lnu.sePublikationer
Ändra sökning
Avgränsa sökresultatet
123456 51 - 100 av 264
RefereraExporteraLänk till träfflistan
Permanent länk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Träffar per sida
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sortering
  • Standard (Relevans)
  • Författare A-Ö
  • Författare Ö-A
  • Titel A-Ö
  • Titel Ö-A
  • Publikationstyp A-Ö
  • Publikationstyp Ö-A
  • Äldst först
  • Nyast först
  • Skapad (Äldst först)
  • Skapad (Nyast först)
  • Senast uppdaterad (Äldst först)
  • Senast uppdaterad (Nyast först)
  • Disputationsdatum (tidigaste först)
  • Disputationsdatum (senaste först)
  • Standard (Relevans)
  • Författare A-Ö
  • Författare Ö-A
  • Titel A-Ö
  • Titel Ö-A
  • Publikationstyp A-Ö
  • Publikationstyp Ö-A
  • Äldst först
  • Nyast först
  • Skapad (Äldst först)
  • Skapad (Nyast först)
  • Senast uppdaterad (Äldst först)
  • Senast uppdaterad (Nyast först)
  • Disputationsdatum (tidigaste först)
  • Disputationsdatum (senaste först)
Markera
Maxantalet träffar du kan exportera från sökgränssnittet är 250. Vid större uttag använd dig av utsökningar.
  • 51.
    Bustin, Stephen A.
    et al.
    Anglia Ruskin University, UK.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Iba, Michael
    Rutgers University, USA.
    International Journal of Molecular Science Best Paper Award 20142014Ingår i: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 15, nr 1, s. 1683-1685Artikel i tidskrift (Övrigt vetenskapligt)
  • 52. Carlenor, E
    et al.
    Persson, Bengt L.
    Department of Biochemistry, Arrhenius Laboratory, University of Stockholm.
    Glaser, E
    Andersson, B
    Rydström, J
    On the presence of a nicotinamide nucleotide transhydrogenase in mitochondria from potato tuber1988Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 88, s. 303-308Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Mitochondria isolated from potato (Solanum tuberosum L.) tuber wereinvestigated for the presence of a nicotinamide nucleotide transhydrogenaseactivity. Submitochondrial particles derived from these mitochondriaby sonication catalyzed a reduction of NAD' or 3-acetylpyridine-NAD'by NADPH, which showed a maximum of about 50 to 150 nanomoles/minute. milligram protein at pH 5 to 6. The Km values for 3-acetylpyridine-NAD' and NADPH were about 24 and 55 micromolar, respectively.Intact mitochondria showed a negligible activity in the absence of detergents.However, in the presence of detergents the specific activity approachedabout 30% of that seen with submitochondrial particles. Thepotato mitochondria transhydrogenase activity was sensitive to trypsinand phenylarsine oxide, both agents that are known to inhibit the mammaliantranshydrogenase. Antibodies raised against rat liver transhydrogenasecrossreacted with two peptides in potato tuber mitochondrialmembranes with a molecular mass of 100 to 115 kilodaltons. Theobserved transhydrogenase activities may be due to an unspecific activityof dehydrogenases and/or to a genuine transhydrogenase. The activitycontributions by NADH dehydrogenases and transhydrogenase to thetotal transhydrogenase activity were investigated by determining theirrelative sensitivities to trypsin. It is concluded that, at high or neutralpH, the observed transhydrogenase activity in potato tuber submitochondrialparticles is due to the presence of a genuine and specific highmolecular weight transhydrogenase. At low pH an unspecific reaction ofan NADH dehydrogenase with NADPH contributes to the total transhydrogenaseactivity. 

  • 53.
    Carlsson, Stina K.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Effects of adenosine and acetylcholine on the lacrimal gland2011Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    A balanced tear film is essential for a healthy ocular surface. Insufficient tear production may result in dry eye, a common disorder in the elderly population. Dry eye causes significant discomfort in the patients and may lead to visual impairment and ocular infections. The lacrimal gland secretes water, proteins and electrolytes to the aqueous layer of the tear film. Lacrimal gland secretion is tightly regulated by e.g. neuronally released acetylcholine. The effect of acetylcholine on lacrimal gland secretion was recently found to be potentiated by adenosine. Adenosine is an important signaling molecule acting upon the adenosine receptors: A1, A2A, A2B and A3.

    The aim of this thesis was to study effects of adenosine and acetylcholine on intracellular signaling pathways and lacrimal gland secretion. Cholinergic stimulation of secretion was shown to be regulated by the mitogen activated protein kinase p38, a protein previously not known to be involved in exocrine secretion. p38 was activated in response to cholinergic stimulation and inhibition of p38 significantly diminished cholinergic secretion.

    When investigating adenosine effects, potentiation of cholinergic secretion was observed by activation of the A2B receptor in addition to the previously studied A1 receptor. An A2 receptor agonist increased cholinergic rabbit lacrimal gland protein secretion at several concentrations. The increase was inhibited by antagonism of the A2B receptor, but not the A2A receptor. When investigating the intracellular signaling pathways following adenosine and acetylcholine receptor activation, adenosine was shown to increase of cAMP levels. An additional increase in cAMP levels was observed after parallel adenosine and cholinergic receptor activation. Inhibition of Ca2+ release from the endoplasmic reticulum had inhibitory effects of cholinergic stimulation of secretion. In addition, the expression of adenosine receptors in a mouse model of autoimmune dry eye was investigated. The results showed a lymphocyte dependent upregulation of A2A receptors in diseased mice compared to controls.

    In conclusion, the results in this thesis provide significant contributions in the search of dry eye therapeutics through studies of adenosine and acetylcholine receptor activation.

  • 54.
    Chapman, Joanne R.
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Waldenström, Jonas
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    With Reference to Reference Genes: A Systematic Review of Endogenous Controls in Gene Expression Studies2015Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 11, artikel-id e0141853Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    The choice of reference genes that are stably expressed amongst treatment groups is a crucial step in real-time quantitative PCR gene expression studies. Recent guidelines have specified that a minimum of two validated reference genes should be used for normalisation. However, a quantitative review of the literature showed that the average number of reference genes used across all studies was 1.2. Thus, the vast majority of studies continue to use a single gene, with beta-actin (ACTB) and/or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) being commonly selected in studies of vertebrate gene expression. Few studies (15%) tested a panel of potential reference genes for stability of expression before using them to normalise data. Amongst studies specifically testing reference gene stability, few found ACTB or GAPDH to be optimal, whereby these genes were significantly less likely to be chosen when larger panels of potential reference genes were screened. Fewer reference genes were tested for stability in non-model organisms, presumably owing to a dearth of available primers in less well characterised species. Furthermore, the experimental conditions under which real-time quantitative PCR analyses were conducted had a large influence on the choice of reference genes, whereby different studies of rat brain tissue showed different reference genes to be the most stable. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies.

  • 55.
    Chavan, Swapnil
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    Karlsson, Björn C. G.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Rosengren, Annika M.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Ballabio, Davide
    University of Milano-Bicocca, Italy.
    Consonni, Viviana
    University of Milano-Bicocca, Italy.
    Todeschini, Roberto
    University of Milano-Bicocca, Italy.
    Towards Global QSAR Model Building for Acute Toxicity: Munro Database Case Study2014Ingår i: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 15, nr 10, s. 18162-18174Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A series of 436 Munro database chemicals were studied with respect to their corresponding experimental LD50 values to investigate the possibility of establishing a global QSAR model for acute toxicity. Dragon molecular descriptors were used for the QSAR model development and genetic algorithms were used to select descriptors better correlated with toxicity data. Toxic values were discretized in a qualitative class on the basis of the Globally Harmonized Scheme: the 436 chemicals were divided into 3 classes based on their experimental LD50 values: highly toxic, intermediate toxic and low to non-toxic. The k-nearest neighbor (k-NN) classification method was calibrated on 25 molecular descriptors and gave a non-error rate (NER) equal to 0.66 and 0.57 for internal and external prediction sets, respectively. Even if the classification performances are not optimal, the subsequent analysis of the selected descriptors and their relationship with toxicity levels constitute a step towards the development of a global QSAR model for acute toxicity.

  • 56.
    Clima, Rosanna
    et al.
    University of Bari, Italy ; University of Bologna, Italy.
    Preste, Roberto
    University of Bari, Italy.
    Calabrese, Claudia
    European Bioinformatics Institute (EMBL-EBI), UK.
    Diroma, Maria Angela
    University of Bari, Italy.
    Santorsola, Mariangela
    University of Bari, Italy.
    Scioscia, Gaetano
    IBM Italia SpA, Italy ; MBLab Bari, Italy.
    Simone, Domenico
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Shen, Lishuang
    Children's Hospital Los Angeles, USA.
    Gasparre, Giuseppe
    University of Bologna, Italy.
    Attimonelli, Marcella
    University of Bari, Italy.
    HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor2017Ingår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 45, nr D1, s. D698-D706Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/.

