Bengt Persson

Summary

Country: Sweden

Publications

  1. pmc The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns
    Hanane Moummou
    Universite de Toulouse, INPT ENSAT, UMR990 Génomique et Biotechnologie des fruits, Avenue de l Agrobiopole, BP 32607, Castanet Tolosan F 31326, France
    BMC Plant Biol 12:219. 2012
  2. doi request reprint Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs)
    Bengt Persson
    IFM Bioinformatics and SeRC Swedish e Science Research Centre, Linkoping University, Linkoping, Sweden
    Chem Biol Interact 202:111-5. 2013
  3. pmc Medium- and short-chain dehydrogenase/reductase gene and protein families : the MDR superfamily
    B Persson
    IFM Bioinformatics, Linkoping University, Sweden
    Cell Mol Life Sci 65:3879-94. 2008
  4. pmc The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative
    Bengt Persson
    IFM Bioinformatics, Linkoping University, Linkoping, Sweden
    Chem Biol Interact 178:94-8. 2009
  5. ncbi request reprint Coenzyme-based functional assignments of short-chain dehydrogenases/reductases (SDRs)
    Bengt Persson
    IFM Bioinformatics, Linkoping University, S 581 83, Linkoping, Sweden
    Chem Biol Interact 143:271-8. 2003
  6. doi request reprint Autoimmune T cell responses to antigenic peptides presented by bronchoalveolar lavage cell HLA-DR molecules in sarcoidosis
    Jan Wahlstrom
    Karolinska Institutet, Department of Medicine, Lung Research Laboratory, L4 01, Karolinska University Hospital, Solna, 171 76 Stockholm, Sweden
    Clin Immunol 133:353-63. 2009
  7. doi request reprint Classification of the short-chain dehydrogenase/reductase superfamily using hidden Markov models
    Yvonne Kallberg
    IFM Bioinformatics, Linkoping University, Linkoping, Sweden
    FEBS J 277:2375-86. 2010
  8. pmc Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement
    Joel Hedlund
    IFM Bioinformatics, Linkoping University, S 581 83 Linkoping, Sweden
    BMC Bioinformatics 11:534. 2010
  9. pmc RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum
    Nicolas Joannin
    Department of Microbiology, Cell and Tumor biology MTC, Karolinska Institutet, SE 17177 Stockholm, Sweden
    BMC Genomics 12:119. 2011
  10. doi request reprint Superfamilies SDR and MDR: from early ancestry to present forms. Emergence of three lines, a Zn-metalloenzyme, and distinct variabilities
    Hans Jornvall
    Department of Medical Biochemistry and Biophysics MBB, Karolinska Institutet, SE 17177 Stockholm, Sweden
    Biochem Biophys Res Commun 396:125-30. 2010

Collaborators

Detail Information

Publications45

  1. pmc The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns
    Hanane Moummou
    Universite de Toulouse, INPT ENSAT, UMR990 Génomique et Biotechnologie des fruits, Avenue de l Agrobiopole, BP 32607, Castanet Tolosan F 31326, France
    BMC Plant Biol 12:219. 2012
    ..Recent classification methods, relying on hidden-Markov models (HMMs), improved identification and enabled the construction of a nomenclature. However, functional annotations of plant SDRs remain scarce...
  2. doi request reprint Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs)
    Bengt Persson
    IFM Bioinformatics and SeRC Swedish e Science Research Centre, Linkoping University, Linkoping, Sweden
    Chem Biol Interact 202:111-5. 2013
    ..The classification method has paved the ground for a sustainable and expandable nomenclature system. Information on the SDR superfamily is continuously updated at http://sdr-enzymes.org/...
  3. pmc Medium- and short-chain dehydrogenase/reductase gene and protein families : the MDR superfamily
    B Persson
    IFM Bioinformatics, Linkoping University, Sweden
    Cell Mol Life Sci 65:3879-94. 2008
    ..Combined, they have specific substrates in metabolic pathways, some with wide substrate specificity, and several with little known functions...
