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  • 1. Babrzadeh, F.
    et al.
    Varghese, V.
    Pacold, M.
    Liu, T. F.
    Nyrén, Pål
    KTH, School of Biotechnology (BIO), Biochemistry.
    Schiffer, C.
    Fessel, W. J.
    Shafer, R. W.
    Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance2013In: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 68, no 2, p. 414-418Article in journal (Refereed)
    Abstract [en]

    Objectives: To determine whether pan-protease inhibitor (PI)-resistant virus populations are composed predominantly of viruses with resistance to all PIs or of diverse virus populations with resistance to different subsets of PIs. Methods: We performed deep sequencing of plasma virus samples from nine patients with high-level genotypic and/or phenotypic resistance to all licensed PIs. The nine virus samples had a median of 12 PI resistance mutations by direct PCR Sanger sequencing. Results: For each of the nine virus samples, deep sequencing showed that each of the individual viruses within a sample contained nearly all of the mutations detected by Sanger sequencing. Indeed, a median of 94.9% of deep sequence reads had each of the PI resistance mutations present as a single chromatographic peak in the Sanger sequence. A median of 5.0% of reads had all but one of the Sanger mutations that were not part of an electrophoretic mixture. Conclusions: The collinearity of PI resistance mutations in the nine virus samples demonstrated that pan-PI-resistant viruses are able to replicate in vivo despite their highly mutated protease enzymes. We hypothesize that the marked collinearity of PI resistance mutations in pan-PI-resistant virus populations results from the unique requirements for multi-PI resistance and the extensive cross-resistance conferred by many of the accessory PI resistance mutations.

  • 2. Babrzadeh, Farbod
    et al.
    Jalili, Roxana
    Wang, Chunlin
    Shokralla, Shadi
    Pierce, Sarah
    Robinson-Mosher, Avi
    Nyrén, Pål
    KTH, School of Biotechnology (BIO), Biochemistry.
    Shafer, Robert W.
    Basso, Luiz C.
    de Amorim, Henrique V.
    de Oliveira, Antonio J.
    Davis, Ronald W.
    Ronaghi, Mostafa
    Gharizadeh, Baback
    Stambuk, Boris U.
    Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-12012In: Molecular Genetics and Genomics, ISSN 1617-4615, E-ISSN 1617-4623, Vol. 287, no 6, p. 485-494Article in journal (Refereed)
    Abstract [en]

    The Saccharomyces cerevisiae strains widely used for industrial fuel-ethanol production have been developed by selection, but their underlying beneficial genetic polymorphisms remain unknown. Here, we report the draft whole-genome sequence of the S. cerevisiae strain CAT-1, which is a dominant fuel-ethanol fermentative strain from the sugarcane industry in Brazil. Our results indicate that strain CAT-1 is a highly heterozygous diploid yeast strain, and the similar to 12-Mb genome of CAT-1, when compared with the reference S228c genome, contains similar to 36,000 homozygous and similar to 30,000 heterozygous single nucleotide polymorphisms, exhibiting an uneven distribution among chromosomes due to large genomic regions of loss of heterozygosity (LOH). In total, 58 % of the 6,652 predicted protein-coding genes of the CAT-1 genome constitute different alleles when compared with the genes present in the reference S288c genome. The CAT-1 genome contains a reduced number of transposable elements, as well as several gene deletions and duplications, especially at telomeric regions, some correlated with several of the physiological characteristics of this industrial fuel-ethanol strain. Phylogenetic analyses revealed that some genes were likely associated with traits important for bioethanol production. Identifying and characterizing the allelic variations controlling traits relevant to industrial fermentation should provide the basis for a forward genetics approach for developing better fermenting yeast strains.

  • 3.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Asymmetric Organic Synthesis with Enzymes: Edited by Vicente Gotor, Ignacio Alfonso and Eduardo Garcia-Urdiales2008In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 47, no 35, p. 6514-6515Article, book review (Other academic)
  • 4.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    BIO-AMINES: Searching for a Novel Approach to Biocatalytic Transaminations – a Vinnova Sponsored Project2009In: Book of abstracts, 2009Conference paper (Other academic)
  • 5.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Biocatalysis with Promiscuous Enzymes2007In: 2007 European BioPerspectives / [ed] Dechema, 2007Conference paper (Refereed)
  • 6.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Enzyme Catalytic Promiscuity and Rational Design2006In: Book of abstracts, 2006Conference paper (Refereed)
  • 7.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Enzymes Engineered for New Reactions - Novel Catalysts for Organic Synthesis2005In: Enzyme Technology / [ed] Pandey, A.; Webb, C.; Soccol, C. R.; Larroche, C., New Delhi: AsiaTech Publishers , 2005, p. 175-188Chapter in book (Refereed)
  • 8.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hydrolases in Organic Synthesis: Regio- and Stereoselective Biotransformation: By Uwe T. Bornscheuer and Romas J. Kazlauskas2006In: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 7, no 8, p. 1280-Article, book review (Other academic)
  • 9.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    omega-Transaminases: Tailored for Chiral Amine Synthesis2010In: Biocat2010 / [ed] Ralf Grote, Garabed Antranikian, Hamburg, Germany: TuTech Verlag , 2010Conference paper (Refereed)
  • 10.
    Berglund, Per
    et al.
    KTH, Superseded Departments, Biotechnology.
    Branneby, Cecilia
    Svedendahl Humble, Maria
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Carlqvist, Peter
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Magnusson, Anders
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Aldol and Michael additions catalyzed by a rationally redesigned hydrolytic enzyme2003In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 226, no 2, p. U155-U156Article in journal (Refereed)
  • 11.
    Berglund, Per
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Christiernin, M.
    Hedenström, E.
    Enantiorecognition of chiral acids by Candida rugosa lipase: Two substrate binding modes evidenced in an organic medium2001In: American Chemical Society Symposium Series (ACS), ISSN 0097-6156, E-ISSN 1947-5918, Vol. 776, p. 263-273Article in journal (Refereed)
    Abstract [en]

