M V Rodnina

Summary

Affiliation: University of Witten/Herdecke
Country: Germany

Publications

  1. pmc Role and timing of GTP binding and hydrolysis during EF-G-dependent tRNA translocation on the ribosome
    Berthold Wilden
    Institutes of Molecular Biology and Physical Biochemistry, University of Witten Herdecke, D 58448 Witten, Germany
    Proc Natl Acad Sci U S A 103:13670-5. 2006
  2. doi Conservation of bacterial protein synthesis machinery: initiation and elongation in Mycobacterium smegmatis
    Christian M Bruell
    Institute of Medical Microbiology, University of Zurich, Switzerland
    Biochemistry 47:8828-39. 2008
  3. ncbi [Mechanism of tRNA translocation on the ribosome]
    M V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Mol Biol (Mosk) 35:655-65. 2001
  4. ncbi Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms
    M V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Annu Rev Biochem 70:415-35. 2001
  5. doi The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation
    Marina V Rodnina
    Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany
    Biochem Soc Trans 39:658-62. 2011
  6. ncbi Ribosome fidelity: tRNA discrimination, proofreading and induced fit
    M V Rodnina
    Institutes of Physical Biochemistry and Molecular Biology, University of Witten Herdecke, 58448, Witten, Germany
    Trends Biochem Sci 26:124-30. 2001
  7. ncbi How ribosomes make peptide bonds
    Marina V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, D 58448 Witten, Germany
    Trends Biochem Sci 32:20-6. 2007
  8. ncbi Mechanism of peptide bond formation on the ribosome
    Marina V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, Witten, Germany
    Q Rev Biophys 39:203-25. 2006
  9. ncbi Structural dynamics of ribosomal RNA during decoding on the ribosome
    Marina V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, Stockumer Str 10, 58448, Witten, Germany
    Biochimie 84:745-54. 2002
  10. ncbi Peptide bond formation on the ribosome: structure and mechanism
    Marina V Rodnina
    Institutes of Physical Biochemistry and Molecular Biology, University of Witten Herdecke, Stockumer Strasse 10, 58448, Witten, Germany
    Curr Opin Struct Biol 13:334-40. 2003

Collaborators

  • RICHARD VANCE WOLFENDEN
  • Malte Beringer
  • W Wintermeyer
  • G Lentzen
  • J Luirink
  • Alexander S Mankin
  • Erik C Bottger
  • Holger Stark
  • S A Strobel
  • Harald Engelhardt
  • Sven N Hobbie
  • CHRISTOPHER HELLEN
  • Jörg M Harms
  • Tatyana Pestova
  • M C Wahl
  • Jens T Kaiser
  • Alexander Tonevitsky
  • Andrey L Konevega
  • Kirill B Gromadski
  • Ute Kothe
  • Andreas Savelsbergh
  • Pohl Milon
  • Frank Peske
  • Ingo Wohlgemuth
  • Vladimir I Katunin
  • Hans Joachim Wieden
  • Niels Fischer
  • Iwona Buskiewicz
  • Alena Paleskava
  • Claudio O Gualerzi
  • Shan Qing Gu
  • Johannes Jöckel
  • Dagmar Mohr
  • Tobias Schümmer
  • Yuri P Semenkov
  • Tina Daviter
  • Iwona A Buskiewicz
  • J R Jagath
  • David A Kingery
  • Thomas Bornemann
  • Lorna E Lancaster
  • Christian M Bruell
  • Charlotte R Knudsen
  • Andriy Kubarenko
  • Berthold Wilden
  • Vera P Pisareva
  • Andrew Kubarenko
  • Peter Bieling
  • T Daviter
  • Louise D Dahl
  • Mihaela Diaconu
  • N B Matassova
  • Annette Sievers
  • Ashley Eversole Hesslein
  • Jörg Schirmer
  • H J Wieden
  • Corinna Pohl
  • Marcello Carotti
  • A Savelsbergh
  • Emmanuel Pfund
  • Carolin Eichholz
  • Sibylle Brenner
  • David E Kitchen
  • Virginia Post
  • Rebecca M Voorhees
  • Kensuke Okuda
  • Colin Kleanthous
  • Attilio Fabbretti
  • Anne Strømgaard
  • Terri Goss Kinzy
  • Enrico Caserta
  • Petr Sergiev