  4. pmc The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative
    Bengt Persson
    IFM Bioinformatics, Linkoping University, Linkoping, Sweden
    Chem Biol Interact 178:94-8. 2009
    ..A functional subdivision of the SDR superfamily into at least 200 SDR families based upon hidden Markov models forms a suitable foundation for such a nomenclature system, which we present in this paper using human SDRs as examples...
  5. ncbi request reprint Coenzyme-based functional assignments of short-chain dehydrogenases/reductases (SDRs)
    Bengt Persson
    IFM Bioinformatics, Linkoping University, S 581 83, Linkoping, Sweden
    Chem Biol Interact 143:271-8. 2003
    ..We also find that NADP(H) is the preferred coenzyme among most classical SDRs, while NAD(H) is that preferred among most extended SDRs...
  6. doi request reprint Autoimmune T cell responses to antigenic peptides presented by bronchoalveolar lavage cell HLA-DR molecules in sarcoidosis
    Jan Wahlstrom
    Karolinska Institutet, Department of Medicine, Lung Research Laboratory, L4 01, Karolinska University Hospital, Solna, 171 76 Stockholm, Sweden
    Clin Immunol 133:353-63. 2009
    ..By using antigenic peptides presented in vivo in the lungs of sarcoidosis patients, we have identified blood and lung T cell autoimmune responses that may help sustain the inflammation in this disease...
  7. doi request reprint Classification of the short-chain dehydrogenase/reductase superfamily using hidden Markov models
    Yvonne Kallberg
    IFM Bioinformatics, Linkoping University, Linkoping, Sweden
    FEBS J 277:2375-86. 2010
    ..About half of the SDR families are only found among bacteria, where the 'classical' SDR type is most prominent. The HMM-based classification is used as a basis for a sustainable and expandable nomenclature system...
  8. pmc Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement
    Joel Hedlund
    IFM Bioinformatics, Linkoping University, S 581 83 Linkoping, Sweden
    BMC Bioinformatics 11:534. 2010
    ..However, gathering good quality training data usually requires manual attention by experts and has therefore been the rate limiting step for expanding the number of available models...
  9. pmc RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum
    Nicolas Joannin
    Department of Microbiology, Cell and Tumor biology MTC, Karolinska Institutet, SE 17177 Stockholm, Sweden
    BMC Genomics 12:119. 2011
    ..These sub-groups require phylogenetic analysis to sort out, which is not practical for large-scale projects, such as the sequencing of patient isolates and meta-genomic analysis...
  10. doi request reprint Superfamilies SDR and MDR: from early ancestry to present forms. Emergence of three lines, a Zn-metalloenzyme, and distinct variabilities
    Hans Jornvall
    Department of Medical Biochemistry and Biophysics MBB, Karolinska Institutet, SE 17177 Stockholm, Sweden
    Biochem Biophys Res Commun 396:125-30. 2010
    ..Differences among structural and catalytic zinc ions may be relative and involve several states. Combined, the comparisons trace evolutionary properties of huge superfamilies, with partially redundant enzymes in cellular redox functions...
  11. ncbi request reprint Short-chain dehydrogenases/reductases (SDRs)
    Yvonne Kallberg
    Department of Medical Biochemistry and Biophysics and Stockholm Bioinformatics Centre, Karolinska Institutet, Sweden
    Eur J Biochem 269:4409-17. 2002
    ..We show that, in spite of the great diversity of the SDR superfamily, the primary structure alone can be used for functional assignments and for predictions of coenzyme preference...
  12. ncbi request reprint Molecular dynamics studies of alpha-helix stability in fibril-forming peptides
    Erik Nordling
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 77, Sweden
    J Comput Aided Mol Des 22:53-8. 2008
    ..The MD results are in several cases compatible with known experimental data, but the correlation is not perfect, indicating that multimerisation tendency and other factors might also be important for fibril formation...
  13. ncbi request reprint Medium-chain dehydrogenases/reductases (MDR). Family characterizations including genome comparisons and active site modeling
    Erik Nordling
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S 171 77 Stockholm, Sweden
    Eur J Biochem 269:4267-76. 2002
    ..Finally, sequence patterns were derived that are diagnostic for the different families and can be used in genome annotations...
