Browsing by Subject "NMR-SPECTROSCOPY"

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  • Pantsar, Tatu; Rissanen, Sami; Dauch, Daniel; Laitinen, Tuomo; Vattulainen, Ilpo; Poso, Antti (2018)
    A mutated KRAS protein is frequently observed in human cancers. Traditionally, the oncogenic properties of KRAS missense mutants at position 12 (G12X) have been considered as equal. Here, by assessing the probabilities of occurrence of all KRAS G12X mutations and KRAS dynamics we show that this assumption does not hold true. Instead, our findings revealed an outstanding mutational bias. We conducted a thorough mutational analysis of KRAS G12X mutations and assessed to what extent the observed mutation frequencies follow a random distribution. Unique tissue-specific frequencies are displayed with specific mutations, especially with G12R, which cannot be explained by random probabilities. To clarify the underlying causes for the nonrandom probabilities, we conducted extensive atomistic molecular dynamics simulations (170 its) to study the differences of G12X mutations on a molecular level. The simulations revealed an allosteric hydrophobic signaling network in KRAS, and that protein dynamics is altered among the G12X mutants and as such differs from the wild-type and is mutation-specific. The shift in long-timescale conformational dynamics was confirmed with Markov state modeling. A G12X mutation was found to modify KRAS dynamics in an allosteric way, which is especially manifested in the switch regions that are responsible for the effector protein binding. The findings provide a basis to understand better the oncogenic properties of KRAS G12X mutants and the consequences of the observed nonrandom frequencies of specific G12X mutations.
  • Borrega, Marc; Larsson, Per Tomas; Ahvenainen, Patrik; Ceccherini, Sara; Maloney, Thaddeus; Rautkari, Lauri; Sixta, Herbert (2018)
    Hydrothermal treatments of birch wood and kraft pulp were compared for their ability to extract the xylan and produce viscose-grade pulp. Water post-hydrolysis of kraft pulp produced a high-purity cellulosic pulp with lower viscosity but higher cellulose yield than traditional pre-hydrolysis kraft pulping of wood. Post-hydrolysis of pulp also increased the crystallite dimensions and degree of crystallinity in cellulose, and promoted a higher extent of fibril aggregation. The lower specific surface area in post-hydrolyzed pulps, derived from their larger fibril aggregates, decreased the accessibility of OH groups. However, this lower accessibility did not seem to decrease the pulp reactivity to derivatizing chemicals. In the aqueous side-stream, the xylose yield was similar in both pre- and post-hydrolysates, although conducting post-hydrolysis of pulp in a flow-through system enabled the recovery of high purity and molar mass (∼10 kDa) xylan for high-value applications.
  • Virtanen, Salla; Kiirikki, Anne M.; Mikula, Kornelia M.; Iwai, Hideo; Ollila, O. H. Samuli (2020)
    Importance of disordered protein regions is increasingly recognized in biology, but their characterization remains challenging due to the lack of suitable experimental and theoretical methods. NMR experiments can detect multiple timescale dynamics and structural details of disordered protein regions, but their detailed interpretation is often difficult. Here we combine protein backbone(15)N spin relaxation data with molecular dynamics (MD) simulations to detect not only heterogeneous dynamics of large partially disordered proteins but also their conformational ensembles. We observed that the rotational dynamics of folded regions in partially disordered proteins is dominated by similar rigid body rotation as in globular proteins, thereby being largely independent of flexible disordered linkers. Disordered regions, on the other hand, exhibit complex rotational motions with multiple timescales below similar to 30 ns which are difficult to detect from experimental data alone, but can be captured by MD simulations. Combining MD simulations and backbone(15)N spin relaxation data, measured applying segmental isotopic labeling with salt-inducible split intein, we resolved the conformational ensemble and dynamics of partially disordered periplasmic domain of TonB protein fromHelicobacter pyloricontaining 250 residues. To demonstrate the universality of our approach, it was applied also to the partially disordered region of chicken Engrailed 2. Our results pave the way in understanding how TonB transfers energy from inner membrane to the outer membrane receptors in Gram-negative bacteria, as well as the function of other proteins with disordered domains.