  • Jerneja Tomsic
  • K B Gromadski
  • Sarah Adio
  • Olga Dontsova
  • Andrey V Pisarev
  • Gert Folkers
  • Cynthia L Pon
  • Rolf Boelens
  • Anna La Teana
  • Eugene Tischenko
  • Frank Schlünzen
  • Jens Warnecke
  • Ignacy Gryczynski
  • Philipp Beinker
  • Natalia G Soboleva
  • Elke Deuerling
  • Bernd Bukau
  • Anne B Kosek

Detail Information

Publications79

  1. pmc Role and timing of GTP binding and hydrolysis during EF-G-dependent tRNA translocation on the ribosome
    Berthold Wilden
    Institutes of Molecular Biology and Physical Biochemistry, University of Witten Herdecke, D 58448 Witten, Germany
    Proc Natl Acad Sci U S A 103:13670-5. 2006
    ..GTP hydrolysis is required for rapid tRNA-mRNA movement, and P(i) release induces further rearrangements of both EF-G and the ribosome that are required for EF-G turnover...
  2. doi Conservation of bacterial protein synthesis machinery: initiation and elongation in Mycobacterium smegmatis
    Christian M Bruell
    Institute of Medical Microbiology, University of Zurich, Switzerland
    Biochemistry 47:8828-39. 2008
    ..smegmatis components as an alternative to that from E. coli to study the mechanisms of translation and to test the action of antibiotics against Gram-positive bacteria...
  3. ncbi [Mechanism of tRNA translocation on the ribosome]
    M V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Mol Biol (Mosk) 35:655-65. 2001
    ....
  4. ncbi Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms
    M V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Annu Rev Biochem 70:415-35. 2001
    ..In utilizing induced fit for substrate discrimination, the ribosome resembles other nucleic acid-programmed polymerases...
  5. doi The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation
    Marina V Rodnina
    Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany
    Biochem Soc Trans 39:658-62. 2011
    ..EF-G acts as a Brownian ratchet providing directional bias for movement at the cost of GTP hydrolysis...
  6. ncbi Ribosome fidelity: tRNA discrimination, proofreading and induced fit
    M V Rodnina
    Institutes of Physical Biochemistry and Molecular Biology, University of Witten Herdecke, 58448, Witten, Germany
    Trends Biochem Sci 26:124-30. 2001
    ..Similar mechanisms are used by other template-programmed enzymes, such as DNA and RNA polymerases...
  7. ncbi How ribosomes make peptide bonds
    Marina V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, D 58448 Witten, Germany
    Trends Biochem Sci 32:20-6. 2007
    ..Proton transfer during the reaction seems to be promoted by a concerted shuttle mechanism that involves ribose hydroxyl groups on the tRNA substrate...
  8. ncbi Mechanism of peptide bond formation on the ribosome
    Marina V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, Witten, Germany
    Q Rev Biophys 39:203-25. 2006
    ..The catalytic mechanism employed by the ribosome suggests how ancient RNA-world enzymes may have functioned...
  9. ncbi Structural dynamics of ribosomal RNA during decoding on the ribosome
    Marina V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, Stockumer Str 10, 58448, Witten, Germany
    Biochimie 84:745-54. 2002
    ....
  10. ncbi Peptide bond formation on the ribosome: structure and mechanism
    Marina V Rodnina
    Institutes of Physical Biochemistry and Molecular Biology, University of Witten Herdecke, Stockumer Strasse 10, 58448, Witten, Germany
    Curr Opin Struct Biol 13:334-40. 2003
    ..According to the kinetics of mutant ribosomes, these effects may be attributed to a candidate catalytic base (A2451) suggested by the crystal structure...