  14. pmc Epstein-barr virus encodes three bona fide ubiquitin-specific proteases
    Ramakrishna Sompallae
    Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
    J Virol 82:10477-86. 2008
    ..DUB activity was confirmed by functional assays and mutation analysis for three high scoring candidates, supporting the usefulness of this bioinformatics approach in predicting distant homologues of cellular enzymes...
  15. ncbi request reprint Analysis of ancient sequence motifs in the H-PPase family
    Joel Hedlund
    IFM Bioinformatics, Linkoping University, Sweden
    FEBS J 273:5183-93. 2006
    ....
  16. pmc Characterization of oligopeptide patterns in large protein sets
    Anders Bresell
    IFM Bioinformatics, Linkoping University, S 581 83 Linkoping, Sweden
    BMC Genomics 8:346. 2007
    ..Therefore, it is important to characterize these informational peptide patterns to shed light on possible new applications and the pitfalls implicit in neglecting bias in peptide patterns...
  17. doi request reprint Origin and evolution of medium chain alcohol dehydrogenases
    Hans Jornvall
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
    Chem Biol Interact 202:91-6. 2013
    ..They further show that simple molecular observations on patterns, multiplicities and occurrence give much information, suggesting common divergence rules not much disturbed by horizontal gene transfers after the initial origins...
  18. pmc Evolutionary conservation of the ribosomal biogenesis factor Rbm19/Mrd1: implications for function
    Yvonne Kallberg
    Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
    PLoS ONE 7:e43786. 2012
    ..The patterns of evolutionary conservation provide information for experimental analyses of the function of Rbm19/Mrd1. In vivo mutational analysis confirmed that a highly conserved loop 5-β4-strand in RBD6 is essential for function...
  19. doi request reprint Characterization of new medium-chain alcohol dehydrogenases adds resolution to duplications of the class I/III and the sub-class I genes
    Ella Cederlund
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
    Chem Biol Interact 191:8-13. 2011
    ....
  20. pmc Investigation and prediction of the severity of p53 mutants using parameters from structural calculations
    Jonas Carlsson
    IFM Bioinformatics, Linkoping University, Sweden
    FEBS J 276:4142-55. 2009
    ..As a result of the severity score calculated for every mutant, valuable knowledge can be gained regarding p53, a protein that is believed to be involved in over 50% of all human cancers...
  21. ncbi request reprint Prediction of coenzyme specificity in dehydrogenases/reductases. A hidden Markov model-based method and its application on complete genomes
    Yvonne Kallberg
    IFM Bioinformatics, Linkoping University, Sweden
    FEBS J 273:1177-84. 2006
    ..The described method is available at http://www.ifm.liu.se/bioinfo, where the preferred coenzyme and its binding region are predicted given an amino acid sequence as input...
  22. doi request reprint Quasispecies dynamics and molecular evolution of human norovirus capsid P region during chronic infection
    Beatrice Carlsson
    Division of Molecular Virology, Department of Clinical and Experimental Medicine, Medical Faculty, 58185 Linköping University, Linkoping, Sweden
    J Gen Virol 90:432-41. 2009
    ..In conclusion, this study provides novel insights to the evolutionary process of norovirus during chronic infection...
  23. pmc Functionally important amino acids in the Arabidopsis thylakoid phosphate transporter: homology modeling and site-directed mutagenesis
    Lorena Ruiz-Pavón
    Division of Molecular Genetics, Department of Physics, Chemistry, and Biology, Linkoping University, Linkoping, Sweden
    Biochemistry 49:6430-9. 2010
    ..Functional characterization of ANTR1 should provide useful insights into the function of other plant and mammalian SLC17 homologous transporters...
  24. ncbi request reprint Short-chain dehydrogenases/reductases (SDR): the 2002 update
    Udo Oppermann
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 17177, Stockholm, Sweden
    Chem Biol Interact 143:247-53. 2003
    ....