    We have identified the existence of different modes of binding the enantiomers of 2-methyl-branched carboxylic acids to a lipase active site by rational substrate engineering. Similar to hydrolysis, previously investigated, we have now evidence for differential binding modes in the Candida rugosa lipase-catalyzed esterifications in cyclohexane. The relevance of considering two different binding modes to understand lipase enantiorecognition is demonstrated by introducing bulky substituents on a chiral carboxylic acid which impose a different orientation of the substrate acyl chain in the active site of Candida rugosa lipase. With this substrate engineering approach based on molecular modeling it is thus possible to markedly alter the enantioselectivity of the lipase. Examples from hydrolysis and new results from esterifications in an organic solvent are presented and discussed.

  • 12.
    Berglund, Per
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hedenström, Erik
    Mid Sweden university.
    Preparation of 2-, 3-, and 4-methylcarboxylic acids and the corresponding alcohols of high enantiopurity by lipase-catalyzed esterification2001In: Enzymes in Nonaqueous Solvents: Methods and Protocols / [ed] Vulfson, E. N.; Halling, P. J.; Holland, H. L., Totowa: Humana Press , 2001, p. 307-317Chapter in book (Refereed)
  • 13.
    Berglund, Per
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Holmquist, M.
    Hult, K.
    Reversed enantiopreference of Candida rugosa lipase supports different modes of binding enantiomers of a chiral acyl donor1998In: Journal of Molecular Catalysis - B Enzymatic, ISSN 13811177 (ISSN), Vol. 5, no 1-4, p. 283-287Article in journal (Refereed)
    Abstract [en]

    Molecular modelling identifies two different productive modes of binding the enantiomers of a 2-methyldecanoic acid ester to the active site of Candida rugosa lipase (CRL). The fast reacting S-enantiomer occupies the previously identified acyl-binding tunnel of the enzyme, whereas the R- enantiomer leaves the tunnel empty. The modelling suggested that if both enantiomers were forced to bind to the active site leaving the tunnel empty, the enzyme would reverse its enantiopreference to become R-enantioselective. To test this hypothesis, we designed a structural analogue to 2- methyldecanoic acid, 2-methyl-6-(2-thienyl)hexanoic acid, which was expected to be too bulky to fit its acyl moiety into the acyl-binding tunnel. The CRL- catalysed hydrolysis of the ethyl ester of this substrate resulted in the preferential conversion of the R-enantiomer as predicted by molecular modelling. This represents the first kinetic evidence supporting the existence of two different modes of binding the enantiomers of a 2- methyldecanoic acid ester to the active site of CRL. We have shown that a rational 3D based approach in combination with substrate engineering can be used to predict and control the stereochemical outcome of a lipase catalysed reaction.

  • 14.
    Berglund, Per
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Biocatalytic synthesis of enantiopure compounds using lipases: Chapter 212000In: Stereoselective Biocatalysis / [ed] Patel, R. N., New York: Marcel Dekker, 2000, p. 633-657Chapter in book (Refereed)
  • 15.
    Berglund, Per
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Högfeldt, Anna-Karin
    KTH, School of Education and Communication in Engineering Science (ECE), Learning.
    Karlsson, Sara
    KTH.
    Klasén, Ida
    KTH, School of Education and Communication in Engineering Science (ECE).
    Sandberg, Teresia
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Wood Chemistry and Pulp Technology.
    Utvärdering för utveckling: KTH:s samtliga utbildningar under belysning2011Conference paper (Other academic)
  • 16.
    Berglund, Per
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Park, S.
    Strategies for altering enzyme reaction specificity for applied biocatalysis2005In: Current organic chemistry, ISSN 1385-2728, E-ISSN 1875-5348, Vol. 9, no 4, p. 325-336Article in journal (Refereed)
    Abstract [en]

    The fact that many enzymes have broad substrate specificity has been a property, of fundamental importance for the widespread applications of enzymes in synthetic chemistry. Many enzymes can, in addition, catalyze completely different reactions compared to their natural ones. The possibility of using molecular biology techniques to control Such catalytic plasticity of enzymes in order to establish completely new reaction specificity in the active site is the topic for this review. The examples are subdivided according to six different approaches used (i - vi) for engineering of the reaction specificity. The first approach (i) is the random method of directed evolution to achieve new reaction specificity. Other approaches involve strategies where tire reaction specificity of a known enzyme is implemented into another, closely related, enzyme by substituting key amino acid residues selected either by (ii) sequence or (iii) structural overlap of the two enzymes. Yet other approaches involve substitution of key amino acid residues to introduce new reaction specificity without comparing with a template enzyme (iv) and the introduction of a complete catalytic machinery (v). The final approach is the introduction of an active site into a non-catalytic protein (vi). These six different approaches for altering the reaction chemistry of enzymes each represent a powerful tool for controlling the catalytic plasticity or enzymes. The prospect for these altered enzymes as catalysts in synthetic chemistry is very large although examples of practical use are rare and still challenging. The progress in the area of altering enzyme reaction specificity will result in a Continued development towards the goal of creating tailor-made enzymes for synthetic chemistry.