  • 57. Clyne, N
    et al.
    Persson, Bengt L.
    Department of Biochemistry, University of Stockholm.
    Havu, N
    Hultman, E
    Lins, L-E
    Pehrsson, S K
    Rydström, J
    Wibom, R
    The intracellular distribution of cobalt in exposed and unexposed rat myocardium1990Ingår i: Scandinavian Journal of Clinical and Laboratory Investigation, ISSN 0036-5513, E-ISSN 1502-7686, Vol. 50, nr 6, s. 605-609Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The intracellular distribution of cobalt was analysed in the myocardium of exposed and unexposed rats. The exposed rats were given a dietary cobalt supplementation of 40 mg CoS04-7 H20/kg body weight for 8 weeks. The mitochondrial fraction showed the greatest relative increase in cobalt: 0.09 ng/mg protein in the unexposed rats to 8.43 ng/mg protein in the exposed rats. In the exposed rats the submitochondrial particles had the highest levels of cobalt: 19.43 ng/mg protein, followed by the sarcoplasmatic reticulum: 12.3 ng/mg protein. The microsomal 44 000g supernatant also showed an increase, although the levels remained low (0.51 ng/mg protein in the exposed animals). Apparently the calcium-storing organelles had the highest levels of cobalt. This could affect calcium flux in myocardial cells and, secondarily, tension development in cardiac muscle.

  • 58. Collinge, M A
    et al.
    Brodelius, Peter
    Institute of Biotechnology ETH-Hönggerberg CH-8093 Zürich, Switzerland.
    Dynamics of Benzophenanthridine Alkaloid Production in Suspension Cultures of Eschscholtzia californica after Treatment with a Yeast Elicitor1989Ingår i: Phytochemistry, ISSN 0031-9422, E-ISSN 1873-3700, Vol. 28, nr 4, s. 1101-1104Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A number of benzophenanthridine alkaloids are induced in suspension cultures of Eschscholtzia californica after treatment with an elicitor prepared from yeast extract. The formation of the alkaloids sanguinarine, chelerythrine and macarpine has been studied in relation to; elicitor concentration, incubation time after elicitation, and culture age. A significant portion of these alkaloids is released into the medium. Sanguinarine and chelerythrine reach maximum levels a few hours after the time of elicitation. Thereafter, their levels decline and the amount of macarpine increases. Viability of elicited cells, as determined by their subsequent growth, is not significantly reduced. There is a good correlation between induced tyrosine decarboxylase activity and alkaloid formation. 

  • 59.
    Crona, Mikael
    et al.
    Arrhenius Laboratories for Natural Sciences.
    Avesson, Lotta
    Swedish University of Agricultural Sciences.
    Sahlin, Margareta
    Arrhenius Laboratories for Natural Sciences ; Stockholm University.
    Lundin, Daniel
    Stockholm University.
    Hinas, Andrea
    Swedish University of Agricultural Sciences.
    Klose, Ralph
    Arrhenius Laboratories for Natural Sciences.
    Söderbom, Fredrik
    Swedish University of Agricultural Sciences.
    Sjöberg, Britt-Marie
    Arrhenius Laboratories for Natural Sciences ; Swedish University of Agricultural Sciences.
    A Rare Combination of Ribonucleotide Reductases in the Social Amoeba Dictyostelium discoideum2013Ingår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 288, nr 12, s. 8198-8208Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ribonucleotide reductases (RNRs) catalyze the only pathway for de novo synthesis of deoxyribonucleotides needed for DNA replication and repair. The vast majority of eukaryotes encodes only a class I RNR, but interestingly some eukaryotes, including the social amoeba Dictyostelium discoideum, encode both a class I and a class II RNR. The amino acid sequence of the D. discoideum class I RNR is similar to other eukaryotic RNRs, whereas that of its class II RNR is most similar to the monomeric class II RNRs found in Lactobacillus spp. and a few other bacteria. Here we report the first study of RNRs in a eukaryotic organism that encodes class I and class II RNRs. Both classes of RNR genes were expressed in D. discoideum cells, although the class I transcripts were more abundant and strongly enriched during mid-development compared with the class II transcript. The quaternary structure, allosteric regulation, and properties of the diiron-oxo/radical cofactor of D. discoideum class I RNR are similar to those of the mammalian RNRs. Inhibition of D. discoideum class I RNR by hydroxyurea resulted in a 90% reduction in spore formation and decreased the germination viability of the surviving spores by 75%. Class II RNR could not compensate for class I inhibition during development, and an excess of vitamin B12 coenzyme, which is essential for class II activity, did not improve spore formation. We suggest that class I is the principal RNR during D. discoideum development and growth and is important for spore formation, possibly by providing dNTPs for mitochondrial replication.

  • 60.
    Daly, Norelle
    et al.
    University of Queensland, Australia.
    Chen, Yi
    University of Queensland, Australia.
    Rosengren, K. Johan
    University of Queensland, Australia.
    Marx, Ute
    University of Queensland, Australia.
    Phillips, Martin
    UCLA, USA.
    Waring, Alan
    UCLA, USA.
    Wang, Wei
    UCLA, USA.
    Lehrer, Robert
    UCLA, USA.
    Craik, David
    University of Queensland, Australia.
    Retrocyclin-2: a potent anti-HIV theta-defensin that forms a cyclic cysteine ladder structural motif2009Ingår i: Peptides for Youth: The Proceedings of the 20th American Peptide Symposium / [ed] Valle S.D., Escher E., Lubell W.D., Springer, 2009, Vol. 611, nr 11, s. 577-578Konferensbidrag (Refereegranskat)
  • 61.
    Dragan, Smiljic
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Studies of small bicoid knock-down and overexpression at early and late stage of development in Drosophila melanogaster.2016Självständigt arbete på avancerad nivå (magisterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 62.
    Dragovich, Branko
    et al.
    University of Belgrade, Serbia ; Serbian Academy of Arts and Sciences, Serbia.
    Khrennikov, Andrei
    Linnéuniversitetet, Fakulteten för teknik (FTK), Institutionen för matematik (MA).
    Mišić, Nata Ž.
    Lola Institute, Serbia.
    Ultrametrics in the genetic code and the genome2017Ingår i: Applied Mathematics and Computation, ISSN 0096-3003, E-ISSN 1873-5649, Vol. 309, s. 350-358Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ultrametric approach to the genetic code and the genome is considered and developed. p-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. It is shown that codons and amino acids can be treated as p-adic ultrametric networks. Ultrametric modification of the Hamming distance is defined and noted how it can be useful. Ultrametric approach with p-adic distance is an attractive and promising trend towards investigation of bioinformation. © 2017 Elsevier Inc.

  • 63. Drakenberg, T
    et al.
    Brodelius, Peter
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    McIntyre, D D
    Vogel, H J
    Structural Studies of Digitoxin and Related Cardenolides by two-dimentional NMR1990Ingår i: Canadian journal of biochemistry, ISSN 0008-4018, Vol. 68, s. 272-277Artikel i tidskrift (Refereegranskat)
  • 64.
    Duong-Thi, Minh-Dao
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Bergström, Gunnar
    Linköping Univ, Sweden.
    Mandenius, Carl-Fredrik
    Linköping Univ, Sweden.
    Bergström, Maria
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Fex, Tomas
    Univ Gothenburg, Sweden.
    Ohlson, Sten
    Nanyang Technol Univ, Singapore.
    Comparison of weak affinity chromatography and surface plasmon resonance in determining affinity of small molecules2014Ingår i: Analytical Biochemistry, ISSN 0003-2697, E-ISSN 1096-0309, Vol. 461, s. 57-59Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this study, we compared affinity data from surface plasmon resonance (SPR) and weak affinity chromatography (WAC), two established techniques for determination of weak affinity (mM-mu M) small molecule-protein interactions. In the current comparison, thrombin was used as target protein. In WAC the affinity constant (K-D) was determined from retention times, and in SPR it was determined by Langmuir isotherm fitting of steady-state responses. Results indicate a strong correlation between the two methods (R-2 = 0.995, P < 0.0001). (C) 2014 Elsevier Inc. All rights reserved.

  • 65.
    Duong-Thi, Minh-Dao
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Bergström, Maria
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Fex, Tomas
    Astra& Zeneca R&D Mölndal, Mölndal, Sweden.
    Isaksson, Roland
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Ohlson, Sten
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    High-Throughput Fragment Screening by Affinity LC-MS2013Ingår i: Journal of Biomolecular Screening, ISSN 1087-0571, E-ISSN 1552-454X, Vol. 18, nr 2, s. 160-171Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fragment screening, an emerging approach for hit finding in drug discovery, has recently been proven effective by its first approved drug, vemurafenib, for cancer treatment. Techniques such as nuclear magnetic resonance, surface plasmon resonance, and isothemal titration calorimetry, with their own pros and cons, have been employed for screening fragment libraries. As an alternative approach, screening based on high-performance liquid chromatography separation has been developed. In this work, we present weak affinity LC/MS as a method to screen fragments under high-throughput conditions. Affinity-based capillary columns with immobilized thrombin were used to screen a collection of 590 compounds from a fragment library. The collection was divided into 11 mixtures (each containing 35 to 65 fragments) and screened by MS detection. The primary screening was performed in < 4 h (corresponding to > 3500 fragments per day). Thirty hits were defined, which subsequently entered a secondary screening using an active site-blocked thrombin column for confirmation of specificity. One hit showed selective binding to thrombin with an estimated dissociation constant (K-D) in the 0.1 mM range. This study shows that affinity LC/MS is characterized by high throughput, ease of operation, and low consumption of target and fragments, and therefore it promises to be a valuable method for fragment screening.

