Dagmar Klostermeier

Summary

Country: Germany

Publications

  1. doi request reprint Mapping the spectrum of conformational states of the DNA- and C-gates in Bacillus subtilis gyrase
    Markus G Rudolph
    F Hoffmann La Roche AG, Pharma Research and Early Development, Discovery Technologies, Grenzacherstrasse 124, CH 4070 Basel, Switzerland
    J Mol Biol 425:2632-40. 2013
  2. pmc Lifelong companions: RNA helicases and their roles in RNA metabolism
    Dagmar Klostermeier
    Institute for Physical Chemistry, University of Muenster, Muenster, Germany
    RNA Biol 10:2-3. 2013
  3. doi request reprint Single-molecule FRET reveals nucleotide-driven conformational changes in molecular machines and their link to RNA unwinding and DNA supercoiling
    Dagmar Klostermeier
    University of Basel, Biozentrum, Klingelbergstrasse 70, 4056 Basel, Switzerland
    Biochem Soc Trans 39:611-6. 2011
  4. pmc The GyrA-box determines the geometry of DNA bound to gyrase and couples DNA binding to the nucleotide cycle
    Martin A Lanz
    Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D 48149 Muenster, Germany
    Nucleic Acids Res 40:10893-903. 2012
  5. pmc Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase
    Bettina Theissen
    Department of Biophysical Chemistry, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
    Proc Natl Acad Sci U S A 105:548-53. 2008
  6. pmc Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling
    Markus G Rudolph
    pRED, Pharma Research and Early Development, Discovery Technologies, Grenzacherstrasse 124, CH 4070 Basel, Switzerland
    Nucleic Acids Res 41:1058-70. 2013
  7. doi request reprint Reverse gyrase transiently unwinds double-stranded DNA in an ATP-dependent reaction
    Agneyo Ganguly
    Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D 48149 Muenster, Germany
    J Mol Biol 425:32-40. 2013
  8. pmc DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage
    Airat Gubaev
    Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D 48149 Muenster, Germany
    Proc Natl Acad Sci U S A 108:14085-90. 2011
  9. pmc The DNA-gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction
    Airat Gubaev
    Biozentrum, Department of Biophysical Chemistry, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
    Proc Natl Acad Sci U S A 106:13278-83. 2009
  10. pmc Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera
    Lenz Steimer
    Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D 48149 Muenster, Germany
    Nucleic Acids Res 41:6259-72. 2013

Collaborators

  • Markus G Rudolph
  • Airat Gubaev
  • Yoandris del Toro Duany
  • Anne R Karow
  • Alexandra Z Andreou
  • Lenz Steimer
  • Agneyo Ganguly
  • Martin A Lanz
  • Manuel Hilbert
  • Martin H Linden
  • Bettina Theissen
  • Stefan P Jungblut
  • Regula Aregger
  • Thomas Göttler
  • Jan Philip Wurm
  • Jens Wöhnert
  • Fabian Kebbel
  • Jürgen Köhler
  • Andreas S Schmidt
  • Roland K Hartmann