  25. pmc Short-chain dehydrogenase/reductase (SDR) relationships: a large family with eight clusters common to human, animal, and plant genomes
    Yvonne Kallberg
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S 171 77 Stockholm, Sweden
    Protein Sci 11:636-41. 2002
    ..Close to half of these gene products represent steroid dehydrogenases, emphasizing the regulatory importance of these enzymes...
  26. pmc Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing
    Fredrik Lysholm
    IFM Bioinformatics and Swedish e Science Research Centre SeRC, Linkoping University, Linkoping, Sweden
    PLoS ONE 7:e30875. 2012
    ..The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin...
  27. doi request reprint Investigating protein variants using structural calculation techniques
    Jonas Carlsson
    IFM Bioinformatics and SeRC Swedish e Science Research Centre, Linkoping University, Linkoping, Sweden
    Methods Mol Biol 857:313-30. 2012
    ..To take this information one step further, we also describe prediction methods that can be used to judge the effects of mutations and how to evaluate these and the interplay between the protein properties...
  28. ncbi request reprint Multiplicity of eukaryotic ADH and other MDR forms
    Hans Jornvall
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77, Stockholm, Sweden
    Chem Biol Interact 143:255-61. 2003
    ....
  29. ncbi request reprint Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes
    Johan Nilsson
    Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    Proteins 60:606-16. 2005
    ..The results strongly support the notion that a biased distribution of Lys and Arg residues between cytoplasmic and extra-cytoplasmic segments (the positive-inside rule) is present in most if not all organisms...
  30. doi request reprint Enrichment of ligands with molecular dockings and subsequent characterization for human alcohol dehydrogenase 3
    Mikko Hellgren
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
    Cell Mol Life Sci 67:3005-15. 2010
    ..Two compounds showed inhibition capacity (deoxycholic acid and doxorubicin), and with these data three different lines for specific inhibitors for ADH3 are suggested: fatty acids, glutathione analogs, and cholic acids...
  31. ncbi request reprint Disruption of the GDNF binding site in NCAM dissociates ligand binding and homophilic cell adhesion
    Dan Sjöstrand
    Division of Molecular Neurobiology, Department of Neuroscience, Karolinska Institute, S 171 77 Stockholm, Sweden
    J Biol Chem 282:12734-40. 2007
    ..The GDNF-NCAM interface allows complex formation with the GDNF family receptor alpha1, shedding light on the molecular architecture of a multicomponent GDNF receptor...
  32. pmc FAAST: Flow-space Assisted Alignment Search Tool
    Fredrik Lysholm
    IFM Bioinformatics and SeRC Swedish e Science Research Centre, Linkoping University, S 581 83 Linkoping, Sweden
    BMC Bioinformatics 12:293. 2011
    ..These errors are less efficiently detected by most conventional alignment programs and may produce inaccurate alignments...
  33. ncbi request reprint A new polymorphism in the coding region of exon four in HSD17B2 in relation to risk of sporadic and hereditary breast cancer
    Agneta Jansson
    Department of Biomedicine and Surgery, Linkoping University, 581 85, Linkoping, Sweden
    Breast Cancer Res Treat 106:57-64. 2007
    ..We suggest that the detected polymorphism does not contribute to a higher risk of developing breast cancer...
  34. doi request reprint Analysis of mammalian alcohol dehydrogenase 5 (ADH5): characterisation of rat ADH5 with comparisons to the corresponding human variant
    Linus J Ostberg
    SciLifeLab, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
    Chem Biol Interact 202:97-103. 2013
    ..Further possibilities are conceivable: the ADH5 protein may have to interact with a stabiliser, or the gene is actually a pseudogene...
  35. ncbi request reprint Evidence for a negative association between schizophrenia and a polymorphism in the insulin receptor substrate-3 (IRS-3) gene
    Kristina Melkersson
    Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
    Neuro Endocrinol Lett 33:321-30. 2012
    ..In the present study, we chose to study the insulin receptor substrate-3 (IRS-3) gene as a candidate gene in schizophrenia...