  11. ncbi Ten remarks on peptide bond formation on the ribosome
    M V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Biochem Soc Trans 33:493-8. 2005
    ..10(7)-fold rate enhancement of peptide bond formation by the ribosome is mainly due to substrate positioning within the active site, rather than to chemical catalysis...
  12. pmc Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY
    J R Jagath
    Institute of Molecular Biology, University of Witten Herdecke, Witten, Germany
    RNA 7:293-301. 2001
    ....
  13. ncbi Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome
    M V Rodnina
    Institute of Molecular Biology, University of Witten Herdecke, Germany
    Nature 385:37-41. 1997
    ..By coupling the free energy of GTP hydrolysis to translocation, EF-G serves as a motor protein to drive the directional movement of transfer and messenger RNAs on the ribosome...
  14. ncbi Mechanisms of elongation on the ribosome: dynamics of a macromolecular machine
    W Wintermeyer
    Institute of Molecular Biology, University of Witten Herdecke, Stockumer Str 10, 58448 Witten, Germany
    Biochem Soc Trans 32:733-7. 2004
    ..This review summarizes recent progress in understanding the mechanisms of the elongation phase of protein synthesis. Results from rapid kinetic analysis of elongation reactions are discussed in the light of recent structural data...
  15. pmc Ribosomal RNA is the target for oxazolidinones, a novel class of translational inhibitors
    N B Matassova
    Institute of Molecular Biology, University of Witten Herdecke, Witten, Germany
    RNA 5:939-46. 1999
    ..Both binding sites and mode of action of oxazolidinones are unique among the antibiotics known to act on the ribosome...
  16. ncbi GTPases mechanisms and functions of translation factors on the ribosome
    M V Rodnina
    Institute of Molecular Biology, University of Witten Herdecke, Germany
    Biol Chem 381:377-87. 2000
    ..GTP hydrolysis by IF2 is triggered upon formation of the 70S initiation complex, and the dissociation of Pi and/or IF2 follows a rearrangement of the ribosome into the elongation-competent state...
  17. ncbi Stimulation of the GTPase activity of translation elongation factor G by ribosomal protein L7/12
    A Savelsbergh
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    J Biol Chem 275:890-4. 2000
    ..L7/12 appears to function by stabilizing the GTPase transition state of EF-G...
  18. pmc Thiostrepton inhibits the turnover but not the GTPase of elongation factor G on the ribosome
    M V Rodnina
    Institute of Molecular Biology, University of Witten Herdecke, D 58448 Witten, Germany
    Proc Natl Acad Sci U S A 96:9586-90. 1999
    ..The results indicate that thiostrepton inhibits a structural transition of the 1067 region of 23S rRNA that is important for functions of EF-G after GTP hydrolysis...
  19. ncbi Essential mechanisms in the catalysis of peptide bond formation on the ribosome
    Malte Beringer
    Institute of Physical Biochemistry, University of Witten Herdecke, Stockumer Strasse 10, 58448 Witten, Germany
    J Biol Chem 280:36065-72. 2005
    ..A2451 seems to function as a pivot point in ordering the structure of the peptidyl transferase center rather than taking part in chemical catalysis...
  20. doi Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates
    Ingo Wohlgemuth
    Institute of Physical Biochemistry, University of Witten Herdecke, Stockumer Strasse 10, D 58448 Witten, Germany
    J Biol Chem 283:32229-35. 2008
    ..On the other hand, the 50-fold increase in the reaction rate for peptidyl-tRNA ending with Pro suggests that full-length aminoacyl-tRNA in the A site greatly accelerates peptide bond formation...
  21. ncbi The ribosome's response to codon-anticodon mismatches
    T Daviter
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Biochimie 88:1001-11. 2006
    ..This review emphasizes the progress made in understanding the mechanisms that determine recognition and selection of tRNA by the translational machinery...