Detail Information

Publications29

  1. doi request reprint Mapping the spectrum of conformational states of the DNA- and C-gates in Bacillus subtilis gyrase
    Markus G Rudolph
    F Hoffmann La Roche AG, Pharma Research and Early Development, Discovery Technologies, Grenzacherstrasse 124, CH 4070 Basel, Switzerland
    J Mol Biol 425:2632-40. 2013
    ..None of the dimers in the crystal structures display an open C-gate that would allow DNA passage, in agreement with a transient opening of this gate during the catalytic cycle of DNA supercoiling. ..
  2. pmc Lifelong companions: RNA helicases and their roles in RNA metabolism
    Dagmar Klostermeier
    Institute for Physical Chemistry, University of Muenster, Muenster, Germany
    RNA Biol 10:2-3. 2013
    ..Ultimately, RNA degradation by the so-called degradosome will end the RNA's life...
  3. doi request reprint Single-molecule FRET reveals nucleotide-driven conformational changes in molecular machines and their link to RNA unwinding and DNA supercoiling
    Dagmar Klostermeier
    University of Basel, Biozentrum, Klingelbergstrasse 70, 4056 Basel, Switzerland
    Biochem Soc Trans 39:611-6. 2011
    ....
  4. pmc The GyrA-box determines the geometry of DNA bound to gyrase and couples DNA binding to the nucleotide cycle
    Martin A Lanz
    Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D 48149 Muenster, Germany
    Nucleic Acids Res 40:10893-903. 2012
    ..Our results implicate the GyrA-box in coordinating DNA binding and the nucleotide cycle...
  5. pmc Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase
    Bettina Theissen
    Department of Biophysical Chemistry, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
    Proc Natl Acad Sci U S A 105:548-53. 2008
    ..These results establish a closure of the interdomain cleft in the helicase core at the beginning of the unwinding reaction, and suggest a conserved mechanism of energy conversion among DEAD box helicases across kingdoms...
  6. pmc Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling
    Markus G Rudolph
    pRED, Pharma Research and Early Development, Discovery Technologies, Grenzacherstrasse 124, CH 4070 Basel, Switzerland
    Nucleic Acids Res 41:1058-70. 2013
    ..A possible mechanism for positive supercoiling by reverse gyrases is presented...
  7. doi request reprint Reverse gyrase transiently unwinds double-stranded DNA in an ATP-dependent reaction
    Agneyo Ganguly
    Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D 48149 Muenster, Germany
    J Mol Biol 425:32-40. 2013
    ..The unwinding activity may provide and stabilize the single-stranded regions required for strand passage by the topoisomerase domain, either de novo or by expanding already existing unpaired regions that may form at high temperatures...
  8. pmc DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage
    Airat Gubaev
    Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D 48149 Muenster, Germany
    Proc Natl Acad Sci U S A 108:14085-90. 2011
    ..The N-gate reopens after ATP hydrolysis, allowing for further catalytic cycles. DNA binding, cleavage, and wrapping and N-gate narrowing are intimately linked events that coordinate conformational changes at the DNA and the N-gate...
  9. pmc The DNA-gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction
    Airat Gubaev
    Biozentrum, Department of Biophysical Chemistry, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
    Proc Natl Acad Sci U S A 106:13278-83. 2009
    ..During the relaxation and supercoiling reactions, gyrase with an open DNA-gate is not significantly populated, consistent with gate-opening as a very rare event that only occurs briefly to allow for strand passage...
  10. pmc Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera
    Lenz Steimer
    Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D 48149 Muenster, Germany
    Nucleic Acids Res 41:6259-72. 2013
    ..The helicase core then unwinds an adjacent RNA duplex. Overall, the mode of RNA binding by Hera is consistent with a possible function as a general RNA chaperone. ..
  11. doi request reprint A structural model for the DEAD box helicase YxiN in solution: localization of the RNA binding domain
    Anne R Karow
    Department of Biophysical Chemistry, Biozentrum, University of Basel, Basel, Switzerland
    J Mol Biol 402:629-37. 2010
    ..Possibly, this region constitutes an adaptable interface that generally allows for the interaction of the helicase core with additional domains or interacting factors...
  12. pmc The latch modulates nucleotide and DNA binding to the helicase-like domain of Thermotoga maritima reverse gyrase and is required for positive DNA supercoiling
    Agneyo Ganguly
    Department of Biophysical Chemistry, University of Basel, Biozentrum, Klingelbergstrasse 70, CH 4056 Basel and Hoffmann La Roche AG, Grenzacher Strasse 124, CH 4070 Basel, Switzerland
    Nucleic Acids Res 39:1789-800. 2011
    ..Thus, the latch coordinates the individual domain activities by modulating the helicase-like domain, and by communicating changes in the nucleotide state to the topoisomerase domain...
  13. pmc Potassium ions are required for nucleotide-induced closure of gyrase N-gate
    Airat Gubaev
    Institute for Physical Chemistry, University of Munster, D 48149 Munster, Germany
    J Biol Chem 287:10916-21. 2012
    ....
  14. doi request reprint The DEAD box helicase YxiN maintains a closed conformation during ATP hydrolysis
    Regula Aregger
    University of Basel, Biozentrum, Biophysical Chemistry, Klingelbergstrasse 70, 4056 Basel, Switzerland
    Biochemistry 48:10679-81. 2009
    ..Our results show that the interdomain cleft in the helicase core closes upon ATP binding at the beginning of the cycle. Reopening occurs after ATP hydrolysis, most likely coupled to phosphate release...
  15. ncbi request reprint Adenosine 5'-O-(3-thio)triphosphate (ATPgammaS) promotes positive supercoiling of DNA by T. maritima reverse gyrase
    Stefan P Jungblut