  • Pawar, Prashant Mohan-Anupama; Derba-Maceluch, Marta; Chong, Sun-Li; Gandla, Madhavi Latha; Bashar, Shamrat Shafiul; Sparrman, Tobias; Ahvenainen, Patrik; Hedenström, Mattias; Ozparpucu, Merve; Ruggeberg, Markus; Serimaa, Ritva; Lawoko, Martin; Tenkanen, Maija; Jönsson, Leif J.; Mellerowicz, Ewa J. (2017)
    Background: Lignocellulose from fast growing hardwood species is a preferred source of polysaccharides for advanced biofuels and "green" chemicals. However, the extensive acetylation of hardwood xylan hinders lignocellulose saccharification by obstructing enzymatic xylan hydrolysis and causing inhibitory acetic acid concentrations during microbial sugar fermentation. To optimize lignocellulose for cost-effective saccharification and biofuel production, an acetyl xylan esterase AnAXE1 from Aspergillus niger was introduced into aspen and targeted to cell walls. Results: AnAXE1-expressing plants exhibited reduced xylan acetylation and grew normally. Without pretreatment, their lignocellulose yielded over 25% more glucose per unit mass of wood (dry weight) than wild-type plants. Glucose yields were less improved (+7%) after acid pretreatment, which hydrolyses xylan. The results indicate that AnAXE1 expression also reduced the molecular weight of xylan, and xylan-lignin complexes and/or lignin co-extracted with xylan, increased cellulose crystallinity, altered the lignin composition, reducing its syringyl to guaiacyl ratio, and increased lignin solubility in dioxane and hot water. Lignin-associated carbohydrates became enriched in xylose residues, indicating a higher content of xylo-oligosaccharides. Conclusions: This work revealed several changes in plant cell walls caused by deacetylation of xylan. We propose that deacetylated xylan is partially hydrolyzed in the cell walls, liberating xylo-oligosaccharides and their associated lignin oligomers from the cell wall network. Deacetylating xylan thus not only increases its susceptibility to hydrolytic enzymes during saccharification but also changes the cell wall architecture, increasing the extractability of lignin and xylan and facilitating saccharification.
  • Steringer, Julia P.; Lange, Sascha; Cujova, Sabina; Sachi, Radek; Poojari, Chetan; Lolicato, Fabio; Beutel, Oliver; Mueller, Hans-Michael; Unger, Sebastian; Coskun, Uenal; Honigmann, Alf; Vattulainen, Ilpo; Hof, Martin; Freund, Christian; Nickel, Walter (2017)
    FGF2 is secreted from cells by an unconventional secretory pathway. This process is mediated by direct translocation across the plasma membrane. Here, we define the minimal molecular machinery required for FGF2 membrane translocation in a fully reconstituted inside-out vesicle system. FGF2 membrane translocation is thermodynamically driven by PI(4,5)P-2-induced membrane insertion of FGF2 oligomers. The latter serve as dynamic translocation intermediates of FGF2 with a subunit number in the range of 8-12 FGF2 molecules. Vectorial translocation of FGF2 across the membrane is governed by sequential and mutually exclusive interactions with PI(4,5)P-2 and heparan sulfates on opposing sides of the membrane. Based on atomistic molecular dynamics simulations, we propose a mechanism that drives PI(4,5)P-2 dependent oligomerization of FGF2. Our combined findings establish a novel type of self-sustained protein translocation across membranes revealing the molecular basis of the unconventional secretory pathway of FGF2.
  • Norppa, Antto J.; Kauppala, Tuuli M.; Heikkinen, Harri A.; Verma, Bhupendra; Iwai, Hideo; Frilander, Mikko J. (2018)
    Mutations in the components of the minor spliceosome underlie several human diseases. A subset of patients with isolated growth hormone deficiency (IGHD) harbors mutations in the RNPC3 gene, which encodes the minor spliceosome-specific U11/U12-65K protein. Although a previous study showed that IGHD patient cells have defects in U12-type intron recognition, the biochemical effects of these mutations on the 65K protein have not been characterized. Here, we show that a proline-to-threonine missense mutation (P474T) and a nonsense mutation (R502X) in the C-terminal RNA recognition motif (C-RRM) of the 65K protein impair the binding of 65K to U12 and U6atac snRNAs. We further show that the nonsense allele is targeted to the nonsense-mediated decay (NMD) pathway, but in an isoform-specific manner, with the nuclear-retained 65K long-3'UTR isoform escaping the NMD pathway. In contrast, the missense P474T mutation leads, in addition to the RNA-binding defect, to a partial defect in the folding of the C-RRM and reduced stability of the full-length protein, thus reducing the formation of U11/U12 di-snRNP complexes. We propose that both the C-RRM folding defect and NMD-mediated decrease in the levels of the U11/U12-65K protein reduce formation of the U12-type intron recognition complex and missplicing of a subset of minor introns leading to pituitary hypoplasia and a subsequent defect in growth hormone secretion.
