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  • 1. Abelein, Axel
    et al.
    Lang, Lisa
    Lendel, Christofer
    Gräslund, Astrid
    Danielsson, Jens
    Transient small molecule interactions kinetically modulate amyloid β peptide self-assembly.2012In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 586, no 22, p. 3991-3995, article id S0014-5793(12)00757-0Article in journal (Refereed)
    Abstract [en]

    Small organic molecules, like Congo red and lacmoid, have been shown to modulate the self-assembly of the amyloid β peptide (Aβ). Here, we show that Aβ forms NMR invisible non-toxic co-aggregates together with lacmoid as well as Congo red. We find that the interaction involves two distinct kinetic processes and at every given time point only a small fraction of Aβ is in the co-aggregate. These weak transient interactions kinetically redirect the aggregation prone Aβ from self-assembling into amyloid fibrils. These findings suggest that even such weak binders might be effective as therapeutics against pathogenic protein aggregation.

  • 2.
    Arnling Bååth, Jenny
    et al.
    Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Giummarella, Nicola
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Wood Chemistry and Pulp Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Klaubauf, Sylvia
    Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Lawoko, Martin
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Wood Chemistry and Pulp Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Olsson, Lisbeth
    Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    A glucuronoyl esterase from Acremonium alcalophilum cleaves native lignin-carbohydrate ester bonds2016In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 590, no 16, p. 2611-2618Article in journal (Refereed)
    Abstract [en]

    The Glucuronoyl esterases (GE) have been proposed to target lignin-carbohydrate (LC) ester bonds between lignin moieties and glucuronic acid side groups of xylan, but to date, no direct observations of enzymatic cleavage on native LC ester bonds have been demonstrated. In the present investigation, LCC fractions from spruce and birch were treated with a recombinantly produced GE originating from Acremonium alcalophilum (AaGE1). A combination of size exclusion chromatography and 31P NMR analyses of phosphitylated LCC samples, before and after AaGE1 treatment provided the first evidence for cleavage of the LC ester linkages existing in wood.

  • 3. Hilden, L.
    et al.
    Johansson, G.
    Pettersson, G.
    Li, Jiebing
    KTH, Superseded Departments, Pulp and Paper Technology.
    Ljungquist, P.
    Henriksson, Gunnar
    KTH, Superseded Departments, Pulp and Paper Technology.
    Do the extracellular enzymes cellobiose dehydrogenase and manganese peroxidase form a pathway in lignin biodegradation?2000In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 477, no 02-jan, p. 79-83Article in journal (Refereed)
    Abstract [en]

    The extracellular enzyme manganese peroxidase is believed to degrade lignin by a hydrogen peroxide-dependent oxidation of Mn(II) to the reactive species Mn(III) that attacks the lignin, However, Mn(III) is not able to directly oxidise the non-phenolic lignin structures that predominate in native lignin, We show here that pretreatment of a non-phenolic lignin model compound with another extracellular fungal enzyme, cellobiose dehydrogenase, allows the manganese peroxidase system to oxidise this molecule. The mechanism behind this effect is demethoxylation and/or hydroxylation, i.e. conversion of a nonphenolic structure to a phenolic one, mediated by hydroxyl radicals generated by cellobiose dehydrogenase, This suggests that cellobiose dehydrogenase and manganese peroxidase may act in an extracellular pathway in fungal lignin biodegradation, Analytical techniques used in this paper are reverse-phase high-pressure liquid chromatography, gas chromatography connected to mass spectroscopy and UV-visible spectroscopy.

  • 4.
    Hober, Sophia
    et al.
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Lundström Ljung, J
    Uhlén, Mathias
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Nilsson, B
    Insulin-like growth factors I and II are unable to form and maintain their native disulfides under in vivo redox conditions.1999In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 443, no 3Article in journal (Refereed)
    Abstract [en]

    Insulin-like growth factor (IGF) I does not quantitatively form its three native disulfide bonds in the presence of 10 mM reduced and 1 mM oxidized glutathione in vitro [Hober, S. et al. (1992) Biochemistry 31, 1749-1756]. In this paper, we show (i) that both IGF-I and IGF-II are unable to form and maintain their native disulfide bonds at redox conditions that are similar to the situation in the secretory vesicles in vivo and (ii) that the presence of protein disulfide isomerase does not overcome this problem. The results indicate that the previously described thermodynamic disulfide exchange folding problem of IGF-I in vitro is also present in vivo. Speculatively, we suggest that the thermodynamic disulfide exchange properties of IGF-I and II are biologically significant for inactivation of the unbound growth factors by disulfide exchange reactions to generate variants destined for rapid clearance.