  • 66.
    Ehrnthaller, Christian
    et al.
    University of Ulm, Germany.
    Huber-Lang, Markus
    University of Ulm, Germany.
    Nilsson, Per H.
    University of Oslo, Norway.
    Bindl, Ronny
    University of Ulm, Germany.
    Redeker, Simon
    University of Ulm, Germany.
    Recknagel, Stefan
    University of Ulm, Germany.
    Rapp, Anna
    University of Ulm, Germany.
    Mollnes, Tom
    University of Oslo, Norway.
    Amling, Michael
    Univ Med Ctr Hamburg Eppendorf, Germany.
    Gebhard, Florian
    University of Ulm, Germany.
    Ignatius, Anita
    University of Ulm, Germany.
    Complement C3 and C5 deficiency affects fracture healing.2013Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, nr 11, artikel-id UNSP e81341Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    There is increasing evidence that complement may play a role in bone development. Our previous studies demonstrated that the key complement receptor C5aR was strongly expressed in the fracture callus not only by immune cells but also by bone cells and chondroblasts, indicating a function in bone repair. To further elucidate the role of complement in bone healing, this study investigated fracture healing in mice in the absence of the key complement molecules C3 and C5. C3(-/-) and C5(-/-) as well as the corresponding wildtype mice received a standardized femur osteotomy, which was stabilized using an external fixator. Fracture healing was investigated after 7 and 21 days using histological, micro-computed tomography and biomechanical measurements. In the early phase of fracture healing, reduced callus area (C3(-/-): -25%, p=0.02; C5(-/-): -20% p=0.052) and newly formed bone (C3(-/-): -38%, p=0.01; C5(-/-): -52%, p=0.009) was found in both C3- and C5-deficient mice. After 21 days, healing was successful in the absence of C3, whereas in C5-deficient mice fracture repair was significantly reduced, which was confirmed by a reduced bending stiffness (-45%; p=0.029) and a smaller callus volume (-17%; p=0.039). We further demonstrated that C5a was activated in C3(-/-) mice, suggesting cleavage via extrinsic pathways. Our results suggest that the activation of the terminal complement cascade in particular may be crucial for successful fracture healing.

  • 67.
    Ekstrand-Hammarström, Barbro
    et al.
    Swedish Def Res Agcy, Linköping.
    Hong, Jaan
    Uppsala University.
    Davoodpour, Padideh
    Uppsala University.
    Sandholm, Kerstin
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Nilsson Ekdahl, Kristina
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    Bucht, Anders
    Umeå University.
    Nilsson, Bo
    Uppsala University.
    TiO2 nanoparticles tested in a novel screening whole human blood model of toxicity trigger adverse activation of the kallikrein system at low concentrations2015Ingår i: Biomaterials, ISSN 0142-9612, E-ISSN 1878-5905, Vol. 51, s. 58-68Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    There is a compelling need to understand and assess the toxicity of industrially produced nanoparticles (NPs). In order to appreciate the long-term effects of NPs, sensitive human-based screening tests that comprehensively map the NP properties are needed to detect possible toxic mechanisms. Animal models can only be used in a limited number of test applications and are subject to ethical concerns, and the interpretation of experiments in animals is also distorted by the species differences. Here, we present a novel easy-to-perform highly sensitive whole-blood model using fresh non-anticoagulated human blood, which most justly reflects complex biological cross talks in a human system. As a demonstrator of the tests versatility, we evaluated the toxicity of TiO2 NPs that are widely used in various applications and otherwise considered to have relatively low toxic properties. We show that TiO2 NPs at very low concentrations (50 ng/mL) induce strong activation of the contact system, which in this model elicits thromboinflammation. These data are in line with the finding of components of the contact system in the protein corona of the TiO2 NPs after exposure to blood. The contact system activation may lead to both thrombotic reactions and generation of bradykinin, thereby representing fuel for chronic inflammation in vivo and potentially long-term risk of autoimmunity, arteriosclerosis and cancer. These results support the notion that this novel whole-blood model represents an important contribution to testing of NP toxicity. (C) 2015 Elsevier Ltd. All rights reserved.

  • 68.
    Elmlund, Louise
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Käck, Camilla
    Attana AB.
    Aastrup, Teodor
    Attana AB.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    Study of the Interaction of Trastuzumab and SKOV3 Epithelial Cancer Cells Using a Quartz Crystal Microbalance Sensor2015Ingår i: Sensors, ISSN 1424-8220, E-ISSN 1424-8220, Vol. 15, nr 3, s. 5884-5894Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Analytical methods founded upon whole cell-based assays are of importance in early stage drug development and in fundamental studies of biomolecular recognition. Here we have studied the binding of the monoclonal antibody trastuzumab to human epidermal growth factor receptor 2 (HER2) on human ovary adenocarcinoma epithelial cancer cells (SKOV3) using quartz crystal microbalance (QCM) technology. An optimized procedure for immobilizing the cells on the chip surface was established with respect to fixation procedure and seeding density. Trastuzumab binding to the cell decorated sensor surface was studied, revealing a mean dissociation constant, K-D, value of 7 +/- 1 nM (standard error of the mean). This study provides a new perspective on the affinity of the antibody-receptor complex presented a more natural context compared to purified receptors. These results demonstrate the potential for using whole cell-based QCM assay in drug development, the screening of HER2 selective antibody-based drug candidates, and for the study of biomolecular recognition. This real time, label free approach for studying interactions with target receptors present in their natural environment afforded sensitive and detailed kinetic information about the binding of the analyte to the target.

  • 69.
    Elmlund, Louise
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Söderberg, Pernilla
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Suriyanarayanan, Subramanian
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    A Phage Display Screening Derived Peptide with Affinity for the Adeninyl Moiety2014Ingår i: Biosensors, ISSN 2079-6374, Vol. 4, nr 2, s. 137-149Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Phage display screening of a surface-immobilized adenine derivative led to the identification of a heptameric peptide with selectivity for adenine as demonstrated through quartz crystal microbalance (QCM) studies. The peptide demonstrated a concentration dependent affinity for an adeninyl moiety decorated surface (KD of 968 ± 53.3 μM), which highlights the power of piezoelectric sensing in the study of weak interactions. 

    Ladda ner fulltext (pdf)
    Biosensors
  • 70.
    Ensterö, Mats
    et al.
    Stockholm University.
    Åkerborg, Örjan
    Stockholm University ; KTH Royal Institute of Technology.
    Lundin, Daniel
    Stockholm University.
    Wang, Bei
    Duke University, USA.
    Furey, Terrence S
    Institute for Genome Sciences and Policy (IGSP), USA ; Duke University, USA.
    Öhman, Marie
    Stockholm University.
    Lagergren, Jens
    Stockholm University ; KTH Royal Institute of Technology.
    A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins2010Ingår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 11, artikel-id 6Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    BACKGROUND: Several bioinformatic approaches have previously been used to find novel sites of ADAR mediated A-to-I RNA editing in human. These studies have discovered thousands of genes that are hyper-edited in their non-coding intronic regions, especially in alu retrotransposable elements, but very few substrates that are site-selectively edited in coding regions. Known RNA edited substrates suggest, however, that site selective A-to-I editing is particularly important for normal brain development in mammals.

    RESULTS: We have compiled a screen that enables the identification of new sites of site-selective editing, primarily in coding sequences. To avoid hyper-edited repeat regions, we applied our screen to the alu-free mouse genome. Focusing on the mouse also facilitated better experimental verification. To identify candidate sites of RNA editing, we first performed an explorative screen based on RNA structure and genomic sequence conservation. We further evaluated the results of the explorative screen by determining which transcripts were enriched for A-G mismatches between the genomic template and the expressed sequence since the editing product, inosine (I), is read as guanosine (G) by the translational machinery. For expressed sequences, we only considered coding regions to focus entirely on re-coding events. Lastly, we refined the results from the explorative screen using a novel scoring scheme based on characteristics for known A-to-I edited sites. The extent of editing in the final candidate genes was verified using total RNA from mouse brain and 454 sequencing.

    CONCLUSIONS: Using this method, we identified and confirmed efficient editing at one site in the Gabra3 gene. Editing was also verified at several other novel sites within candidates predicted to be edited. Five of these sites are situated in genes coding for the neuron-specific RNA binding proteins HuB and HuD.