  36. pmc An efficient simulator of 454 data using configurable statistical models
    Fredrik Lysholm
    IFM Bioinformatics and SeRC Swedish e Science Research Centre, Linkoping University, S 581 83 Linkoping, Sweden
    BMC Res Notes 4:449. 2011
    ..abstract:..
  37. ncbi request reprint Ontology annotation treebrowser : an interactive tool where the complementarity of medical subject headings and gene ontology improves the interpretation of gene lists
    Anders Bresell
    IFM Bioinformatics, Linkoping University, Linkoping, Sweden
    Appl Bioinformatics 5:225-36. 2006
    ..With OAT, we illustrate the benefits of combining MeSH and GO for understanding gene lists. OAT is available as a public web service at: http://www.ifm.liu.se/bioinfo/oat...
  38. doi request reprint The fellowship of the RING: the RING-B-box linker region interacts with the RING in TRIM21/Ro52, contains a native autoantigenic epitope in Sjögren syndrome, and is an integral and conserved region in TRIM proteins
    Janosch Hennig
    Molecular Biotechnology, IFM, Campus Valla, Linkoping University, SE 581 83 Linkoping, Sweden
    J Mol Biol 377:431-49. 2008
    ..Sequence similarities and evolutionary sequence patterns suggest that the results obtained from Ro52 are extendable to the entire TRIM protein family...
  39. ncbi request reprint Bioinformatic and enzymatic characterization of the MAPEG superfamily
    Anders Bresell
    IFM Bioinformatics, Linkoping University, Sweden
    FEBS J 272:1688-703. 2005
    ....
  40. ncbi request reprint Folding into a beta-hairpin can prevent amyloid fibril formation
    Waltteri Hosia
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S 171 77 Stockholm, Sweden
    Biochemistry 43:4655-61. 2004
    ..These data indicate that the structural context in which a potential fibril forming sequence is present can prevent fibril formation by favoring self-limiting oligomerization over polymerization...
  41. ncbi request reprint Mutation analysis of the human 5-lipoxygenase C-terminus: support for a stabilizing C-terminal loop
    Hisayo Okamoto
    Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, S 171 77 Stockholm, Sweden
    Biochim Biophys Acta 1749:123-31. 2005
    ..In the structure of soybean lipoxygenase-1, a C-terminal loop was pointed out as important for correct orientation of the C-terminus. Accordingly, a hydrogen bond appears to stabilize such a C-terminal loop also in 5LO...
  42. pmc Model of the complex of Parathyroid hormone-2 receptor and Tuberoinfundibular peptide of 39 residues
    Mirna Abraham-Nordling
    Division of Surgery, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
    BMC Res Notes 3:270. 2010
    ..The two related peptides parathyroid hormone (PTH) and parathyroid hormone related protein (PTHrP) are compared with the complex to examine their interactions...
  43. pmc Identification of HLA-DR-bound peptides presented by human bronchoalveolar lavage cells in sarcoidosis
    Jan Wahlstrom
    Lung Research Laboratory, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
    J Clin Invest 117:3576-82. 2007
    ..For the first time, to our knowledge, we have identified HLA-bound peptides presented in vivo during an inflammatory condition. This approach can be extended to characterize HLA-bound peptides in various autoimmune settings...
  44. pmc Prediction of partial membrane protein topologies using a consensus approach
    Johan Nilsson
    Stockholm Bioinformatics Centre, AlbaNova, Sweden
    Protein Sci 11:2974-80. 2002
    ..Reliably predicted partial topologies may simplify experimental determinations of membrane protein topology...
  45. ncbi request reprint Molecular model of human CYP21 based on mammalian CYP2C5: structural features correlate with clinical severity of mutations causing congenital adrenal hyperplasia
    Tiina Robins
    Department of Molecular Medicine and Surgery, Center for Molecular Medicine CMM L8 02, Karolinska Institutet Karolinska University Hospital, S 17176 Stockholm, Sweden
    Mol Endocrinol 20:2946-64. 2006
    ..Structural features deduced from the models are in good correlation with clinical severity of CYP21 mutants, which shows the applicability of a modeling approach in assessment of new CYP21 mutations...