  22. ncbi Kinetic determinants of high-fidelity tRNA discrimination on the ribosome
    Kirill B Gromadski
    Institute of Physical Biochemistry, University of Witten Herdecke, D 58448 Witten, Germany
    Mol Cell 13:191-200. 2004
    ..tRNA selection at the initial selection step is entirely kinetically controlled and is due to much faster (650-fold) GTP hydrolysis of cognate compared to near-cognate substrate...
  23. ncbi A common structural motif in elongation factor Ts and ribosomal protein L7/12 may be involved in the interaction with elongation factor Tu
    H J Wieden
    Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany
    J Mol Evol 52:129-36. 2001
    ..The motif is remarkably similar with respect to fold, bulkiness, and charge distribution of the solution surface, suggesting that it has a common function in binding EF-Tu...
  24. ncbi Essential role of histidine 84 in elongation factor Tu for the chemical step of GTP hydrolysis on the ribosome
    Tina Daviter
    Institute of Physical Biochemistry, University of Witten Herdecke, Stockumer Strasse 10, 58448, Witten, Germany
    J Mol Biol 332:689-99. 2003
    ..We propose that the catalytic role of His84 is to stabilize the transition state of GTP hydrolysis by hydrogen bonding to the attacking water molecule or, possibly, the gamma-phosphate group of GTP...
  25. ncbi Peptide bond formation does not involve acid-base catalysis by ribosomal residues
    Peter Bieling
    Institute of Physical Biochemistry, University of Witten Herdecke, Stockumer Strasse 10, 58448 Witten, Germany
    Nat Struct Mol Biol 13:423-8. 2006
    ..The rate of peptide bond formation with unmodified Phe-tRNA(Phe) is estimated to be >300 s(-1)...
  26. ncbi The ribosomal peptidyl transferase
    Malte Beringer
    Institute of Physical Biochemistry, University of Witten Herdecke, Witten, Germany
    Mol Cell 26:311-21. 2007
    ..Proton transfer during the reaction appears to be promoted by a concerted proton shuttle mechanism that involves ribose hydroxyl groups on the tRNA substrate...
  27. ncbi Interaction of guanine nucleotides with the signal recognition particle from Escherichia coli
    J R Jagath
    Institute of Molecular Biology, University of Witten Herdecke, Germany
    Biochemistry 37:15408-13. 1998
    ..Binding of both GTP and GDP to Ffh was independent of Mg2+ ions. The data suggest that, at conditions in vivo, (i) there will be rapid spontaneous GDP-GTP exchange, and (ii) the GTP-bound form of Ffh, or of SRP, will be predominant...
  28. pmc Control of phosphate release from elongation factor G by ribosomal protein L7/12
    Andreas Savelsbergh
    Institute of Molecular Biology, University of Witten Herdecke, Witten, Germany
    EMBO J 24:4316-23. 2005
    ....
  29. ncbi A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity
    Kirill B Gromadski
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Mol Cell 21:369-77. 2006
    ..The forward reactions on mismatched codons were particularly sensitive to the disruption of the A-minor interactions with 16S rRNA and determined the variations in the misreading efficiency of near-cognate codons...
  30. pmc Thermodynamic and kinetic framework of selenocysteyl-tRNASec recognition by elongation factor SelB
    Alena Paleskava
    Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
    J Biol Chem 285:3014-20. 2010
    ..The mode of tRNA recognition by SelB is reminiscent of another specialized factor, eIF2, rather than of EF-Tu, the common delivery factor for all other aminoacyl-tRNAs, in line with a common evolutionary ancestry of SelB and eIF2...
  31. pmc Truncated elongation factor G lacking the G domain promotes translocation of the 3' end but not of the anticodon domain of peptidyl-tRNA
    C Borowski
    Institute of Molecular Biology, University of Witten Herdecke, Germany
    Proc Natl Acad Sci U S A 93:4202-6. 1996
    ..The G domain's intramolecular interactions are likely to be modulated by GTP binding and hydrolysis...