    Ladda ner fulltext (pdf)
    fulltext
  • 71.
    Ersmark, Karolina
    et al.
    Uppsala University.
    Feierberg, Isabella
    Uppsala University.
    Bjelic, Sinisa
    Uppsala University.
    Hamelink, Elizabeth
    National Institute for Medical Research, UK.
    Hackett, Fiona
    Medivir AB.
    Blackman, Michael J
    Medivir AB.
    Hultén, Johan
    Uppsala University.
    Samuelsson, Bertil
    Medivir AB.
    Aqvist, Johan
    Uppsala University.
    Hallberg, Anders
    Uppsala University.
    Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity2004Ingår i: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 47, nr 1, s. 110-122Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The hemoglobin-degrading aspartic proteases plasmepsin I (Plm I) and plasmepsin II (Plm II) of the malaria parasite Plasmodium falciparum have lately emerged as putative drug targets. A series of C(2)-symmetric compounds encompassing the 1,2-dihydroxyethylene scaffold and a variety of elongated P1/P1' side chains were synthesized via microwave-assisted palladium-catalyzed coupling reactions. Binding affinity calculations with the linear interaction energy method and molecular dynamics simulations reproduced the experimental binding data obtained in a Plm II assay with very good accuracy. Bioactive conformations of the elongated P1/P1' chains were predicted and agreed essentially with a recent X-ray structure. The compounds exhibited picomolar to nanomolar inhibition constants for the plasmepsins and no measurable affinity to the human enzyme cathepsin D. Some of the compounds also demonstrated significant inhibition of parasite growth in cell culture. To the best of our knowledge, these plasmepsin inhibitors represent the most selective reported to date and constitute promising lead compounds for further optimization.

  • 72.
    Ersmark, Karolina
    et al.
    Uppsala University.
    Feierberg, Isabella
    Uppsala University.
    Bjelic, Sinisa
    Uppsala University.
    Hultén, Johan
    Uppsala University.
    Samuelsson, Bertil
    Medivir AB.
    Åqvist, Johan
    Uppsala University.
    Hallberg, Anders
    Uppsala University.
    C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: synthesis and theoretical predictions2003Ingår i: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, E-ISSN 1464-3391, Vol. 11, nr 17, s. 3723-3733Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A series of C(2)-symmetric compounds with a mannitol-based scaffold has been investigated, both theoretically and experimentally, as Plm II inhibitors. Four different stereoisomers with either benzyloxy or allyloxy P1/P1' side chains were studied. Computational ranking of the binding affinities of the eight compounds was carried out using the linear interaction energy (LIE) method relying on a complex previously determined by crystallography. Within both series of isomers the theoretical binding energies were in agreement with the enzymatic measurements, illustrating the power of the LIE method for the prediction of ligand affinities prior to synthesis. The structural models of the enzyme-inhibitor complexes obtained from the MD simulations provided a basis for interpretation of further structure-activity relationships. Hence, the affinity of a structurally similar ligand, but with a different P2/P2' substituent was examined using the same procedure. The predicted improvement in binding constant agreed well with experimental results.

  • 73. Eytan, G D
    et al.
    Persson, Bengt L.
    UNIV STOCKHOLM, ARRHENIUS LAB, DEPT BIOCHEM.
    Ekebacke, A
    Rydström, J
    Energy-linked nicotinamide-nucleotide transhydrogenase. Characterization of reconstituted ATP-driven transhydrogenase from beef heart mitochondria.1987Ingår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 262, s. 5008-5014Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The interaction between pure transhydrogenase and ATPase (Complex V) from beef heart mitochondria was investigated with transhydrogenase-ATPase vesicles in which the two proteins were co-reconstituted by dialysis or dilution procedures. In addition to phosphatidylcholine and phosphatidylethanolamine, reconstitution required phosphatidylserine and lysophosphatidylcholine. Transhydrogenase-ATPase vesicles catalyzed a 20-30-fold stimulation of the reduction of NADP+ or thio-NADP+ by NADH and a 70-fold shift of the apparent equilibrium expressed as the nicotinamide nucleotide ratio [NADPH][NAD+]/[NADP+][NADH]. In both of these respects, the transhydrogenase-ATPase vesicles were severalfold more efficient than beef heart submitochondrial particles. By measuring the ATP-driven transhydrogenase and the oligomycin-sensitive ATPase activities simultaneously and under the same conditions at low ATP concentrations, i.e. below 15 microM, the ATP-driven transhydrogenase/oligomycin-sensitive ATPase activity ratio was found to be about 3. This value is consistent with the stoichiometries of three protons translocated per ATP hydrolyzed and one proton translocated per NADPH formed and with a mechanism where the two enzymes interact through a delocalized proton-motive force. 

  • 74.
    Fagerqvist, Therese
    et al.
    Uppsala University.
    Näsström, Thomas
    Uppsala University.
    Ihse, Elisabet
    Uppsala University.
    Lindström, Veronica
    Uppsala University.
    Sahlin, Charlotte
    Uppsala University.
    Tucker, Stina M. Fangmark
    BioArctic Neurosci AB, Stockholm.
    Kasaryan, Alex
    BioArctic Neurosci AB, Stockholm.
    Karlsson, Mikael
    Uppsala University.
    Nikolajeff, Fredrik
    Uppsala University.
    Schell, Heinrich
    Hertie Inst Clin Brain Res, Germany;German Ctr Neurodegenerat Dis, Germany.
    Outeiro, Tiago F.
    Univ Med Ctr Göttingen, Germany.
    Kahle, Philipp J.
    Hertie Inst Clin Brain Res, Germany;German Ctr Neurodegenerat Dis, Germany.
    Lannfelt, Lars
    Uppsala University.
    Ingelsson, Martin
    Uppsala University.
    Bergström, Joakim
    Uppsala University.
    Off-pathway α-synuclein oligomers seem to alter α-synuclein turnover in a cell model but lack seeding capability in vivo2013Ingår i: Amyloid: Journal of Protein Folding Disorders, ISSN 1350-6129, E-ISSN 1744-2818, Vol. 20, nr 4, s. 233-244Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Aggregated alpha-synuclein is the major component of Lewy bodies, protein inclusions observed in the brain in neurodegenerative disorders such as Parkinson's disease and dementia with Lewy bodies. Experimental evidence indicates that alpha-synuclein potentially can be transferred between cells and act as a seed to accelerate the aggregation process. Here, we investigated in vitro and in vivo seeding effects of alpha-synuclein oligomers induced by the reactive aldehyde 4-oxo-2-nonenal (ONE). As measured by a Thioflavin-T based fibrillization assay, there was an earlier onset of aggregation when alpha-synuclein oligomers were added to monomeric alpha-synuclein. In contrast, exogenously added alpha-synuclein oligomers did not induce aggregation in a cell model. However, cells overexpressing alpha-synuclein that were treated with the oligomers displayed reduced alpha-synuclein levels, indicating that internalized oligomers either decreased the expression or accelerated the degradation of transfected alpha-synuclein. Also in vivo there were no clear seeding effects, as intracerebral injections of alpha-synuclein oligomers into the neocortex of alpha-synuclein transgenic mice did not induce formation of proteinase K resistant alpha-synuclein pathology. Taken together, we could observe a seeding effect of the ONE-induced alpha-synuclein oligomers in a fibrillization assay, but neither in a cell nor in a mouse model.

  • 75. Felix, H
    et al.
    Brodelius, Peter
    Lunds Universitet.
    Mosbach, K
    Enzyme Activities of the Primary and Secondary Metabolism of Simultaneously Permeabilized and Immobilized Plant Cells1981Ingår i: Analytical biochemistry, Vol. 116, nr 2, s. 462-470Artikel i tidskrift (Refereegranskat)
  • 76.
    Fischer, Benjamin
    et al.
    Fraunhofer Inst Biomed Engn, Germany.
    Meier, Anna
    Fraunhofer Inst Biomed Engn, Germany;Tech Univ Munich, Germany.
    Dehne, Annika
    Fraunhofer Inst Biomed Engn, Germany.
    Salhotra, Aseem
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Fraunhofer Inst Biomed Engn, Germany.
    Tran, Thao Anh
    Neumann, Sascha
    Fraunhofer Inst Biomed Engn, Germany;Univ Clin Essen, Germany.
    Schmidt, Katharina
    Fraunhofer Inst Biomed Engn, Germany.
    Meiser, Ina
    Fraunhofer Inst Biomed Engn, Germany.
    Neubauer, Julia C.
    Fraunhofer Inst Biomed Engn, Germany;Fraunhofer Project Ctr Stem Cell Proc Engn, Germany.
    Zimmermann, Heiko
    Fraunhofer Inst Biomed Engn, Germany;Fraunhofer Project Ctr Stem Cell Proc Engn, Germany;Saarland Univ, Germany;Univ Catolica Norte, Chile.
    Gentile, Luca
    Fraunhofer Inst Biomed Engn, Germany;Univ Appl Sci Kaiserslautern, Germany;Hasselt Univ, Belgium.
    A complete workflow for the differentiation and the dissociation of hiPSC-derived cardiospheres2018Ingår i: Stem Cell Research, ISSN 1873-5061, E-ISSN 1876-7753, Vol. 32, s. 65-72Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) are an invaluable tool for both basic and translational cardiovascular research. The potential that these cells hold for therapy, disease modeling and drug discovery is hampered by several bottlenecks that currently limit both the yield and the efficiency of cardiac induction. Here, we present a complete workflow for the production of ready-to-use hiPSC-CMs in a dynamic suspension bioreactor. This includes the efficient and highly reproducible differentiation of hiPSCs into cardiospheres, which display enhanced physiological maturation compared to static 3D induction in hanging drops, and a novel papain-based dissociation method that offers higher yield and viability than the broadly used dissociation reagents TrypLE and Accutase. Molecular and functional analyses of the cardiomyocytes reseeded after dissociation confirmed both the identity and the functionality of the cells, which can be used in down-stream applications, either as monolayers or spheroids.