  • Bautista, Godofredo; Pfisterer, Simon G.; Huttunen, Mikko J.; Ranjan, Sanjeev; Kanerva, Kristiina; Ikonen, Elina; Kauranen, Martti (2014)
  • Taboada-Puig, Roberto; Lu-Chau, Thelmo A.; Moreira, Maria T.; Feijoo, Gumersindo; Lema, Juan M.; Fagerstedt, Kurt; Ohra-Aho, Taina; Liitia, Tiina; Heikkinen, Harri; Ropponen, Jarmo; Tamminen, Tarja (2018)
    The objective of this study was to evaluate the ability of one versatile peroxidase and the biocatalytically generated complex Mn(III)-malonate to polymerize coniferyl alcohol (CA) to obtain dehydrogenation polymers (DHPs) and to characterize how closely the structures of the formed DHPs resemble native lignin. Hydrogen peroxide was used as oxidant and Mn2+ as mediator. Based on the yields of the polymerized product, it was concluded that the enzymatic reaction should be performed in aqueous solution without organic solvents at 4.5pH6.0 and with 0.75H(2)O(2):CA ratio1. The results obtained from the Mn3+-malonate-mediated polymerization showed that the yield was almost 100%. Reaction conditions had, however, effect on the structures of the formed DHPs, as detected by size exclusion chromatography and pyrolysis-GC/MS. It can be concluded that from the structural point of view, the optimal pH for DHP formation using the presently studied system was 3 or 4.5. Low H2O2/CA ratio was beneficial to avoid oxidative side reactions. However, the high frequency of - linkages in all cases points to dimer formation between monomeric CA rather than endwise polymerization. (c) 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:81-90, 2018
  • Stepanek, Petr; Coriani, Sonia; Sundholm, Dage; Ovchinnikov, Vasily A.; Vaara, Juha (2017)
    The recently theoretically described nuclear spin-induced circular dichroism (NSCD) is a promising method for the optical detection of nuclear magnetization. NSCD involves both optical excitations of the molecule and hyperfine interactions and, thus, it offers a means to realize a spectroscopy with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine). The NSCD signal correlates with the spatial distribution of the excited states and couplings between them, reflecting changes in molecular structure and conformation. This constitutes a marked difference to the nuclear magnetic resonance (NMR) chemical shift, which only reflects the local molecular structure in the ground electronic state. The calculated NSCD spectra are rationalized by means of changes in the electronic density and by a sum-over-states approach, which allows to identify the contributions of the individual excited states. Two separate contributions to NSCD are identified and their physical origins and relative magnitudes are discussed. The results underline NSCD spectroscopy as a plausible tool with a power for the identification of not only different molecules, but their specific structures as well.
  • Khanjani, Pegah; King, Alistair W. T.; Part, Gabriel J.; Johansson, Leena-Sisko; Kostiainen, Mauri A.; Ras, Robin H. A. (2018)
    The development of economically and ecologically viable strategies for sup erhydrophobization offers a vast variety of interesting applications in self-cleaning surfaces. Examples include packaging materials, textiles, outdoor clothing, and microfluidic devices. In this work, we produced superhydrophobic paper by spin-coating a dispersion of nanostructured fluorinated cellulose esters. Modification of cellulose nanocrystals was accomplished using 2H,2H,3H,3H-perfluorononanoyl chloride and 2H,2H,3H,3H-perfluoroundecanoyl chloride, which are well-known for their ability to reduce surface energy. A stable dispersion of nanospherical fluorinated cellulose ester was obtained by using the nanoprecipitation technique. The hydrophobized fluorinated cellulose esters were characterized by both solid- and liquid-state nuclear magnetic resonance, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and contact angle measurements. Further, we investigated the size, shape, and structure morphology of nanostructured fluorinated cellulose esters by dynamic light scattering, scanning electron microscopy, and X-ray diffraction measurements.
  • Laaksonen, Tiina; Helminen, Jussi K. J.; Lemetti, Laura; Långbacka, Jesper; del Cerro, Daniel Rico; Hummel, Michael; Filpponen, Ilari; Rantamaki, Antti H.; Kakko, Tia; Kemell, Marianna L.; Wiedmer, Susanne K.; Heikkinen, Sami; Kilpeläinen, Ilkka; King, Alistair W. T. (2017)
    Ionic liquids are used to dewater a suspension of birch Kraft pulp cellulose nanofibrils (CNF) and as a medium for water-free topochemical modification of the nanocellulose (a process denoted as "WtF-Nano"). Acetylation was applied as a model reaction to investigate the degree of modification and scope of effective ionic liquid structures. Little difference in reactivity was observed when water was removed, after introduction of an ionic liquid or molecular co-solvent. However, the viscoelastic properties of the CNF suspended in two ionic liquids show that the more basic, but non-dissolving ionic liquid, allows for better solvation of the CNF. Vibrio fischeri bacterial tests show that all ionic liquids in this study were harmless. Scanning electron microscopy and wide-angle X-ray scattering on regenerated samples show that the acetylated CNF is still in a fibrillar form. 1D and 2D NMR analyses, after direct dissolution in a novel ionic liquid electrolyte solution, indicate that both cellulose and residual xylan on the surface of the nanofibrils reacts to give acetate esters.