  • 5.
    Jansson, Magnus
    et al.
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Dixelius, J
    Uhlén, M
    Nilsson, B O
    Binding affinities of insulin-like growth factor-I (IGF-I) fusion proteins to IGF binding protein 1 and IGF-I receptor are not correlated with mitogenic activity.1997In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 416, no 3, p. 259-264Article in journal (Refereed)
    Abstract [en]

    In this report, comparisons between molecular affinities and cellular proliferation activities have been made for insulin-like growth factor-I (IGF-I) and two IGF-I fusion proteins in order to evaluate fusion proteins as tools for receptor binding studies. Binding affinities and growth promoting effects of the N-terminal fusion Z-IGF-I and the C-terminal fusion IGF-I-Z, and native recombinant human IGF-I, were analyzed. Binding kinetic properties of the three IGF-I variants were analyzed using BIAcore kinetic interaction analysis testing for binding to both human IGF binding protein 1 (IGFBP-1) and a soluble form of the human IGF type I receptor extracellular domains (sIGF-IR). The growth promoting effects on SaOS-2 human osteosarcoma cells of the different fusion proteins were analyzed. A comparison of receptor binding affinities and growth promoting effects shows that the fusion protein receptor affinity does not correlate with proliferative potential. The IGF-I-Z fusion, with the lowest receptor affinity, shows similar proliferative potential to native IGF-I. However, the Z-IGF-I fusion protein, with twice the receptor affinity of IGF-I-Z, displays only about 70% of the IGF-I-Z growth promoting activity. Both IGF-I fusion proteins possess similar affinity to IGFBP-1. These results indicate that determinants other than the receptor affinity could be involved in the regulation of IGF-I proliferative action. This study demonstrates that ligand fusion proteins may be useful to study mechanisms of ligand induced receptor activation.

  • 6.
    Käll, Lukas
    et al.
    Ctr. for Genomics and Bioinformatics, Karolinska Institutet.
    Sonnhammer, Erik L. L.
    Reliability of transmembrane predictions in whole-genome data2002In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 532, no 3, p. 415-418Article in journal (Refereed)
    Abstract [en]

    Transmembrane prediction methods are generally benchmarked on a set of proteins with experimentally verified topology. We have investigated if the accuracy measured on such datasets can be expected in an unbiased genomic analysis, or if there is a bias towards 'easily predictable' proteins in the benchmark datasets. As a measurement of accuracy, the concordance of the results from five different prediction methods was used (TMHMM, PHD, HMMTOP, MEMSAT, and TOPPRED). The benchmark dataset showed significantly higher levels (up to five times) of agreement between different methods than in 10 tested genomes. We have also analyzed which programs are most prone to make mispredictions by measuring the frequency of one-out-of-five disagreeing predictions.

  • 7. Lundin, Carolina
    et al.
    Käll, Lukas
    Stockholm Bioinformatics Center, AlbaNova.
    Kreher, Scott A.
    Kapp, Katja
    Sonnhammer, Erik L.
    Carlson, John R.
    Heijne, Gunnar von
    Nilsson, IngMarie
    Membrane topology of the Drosophila OR83b odorant receptor2007In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 581, no 29, p. 5601-5604Article in journal (Refereed)
    Abstract [en]

    By analogy to mammals, odorant receptors (ORs) in insects, such as Drosophila melanogaster, have long been thought to belong to the G-protein coupled receptor (GPCR) superfamily. However, recent work has cast doubt on this assumption and has tentatively suggested an inverted topology compared to the canonical N(out) - C(in) 7 transmembrane (TM) GPCR topology, at least for some Drosophila ORs. Here, we report a detailed topology mapping of the Drosophila OR83b receptor using engineered glycosylation sites as topology markers. Our results are inconsistent with a classical GPCR topology and show that OR83b has an intracellular N-terminus, an extracellular C-terminus, and 7TM helices.

  • 8.
    Löfblom, John
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Feldwisch, J.
    Tolmachev, V.
    Carlsson, J.
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Frejd, F. Y.
    Affibody molecules: Engineered proteins for therapeutic, diagnostic and biotechnological applications2010In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 584, no 12, p. 2670-2680Article, review/survey (Refereed)
    Abstract [en]

    Affibody molecules are a class of engineered affinity proteins with proven potential for therapeutic, diagnostic and biotechnological applications. Affibody molecules are small (6.5 kDa) single domain proteins that can be isolated for high affinity and specificity to any given protein target. Fifteen years after its discovery, the Affibody technology is gaining use in many groups as a tool for creating molecular specificity wherever a small, engineering compatible tool is warranted. Here we summarize recent results using this technology, propose an Affibody nomenclature and give an overview of different HER2-specific Affibody molecules. Cumulative evidence suggests that the three helical scaffold domain used as basis for these molecules is highly suited to create a molecular affinity handle for vastly different applications.

  • 9. RAICES, M
    et al.
    PAIFER, E
    CREMATA, J
    MONTESINO, R
    STAHLBERG, J
    DIVNE, Christina
    Uppsala University, Sweden.
    SZABO, IJ
    HENRIKSSON, G
    JOHANSSON, G
    PETTERSSON, G
    Cloning and characterization of a cDNA encoding a cellobiose dehydrogenase from the white rot fungus Phanerochaete chrysosporium1995In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 369, no 2-3, p. 233-238Article in journal (Refereed)
    Abstract [en]

    The cDNA of cellobiose dehydrogenase (CDH) from Phanerochaete chrysosporium has been cloned and sequenced. The 5′ end was obtained by PCR amplification. The cDNA contains 2310 translated bases excluding the poly(A) tail. The deduced mature protein contains 770 amino acid residues and is preceded by a 18 residue long signal peptide. The regions of the amino acid sequence corresponding to the heme and FAD domains of CDH were identified as well as the nucleotide-binding motif, the disulfide pairing and a methionine residue chelating the heme iron. No homologous sequences were found for the heme domain, however, the FAD domain appears to be distantly related to the GMC oxidoreductase family.

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