  • 17.
    Berglund, Per
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Svedendahl Humble, Maria
    Branneby, Cecilia
    7.18 C-X Bond Formation: Transaminases as Chiral Catalysts: Mechanism, Engineering, and Applications2012In: Comprehensive Chirality, Elsevier, 2012, Vol. 7, p. 390-401Chapter in book (Refereed)
    Abstract [en]

    Enantiomerically pure amines and amino acids are important building blocks in academic research as well as in industrial-scale chemical production. Transaminases are versatile enzymes providing access to such compounds of high enantiomeric excess. This chapter illustrates the available strategies with transaminases such as kinetic resolution or stereoselective synthesis and highlights many successful examples for amino acid and chiral amines synthesis. There are some known challenges linked to the use of transaminases, for example in terms of unfavorable equilibria and inhibition. Several successful examples to overcome these limitations are presented. Also, the classification of transaminases, mechanistic details, and various strategies for optimization are discussed.

  • 18.
    Berglund, Per
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Svedendahl, Maria
    KTH, School of Biotechnology (BIO), Biochemistry.
    Engelmark Cassimjee, Karim
    KTH, School of Biotechnology (BIO), Biochemistry.
    Branneby, Cecilia
    Cambrex Karlskoga AB.
    Abedi, Vahak
    AstraZeneca.
    Wells, Andrew
    AstraZeneca.
    Federsel, Hans-Jürgen
    AstraZeneca.
    Omega-Transaminases Redesigned for Chiral Amine Synthesis2011In: BIT Life Sciences’ 2nd Symposium on Enzymes & Biocatalysis, Dalian, China: BIT Life Sciences , 2011Conference paper (Refereed)
  • 19.
    Bernhardt, Peter
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Kazlauskas, R. J.
    Molecular basis of perhydrolase activity in serine hydrolases2005In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 44, no 18, p. 2742-2746Article in journal (Refereed)
    Abstract [en]

    (Chemical Equation Presented) Changing substrates: A mutation that forms a cis-proline-peptide bond in a loop structure close to the active site of an aryl esterase from Pseudomonas fluorescens converts the enzyme into a perhydrolase (see picture). The switch in activity is explained by a new hydrogen bond formed between a backbone carbonyl oxygen atom and the peroxy deacylation intermediate.

  • 20.
    Branneby, Cecilia
    KTH, School of Biotechnology (BIO), Biochemistry.
    Epoxidation catalyzed by a CALB mutantManuscript (preprint) (Other academic)
  • 21.
    Branneby, Cecilia
    KTH, School of Biotechnology (BIO), Biochemistry.
    Exploiting enzyme promiscuity for rational design2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Enzymes are today well recognized in various industrial applications, being an important component in detergents, and catalysts in the production of agrochemicals, foods, pharmaceuticals, and fine chemicals. Their large use is mainly due to their high selectivity and environmental advantage, compared to traditional catalysts. Tools and techniques in molecular biology offer the possibility to screen the natural sources and engineer new enzyme activities which further increases their usefulness as catalysts, in a broader area.

    Although enzymes show high substrate and reaction selectivity many enzymes are today known to catalyze other reactions than their natural ones. This is called enzyme promiscuity. It has been suggested that enzyme promiscuity is Nature’s way to create diversity. Small changes in the protein sequence can give the enzyme new reaction specificity.

    In this thesis I will present how rational design, based on molecular modeling, can be used to explore enzyme promiscuity and to change the enzyme reaction specificity. The first part of this work describes how Candida antarctica lipase B (CALB), by a single point mutation, was mutated to give increased activity for aldol additions, Michael additions and epoxidations. The activities of these reactions were predicted by quantum chemical calculations, which suggested that a single-point mutant of CALB would catalyze these reactions. Hence, the active site of CALB, which consists of a catalytic triad (Ser, His, Asp) and an oxyanion hole, was targeted by site-directed mutagenesis and the nucleophilic serine was mutated for either glycine or alanine. Enzymes were expressed in Pichia pastoris and analyzed for activity of the different reactions. In the case of the aldol additions the best mutant showed a four-fold initial rate over the wild type enzyme, for hexanal. Also Michael additions and epoxidations were successfully catalyzed by this mutant.

    In the last part of this thesis, rational design of alanine racemase from Geobacillus stearothermophilus was performed in order to alter the enzyme specificity. Active protein was expressed in Escherichia coli and analyzed. The explored reaction was the conversion of alanine to pyruvate and 2-butanone to 2-butylamine. One of the mutants showed increased activity for transamination, compared to the wild type.

