9, 877160. https://doi.org/10.3389/fmats.2022.877160 https://doi.org/10.3389/fmats.2022.877160 Rinnakkaistallennettu versio Kursula, K., Illikainen, M., &amp; Perumal, P. (2023). Recycling alkali activated slag into artificial aggregate: Influence of particle size distribution of the starting material on granulation. Low-Carbon Materials and Green Construction, 1(1), 28. https://doi.org/10.1007/s44242-023-00031-5 https://doi.org/10.1007/s44242-023-00031-5 Rinnakkaistallennettu versio Kursula, K., Mistri, A., Illikainen, M., &amp; Perumal, P. (2024). Utilization of fine concrete waste as a lightweight aggregate via granulation: Technical and environmental assessment. Journal of Cleaner Production, 434, 139938. https://doi.org/10.1016/j.jclepro.2023.139938 https://doi.org/10.1016/j.jclepro.2023.139938 Rinnakkaistallennettu versio Academic dissertation to be presented with the assent of the Doctoral Programme Committee of Technology and Natural Sciences of the University of Oulu for public defence in the Arina auditorium (TA105), Linnanmaa, on 12 April 2024, at 12 noonAbstract In recent years, a large amount of construction and demolition waste has been generated by many demolition and construction projects because of fast urbanization. There is therefore a growing need for the sustainable management of construction waste and its recycling. The fine fraction of construction waste is especially challenging to reuse, and the problem is that it is yet to be fully utilized. Current options for the recycling of recycled concrete fines are limited, and there is a lack of research related to this. Today, recycled concrete fines are typically dumped in landfill, which requires large areas and may cause environmental contamination through water and soil pollution. The recycling and utilization of recycled concrete fines could make a significant contribution to sustainable development and the environment. This thesis, examined the possibility of the utilization of the recycled concrete fines. The general aim was to produce artificial aggregates from different recycled concrete fines by granulation. The results of this thesis show that with suitable co-binders and curing methods, it is possible to produce artificial aggregates from recycled concrete fines that have comparable engineering properties as commercial lightweight aggregates. Most of the produced artificial aggregates can be classified as lightweight aggregates according to the EN 13055-1 standard. It was observed that the strength of the produced aggregates was highly dependent on their reactivity, particle size, and the different co-binders and curing methods used. The lightweight concrete produced from these artificial aggregates showed almost similar strength to lightweight concrete produced from commercial lightweight aggregate.Tiivistelmä Kaupungistuminen on johtanut viime vuosina moniin rakennus- ja purkuprojekteihin, joka on tuottanut valtavan määrän erilaista rakennus- ja purkujätettä. Näin ollen rakennus- ja purkujätteen kierrättämiselle ja ympäristöystävälliselle uudelleenkäytölle on kasvavaa kysyntää. Erityisesti betonijätteestä syntyvä hienoaines on haastavaa kierrättää ja ongelmana on, ettei sitä pystytä täysin hyödyntämään. Nykyiset vaihtoehdot jätebetonijauheen kierrättämiselle ovat vähäiset ja tutkimusta sen hyödyntämisestä on tehty vähän. Yleensä jätebetonin hienoaine on viety kaatopaikalle, mikä vaatii suuria maapinta-aloja ja on ympäristölle haitallista sillä se saattaa saastuttaa maaperää ja luonnonvesiä. Näin ollen jätebetonijauheen hyödyntämisellä olisi suuria etuja kestävän kehityksen ja ympäristön kannalta. Tässä väitöskirjassa tarkoituksena on tutkia jätebetonin hienoaineksen hyödyntämismahdollisuuksia. Erityinen tavoite oli tuottaa aggregaatteja erilaisista jätebetonijauheista rakeistusprosessin avulla. Väitöskirjan tulokset osoittavat, että sopivien sideaineiden ja kovetusmenetelmien avulla on mahdollista tuottaa jätebetonijauheesta aggregaatteja, joilla on vertailukelpoiset ominaisuudet kaupallisen kevytsoran kanssa. Suurin osa tuotetuista aggregaateista voidaan luokitella kevytsoraksi standardin EN 13055-1 mukaan. Tutkimuksessa havaittiin, että tuotettujen aggregaattien lujuus riippui suuresti käytetyn betonijauheen reaktiivisuudesta ja partikkelikoosta, sekä käytetystä sideaineesta ja kovetusmenetelmästä. Näillä aggregaateilla valmistettujen kevytbetonien lujuus oli vertailukelpoinen kaupallisella kevytsoralla valmistettuun betoniin