  • 77.
    Fjällström, Ann-Kristin
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Evertsson, Kim
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Norrby, Marlene
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Tågerud, Sven
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Forkhead box O1 and muscle RING finger 1protein expression in atrophic and hypertrophicdenervated mouse skeletal muscle2014Ingår i: Journal of Molecular Signaling, ISSN 1750-2187, E-ISSN 1750-2187, Vol. 9, artikel-id 9Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Forkhead box O (FoxO) transcription factors and E3 ubiquitin ligases such as Muscle RING finger 1 (MuRF1) are believed to participate in the regulation of skeletal muscle mass. The function of FoxO transcription factors is regulated by post-translational modifications such as phosphorylation and acetylation. In the present study FoxO1 protein expression, phosphorylation and acetylation as well as MuRF1 protein expression, were examined in atrophic and hypertrophic denervated skeletal muscle. Methods: Protein expression, phosphorylation and acetylation were studied semi-quantitatively using Western blots. Muscles studied were 6-days denervated mouse hind-limb muscles (anterior tibial as well as pooled gastrocnemius and soleus muscles, all atrophic), 6-days denervated mouse hemidiaphragm muscles (hypertrophic) and innervated control muscles. Total muscle homogenates were used as well as separated nuclear and cytosolic fractions of innervated and 6-days denervated anterior tibial and hemidiaphragm muscles. Results: Expression of FoxO1 and MuRF1 proteins increased 0.3-3.7-fold in all 6-days denervated muscles studied, atrophic as well as hypertrophic. Phosphorylation of FoxO1 at S256 increased about 0.8-1-fold after denervation in pooled gastrocnemius and soleus muscles and in hemidiaphragm but not in unfractionated anterior tibial muscle. A small (0.2-fold) but statistically significant increase in FoxO1 phosphorylation was, however, observed in cytosolic fractions of denervated anterior tibial muscle. A statistically significant increase in FoxO1 acetylation (0.8-fold) was observed only in denervated anterior tibial muscle. Increases in total FoxO1 and in phosphorylated FoxO1 were only seen in cytosolic fractions of denervated atrophic anterior tibial muscle whereas in denervated hypertrophic hemidiaphragm both total FoxO1 and phosphorylated FoxO1 increased in cytosolic as well as in nuclear fractions. MuRF1 protein expression increased in cytosolic as well as in nuclear fractions of both denervated atrophic anterior tibial muscle and denervated hypertrophic hemidiaphragm muscle. Conclusions: Increased expression of FoxO1 and MuRF1 in denervated muscles (atrophic as well as hypertrophic) suggests that these proteins participate in the tissue remodelling occurring after denervation. The effect of denervation on the level of phosphorylated and acetylated FoxO1 differed in the muscles studied and may be related to differences in fiber type composition of the muscles.

  • 78.
    Fjällström, Ann-Kristin
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Norrby, Marlene
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Tågerud, Sven
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Expression and phosphorylation of eukaryotic translation initiation factor 4-gamma (eIF4G) in denervated atrophic and hypertrophic mouse skeletal muscle2015Ingår i: Cell Biology International, ISSN 1065-6995, E-ISSN 1095-8355, Vol. 39, nr 4, s. 496-501Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The eukaryotic translation initiation factor 4-gamma (eIF4G) is important for the initiation of protein synthesis and phosphorylation on S1108 regulates this function of eIF4G. Thus, increased phosphorylation has been reported in conditions associated with increased protein synthesis such as meal feeding and insulin/IGF-1 treatment whereas decreased phosphorylation occurs following starvation, dexamethasone treatment, in sepsis and in atrophic denervated hind-limb muscle. The aim of the present study was to test the hypothesis that S1108 phosphorylation of eIF4G is differentially affected in denervated atrophic hind-limb muscles and denervated hypertrophic hemidiaphragm muscle. Protein expression and phosphorylation in innervated and 6-days denervated atrophic hind-limb muscles (pooled gastrocnemius and soleus) and hypertrophic hemidiaphragms were studied semi-quantitatively using Western blots. Total expression of eIF4G did not change in denervated hind-limb muscles but increased about 77% in denervated hemidiaphragm. S1108 phosphorylated eIF4G decreased about 64% in denervated hind-limb muscles but increased about 1.3-fold in denervated hemidiaphragm. The ratio of S1108 phosphorylated eIF4G to total eIF4G decreased about 60% in denervated hind-limb muscles but no statistically significant change was observed in denervated hemidiaphragm. The differential effect of denervation on eIF4G expression and S1108 phosphorylation in hemidiaphragm (hypertrophic) and hind-limb muscle (atrophic) may represent a regulatory mechanism that helps clarify the differential response of these muscles following denervation.

  • 79.
    Friedman, Ran
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Aggregation of amyloids in a cellular context: modelling and experiment2011Ingår i: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 438, s. 415-426Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Amyloid-related diseases are a group of illnesses in which an abnormal accumulation of proteins into fibrillar structures is evident. Results from a wide range of studies, ranging from identification of amyloid-β dimers in the brain to biophysical characterization of the interactions between amyloidogenic peptides and lipid membranes during fibril growth shed light on the initial events which take place during amyloid aggregation. Accounts of fibril disaggregation and formation of globular aggregates due to interactions with lipids or fatty acids further demonstrate the complexity of the aggregation process and the difficulty to treat amyloid-related diseases. There is an inherent difficulty in generalizing from studies of aggregation in vitro, but the involvement of too many cellular components limits the ability to follow amyloid aggregation in a cellular (or extracellular) context. Fortunately, the development of experimental methods to generate stable globular aggregates suggests new means of studying the molecular events associated with amyloid aggregation. Furthermore, simulation studies enable deeper understanding of the experimental results and provide useful predictions that can be tested in the laboratory. Computer simulations can nowadays provide molecular or even atomistic details that are experimentally not available or very difficult to obtain. In the present review, recent developments on modelling and experiments of amyloid aggregation are reviewed, and an integrative account on how isolated interactions (as observed in vitro and in silico) combine during the course of amyloid-related diseases is presented. Finally, it is argued that an integrative approach is necessary to get a better understanding of the protein aggregation process.

  • 80.
    Friedman, Ran
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Drug Resistance Missense Mutations in Cancer Are Subject to Evolutionary Constraints2013Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, nr 12, artikel-id e82059Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Several tumor types are sensitive to deactivation of just one or very few genes that are constantly active in the cancer cells,a phenomenon that is termed oncogene addiction'. Drugs that target the products of those oncogenes can yield a temporary relief, and even complete remission. Unfortunately, many patients receiving oncogene-targeted therapies relapse on treatment. This often happens due to somatic mutations in the oncogene (resistance mutations"). 'Compound mutations', which in the context of cancer drug resistance are defined as two or more mutations of the drug target in the same clone may lead to enhanced resistance against the most selective inhibitors. Here, it is shown that the vast majority the resistance mutations occurring in cancer patients treated with tyrosin kinase inhibitors aimed at three different proteins follow an evolutionary pathway. Using bioinforrnatic analysis tools, found that the drug-resistance mutations in the tyrosine kinase domains of Abl1, ALK and exons 20 and 21 of EGFR favour transformations to residues that can be identified in similar positions in evolutionary related proteins. The results demonstrate that evolutionary pressure shapes the mutational landscape in the case of drug-resistance somatic mutations. The constraints on the mutational landscape suggest that it may be possible to counter single drug-resistance point mutations. The observation of relatively many resistance mutations in Abl1, but not in the other genes, is explained by the fact that mutations in Abl1 tend to be biochemically conservative, whereas mutations in EGFR and ALK tend to be radical. Analysis of Abl1 compound mutations suggests that such mutations are more prevalent than hitherto reported and may be more difficult to counter. This supports the notion that such mutations may provide an escape route for targeted cancer drug resistance.