  • 22. Branneby, Cecilia
    et al.
    Carlqvist, Peter
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Berglund, Per
    KTH, Superseded Departments, Biotechnology.
    Rational redesign of a lipase to an aldolase2003In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 42, no 28, p. 8633-8633Article in journal (Refereed)
  • 23.
    Branneby, Cecilia
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Park, Seongsoon
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Investigation of Substrate Specificity of Geobacillus stearothermophilus Alanine RacemaseManuscript (preprint) (Other academic)
  • 24.
    Branneby, Cecilia
    et al.
    Cambrex Karlskoga AB.
    Svedendahl, Maria
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Lipase-Catalyzed Aldol and Michael-Type Reactions2006Conference paper (Refereed)
  • 25.
    Branneby, Cecilia
    et al.
    Cambrex Karlskoga AB.
    Svedendahl, Maria
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Lipase-Catalyzed Aldol and Michael-Type Reactions2005In: Book of abstracts, 2005Conference paper (Refereed)
  • 26. Cammenberg, Maria
    et al.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Park, Seongsoon
    Molecular basis for the enhanced lipase-catalyzed N-acylation of 1-phenylethanamine with methoxyacetate2006In: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 7, no 11, p. 1745-1749Article in journal (Refereed)
    Abstract [en]

    One of the commercial methods for preparing enantiopure amines is lipase-catalyzed kinetic resolution, although lipases catalyze, aminolysis with only low activity. Interestingly, in 1997 Balkenhohl et al. used, ethyl methoxyacetate instead of ethyl butyrate as an acylation reagent for the aminolysis of 1-phenylethanamine and increased the reaction rate more than a 100-fold. This method has been applied to other aminolysis reactions, but the molecular basis for the enhanced rate is not understood. A moecular-modeling study of the transition-state analogue for the aminolysis showed that an interaction between the beta-oxygen atom in methoxyacetate and the amine nitrogen atom might be a key factor in the rate enhancement. Other acylation reagents, such as methyl 3-methoxypropionate and methyl 4-methoxybutyrate, were chosen to test the influence of this interaction because these molecules can be spatially arranged to have similar to that in the acylation with methyoxyacetate. The initial aminolysis rates were improved (11-fold and sixfold, respectively) compared to that with butyrate. In with 1-phenylethanol afforded the same rate with all acyl donors.

  • 27.
    Carlqvist, Peter
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Svedendahl, Maria
    KTH, School of Biotechnology (BIO), Biochemistry.
    Branneby, Cecilia
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Exploring the Active-Site of a Rationally Redesigned Lipase for Catalysis of Michael-Type Additions2005In: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 6, p. 331-336Article in journal (Refereed)
    Abstract [en]

    Michael-type additions of various thiols and alpha,beta-unsaturated carbonyl compounds were performed in organic solvent catalyzed by wild-type and a rationally redesigned mutant of Candida antarctica lipase B. The mutant locks the nucleophilic serine 105 in the active-site; this results in a changed catalytic mechanism of the enzyme. The possibility of utilizing this mutant for Michael-type additions was initially explored by quantum-chemical calculations on the reaction between acrolein and methanethiol in a model system. The model system was constructed on the basis of docking and molecular-dynamics simulations and was designed to simulate the catalytic properties of the active site. The catalytic system was explored experimentally with a range of different substrates. The k(cat) values were found to be in the range of 10(-3) to 4 min(-1), similar to the values obtained with aldolase antibodies. The enzyme proficiency was 10(7). Furthermore, the Michael-type reactions followed saturation kinetics and were confirmed to take place in the enzyme active site.

  • 28.
    Cassimjee, Karim Engelmark
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Humble, Maria Svedendahl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Land, Henrik
    KTH, School of Biotechnology (BIO), Biochemistry.
    Abedi, Vahak
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Chromobacterium violaceum omega-transaminase variant Trp60Cys shows increased specificity for (S)-1-phenylethylamine and 4 '-substituted acetophenones, and follows Swain-Lupton parameterisation2012In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 10, no 28, p. 5466-5470Article in journal (Refereed)
    Abstract [en]

    For biocatalytic production of pharmaceutically important chiral amines the.-transaminase enzymes have proven useful. Engineering of these enzymes has to some extent been accomplished by rational design, but mostly by directed evolution. By use of a homology model a key point mutation in Chromobacterium violaceum omega-transaminase was found upon comparison with engineered variants from homologous enzymes. The variant Trp60Cys gave increased specificity for (S)-1-phenylethylamine (29-fold) and 4'-substituted acetophenones (similar to 5-fold). To further study the effect of the mutation the reaction rates were Swain-Lupton parameterised. On comparison with the wild type, reactions of the variant showed increased resonance dependence; this observation together with changed pH optimum and cofactor dependence suggests an altered reaction mechanism.