Cytoplasmic domains of the myelin-associated glycoprotein

AbstractThe function of the vertebrate nervous system is based on the rapid and accurate transmission of electrical impulses. The myelin sheath is a lipid-rich membrane that envelops the axon, preventing the leakage of the nervous impulse to the environment. Myelin is formed when the plasma membrane of a myelinating glial cell differentiates and wraps around an axon. The compaction of myelin leads to the extrusion of most of the glial cell cytoplasm from the structure. Both the compact and noncompact regions of myelin carry distinct subsets of proteins.The myelin-associated glycoprotein (MAG) is present in noncompact myelin. It is a cell adhesion molecule expressed only by myelinating glial cells. Two isoforms of MAG, S- and L-MAG, exist, and these forms differ from each other only by their cytoplasmic domains. Until now, little information has been available on the differences between the MAG isoforms. This study was carried out in order to gain information on the cytoplasmic domains of S- and L-MAG.Significant differences were observed in the properties of the MAG cytoplasmic domains. An interaction between the L-MAG cytoplasmic domain and the S100b protein was characterised, and a role for this interaction was found in the regulation of L-MAG phosphorylation. Evidence was also obtained for the dimerisation of the L-MAG cytoplasmic domain. The S-MAG cytoplasmic domain bound zinc, which induced a change in the surface properties of the protein. The S-MAG cytoplasmic domain was also found to interact directly with tubulin, the core component of microtubules.In conclusion, this study has brought information on the functions of the MAG cytoplasmic domains. The results are complementary with ealier hypotheses on the roles of the MAG isoforms in myelinating glia. While the properties of L-MAG suggest a role as a signaling molecule, a dynamic structural role for S-MAG during myelin formation and maintenance can be envisaged.Academic Dissertation to be presented with the assent of the Faculty of Medicine, University of Oulu, for public discussion in the Auditorium of the Department of Pharmacology and Toxicology, on June 21st, 2000, at 12 noon.Abstract The function of the vertebrate nervous system is based on the rapid and accurate transmission of electrical impulses. The myelin sheath is a lipid-rich membrane that envelops the axon, preventing the leakage of the nervous impulse to the environment. Myelin is formed when the plasma membrane of a myelinating glial cell differentiates and wraps around an axon. The compaction of myelin leads to the extrusion of most of the glial cell cytoplasm from the structure. Both the compact and noncompact regions of myelin carry distinct subsets of proteins. The myelin-associated glycoprotein (MAG) is present in noncompact myelin. It is a cell adhesion molecule expressed only by myelinating glial cells. Two isoforms of MAG, S- and L-MAG, exist, and these forms differ from each other only by their cytoplasmic domains. Until now, little information has been available on the differences between the MAG isoforms. This study was carried out in order to gain information on the cytoplasmic domains of S- and L-MAG. Significant differences were observed in the properties of the MAG cytoplasmic domains. An interaction between the L-MAG cytoplasmic domain and the S100b protein was characterised, and a role for this interaction was found in the regulation of L-MAG phosphorylation. Evidence was also obtained for the dimerisation of the L-MAG cytoplasmic domain. The S-MAG cytoplasmic domain bound zinc, which induced a change in the surface properties of the protein. The S-MAG cytoplasmic domain was also found to interact directly with tubulin, the core component of microtubules. In conclusion, this study has brought information on the functions of the MAG cytoplasmic domains. The results are complementary with ealier hypotheses on the roles of the MAG isoforms in myelinating glia. While the properties of L-MAG suggest a role as a signaling molecule, a dynamic structural role for S-MAG during myelin formation and maintenance can be envisaged

A multistage antimalarial targets the plasmepsins IX and X essential for invasion and egress.

: Regulated exocytosis by secretory organelles is important for malaria parasite invasion and egress. Many parasite effector proteins, including perforins, adhesins, and proteases, are extensively proteolytically processed both pre- and postexocytosis. Here we report the multistage antiplasmodial activity of the aspartic protease inhibitor hydroxyl-ethyl-amine-based scaffold compound 49c. This scaffold inhibits the preexocytosis processing of several secreted rhoptry and microneme proteins by targeting the corresponding maturases plasmepsins IX (PMIX) and X (PMX), respectively. Conditional excision of PMIX revealed its crucial role in invasion, and recombinantly active PMIX and PMX cleave egress and invasion factors in a 49c-sensitive manner.<br/