  • 81.
    Friedman, Ran
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Bjelic, Sinisa
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Simulations Studies of Protein Kinases that are Molecular Targets in Cancer2020Ingår i: Israel Journal of Chemistry, ISSN 0021-2148, s. 1-15Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Protein kinases are enzymes with partially overlapping specificities, many of which are important clinical targets. In this article, we give some background on protein kinases and discuss in more depth four such enzymes that have been studied in our labs using computer simulations. The combination of molecular dynamics simulations and enzyme or cell growth experiments was instrumental to explain why certain mutations lead (or do not lead) to resistance to targeted therapy aimed at these proteins. Stochastic network simulations were used to study protein-protein interactions and suggest points for intervention against tumour growth.

  • 82.
    Friedman, Ran
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Caflisch, Amedeo
    Department of Biochemistry, University of Zürich.
    Surfactant Effects on Amyloid Aggregation Kinetics2011Ingår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 414, s. 303-312Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    There is strong experimental evidence of the influence of surfactants (e.g., fatty acids) on the kinetics of amyloid fibril formation. However, the structures of mixed assemblies and interactions between surfactants and fibril-forming peptides are still not clear. Here, coarse-grained simulations are employed to study the aggregation kinetics of amyloidogenic peptides in the presence of amphiphilic lipids. The simulations show that the lower the fibril formation propensity of the peptides, the higher the influence of the surfactants on the peptide self-assembly kinetics. In particular, the lag phase of weakly aggregating peptides increases because of the formation of mixed oligomers, which are promoted by hydrophobic interactions and favorable entropy of mixing. A transient peak in the number of surfactants attached to the growing fibril is observed before reaching the mature fibril in some of the simulations. This peak originates from transient fibrillar defects consisting of exposed hydrophobic patches on the fibril surface, which provide a possible explanation for the temporary maximum of fluorescence observed sometimes in kinetic traces of the binding of small-molecule dyes to amyloid fibrils.

    Ladda ner fulltext (pdf)
    fulltext
  • 83.
    Friedman, Ran
    et al.
    University of Zürich, Switzerland.
    Pellarin, R
    Caflisch, A
    Amyloid aggregation on lipid bilayers and its impact on membrane permeability2009Ingår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 387, nr 2, s. 407-415Artikel i tidskrift (Refereegranskat)
  • 84.
    Friedman, Ran
    et al.
    University of Zürich, Switzerland.
    Pellarin, R
    Caflisch, A
    Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles2010Ingår i: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 1, nr 2, s. 471-474Artikel i tidskrift (Refereegranskat)
  • 85. Funk, C
    et al.
    Brodelius, Peter
    Institute of Biotechnology ETH-Hönggerberg CH-8093 Zürich, Switzerland.
    Influence of Growth Regulators and an Elicitor on Phenylpropanoid Metabolism in Suspension Cultures of Vanilla planifolia1990Ingår i: Phytochemistry, ISSN 0031-9422, E-ISSN 1873-3700, Vol. 29, nr 3, s. 845-848Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A cell suspension culture of Vanilla planifolia has been established in MS-medium. 2,4-D suppressed while NAA enhanced the formation of extractable phenolics. Cytokinins appeared to favour lignin biosynthesis. Treatment of the culture with chitosan resulted in the induction of various enzymes of phenylpropanoid metabolism, while the amount of extractable phenolics decreased due to their rapid incorporation into polymeric ligneous material. 

  • 86. Funk, C
    et al.
    Brodelius, Peter
    Department of Plant Biochemistry, University of Lund.
    Phenylpropanoid Metabolism in Suspension Cultures of Vanilla planifolia. Andr. II. Effects of Precursor Feeding and Metabolic Inhibitors1990Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 94, s. 95-101Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Feeding of cinnamic acid and ferulic acid to non-treated andchitosan-treated cell suspension cultures of Vanilla planifoIiaresulted in the formation of trace amounts of p-hydroxy benzoicacid (5.2 micrograms per gram fresh weight of cells) and vanillicacid (6.4 micrograms per gram fresh weight of cells), respectively.Addition of a 4-hydroxycinnamate: CoA-ligase inhibitor, 3,4-(methylenedioxy)-cinnamic acid (MDCA), resulted in a reducedbiosynthesis of ligneous material with a simultaneous significantincreased vanillic acid formation (around 75 micrograms per gramfresh weight of cells). A K, of 100 micromolar for 4-hydroxycinnamate:CoA-ligase in a crude preparation was estimated for thisinhibitor. It is suggested that the conversion of cinnamic acidsinto benzoic acids does not involve cinnamoyl CoA esters asintermediates. Feeding of 14C-cinnamic acid and 14C-ferulic acidto cells treated with MDCA indicate that cinnamic acid, but notferulic acid, is a precursor of vanillic acid in these cultivated cellsof V. planifolia. 

  • 87. Funk, C
    et al.
    Brodelius, Peter
    Department of Plant Biochemistry, University of Lund.
    Phenylpropanoid Metabolism in Suspension Cultures of Vanilla planifolia. Andr. III. Conversion of 4-Methoxycinnamic acids into 4-Hydroxybenzoic acids1990Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 94, s. 102-108Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Feeding of 4-methoxycinnamic acid, 3,4-dimethoxycinnamicacid and 3,4,5-trimethoxycinnamic acid to cell suspension culturesof Vanilla planifolia resulted in the formation of 4-hydroxybenzoicacid, vanillic acid, and syringic acid, respectively. Thehomologous 4-methoxybenzoic acids were demethylated to thesame products. It is concluded that the side chain degradingenzyme system accepts the 4-methoxylated substrates while thedemethylation occurs at the benzoic acid level. The demethylatingenzyme is specific for the 4-position. Feeding of [10_4Cmethyl]-3,4-dimethoxycinnamic acid revealed that the first stepin the conversion is the glycosylation of the cinnamic acid to itsglucose ester. A partial purification of a UDP-glucose: transcinnamicacid glucosyltransferase is reported. 4-Methoxy substitutedcinnamic acids are better substrates for this enzyme than4-hydroxy substituted cinnamic acid. It is suggested that 4-methoxysubstituted cinnamic acids are intermediates in the biosyntheticconversion of cinnamic acids to benzoic acids in cells ofV. planifolia. 

  • 88. Funk, C
    et al.
    Gügler, K
    Brodelius, Peter
    Institute of Biotechnology, ETH/Hönggerberg, CH-8093 Zürich, Switzerland.
    Increased Secondary Product Formation in Plant Cell Suspension Cultures after Treatment with a Yeast Carbohydrate (Elicitor)1987Ingår i: Phytochemistry, ISSN 0031-9422, E-ISSN 1873-3700, Vol. 26, s. 401-405Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A carbohydrate fraction isolated from yeast extract by ethanolic precipitation was used as an elicitor to induce secondary product formation in plant cell suspension cultures. The elicitor preparation is effective in inducing glyceollin isomer synthesis (up to 200 μg glyceollin per g dry wt) in cells of Glycine max and enhancing berberine biosynthesis (up to four-fold) in cells of Thalictrum rugosum. The response of the cell cultures to the elicitor treatment is dependent on the amount of carbohydrate per unit of biomass and on the physiological state of the cells. Cells are optimally induced in late exponential or early stationary growth phases. 

  • 89.
    Georgoulia, Panagiota S.
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). University of Gothenburg, Sweden.
    Bjelic, Sinisa
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Friedman, Ran
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Deciphering the molecular mechanism of FLT3 resistance mutations2020Ingår i: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    FMS-like tyrosine kinase 3 (FLT3) has been found to be mutated in 30% of acute myeloid leukaemia patients. Small-molecule inhibitors targeting FLT3 that are currently approved or still undergoing clinical trials are subject to drug resistance due to FLT3 mutations. How these mutations lead to drug resistance is hitherto poorly understood. Herein, we studied the molecular mechanism of the drug resistance mutations D835N, Y842S and M664I, which confer resistance against the most advanced inhibitors, quizartinib and PLX3397 (pexidartinib), using enzyme kinetics and computer simulations. In vitro kinase assays were performed to measure the comparative catalytic activity of the native protein and the mutants, using a bacterial expression system developed to this aim. Our results reveal that the differential drug sensitivity profiles can be rationalised by the dynamics of the protein-drug interactions and perturbation of the intraprotein contacts upon mutations. Drug binding induced a single conformation in the native protein, whereas multiple conformations were observed otherwise (in the mutants or in the absence of drugs). The end-point kinetics measurements indicated that the three resistant mutants conferred catalytic activity that is at least as high as that of the reference without such mutations. Overall, our calculations and measurements suggest that the structural dynamics of the drug-resistant mutants that affect the active state and the increased conformational freedom of the remaining inactive drug-bound population are the two major factors that contribute to drug resistance in FLT3 harbouring cancer cells. Our results explain the mechanism of drug resistance mutations and can aid to the design of more effective tyrosine kinase inhibitors.