  • 29.
    Cassimjee, Karim Engelmark
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Humble, Maria Svedendahl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Miceli, Valentina
    KTH, School of Biotechnology (BIO), Biochemistry.
    Colomina, Carla Granados
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Active Site Quantification of an omega-Transaminase by Performing a Half Transamination Reaction2011In: ACS CATAL, ISSN 2155-5435, Vol. 1, no 9, p. 1051-1055Article in journal (Refereed)
    Abstract [en]

    Measurement of the active enzyme fraction in a given enzyme preparation is a requirement for accurate kinetic measurements and activity comparisons of, for example, engineered mutants. omega-Transaminases, enzymes capable of interconverting ketones and amines by use of pyridoxal-5'-phosphate (PIP), can be used for the production of pharmaceutically important chiral amines but are subject to engineering to meet the practical requirements in synthesis reactions. Therefore, an active site quantification method is needed. Such a method was developed by quantifying the amount of consumed substrate in a virtually irreversible half transamination reaction. (S)-1-phenylethylamine was converted to acetophenone, while the holo enzyme (E-PLP) was converted to apo enzyme with bound pyridoxamine-5'-phosphate (E:PMP). Further, the mass of active enzyme was correlated to the absorbance of the holo enzyme to achieve a direct measurement method. The active Chromobacterium violaceum omega-transaminase with bound PLP can be quantified at 395 nm with an apparent extinction coefficient of 8.1 mM(-1) cm(-1).

  • 30.
    Cassimjee, Karim Engelmark
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Kourist, Robert
    Lindberg, Diana
    Larsen, Marianne Wittrup
    KTH, School of Biotechnology (BIO), Biochemistry.
    Thanh, Nguyen Hong
    KTH, School of Biotechnology (BIO), Biochemistry.
    Widersten, Mikael
    Bornscheuer, Uwe T.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    One-step enzyme extraction and immobilization for biocatalysis applications2011In: Biotechnology Journal, ISSN 1860-6768, E-ISSN 1860-7314, Vol. 6, no 4, p. 463-469Article in journal (Refereed)
    Abstract [en]

    An extraction/immobilization method for His(6)-tagged enzymes for use in synthesis applications is presented. By modifying silica oxide beads to be able to accommodate metal ions, the enzyme was tethered to the beads after adsorption of Co(II). The beads were successfully used for direct extraction of C. antarctica lipase B (CalB) from a periplasmic preparation with a minimum of 58% activity yield, creating a quick one-step extraction-immobilization protocol. This method, named HisSi Immobilization, was evaluated with five different enzymes [Candida antarctica lipase B (CalB), Bacillus subtilis lipase A (BslA), Bacillus subtilis esterase (BS2), Pseudomonas fluorescence esterase (PFE), and Solanum tuberosum epoxide hydrolase 1 (StEH1)]. Immobilized CalB was effectively employed in organic solvent (cyclohexane and acetonitrile) in a transacylation reaction and in aqueous buffer for ester hydrolysis. For the remaining enzymes some activity in organic solvent could be shown, whereas the non-immobilized enzymes were found inactive. The protocol presented in this work provides a facile immobilization method by utilization of the common His 6 tag, offering specific and defined means of binding a protein in a specific location, which is applicable for a wide range of enzymes.

  • 31.
    Cassimjee, Karim Engelmark
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Trummer, Martin
    KTH, School of Biotechnology (BIO), Biochemistry.
    Branneby, Cecilia
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Silica-immobilized His(6)-tagged enzyme: Alanine racemase in hydrophobic solvent2008In: Biotechnology and Bioengineering, ISSN 0006-3592, E-ISSN 1097-0290, Vol. 99, no 3, p. 712-716Article in journal (Refereed)
    Abstract [en]

    A new immobilization method for enzymes is presented to facilitate synthetic applications in aqueous as well as organic media. The enzyme Alanine racemase (AlaR) from Geobacillus stearothermophilus was cloned, overexpressed and then immobilized on a silica-coated thin-layer chromatography plate to create an enzyme surface. The enzyme, fused to a His(6)-tag at its N-terminal, was tethered to the chemically modified silica-coated TLC plate through cobalt ions. The immobilized enzyme showed unaltered kinetic parameters in small-scale stirred reactions and retained its activity after rinsing, drying, freezing or immersion in n-hexane. This practical method is a first step towards a general immobilization method for synthesis applications with any enzyme suitable for His(6)-tagging.

  • 32. Cheung, Louisa
    et al.
    Andersen, Malin
    KTH, School of Biotechnology (BIO), Gene Technology.
    Gustavsson, Carolina
    Odeberg, Jacob
    KTH, School of Biotechnology (BIO), Biochemistry.
    Fernández-Pérez, Leandro
    Norsteds, Gunnar
    Tollet-Egnell, Petra
    Hormonal and nutritional regulation of alternative CD36 transcripts in rat liver: a role for growth hormone in alternative exon usage2007In: BMC Molecular Biology, ISSN 1471-2199, E-ISSN 1471-2199, Vol. 8, no 60, p. 12-Article in journal (Refereed)
    Abstract [en]

    Background: CD36 is a multiligand receptor involved in various metabolic pathways, including cellular uptake of long-chain fatty acids. Defect function or expression of CD36 can result in dyslipidemia or insulin resistance. We have previously shown that CD36 expression is female-predominant in rat liver. In the present study, hormonal and nutritional regulation of hepatic CD36 expression was examined in male and female rats. Since alternative transcription start sites have been described in murine and human Cd36, we investigated whether alternative CD36 transcripts are differentially regulated in rat liver during these conditions.