  32. ncbi Delayed release of inorganic phosphate from elongation factor Tu following GTP hydrolysis on the ribosome
    Ute Kothe
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Biochemistry 45:12767-74. 2006
    ..Rather, the slow P(i) release may be a consequence of the tight interaction of the switch regions of EF-Tu with the gamma-phosphate and the ribosome in the GTPase activated state of the factor...
  33. ncbi GTPase activation of elongation factors Tu and G on the ribosome
    Dagmar Mohr
    Institute of Physical Biochemistry, University of Witten Herdecke, Stockumer Strasse 10, D 58448 Witten, Germany
    Biochemistry 41:12520-8. 2002
    ..This effect appears to be augmented by interactions of other structural elements of the large ribosomal subunit with the switch regions of the factors...
  34. pmc The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome
    Shan Qing Gu
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    RNA 9:566-73. 2003
    ..These results indicate a model of the topographical arrangement of SRP at the peptide exit of the 50S ribosomal subunit...
  35. pmc Conformation of 4.5S RNA in the signal recognition particle and on the 30S ribosomal subunit
    Shan Qing Gu
    Institute of Molecular Biology, University of Witten Herdecke, Stockumer Str 10, 58448 Witten, Germany
    RNA 11:1374-84. 2005
    ..The functional role of 4.5S RNA binding to the 30S subunit is unclear, as the RNA had no effect on translation or tRNA translocation on the ribosome...
  36. ncbi Sequence of steps in ribosome recycling as defined by kinetic analysis
    Frank Peske
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    Mol Cell 18:403-12. 2005
    ..IF3 is required for the subsequent ejection of tRNA and mRNA from the small subunit. The latter step is slower than subunit dissociation and constitutes the rate-limiting step of ribosome recycling...
  37. pmc Rapid peptide bond formation on isolated 50S ribosomal subunits
    Ingo Wohlgemuth
    Institute of Physical Biochemistry, University of Witten Herdecke, Stockumer Strasse 10, 58448 Witten, Germany
    EMBO Rep 7:699-703. 2006
    ....
  38. ncbi Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex
    Holger Stark
    Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany
    Nat Struct Biol 9:849-54. 2002
    ..These results provide a detailed snapshot view of an important functional state of the ribosome and suggest mechanisms of decoding and GTPase activation...
  39. pmc Optimization of speed and accuracy of decoding in translation
    Ingo Wohlgemuth
    Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
    EMBO J 29:3701-9. 2010
    ..The GTP hydrolysis step is crucial for the optimization of both the speed and accuracy, which explains the necessity for the trade-off between the two fundamental parameters of translation...
  40. doi Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy
    Niels Fischer
    3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
    Nature 466:329-33. 2010
    ..The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement...
  41. ncbi Codon reading by tRNAAla with modified uridine in the wobble position
    Ute Kothe
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Mol Cell 25:167-74. 2007
    ..g., the GCC codon. The ribosome accepts the C-cmo(5)U pair as an almost-correct base pair, unlike third-position mismatches, which lead to the incorporation of incorrect amino acids and are efficiently rejected...
  42. ncbi Recognition and selection of tRNA in translation
    Marina V Rodnina
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    FEBS Lett 579:938-42. 2005
    ..Recent results of kinetic measurements, ribosome crystallography, single molecule FRET measurements, and cryo-electron microscopy suggest the mechanism of tRNA recognition and selection...
  43. ncbi Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation
    Frank Peske
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    J Mol Biol 343:1183-94. 2004
    ....
  44. pmc Conformation of the signal recognition particle in ribosomal targeting complexes
    Iwona A Buskiewicz
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    RNA 15:44-54. 2009
    ..Binding of FtsY to the RNC-SRP complex results in a limited conformational change of SRP, which may initiate subsequent targeting steps...
  45. ncbi Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome
    Kirill B Gromadski
    Institute of Physical Biochemistry, University of Witten Herdecke, D 58448 Witten, Germany
    Nat Struct Mol Biol 11:316-22. 2004
    ..These results indicate that movements within the 30S subunit at the streptomycin-binding site are essential for the coupling between base pair recognition and GTP hydrolysis, thus modulating the fidelity of aa-tRNA selection...