    University of Basel, Biozentrum, Dept of Biophysical Chemistry, Klingelbergstrasse 70, CH 4056 Basel, Switzerland
    J Mol Biol 371:197-209. 2007
    ....
  16. doi request reprint The conformational flexibility of the helicase-like domain from Thermotoga maritima reverse gyrase is restricted by the topoisomerase domain
    Yoandris del Toro Duany
    Biozentrum, Department of Biophysical Chemistry, University of Basel, Klingelbergstrasse 70, CH 4056 Basel, Switzerland
    Biochemistry 50:5816-23. 2011
    ..Counterparts of this insert region are located at very different positions in other DNA-processing enzymes but may point toward a general role in DNA strand separation...
  17. pmc The putative RNase P motif in the DEAD box helicase Hera is dispensable for efficient interaction with RNA and helicase activity
    Martin H Linden
    Department of Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
    Nucleic Acids Res 36:5800-11. 2008
    ..In addition, the specificity of Hera for RNase P RNA may be required for RNase P RNA folding or RNase P assembly...
  18. pmc A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility
    Dagmar Klostermeier
    Division of Biophysical Chemistry, Biozentrum, University of Basel, CH 4056 Basel, Switzerland
    Nucleic Acids Res 37:421-30. 2009
    ..Combination of the previously determined N-terminal Hera structure with the C-terminal Hera structures allows generation of a model for the entire Hera dimer, where two helicase cores can work in conjunction on large RNA substrates...
  19. pmc The reverse gyrase helicase-like domain is a nucleotide-dependent switch that is attenuated by the topoisomerase domain
    Yoandris del Toro Duany
    University of Basel, Biozentrum, Biophysical Chemistry, Klingelbergstrasse 70, 4056 Basel, Switzerland
    Nucleic Acids Res 36:5882-95. 2008
    ..This inhibitory effect of the topoisomerase domain decelerates the progression of reverse gyrase through the nucleotide cycle, possibly providing optimal coordination of ATP hydrolysis with the complex reaction of DNA supercoiling...
  20. doi request reprint The mechanism of ATP-dependent RNA unwinding by DEAD box proteins
    Manuel Hilbert
    Biozentrum, Biophysical Chemistry, University of Basel, Klingelbergstrasse 70, CH 4056 Basel, Switzerland
    Biol Chem 390:1237-50. 2009
    ..After ATP hydrolysis and phosphate release, the DEAD box protein returns to a low-affinity state for RNA. Dissociation of the second RNA strand and reopening of the cleft in the helicase core allow for further catalytic cycles...
  21. pmc Guiding strand passage: DNA-induced movement of the gyrase C-terminal domains defines an early step in the supercoiling cycle
    Martin A Lanz
    University of Basel, Biozentrum, Biophysical Chemistry, Klingelbergstrasse 70, CH 4056 Basel, Switzerland
    Nucleic Acids Res 39:9681-94. 2011
    ....
  22. doi request reprint Nucleotide-driven conformational changes in the reverse gyrase helicase-like domain couple the nucleotide cycle to DNA processing
    Yoandris del Toro Duany
    University of Basel, Biozentrum, Dept of Biophysical Chemistry, Klingelbergstrasse 70, CH 4056 Basel, Switzerland
    Phys Chem Chem Phys 13:10009-19. 2011
    ....
  23. ncbi request reprint Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains
    Anne R Karow
    Department of Biophysical Chemistry, University of Basel, Switzerland
    FEBS J 274:463-73. 2007
    ..Finally, ligated YxiN unwinds a minimal RNA substrate to an extent comparable to that of the wild-type helicase, confirming authentic interdomain communication...
  24. doi request reprint Conformational changes of DEAD-box helicases monitored by single molecule fluorescence resonance energy transfer
    Alexandra Z Andreou
    Institute for Physical Chemistry, University of Muenster, Muenster, Germany
    Methods Enzymol 511:75-109. 2012
    ..We further outline smFRET strategies to determine the orientation of flanking N- and C-terminal domains of DEAD-box helicases and to assess the effects of regulatory proteins on DEAD-box helicase conformation...
  25. pmc eIF4G stimulates the activity of the DEAD box protein eIF4A by a conformational guidance mechanism
    Manuel Hilbert
    Dept of Biophysical Chemistry, University of Basel, Biozentrum, Klingelbergstrasse 70, CH 4056 Basel, Switzerland
    Nucleic Acids Res 39:2260-70. 2011
    ..Subtle changes induced by eIF4G may be amplified by input signals from other translation factors, leading to an efficient regulation of translation initiation...
  26. pmc A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN
    Anne R Karow
    University of Basel, Biozentrum, Biophysical Chemistry, Klingelbergstrasse 70, 4056 Basel, Switzerland
    Nucleic Acids Res 37:4464-71. 2009
    ..Possibly, the K52Q and motif III mutants still introduce a kink into the backbone of bound RNA, whereas G303A fails to kink the RNA substrate...
  27. ncbi request reprint Dissection of the nucleotide cycle of B. subtilis DNA gyrase and its modulation by DNA
    Thomas Göttler
    Division of Biophysical Chemistry, Biozentrum, University of Basel, CH 4056 Basel, Switzerland
    J Mol Biol 367:1392-404. 2007
    ..This suggests that each topoisomerase represents a different solution to the complex reaction sequence in DNA supercoiling...
  28. doi request reprint RNA helicases in infection and disease
    Lenz Steimer
    University of Muenster, Institute for Physical Chemistry, Muenster, Germany
    RNA Biol 9:751-71. 2012
    ..This review summarizes the current knowledge on RNA helicases in infection and disease, and their growing potential as drug targets...
  29. pmc The DEAD-box helicase eIF4A: Paradigm or the odd one out?
    Alexandra Z Andreou
    University of Muenster Institute for Physical Chemistry Muenster, Germany
    RNA Biol 10:19-32. 2013
    ..This review summarizes the current knowledge on eIF4A and its regulation, and discusses to what extent eIF4A serves as a model DEAD-box protein...