    Results: Sequence information of the rat Cd36 5'-UTR was extended, showing that the gene structure of Cd36 in rat is similar to that previously described in mouse with at least two alternative first exons. The rat Cd36 exon 1a promoter was sequenced and found to be highly similar to murine and human Cd36. We show that alternative first exon usage is involved in the female-predominant expression of CD36 in rat liver and during certain hormonal states that induce CD36 mRNA abundance. Estrogen treatment or continuous infusion of growth hormone (GH) in male rats induced CD36 expression preferentially through the exon 1a promoter. Old age was associated with increased CD36 expression in male rats, albeit without any preferential first exon usage. Intermittent GH treatment in old male rats reversed this effect. Mild starvation (12 hours without food) reduced CD36 expression in female liver, whereas its expression was increased in skeletal muscle.

    Conclusion: The results obtained in this study confirm and extend our previous observation that GH is an important regulator of hepatic CD36, and depending on the mode of treatment (continuous or intermittent) the gene might be either induced or repressed. We suggest that the effects of continuous GH secretion in females (which is stimulatory) and intermittent GH secretion in males (which is inhibitory) explains the sex-different expression of this gene. Furthermore, a female-specific repression of hepatic CD36 in response to food deprivation was found, which was in contrast to a stimulatory effect in skeletal muscle. This demonstrates a tissue-specific regulation of Cd36.

  • 33.
    Christiernin, Maria
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Ohlsson, Anna B.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Torkel
    KTH, School of Biotechnology (BIO), Biochemistry.
    Henriksson, Gunnar
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Lignin isolated from primary walls of hybrid aspen cell cultures indicates significant differences in lignin structure between primary and secondary cell wall2005In: Plant physiology and biochemistry (Paris), ISSN 0981-9428, E-ISSN 1873-2690, Vol. 43, no 8, p. 777-785Article in journal (Refereed)
    Abstract [en]

    Hybrid aspen (Populus tremula x tremuloides) cell cultures were grown for 7, 14 and 21 days. The cell cultures formed primary cell walls but no secondary cell wall according to carbohydrate analysis and microscopic characterization. The primary walls were lignified, increasingly with age, according to Klason lignin analysis. Presence of lignin in the primary walls, with a higher content in 21-day old cells than in 7-day old cells, was further Supported by phloroglucinol/HCI reagent test and confocal microscopy after both immunolocalization and staining with acriflavin. Both laccase and peroxidase activity were found in the cultures and the activity increased during lignin formation. The lignin from the cell culture material was compared to lignin from mature aspen wood, where most of the lignin originates in the secondary cell wall, and which served as our secondary cell wall control. Lignin from the cell walls was isolated and characterized by thioacidolysis followed by gas chromatography and mass spectrometry. The lignin in the cell cultures differed from lignin of mature aspen wood in that it consisted exclusively of guaiacyl units, and had a more condensed structure. Five lignin structures were identified by mass spectrometry in the cell suspension cultures. The results indicate that the hybrid aspen cell culture used in this investigation may be a convenient experimental system for studies of primary cell wall lignin.

  • 34.
    Christiernin, Maria
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Wood Chemistry and Pulp Technology.
    Ohlsson, Anna
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Torkil
    KTH, School of Biotechnology (BIO), Biochemistry.
    Henriksson, Gunnar
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Wood Chemistry and Pulp Technology.
    Analysis of lignin isolated from poplar cell suspension cultures2005In: 59th Appita Annual Conference and Exhibition, incorporating the 13th ISWFPC: International Symposium on Wood, Fibre and Pulping Chemistry, 2005, p. 81-86Conference paper (Refereed)
    Abstract [en]

    We have investigated lignin structures in pure primary cell walls. Poplar cell suspension cultures, Populus tremula x tremuloides, were harvested after 7, 14 and 21 days of growth. Carbohydrate monomer analysis also points at the presence of primary wall exclusively. Confocal microscopy of the cells dyed with acriflavin demonstrates that lignin is present. Klason content increases during growth from 0.7 to 3.9 percent. GC analysis of samples subjected to thioacidolysis shows that the lignin constitutes of guaiacyl units as compared to poplar wood which have syringyl as the main monomer. The amount of monomers per unit Klason lignin is lower than in wood and it decreases during cultivation possibly indicating a larger relative content of carbon-carbon bonds in the polymeric lignin in the cell cultures as compared to wood. Five lignin structures were identified with massspectrometry.

