Browsing by Subject "RESIDUES"

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  • Zhou, Kecheng; Dichlberger, Andrea; Martinez-Seara, Hector; Nyholm, Thomas K. M.; Li, Shiqian; Kim, Young Ah; Vattulainen, Ilpo; Ikonen, Elina; Blom, Tomas (2018)
    Membrane proteins are functionally regulated by the composition of the surrounding lipid bilayer. The late endosomal compartment is a central site for the generation of ceramide, a bioactive sphingolipid, which regulates responses to cell stress. The molecular interactions between ceramide and late endosomal transmembrane proteins are unknown. Here, we uncover in atomistic detail the ceramide interaction of Lysosome Associated Protein Transmembrane 4B (LAPTM4B), implicated in ceramide-dependent cell death and autophagy, and its functional relevance in lysosomal nutrient signaling. The ceramide-mediated regulation of LAPTM4B depends on a sphingolipid interaction motif and an adjacent aspartate residue in the protein's third transmembrane (TM3) helix. The interaction motif provides the preferred contact points for ceramide while the neighboring membrane-embedded acidic residue confers flexibility that is subject to ceramide-induced conformational changes, reducing TM3 bending. This facilitates the interaction between LAPTM4B and the amino acid transporter heavy chain 4F2hc, thereby controlling mTORC signaling. These findings provide mechanistic insights into how transmembrane proteins sense and respond to ceramide.
  • Lassfolk, Robert; Rahkila, Jani; Johansson, Mikael Peter; Ekholm, Filip Sebastian; Wärnå, Johan; Leino, Reko (2019)
    Acetylated oligosaccharides are common in nature. While they are involved in several biochemical and biological processes, the role of the acetyl groups and the complexity of their migration has largely gone unnoticed. In this work, by combination of organic synthesis, NMR spectroscopy and quantum chemical modeling, we show that acetyl group migration is a much more complex phenomenon than previously known. By use of synthetic oligomannoside model compounds, we demonstrate, for the first time, that the migration of acetyl groups in oligosaccharides and polysaccharides may not be limited to transfer within a single monosaccharide moiety, but may also involve migration over a glycosidic bond between two different saccharide units. The observed phenomenon is not only interesting from the chemical point of view, but it also raises new questions about the potential biological role of acylated carbohydrates in nature.
  • Morais de Carvalho, Danila; Lahtinen, Maarit; Bhattarai, Mamata; Lawoko, Martin; Mikkonen, Kirsi S. (2021)
    Hemicellulose-rich wood extracts show efficient capacity to adsorb at emulsion interfaces and stabilize them. Their functionality is enhanced by lignin moieties accompanying the hemicellulose structures, in the form of lignin-carbohydrate complexes (LCCs) and, potentially, other non-covalent associations. The formation and stability of emulsions is determined by their interfacial regions. These are largely unexplored assemblies when formed from natural stabilizers with a complex chemical composition. Understanding the structure of the interfacial region could facilitate both designing the extraction processes of abundant biomasses and unraveling a valuable industrial application potential for the extracts. Herein, we characterized the LCCs from the interface of oil-in-water emulsions stabilized by galactoglucomannan (GGM) or glucuronoxylan (GX)-rich wood extracts, using two-dimensional nuclear magnetic resonance (NMR) spectroscopy analysis. The type of covalent linkage between residual lignin and hemicelluloses determined their partitioning between the continuous and interfacial emulsion phases. Benzylether structures, only found in the interface, were suggested to participate in the physical stabilization of the emulsion droplets. In turn, the phenylglycosides, preferentially observed in the continuous phase, were suggested to interact with adsorbed stabilizers by electrostatic interaction. More hydrophobic lignin structures, such as guaiacyl lignin type, dibenzodioxocin substructures, and certain end groups also contributed to droplet stabilization. The elucidation of such attributes is of paramount importance for the biorefinery industry, enabling the optimization of extraction processes for the preparation of wood-based stabilizers and designed interfaces for novel and sustainable emulsion systems.