Shanks — multidomain molecular scaffolds of the postsynaptic density

AbstractThe postsynaptic density (PSD) is a protein-rich assembly below the postsynaptic membrane, formed of large scaffolding proteins. These proteins carry a combination of protein interaction domains, which may interact with several alternative partners; the structure of the protein assembly can be regulated in an activity-dependent manner. A major scaffolding molecule in the PSD is Shank, a family of three main isoforms with highly similar domain structure. Proteins of the Shank family are targets of mutations in neurological disorders, such as autism and schizophrenia. All the predicted folded domains of Shank have now been crystallized. However, for an understanding of the structure and function of full-length Shank and its complexes in the supramolecular PSD assembly, novel complementary approaches and hybrid techniques must be employed.Abstract The postsynaptic density (PSD) is a protein-rich assembly below the postsynaptic membrane, formed of large scaffolding proteins. These proteins carry a combination of protein interaction domains, which may interact with several alternative partners; the structure of the protein assembly can be regulated in an activity-dependent manner. A major scaffolding molecule in the PSD is Shank, a family of three main isoforms with highly similar domain structure. Proteins of the Shank family are targets of mutations in neurological disorders, such as autism and schizophrenia. All the predicted folded domains of Shank have now been crystallized. However, for an understanding of the structure and function of full-length Shank and its complexes in the supramolecular PSD assembly, novel complementary approaches and hybrid techniques must be employed

SEM-EDS and PIXE analyses of Medieval glass from the museum Aboa Vetus in Turku

The scanning electron microscopy (SEM) with an energy-dispersive spectrometer (EDS) and the proton induced X-ray emission (PIXE) methods were used to determine the major, minor and trace elements in 54 fragments of medieval glass vessels from the museum Aboa vetus in Turku. The absolute concentrations of silicon, sodium, potassium, calcium, magnesium, aluminium, phosphorus, sulphur, chlorine, titanium, manganese, iron, copper, zinc, lead, arsenic, rubidium, strontium, zirconium and barium were measured. The possibilities of using analytical methods to reconstruct vessels and to obtain information on the origin of the glasses are discussed

Structural similarities and functional differences clarify evolutionary relationships between tRNA healing enzymes and the myelin enzyme CNPase

AbstractBackground: Eukaryotic tRNA splicing is an essential process in the transformation of a primary tRNA transcript into a mature functional tRNA molecule. 5′-phosphate ligation involves two steps: a healing reaction catalyzed by polynucleotide kinase (PNK) in association with cyclic phosphodiesterase (CPDase), and a sealing reaction catalyzed by an RNA ligase. The enzymes that catalyze tRNA healing in yeast and higher eukaryotes are homologous to the members of the 2H phosphoesterase superfamily, in particular to the vertebrate myelin enzyme 2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase).Results: We employed different biophysical and biochemical methods to elucidate the overall structural and functional features of the tRNA healing enzymes yeast Trl1 PNK/CPDase and lancelet PNK/CPDase and compared them with vertebrate CNPase. The yeast and the lancelet enzymes have cyclic phosphodiesterase and polynucleotide kinase activity, while vertebrate CNPase lacks PNK activity. In addition, we also show that the healing enzymes are structurally similar to the vertebrate CNPase by applying synchrotron radiation circular dichroism spectroscopy and small-angle X-ray scattering.Conclusions: We provide a structural analysis of the tRNA healing enzyme PNK and CPDase domains together. Our results support evolution of vertebrate CNPase from tRNA healing enzymes with a loss of function at its N-terminal PNK-like domain.Abstract Background: Eukaryotic tRNA splicing is an essential process in the transformation of a primary tRNA transcript into a mature functional tRNA molecule. 5′-phosphate ligation involves two steps: a healing reaction catalyzed by polynucleotide kinase (PNK) in association with cyclic phosphodiesterase (CPDase), and a sealing reaction catalyzed by an RNA ligase. The enzymes that catalyze tRNA healing in yeast and higher eukaryotes are homologous to the members of the 2H phosphoesterase superfamily, in particular to the vertebrate myelin enzyme 2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase). Results: We employed different biophysical and biochemical methods to elucidate the overall structural and functional features of the tRNA healing enzymes yeast Trl1 PNK/CPDase and lancelet PNK/CPDase and compared them with vertebrate CNPase. The yeast and the lancelet enzymes have cyclic phosphodiesterase and polynucleotide kinase activity, while vertebrate CNPase lacks PNK activity. In addition, we also show that the healing enzymes are structurally similar to the vertebrate CNPase by applying synchrotron radiation circular dichroism spectroscopy and small-angle X-ray scattering. Conclusions: We provide a structural analysis of the tRNA healing enzyme PNK and CPDase domains together. Our results support evolution of vertebrate CNPase from tRNA healing enzymes with a loss of function at its N-terminal PNK-like domain