  • 35. Cordova, A
    et al.
    Iversen, T
    Martinelle, M
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Lipase-catalysed formation of macrocycles by ring-opening polymerisation of epsilon-caprolactone1998In: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 39, no 25, p. 6519-6524Article in journal (Refereed)
    Abstract [en]

    Studies were undertaken to gain mechanistic information on lactone ring-opening polymerisation reactions using Candida antarctica lipase B (Novozym 435) as the catalyst and epsilon-caprolactone as the monomer. Polymerisations were performed in organic solvents as well as without solvent at 60 degrees C. Candida antarctica lipase B catalysed concurrently with the intermolecular ring-opening polymerisation, and also the formation of macrocycles by an intramolecular condensation reaction. Candida antarctica lipase B had the highest initial rate of consumption of epsilon-caprolactone (1.2 mu mol mg(-1) min(-1)) in the bulk polymerisation, without solvent. Under these conditions, the highest average M-w, 4701 D, of poly(epsilon-caprolactone) was obtained. There were small amounts of cyclic oligomers present. When comparing the polymerisations performed in dioxane, acetonitrile and THF after 24 h reaction time with the bulk polymerisation, the average M-w of poly(epsilon-caprolactone) [2984, 1297, 1862 D, respectively] and the initial rates of monomer conversion of the enzyme (0.1, 0.05, 0.013 mu mol mg(-1) min(-1), respectively) were lower, however, the formation of cyclic oligomers was high. In dioxane, macrocycles of up to 2623 D corresponding to 23 monomer units were formed, and in acetonitrile there were mostly cyclic oligomers present. (C) 1998 Elsevier Science Ltd. All rights reserved.

  • 36.
    Engelmark Cassimjee, Karim
    KTH, School of Biotechnology (BIO), Biochemistry.
    Tools in biocatalysis: enzyme immobilisation on silica and synthesis of enantiopure amines2010Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis presents two techniques in the field of biocatalysis:

    An enzyme immobilisation method based on the His6-tag for attachment on modified silica oxide beads, and it’s employment in aqueous and organic medium for synthesis applications. The method functions as a one step extraction and immobilisation protocol.

    An equilibrium displacement system which enables complete conversion in reactions with ω-transaminases where isopropylamine is the donor, a route for synthesis of pharmaceutically interesting enantiopure amines.

    Biocatalysis is predicted to be a paramount technology for an environmentally sustainable chemical industry, to which every newly developed method represents a small but important step. The work done here is aimed to be a part of this development.

     

  • 37.
    Engelmark Cassimjee, Karim
    KTH, School of Biotechnology (BIO), Biochemistry.
    ω-Transaminase in Biocatalysis: Methods, Reactions and Engineering2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biocatalysis offers an alternative to classic chemistry by using enzymes, the protein catalysts of Nature, for production of fine chemicals. Evolution has created enzymes capable of catalysis at moderate temperature of a specific reaction in the presence of a plethora of compounds in the aqueous cell environment. The focal point of biocatalysis is to utilise these traits in vitro, for creation of valuable molecules.

    The ω-transaminase is an enzyme capable of producing chiral amines, compounds used to great extent in pharmaceuticals. Much effort has in recent years been invested in the research and engineering of this enzyme type since the catalysed reaction offers an advantageous alternative to classical techniques. Nevertheless, there is a need for method development, adaptation of the enzyme and increased understanding of the catalytic mechanism for feasibility as an effective biocatalyst for unnatural substrates. This thesis addresses a chosen set of obstacles as a contribution to meeting the demands at hand. ω-Transaminase from Chromobacterium violaceum and Arthrobacter citreus was used.

    Many homologous ω-transaminases are available, which are also subject to engineering where variants are produced. To accurately compare their kinetic constants an active site quantification method is required but has not been available. Here such a method is presented (Paper 1) which encompasses a virtually irreversible half transamination reaction.

    In stereoselective synthesis the ω-transaminase catalysed equilibrium reaction inherently results in incomplete conversion. An equilibrium displacement system is presented (Paper II) where isopropylamine is the amino donor for transamination of acetophenone and derivatives thereof, coupled to an enzymatic cascade reaction.

    For many unnatural substrates the specificity and enantiospecificity is insufficient. Rationally redesigned variants were produced with improved properties for chosen substrates (Paper III and IV). The catalytic contributions of field and resonance of a variant compared to the wild type were investigated (Paper IV) for increased knowledge of the mechanism.

    For rational redesign of an enzyme the three-dimensional structure is required, of which only a few are available for the ω-transaminases. X-ray crystallographic structures of the holo and apo form of Chromobacterium violaceum ω-transaminase were made (Paper V) which revealed significant structural rearrangements upon coenzyme binding which may be of consequence for future engineering.

  • 38.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Affinity Tag Purification Method and Immobilization of the Promiscuous Enzyme Alanine Racemase2006Conference paper (Refereed)
  • 39.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Affinity Tag Purification Method of the Promiscuous Enzyme Alanine Racemase2006In: Book of abstracts, 2006Conference paper (Other academic)
  • 40.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Immobilization Method for the Promiscuous Enzyme Alanine Racemase2007In: BIOTRANS Oviedo 2007 / [ed] Vicente Gotor, 2007Conference paper (Refereed)
  • 41.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Branneby, Cecilia
    Abedi, Vahak
    Wells, Andrew
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Transaminations with isopropyl amine: equilibrium displacement with yeast alcohol dehydrogenase coupled to in situ cofactor regeneration2010In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 46, no 30, p. 5569-5571Article in journal (Refereed)
    Abstract [en]

    Enantiopure chiral amines synthesis using omega-transaminases is hindered by an unfavourable equilibrium, but when using isopropylamine as the amine donor the equilibrium can be completely displaced by using a specific dehydrogenase in situ for removal of formed acetone.