  46. ncbi Mechanism of elongation factor (EF)-Ts-catalyzed nucleotide exchange in EF-Tu. Contribution of contacts at the guanine base
    Hans Joachim Wieden
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    J Biol Chem 277:6032-6. 2002
    ....
  47. ncbi Interaction of helix D of elongation factor Tu with helices 4 and 5 of protein L7/12 on the ribosome
    Ute Kothe
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    J Mol Biol 336:1011-21. 2004
    ..By analogy to the interaction of helix D of EF-Tu with the N-terminal domain of EF-Ts, the contact area is likely to consist of a hydrophobic patch flanked by two salt-bridges...
  48. ncbi Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs
    Malte Beringer
    Institute of Physical Biochemistry, University of Witten Herdecke, Witten, Germany
    Biol Chem 388:687-91. 2007
    ..The tRNA-rRNA interactions lead to a robust reaction that is insensitive to pH changes or base substitutions in 23S rRNA at the active site of the ribosome...
  49. ncbi Spontaneous reverse movement of mRNA-bound tRNA through the ribosome
    Andrey L Konevega
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Nat Struct Mol Biol 14:318-24. 2007
    ..These results lend support to the diffusion model of tRNA movement during translocation. In the cell, tRNA movement is biased in the forward direction by EF-G, which acts as a Brownian ratchet and prevents backward movement...
  50. ncbi Mechanism of EF-Ts-catalyzed guanine nucleotide exchange in EF-Tu: contribution of interactions mediated by helix B of EF-Tu
    Tobias Schümmer
    Institute of Physical Biochemistry, University of Witten Herdecke, D 58448 Witten, Germany
    Biochemistry 46:4977-84. 2007
    ....
  51. doi Signal sequence-independent membrane targeting of ribosomes containing short nascent peptides within the exit tunnel
    Thomas Bornemann
    Institute of Molecular Biology, University of Witten Herdecke, Stockumer Strasse 10, 55448 Witten, Germany
    Nat Struct Mol Biol 15:494-9. 2008
    ....
  52. pmc Colicin E3 cleavage of 16S rRNA impairs decoding and accelerates tRNA translocation on Escherichia coli ribosomes
    Lorna E Lancaster
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    Mol Microbiol 69:390-401. 2008
    ..The tRNA-mRNA translocation is faster on colicin E3-cleaved than on intact ribosomes and is less sensitive to inhibition by the antibiotic viomycin...
  53. ncbi Coupling of GTP hydrolysis by elongation factor G to translocation and factor recycling on the ribosome
    Vladimir I Katunin
    Institutes of Molecular Biology and Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    Biochemistry 41:12806-12. 2002
    ....
  54. ncbi An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation
    Andreas Savelsbergh
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    Mol Cell 11:1517-23. 2003
    ..These results indicate that the energy of GTP hydrolysis is utilized to promote the ribosome rearrangement and to bias spontaneous fluctuations within the ribosome-EF-G complex toward unidirectional movement of mRNA and tRNA...
  55. pmc Kinetics of the interactions between yeast elongation factors 1A and 1Balpha, guanine nucleotides, and aminoacyl-tRNA
    Kirill B Gromadski
    Institute of Physical Biochemistry, University of Witten Herdecke, Stockumer Strasse 10, D 58448 Witten, Germany
    J Biol Chem 282:35629-37. 2007
    ..eEF1A.GTP binds Phe-tRNA(Phe) with a K(d) of 3 nm, whereas eEF1A.GDP shows no significant binding, indicating that eEF1A has similar tRNA binding properties as its prokaryotic homolog, EF-Tu...
  56. pmc Distinct functions of elongation factor G in ribosome recycling and translocation
    Andreas Savelsbergh
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    RNA 15:772-80. 2009
    ....
  57. pmc Trigger factor binds to ribosome-signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor
    Iwona Buskiewicz
    Institute für Molekularbiologie und Physikalische Biochemie, Universitat Witten Herdecke, 58448 Witten, Germany
    Proc Natl Acad Sci U S A 101:7902-6. 2004
    ....
  58. ncbi Kinetic mechanism of elongation factor Ts-catalyzed nucleotide exchange in elongation factor Tu
    Kirill B Gromadski
    Institute of Physical Biochemistry, University of Witten Herdecke, D 58448 Witten, Germany
    Biochemistry 41:162-9. 2002
    ..At in vivo concentrations of nucleotides and factors, the overall exchange rate, as calculated from the elemental rate constants, is 30 s(-1), which is compatible with the rate of protein synthesis in the cell...
  59. ncbi Involvement of helix 34 of 16 S rRNA in decoding and translocation on the ribosome
    Andrew Kubarenko
    Institute of Physical Biochemistry, University of Witten Herdecke, 58448 Witten, Germany
    J Biol Chem 281:35235-44. 2006
    ..The data indicate that helix 34 is involved in controlling the maintenance of the reading frame and in tRNA translocation...
  60. ncbi Conformations of the signal recognition particle protein Ffh from Escherichia coli as determined by FRET
    Iwona Buskiewicz
    Institute of Molecular Biology, University of Witten Herdecke, 58448 Witten, Germany
    J Mol Biol 351:417-30. 2005
    ..The domain rearrangement of Ffh that takes place upon formation of the SRP is probably important for subsequent steps of membrane targeting, including interactions with the translating ribosome and the SRP receptor...
  61. ncbi Single-step purification of specific tRNAs by hydrophobic tagging
    Ute Kothe
    Institute of Physical Biochemistry, University of Witten Herdecke, D 58448 Witten, Germany
    Anal Biochem 356:148-50. 2006
  62. pmc Domain rearrangement of SRP protein Ffh upon binding 4.5S RNA and the SRP receptor FtsY
    Iwona Buskiewicz
    Institute of Molecular Biology, University of Witten Herdecke, Germany
    RNA 11:947-57. 2005
    ..These results suggest that in free Ffh, the binding sites for 4.5S RNA and FtsY are occluded by strong domain-domain interactions which must be disrupted for the formation of SRP or the Ffh-FtsY complex...
  63. pmc The ribosome-bound initiation factor 2 recruits initiator tRNA to the 30S initiation complex
    Pohl Milon
    Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
    EMBO Rep 11:312-6. 2010
    ..The mechanism of action of IF2 seems to be different from that of tRNA carriers such as EF-Tu, SelB and eukaryotic initiation factor 2 (eIF2), instead resembling that of eIF5B, the eukaryotic subunit association factor...
  64. doi Recent mechanistic insights into eukaryotic ribosomes
    Marina V Rodnina
    Max Planck Institute for Biophysical Chemistry, Department of Physical Biochemistry, 37077 Gottingen, Germany
    Curr Opin Cell Biol 21:435-43. 2009
    ..Here, we summarize recent progress in deciphering molecular mechanisms of eukaryotic translation. Comparisons with prokaryotic translation are included, emphasizing emerging patterns of common design...
  65. doi The ribosome goes Nobel
    Marina V Rodnina
    Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
    Trends Biochem Sci 35:1-5. 2010
    ..The award of this year's Nobel Prize in Chemistry to Ada E. Yonath, Venkatraman Ramakrishnan and Thomas A. Steitz honors their breakthrough achievement in determining the atomic structure of the ribosome...
  66. ncbi Towards understanding selenocysteine incorporation into bacterial proteins
    Niels Fischer
    3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, D 37077 Gottingen, Germany
    Biol Chem 388:1061-7. 2007
    ..The results indicate that mthSelA forms a homodecamer that has a ring-like structure with five bilobed wings, similar to the structure of the E. coli complex determined previously...
  67. pmc Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions
    Andrey L Konevega
    Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188300 Gatchina, Russia
    RNA 10:90-101. 2004
    ....
  68. ncbi Kinetic analysis of interaction of eukaryotic release factor 3 with guanine nucleotides
    Vera P Pisareva
    Department of Microbiology and Immunology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
    J Biol Chem 281:40224-35. 2006
    ..Guanine nucleotide binding and exchange on eRF3, which therefore depends on stimulation by eRF1, is entirely different from that on prokaryotic RF3 and unusual among GTPases...
  69. pmc The ribosome as an entropy trap
    Annette Sievers
    Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
    Proc Natl Acad Sci U S A 101:7897-901. 2004
    ..These results are consistent with the view that the ribosome enhances the rate of peptide bond formation mainly by positioning the substrates and/or water exclusion within the active site, rather than by conventional chemical catalysis...
  70. ncbi Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation
    Mihaela Diaconu
    Röntgenkristallographie, Max Planck Institut fur biophysikalische Chemie, Am Fassberg 11, D 37077 Gottingen, Germany
    Cell 121:991-1004. 2005
    ..Highly mobile L7/12 C-terminal domains promote recruitment of translation factors to the ribosome and stimulate GTP hydrolysis by the ribosome bound factors through stabilization of their active GTPase conformation...
  71. ncbi Structural and functional investigation of a putative archaeal selenocysteine synthase
    Jens T Kaiser
    Division of Chemistry and Chemical Engineering, California Institute of Technology, M C 114 96, Pasadena, California 91125, USA
    Biochemistry 44:13315-27. 2005
    ....
  72. pmc The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor
    Pohl Milon
    Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino MC, Italy
    Proc Natl Acad Sci U S A 103:13962-7. 2006
    ....
  73. ncbi Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome
    Vladimir I Katunin
    Sankt Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russia
    Mol Cell 10:339-46. 2002
    ..These results suggest a contribution to overall catalysis of general acid-base and/or conformational catalysis involving an ionizing group at the active site...
  74. pmc Exploration of the conserved A+C wobble pair within the ribosomal peptidyl transferase center using affinity purified mutant ribosomes
    Ashley Eversole Hesslein
    Yale University, Department of Molecular Biophysics and Biochemistry, 260 Whitney Avenue, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 32:3760-70. 2004
    ....
  75. ncbi The importance of P-loop and domain movements in EF-Tu for guanine nucleotide exchange
    Louise D Dahl
    Department of Molecular Biology, Aarhus University, Denmark
    J Biol Chem 281:21139-46. 2006
    ..The mutations had no effect on EF-Tu-dependent delivery of aminoacyl-tRNA to the ribosome...
  76. doi Kinetic checkpoint at a late step in translation initiation
    Pohl Milon
    Department of Biology MCA, Laboratory of Genetics, University of Camerino, 62032 Camerino, Italy
    Mol Cell 30:712-20. 2008
    ....
  77. ncbi Transient kinetics, fluorescence, and FRET in studies of initiation of translation in bacteria
    Pohl Milon
    Laboratory of Genetics, Department of Biology MCA, University of Camerino, Camerino, Italy
    Methods Enzymol 430:1-30. 2007
    ..The methods described here are based on results obtained with initiation components from Escherichia coli but can be adopted for mechanistic studies of initiation in other prokaryotic or eukaryotic systems...
  78. pmc An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction
    David A Kingery
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Chem Biol 15:493-500. 2008
    ..Such a transition state is significantly different from that of uncatalyzed aminolysis reactions in solution...
  79. pmc Inactivation of the elongation factor Tu by mosquitocidal toxin-catalyzed mono-ADP-ribosylation
    Jörg Schirmer
    Institut fur Experimentelle und Klinische Pharmakologie und Toxikologie, Albert Ludwigs Universitat Freiburg, D 79104 Freiburg, Germany
    Appl Environ Microbiol 68:4894-9. 2002
    ..The inactivation of EF-Tu by MTX-mediated ADP-ribosylation and the resulting inhibition of bacterial protein synthesis are likely to play important roles in the cytotoxicity of the 27-kDa enzyme fragment of MTX toward E. coli...