  • 90.
    Georgoulia, Panagiota S.
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Glykos, Nicholas M.
    University of Thrace, Greece.
    Molecular simulation of peptides coming of age: accurate prediction of folding, dynamics and structures2019Ingår i: Archives of Biochemistry and Biophysics, ISSN 0003-9861, E-ISSN 1096-0384, Vol. 664, nr March, s. 76-88Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The application of molecular dynamics simulations to study the folding and dynamics of peptides has attracted a lot of interest in the last couple of decades. Following the successful prediction of the folding of several proteins using molecular simulation, foldable peptides emerged as a favourable system mainly due to their application in improving protein structure prediction methods and in drug design studies. However, their performance is inherently linked to the accuracy of the empirical force fields used in the simulations, whose optimisation and validation is of paramount importance. Here we review the most important findings in the field of molecular peptide simulations and highlight the significant advancements made over the last twenty years. Special reference is made on the simulation of disordered peptides and the remaining challenge to find a force field able to describe accurately their conformational landscape.

  • 91.
    Georgoulia, Panagiota S.
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Todde, Guido
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Bjelic, Sinisa
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Friedman, Ran
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    The catalytic activity of Abl1 single and compound mutations: Implications for the mechanism of drug resistance mutations in chronic myeloid leukaemia2019Ingår i: Biochimica et Biophysica Acta - General Subjects, ISSN 0304-4165, E-ISSN 1872-8006, Vol. 1863, nr 4, s. 732-741Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background

    Abl1 is a protein tyrosine kinase whose aberrant activation due to mutations is the culprit of several cancers, most notably chronic myeloid leukaemia. Several Abl1 inhibitors are used as anti-cancer drugs. Unfortunately, drug resistance limits their effectiveness. The main cause for drug resistance is mutations in the kinase domain (KD) of Abl1 that evolve in patients. The T315I mutation confers resistance against all clinically-available inhibitors except ponatinib. Resistance to ponatinib can develop by compound (double) mutations.

    Methods

    Kinetic measurements of the KD of Abl1 and its mutants were carried out to examine their catalytic activity. Specifically, mutants that lead to drug resistance against ponatinib were considered. Molecular dynamics simulations and multiple sequence analysis were used for explanation of the experimental findings.

    Results

    The catalytic efficiency of the T315I pan-resistance mutant is more than two times lower than that of the native KD. All ponatinib resistant mutations restore the catalytic efficiency of the enzyme. Two of them (G250E/T315I and Y253H/E255V) have a catalytic efficiency that is more than five times that of the native KD.

    Conclusions

    The measurements and analysis suggest that resistance is at least partially due to the development of a highly efficient kinase through subsequent mutations. The simulations highlight modifications in two structurally important regions of Abl1, the activation and phosphate binding loops, upon mutations.

    General significance

    Experimental and computational methods were used together to explain how mutations in the kinase domain of Abl1 lead to resistance against the most advanced drug currently in use to treat chronic myeloid leukaemia.

  • 92.
    Gliszczynska, Anna
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Brodelius, Peter E.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Sesquiterpene coumarins2012Ingår i: Phytochemistry Reviews, ISSN 1568-7767, E-ISSN 1572-980X, Vol. 11, nr 1, s. 77-96Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Plants have a long history as therapeutic tools in the treatment of human diseases and have been used as a source of medicines for ages. In search of new biologically active natural products, many plants and herbs used in traditional medicine are screened for natural products with pharmacological activity. In this paper, we present a group of natural products, the sesquiterpene coumarins isolated from plants, and describe their wide range of biological activity. Sesquiterpene coumarins are found in some plants of the families Apiaceae (Umbelliferae), Asteraceae (Compositae) and Rutaceae. The coumarin moiety is often umbelliferone (7-hydroxycoumarin) but scopo- letin (7-hydroxy-6-methoxycoumarin) and isofraxidin (7-hydroxy-6,8-dimethoxycoumarin) are also found. These coumarins are linked to a C15 terpene moiety through an ether linkage. Another group of sesquiter- pene coumarins is the prenylated 4-hydroxycoumarins where the link between the coumarin and the C15 terpene moiety is a C–C-bond at carbon 3 of the coumarin moiety. Finally, the prenylfurocoumarin-type sesquiterpenoids are a separate group of sesquiterpene coumarins based on the suggested biosynthetic pathway. Our relatively limited knowledge on the biosynthesis of sesquiterpene coumarins is reviewed.

  • 93.
    Gonzalez Palmén, Lorena
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Homotrimeric dUTPases: Principles of Catalysis and Inhibitor Design2009Doktorsavhandling, monografi (Övrigt vetenskapligt)
    Abstract [en]

    The ubiquitous enzyme dUTPase hydrolyzes dUTP into dUMP and pyrophosphate, preventing DNA fragmentation and cell death due to accumulation of dUTP. Inhibitors of dUTPase could serve as drugs in the treatment of cancers and infectious diseases. This thesis presents five studies. A mutational study on the Escherichia coli dUTPase (S72A) provides new insights about the catalytic principles of the homotrimeric dUTPases. A model is presented in which transition state formation is associated with a rotation of the conserved Ser72 side chain. The model can explain the strict order of deamination and hydrolysis catalyzed by the bifunctional dCTP deaminase:dUTPases. The S72A/D90N double mutant is currently investigated. Preliminary data indicate that this form preserves the binding properties of the S72A mutant but is completely inactive, making it attractive for structural studies. In the remaining studies we compare the binding of substrate analogues to the human, the E. coli and the equine infectious anemia virus (EIAV) homotrimeric dUTPases. One study concerns 2´,3´-dideoxy-UTP (ddUTP) and shows that removal of the 3´-hydroxyl group increases KM, ten times with the cellular dUTPases and fifty times with the viral dUTPase, but does not affect kcat with any of these enzymes. Another study concerns the inhibitory effects of 3´-azido-2´,3´-dideoxy-UTP. This derivative binds to the bacterial dUTPase but not to the other forms making it a potential lead for the development of antibacterial dUTPase inhibitors. Yet another study investigates two uracil derivatives. Both compounds are found to inhibit the human, the bacterial but not the viral dUTPase. The inhibition is shown to be competitive.

    Ladda ner fulltext (pdf)
    FULLTEXT01
  • 94.
    Gonzalez Palmén, Lorena
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Becker, Kristian
    Department of Pure and Applied Biochemistry, Lund UniVersity, Lund, Sweden.
    Bülow, Leif
    Department of Pure and Applied Biochemistry, Lund UniVersity, Lund, Sweden.
    Kvassman, Jan-Olov
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    A Double Role for a Strictly Conserved Serine: Further Insights into the dUTPase Catalytic Mechanism2008Ingår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 47, nr 30, s. 7863-7874Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ser72 at the active site of the Escherichia coli dUTPase has been mutated to an alanine, and the properties of the mutant have been investigated. The serine is absolutely conserved among the monomeric and trimeric dUTPases (including the bifunctional dCTP deaminase:dUTPases), and it has been proposed to promote catalysis by balancing negative charge at the oxygen that bridges the α- and  β-phosphorus of the substrate. In all reported complexes of dUTPases with the substrate analogue α,β-imido-dUTP·Mg, the serine β-OH is indeed hydrogen bonded to the α,β-bridging nitrogen of the analogue. However, in the complex of the Asp90→Asn mutant dUTPase with the true substrate dUTP·Mg, the serine β-OH points in the opposite direction and may form a hydrogen bond to Asn84 at the bottom of the pyrimidine pocket. Here we show that the replacement of the β-OH by hydrogen reduces kcat from 5.8 to 0.008 s-1 but also k-1, the rate of substrate dissociation, from 6.2 to 0.1 s-1 (KM = 6 × 10-9 M). We conclude that the serine β-OH exercises both ground state (GS) destabilization and transition state (TS) stabilization, effects not usually linked to a single residue. With experimental support, we argue that the β-OH destabilizes the GS by imposing conformational constraints on the enzyme and that formation ofthe TS depends on a rotation of the serine side chain that not only relieves the constraints but brings the β-OH into a position where it can electrostatically stabilize the TS. This rotation would also allow the β-OH to promote both deamination and hydrolysis in the bifunctional deaminases. We find that the E. coli dUTPase does not catalyze the hydrolysis of the α,β-imido-dUTP·Mg, suggesting that the analogue provides the hydrogen in the bond to the serine β-OH.