  • Kilpeläinen, A.; Strandman, H.; Grönholm, T.; Ikonen, V. -P.; Torssonen, P.; Kellomaki, S.; Peltola, H. (2017)
    We investigated how the initial age structure of a managed, middle boreal (62A degrees N), Norway spruce-dominated (Picea abies L. Karst.) forest area affects the net climate impact of using forest biomass for energy. The model-based analysis used a gap-type forest ecosystem model linked to a life cycle assessment (LCA) tool. The net climate impact of energy biomass refers to the difference in annual net CO2 exchange between the biosystem using forest biomass (logging residues from final felling) and the fossil (reference) system using coal. In the simulations over the 80-year period, the alternative initial age structures of the forest areas were (i) skewed to the right (dominated by young stands), (ii) normally distributed (dominated by middle-aged stands), (iii) skewed to the left (dominated by mature stands), and (iv) evenly distributed (same share of different age classes). The effects of management on net climate impacts were studied using current recommendations as a baseline with a fixed rotation period of 80 years. In alternative management scenarios, the volume of the growing stock was maintained 20% higher over the rotation compared to the baseline, and/or nitrogen fertilization was used to enhance carbon sequestration. According to the results, the initial age structure of the forest area affected largely the net climate impact of using energy biomass over time. An initially right-skewed age structure produced the highest climate benefits over the 80-year simulation period, in contrast to the left-skewed age structure. Furthermore, management that enhanced carbon sequestration increased the potential of energy biomass to replace coal, reducing CO2 emissions and enhancing climate change mitigation.
  • Muurinen, Johanna; Pasupulate, Avinash; Lappalainen, Juha; Virta, Marko (2019)
    Whole-cell bioreporters are living organisms and thus using them for detecting environmental contaminants would reflect biological effects of these pollutants. However, bioreporters are not widely used in field studies. Many of the bioreporter field protocols are suitable for liquid samples or include pipetting steps, which is a demanding task outside the laboratory. We present a bioreporter protocol without pipetting or sample type requirements. The protocol utilizes polyester swabs, commonly used in cleanroom technology. As an example contaminant, we used tetracycline and generated test samples with known concentrations up to the maximum tetracycline residue limit of milk set by the European Union (EU) regulation. The matrices of the test samples were Milli-Q water, milk and soil. The swabs were first dipped in the bioreporter cell cultures and then to test samples and luminescence was measured after incubation. The standard deviation of measurements from ten replicate swabs was in the same range as commonly in pipetting protocols (4-19%). The test samples with lowest tetracycline concentration (5 ng mL(-1)) were distinguished from the control samples (0 ng mL(-1) tetracycline). Our results show that swabs can be used together with luminescent whole cell bioreporters, making it possible to conduct the measurements in field conditions.
  • Perez-Loureiro, D.; Benlliure, J.; Diaz-Cortes, J.; Rodriguez-Sanchez, J. L.; Alvarez-Pol, H.; Blank, B.; Casarejos, E.; Dragosavac, D.; Foehr, C.; Gascon, M.; Gawlikowicz, W.; Heinz, A.; Helariutta, K.; Kelic-Heil, A.; Lukic, S.; Montes, F.; Pienkowski, L.; Schmidt, K-H; Staniou, M.; Subotic, K.; Suemmerer, K.; Taieb, J.; Trzcinska, A. (2019)
    The production cross sections of neutron-rich fission residues in reactions induced by U-238 projectiles at 950A MeV impinging on Pb and Be targets are investigated at the Fragment Separator at GSI. These two targets allow us to investigate fission processes induced by two reaction mechanisms, Coulomb and nuclear excitations, and to study the role of these mechanisms in the neutron excess of the final fragments.
  • Haapanen, Outi; Sharma, Vivek (2021)
    Respiratory complex I is a key enzyme in the electron transport chains of mitochondria and bacteria. It transfers two electrons to quinone and couples this redox reaction to proton pumping to electrically charge the membrane it is embedded in. The charge and pH gradient across the membrane drives the synthesis of ATP. The redox reaction and proton pumping in complex I are separated in space and time, which raises the question of how the two reactions are coupled so efficiently. Here, we focus on the unique similar to 35 angstrom long tunnel of complex I, which houses the binding site of quinone reduction. We discuss the redox and protonation reactions that occur in this tunnel and how they influence the dynamics of protein and substrate. On the basis of recent structural data and results from molecular simulations, we review how quinone reduction and dynamics may be coupled to proton pumping in complex I.
  • Stepanenko, Olesya V.; Stepanenko, Olga V.; Bublikov, G. S.; Kuznetsova, I. M.; Verkhusha, Vladislav; Turoverov, K. K. (2017)
    Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes and their mutants with different location of Cys residues, which able to bind a biliverdin chromophore, or without these Cys residues were studied using intrinsic tryptophan fluorescence, NIR fluorescence and circular dichroism. It was shown that a covalent binding of the biliverdin chromophore to a Cys residue via thioether group substantially stabilizes the spatial structure of NIR FPs. The stability of the protein structure and the chromophore association strength strongly depends on the location of Cys residues and decreases in the following order: a protein with Cys residues in both domains, a protein with Cys in PAS domains, and a protein with Cys in GAF domains. NIR FPs without Cys residues capable to covalently attach biliverdin have the lowest stability, comparable to NIR FP apoforms. (C) 2016 Elsevier B.V. All rights reserved.