  • 42.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Branneby, Cecilia
    Cambrex Karlskoga AB.
    Sjöstrand, Ulf
    Cambrex Karlskoga AB.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    High Yield Transamination with Isopropyl Amine as Donor, by Employment of YADH and in situ Cofactor Regeneration2009Conference paper (Refereed)
  • 43.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Branneby, Cecilia
    Cambrex Karlskoga AB.
    Sjöstrand, Ulf
    Cambrex Karlskoga AB.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    High Yield Transamination with Isopropyl Amine as Donor, by Employment of YADH and in situ Cofactor Regeneration2009In: Book of abstracts, 2009Conference paper (Refereed)
  • 44.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Kourist, Robert
    University of Greifswald, Germany.
    Lindberg, Diana
    Uppsala university, SE.
    Wittrup Larsen, Marianne
    KTH, School of Biotechnology (BIO), Biochemistry.
    Widersten, Mikael
    Uppsala university, SE.
    Bornscheuer, Uwe T
    University of Greifswald, DE.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    A One Step Enzyme Extraction and Immobilization Method for Organic and Aqueous Solvents2008In: Biocat2008 / [ed] Ralf Grote, Garabed Antranikian, Hamburg, Germany: TuTech Innovation GmbH , 2008Conference paper (Refereed)
  • 45.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Kourist, Robert
    University of Greifswald, Germany.
    Lindberg, Diana
    Uppsala university, SE.
    Wittrup Larsen, Marianne
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Widersten, Mikael
    Uppsala university, SE.
    Bornscheuer, Uwe T
    University of Greifswald, DE.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    A One Step General Enzyme Immobilization Method for Organic and Aqueous Solvents2008In: Book of Abstracts, 2008Conference paper (Refereed)
  • 46.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Marí­n, Sílvia Rodríguez
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Synthesis of cyclic polyamines by enzymatic generation of an amino aldehyde in situ2012In: Macromolecular rapid communications, ISSN 1022-1336, E-ISSN 1521-3927, Vol. 33, no 18, p. 1580-1583Article in journal (Refereed)
    Abstract [en]

    Multifunctional polycationic polyamines, for example, used in drug and gene delivery, have product range limitations in their synthesis methods. Here, we synthesize a polyamine by forming a self-assembling amino aldehyde from the corresponding amino alcohol with horse liver alcohol dehydrogenase (HLADH), followed by reduction. Circular polyamines were synthesized from 3-amino-propan-1-ol as starting material, analogous to cyclic polyamines formed from azetidin. The product had an isolated yield of 89.7% or 15.3 g L -1. The predicted range of possible polyamine products by this method is broad since many amino alcohols are putative substrates for HLADH. The enzyme also had activity for 2-amino-propan-1-ol and 2-amino-2-phenyl-ethanol, for which the enantioselectivity was 330 (S) and 32 (R), respectively.

  • 47.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Svedendahl Humble, Maria
    KTH, School of Biotechnology (BIO), Biochemistry.
    Land, Henrik
    KTH, School of Biotechnology (BIO), Biochemistry.
    Abedi, Vahak
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Chromobacterium violaceum ω-Transaminase VariantTrp60Cys Shows Increased Specificity for (S)-1-Phenylethylamine and 4’-Substituted Acetophenones, andFollows Swain-Lupton ParameterisationManuscript (preprint) (Other academic)
  • 48.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Svedendahl, Maria
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Rational Redesign of omega-Transaminase2010In: Biocat2010, Hamburg, Germany: TuTech Verlag , 2010Conference paper (Refereed)
  • 49. Engstrom, Karin
    et al.
    Vallin, Michaela
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Backvall, Jan-E.
    Kinetic resolution of diarylmethanols using a mutated variant of lipase CALB2012In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 68, no 37, p. 7613-7618Article in journal (Refereed)
    Abstract [en]

    An enzymatic kinetic resolution of diarylmethanols via acylation has been developed. This was achieved by the use of a mutated variant of CALB that accepts larger substrates compared to the wild type. By the use of diarylmethanols with two differently sized aryl groups, enantioselective transformations were achieved. A larger size-difference led to a higher enantioselectivity. In addition, substrates with electronically different aryl groups, such as phenyl and pyridyl, also gave an enantioselective reaction. The highest E value was observed with a substrate where steric and electronic effects were combined.

  • 50.
    Engström, Karin
    et al.
    Stockholm Univ, Arrhenius Lab, Dept Organ Chem.
    Vallin, Michaela
    KTH, School of Biotechnology (BIO), Biochemistry.
    Syrén, Per-Olof
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Bäckvall, Jan-E.
    Stockholm Univ, Arrhenius Lab, Dept Organ Chem.
    Mutated variant of Candida antarctica lipase B in (S)-selective dynamic kinetic resolution of secondary alcohols2011In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 9, no 1, p. 81-82Article in journal (Refereed)
    Abstract [en]

    An (S)-selective dynamic kinetic resolution of secondary alcohols, employing a mutated variant of Candida antarctica lipase B (CalB) gave products in 84-88% yield and in 90-97% ee.

1234 1 - 50 of 168
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