  • 95.
    Grimberg, Kristian Björk
    et al.
    Stockholm University.
    Beskow, Anne
    Stockholm University.
    Lundin, Daniel
    Stockholm University.
    Davis, Monica M
    Stockholm University.
    Young, Patrick
    Stockholm University.
    Basic Leucine Zipper Protein Cnc-C Is a Substrate and Transcriptional Regulator of the Drosophila 26S Proteasome2011Ingår i: Molecular and Cellular Biology, ISSN 0270-7306, E-ISSN 1098-5549, Vol. 31, nr 4, s. 897-909Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    While the 26S proteasome is a key proteolytic complex, little is known about how proteasome levels are maintained in higher eukaryotic cells. Here we describe an RNA interference (RNAi) screen of Drosophila melanogaster that was used to identify transcription factors that may play a role in maintaining levels of the 26S proteasome. We used an RNAi library against 993 Drosophila transcription factor genes to identify genes whose suppression in Schneider 2 cells stabilized a ubiquitin-green fluorescent protein reporter protein. This screen identified Cnc (cap 'n' collar [CNC]; basic region leucine zipper) as a candidate transcriptional regulator of proteasome component expression. In fact, 20S proteasome activity was reduced in cells depleted of cnc. Immunoblot assays against proteasome components revealed a general decline in both 19S regulatory complex and 20S proteasome subunits after RNAi depletion of this transcription factor. Transcript-specific silencing revealed that the longest of the seven transcripts for the cnc gene, cnc-C, was needed for proteasome and p97 ATPase production. Quantitative reverse transcription-PCR confirmed the role of Cnc-C in activation of transcription of genes encoding proteasome components. Expression of a V5-His-tagged form of Cnc-C revealed that the transcription factor is itself a proteasome substrate that is stabilized when the proteasome is inhibited. We propose that this single cnc gene in Drosophila resembles the ancestral gene family of mammalian nuclear factor erythroid-derived 2-related transcription factors, which are essential in regulating oxidative stress and proteolysis.

  • 96.
    Grinberg, Inna Rozman
    et al.
    Stockholm University.
    Lundin, Daniel
    Stockholm University.
    Hasan, Mahmudul
    Stockholm University ; Lund University.
    Crona, Mikael
    Swedish Ophan Biovitrum AB.
    Jonna, Venkateswara Rao
    Umeå University.
    Loderer, Chrishtoph
    Stockholm University.
    Sahlin, Margareta
    Stockholm University.
    Markova, Natalia
    Malvern Instruments Inc.
    Borovok, Ilya
    Tel Aviv University, Israel.
    Berggren, Gustav
    Uppsala University.
    Hofer, Anders
    Umeå University.
    Logan, Derek T.
    Lund University.
    Sjöberg, Britt-Marie
    Stockholm University.
    Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit2018Ingår i: eLIFE, E-ISSN 2050-084X, Vol. 7, artikel-id e31529Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ribonucleotide reductases (RNRs) are key enzymes in DNA metabolism, with allosteric mechanisms controlling substrate specificity and overall activity. In RNRs, the activity master-switch, the ATP-cone, has been found exclusively in the catalytic subunit. In two class I RNR subclasses whose catalytic subunit lacks the ATP-cone, we discovered ATP-cones in the radical-generating subunit. The ATP-cone in the Leeuwenhoekiella blandensis radical-generating subunit regulates activity via quaternary structure induced by binding of nucleotides. ATP induces enzymatically competent dimers, whereas dATP induces non-productive tetramers, resulting in different holoenzymes. The tetramer forms by interactions between ATP-cones, shown by a 2.45 A crystal structure. We also present evidence for an (MnMnIV)-Mn-III metal center. In summary, lack of an ATP-cone domain in the catalytic subunit was compensated by transfer of the domain to the radical-generating subunit. To our knowledge, this represents the first observation of transfer of an allosteric domain between components of the same enzyme complex.

    Ladda ner fulltext (pdf)
    fulltext
  • 97.
    Grinberg, Inna Rozman
    et al.
    Stockholm University.
    Lundin, Daniel
    Stockholm University.
    Sahlin, Margareta
    Uppsala University.
    Crona, Mikael
    Stockholm University.
    Berggren, Gustav
    Uppsala University.
    Hofer, Anders
    Umeå University.
    Sjöberg, Britt-Marie
    Stockholm University.
    A glutaredoxin domain fused to the radical-generating subunit of ribonucleotide reductase (RNR) functions as an efficient RNR reductant2018Ingår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 293, nr 41, s. 15889-15900Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Class I ribonucleotide reductase (RNR) consists of a catalytic subunit (NrdA) and a radical-generating subunit (NrdB) that together catalyze reduction of ribonucleotides to their corresponding deoxyribonucleotides. NrdB from the firmicute Facklamia ignava is a unique fusion protein with N-terminal add-ons of a glutaredoxin (Grx) domain followed by an ATP-binding domain, the ATP cone. Grx, usually encoded separately from the RNR operon, is a known RNR reductant. We show that the fused Grx domain functions as an efficient reductant of the F. ignava class I RNR via the common dithiol mechanism and, interestingly, also via a monothiol mechanism, although less efficiently. To our knowledge, a Grx that uses both of these two reaction mechanisms has not previously been observed with a native substrate. The ATP cone is in most RNRs an N-terminal domain of the catalytic subunit. It is an allosteric on/off switch promoting ribonucleotide reduction in the presence of ATP and inhibiting RNR activity in the presence of dATP. We found that dATP bound to the ATP cone of F. ignava NrdB promotes formation of tetramers that cannot form active complexes with NrdA. The ATP cone bound two dATP molecules but only one ATP molecule. F. ignava NrdB contains the recently identified radical-generating cofactor MnIII/MnIV. We show that NrdA from F. ignava can form a catalytically competent RNR with the MnIII/MnIV-containing NrdB from the flavobacterium Leeuwenhoekiella blandensis. In conclusion, F. ignava NrdB is fused with a Grx functioning as an RNR reductant and an ATP cone serving as an on/off switch.

  • 98.
    Guo, Ming
    et al.
    Zhejiang A & F University, China.
    Lu, Xiaowang
    Zhejiang A & F University, China.
    Wang, Yan
    Zhejiang A & F University, China.
    Brodelius, Peter E.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Comparison of the interaction between lactoferrin and isomeric drugs2017Ingår i: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 173, s. 593-607Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The binding properties of pentacyclic triterpenoid isomeric drugs, i.e. ursolic acid (UA) and oleanolic acid (OA), to bovine lactoferrin (BLF) have been studied by molecule modeling, fluorescence spectroscopy, UV-visible absorbance spectroscopy and infrared spectroscopy (IR). Molecular docking, performed to reveal the possible binding mode or mechanism, suggested that hydrophobic interaction and hydrogen bonding play important roles to stabilize the complex. The results of spectroscopic measurements showed that the two isomeric drugs both strongly quenched the intrinsic fluorescence of BLF through a static quenching procedure although some differences between UM and OA binding strength and non-radiation energy transfer occurred within the molecules. The number of binding sites was 3.44 and 3.10 for UA and OA, respectively, and the efficiency of Forster energy transfer provided a distance of 0.77 and 1.21 nm for UA and OA, respectively. The conformation transformation of BLF affected by the drugs conformed to the "all-or-none" pattern. In addition, the changes of the ratios of alpha-helices, beta-sheets and beta-turns of BLF during the process of the interaction were obtained. The results of the experiments in combination with the calculations showed that there are two modes of pentacyclic triterpenoid binding to BLF instead of one binding mode only governed by the principle of the lowest bonding energy.

  • 99.
    Göransson, Ulf
    et al.
    Uppsala University.
    Gunasekera, Sunithi
    Uppsala university.
    Malik, Sohaib
    Uppsala university.
    Park, Sungkyu
    Uppsala university.
    Slazak, Blazej
    Uppsala university.
    Jacobsson, Erik
    Uppsala University.
    Andersson, Håkan S.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Strömstedt, Adam
    Uppsala university.
    Peptide biodiscovery from plants and animals: structure to function2016Ingår i: Planta Medica, ISSN 0032-0943, E-ISSN 1439-0221, Vol. 82, nr Supplement 1, artikel-id SL49Artikel i tidskrift (Övrigt vetenskapligt)
  • 100. Gügler, K
    et al.
    Funk, C
    Brodelius, Peter
    Institute of Biotechnology, Swiss Federal Institute of Technology, Hönggerberg, CH-8093 Zfirich, Switzerland.
    Elicitor-induced Tyrosine Decarboxylase in Berberine Synthesizing Suspension Cultures of Thalictrum rugosum1988Ingår i: European Journal of Biochemistry, ISSN 0014-2956, E-ISSN 1432-1033, Vol. 170, nr 3, s. 661-666Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Tyrosine decarboxylase (EC 4.1.1.25) was induced in suspension cultures of Thalictrum rugosum by treatment with a yeast glucan elicitor. Maximum induction was observed at a carbohydrate concentration of 0.4 mg/g fresh weight of cells and maximum enzyme activity was reached 20 h after addition of elicitor. The enzyme was inducible in late exponential and early stationary growth phases. A good correlation between induced tyrosine decarboxylase activity and berberine biosynthesis has been established. It is suggested that tyrosine decarboxylase may be a key enzyme between primary and secondary metabolisms in the biosynthesis of norlaudanosoline-derived alkaloids. 

123456 51 - 100 av 264
RefereraExporteraLänk till träfflistan
Permanent länk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf