Stanislaw Dunin-Horkawicz

Summary

Affiliation: International Institute of Molecular and Cell Biology
Country: Poland

Publications

  1. doi request reprint Prokaryotic ancestry of eukaryotic protein networks mediating innate immunity and apoptosis
    Stanislaw Dunin-Horkawicz
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany Electronic address
    J Mol Biol 426:1568-82. 2014
  2. pmc MODOMICS: a database of RNA modification pathways
    Stanislaw Dunin-Horkawicz
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, PL 02 190 Warsaw, Poland
    Nucleic Acids Res 34:D145-9. 2006
  3. pmc Phylogenomic analysis of the GIY-YIG nuclease superfamily
    Stanislaw Dunin-Horkawicz
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    BMC Genomics 7:98. 2006
  4. doi request reprint Mechanism of regulation of receptor histidine kinases
    Hedda U Ferris
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 20:56-66. 2012
  5. doi request reprint The mechanisms of HAMP-mediated signaling in transmembrane receptors
    Hedda U Ferris
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 19:378-85. 2011
  6. pmc The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase
    Elzbieta Purta
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks, Trojdena 4, 02 109 Warsaw, Poland
    BMC Mol Biol 7:23. 2006
  7. doi request reprint A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins
    Birte Hernandez Alvarez
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    J Struct Biol 170:236-45. 2010
  8. pmc Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria
    Marcus D Hartmann
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Proc Natl Acad Sci U S A 109:20907-12. 2012
  9. ncbi request reprint A soluble mutant of the transmembrane receptor Af1503 features strong changes in coiled-coil periodicity
    Marcus D Hartmann
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    J Struct Biol 186:357-66. 2014
  10. doi request reprint Measuring the conformational space of square four-helical bundles with the program samCC
    Stanislaw Dunin-Horkawicz
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, 72076 Tubingen, Germany
    J Struct Biol 170:226-35. 2010

Collaborators

Detail Information

Publications20

  1. doi request reprint Prokaryotic ancestry of eukaryotic protein networks mediating innate immunity and apoptosis
    Stanislaw Dunin-Horkawicz
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany Electronic address
    J Mol Biol 426:1568-82. 2014
    ..This analysis supports the notion that the innate immunity networks of eukaryotes originated from their endosymbionts and that increases in the complexity of these networks accompanied the emergence of multicellularity. ..
  2. pmc MODOMICS: a database of RNA modification pathways
    Stanislaw Dunin-Horkawicz
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, PL 02 190 Warsaw, Poland
    Nucleic Acids Res 34:D145-9. 2006
    ..The contents of MODOMICS can be accessed through the World Wide Web at http://genesilico.pl/modomics/...
  3. pmc Phylogenomic analysis of the GIY-YIG nuclease superfamily
    Stanislaw Dunin-Horkawicz
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    BMC Genomics 7:98. 2006
    ..However, to date no systematic search for novel members of the GIY-YIG superfamily or comparative analysis of these enzymes has been reported...
  4. doi request reprint Mechanism of regulation of receptor histidine kinases
    Hedda U Ferris
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 20:56-66. 2012
    ..We propose that altered recognition of the catalytic domain by DHp, rather than a shift in position of the phospho-accepting histidine, forms the basis for regulation of kinase activity...
  5. doi request reprint The mechanisms of HAMP-mediated signaling in transmembrane receptors
    Hedda U Ferris
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 19:378-85. 2011
    ..These are correlated with activity and ligand response in vitro and in vivo by incorporating Af1503 HAMP into mycobacterial adenylyl cyclase assay systems...
  6. pmc The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase
    Elzbieta Purta
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks, Trojdena 4, 02 109 Warsaw, Poland
    BMC Mol Biol 7:23. 2006
    ....
  7. doi request reprint A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins
    Birte Hernandez Alvarez
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    J Struct Biol 170:236-45. 2010
    ..Here we present the first detailed analysis of two fundamentally different coiled-coil periodicities being accommodated in the same structure...
  8. pmc Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria
    Marcus D Hartmann
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Proc Natl Acad Sci U S A 109:20907-12. 2012
    ....
  9. ncbi request reprint A soluble mutant of the transmembrane receptor Af1503 features strong changes in coiled-coil periodicity
    Marcus D Hartmann
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    J Struct Biol 186:357-66. 2014
    ..The structure offers the first view of the junction between the transmembrane region and HAMP and explains the conservation of a key sequence motif in HAMP domains. ..
  10. doi request reprint Measuring the conformational space of square four-helical bundles with the program samCC
    Stanislaw Dunin-Horkawicz
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, 72076 Tubingen, Germany
    J Struct Biol 170:226-35. 2010
    ..We also find that one of the originally proposed Alacoil proteins, Rop, in fact has canonical packing. SamCC is freely available as a web service athttp://toolkit.tuebingen.mpg.de/samcc...
  11. ncbi request reprint Axial helix rotation as a mechanism for signal regulation inferred from the crystallographic analysis of the E. coli serine chemoreceptor
    Hedda U Ferris
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    J Struct Biol 186:349-56. 2014
    ..The presented findings extend the cogwheel model for signal transmission to chemoreceptors. ..
  12. pmc The GD box: a widespread noncontiguous supersecondary structural element
    Vikram Alva
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Protein Sci 18:1961-6. 2009
    ....
  13. pmc Delineation of structural domains and identification of functionally important residues in DNA repair enzyme exonuclease VII
    Katarzyna Poleszak
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Ks Trojdena 4, PL 02 109 Warsaw, Poland
    Nucleic Acids Res 40:8163-74. 2012
    ..Altogether, we propose a model of sequence-structure-function relationships in ExoVII...
  14. pmc The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification
    Karolina A Majorek
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, PL 02 109 Warsaw, Poland, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA USA 22908, USA, Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL 61 614 Poznan, Poland, Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, PL 02 089 Warsaw, Poland, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, PL 02 106 Warsaw, Poland and Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, PL 02 109 Warsaw, Poland
    Nucleic Acids Res 42:4160-79. 2014
    ..Our analysis provides a comprehensive picture of sequence-structure-function relationships in the RNHL superfamily that may guide functional studies of the previously uncharacterized protein families. ..
  15. pmc Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases
    Karolina L Tkaczuk
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
    BMC Bioinformatics 8:73. 2007
    ..However, no comprehensive comparative analysis of these proteins has been carried out to classify them based on structural and evolutionary criteria and to guide functional predictions...
  16. doi request reprint Comprehensive analysis of HAMP domains: implications for transmembrane signal transduction
    Stanislaw Dunin-Horkawicz
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, D 72076 Tuebingen, Germany
    J Mol Biol 397:1156-74. 2010
    ....
  17. doi request reprint Two unique membrane-bound AAA proteins from Sulfolobus solfataricus
    Justyna Serek-Heuberger
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Biochem Soc Trans 37:118-22. 2009
    ..They form ring complexes, which are stable after solubilization in a mild detergent and whose formation is dependent on the presence of the N-terminal extensions...
  18. pmc A coiled-coil motif that sequesters ions to the hydrophobic core
    Marcus D Hartmann
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Proc Natl Acad Sci U S A 106:16950-5. 2009
    ..More generally, we think that polar motifs that are both periodic and conserved may often reflect special folding requirements, rather than an unstructured state of the mature proteins...
  19. pmc MODOMICS: a database of RNA modification pathways--2013 update
    Magdalena A Machnicka
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, PL 02 109 Warsaw, Poland
    Nucleic Acids Res 41:D262-7. 2013
    ..New options for database searching and querying have been implemented, including a BLAST search of protein sequences and a PARALIGN search of the collected nucleic acid sequences...
  20. doi request reprint Computational modeling of protein-RNA complex structures
    Irina Tuszynska
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul ks Trojdena 4, PL 02 109 Warsaw, Poland Electronic address
    Methods 65:310-9. 2014
    ..In this article we present an overview of strategies and methods for computational modeling of protein-RNA complexes, including software developed in our laboratory, and illustrate it with practical examples of structural predictions. ..