Harry F Noller

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint RNA structure: reading the ribosome
    Harry F Noller
    Center for Molecular Biology of RNA, Department of Molecular, Cell, and Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Science 309:1508-14. 2005
  2. pmc Spontaneous intersubunit rotation in single ribosomes
    Peter V Cornish
    Department of Physics, University of Illinois, 1110 West Green Street, Urbana, IL 61801, USA
    Mol Cell 30:578-88. 2008
  3. ncbi request reprint The 30S ribosomal P site: a function of 16S rRNA
    Harry F Noller
    Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz, CA 95064, USA
    FEBS Lett 579:855-8. 2005
  4. pmc Crystal structure of a translation termination complex formed with release factor RF2
    Andrei Korostelev
    Center for Molecular Biology of RNA and Departments of Molecular, Cell and Developmental Biology and Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 105:19684-9. 2008
  5. ncbi request reprint Structural basis for translation termination on the 70S ribosome
    Martin Laurberg
    Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Nature 454:852-7. 2008
  6. pmc Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome
    Jie Zhou
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, CA 95064, USA
    RNA 18:230-40. 2012
  7. pmc Creating ribosomes with an all-RNA 30S subunit P site
    Lee Hoang
    Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 101:12439-43. 2004
  8. pmc Recognition of the amber UAG stop codon by release factor RF1
    Andrei Korostelev
    Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, UCSC, Santa Cruz, CA, USA
    EMBO J 29:2577-85. 2010
  9. pmc Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome
    Andrei Korostelev
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95060, USA
    Proc Natl Acad Sci U S A 104:16840-3. 2007
  10. ncbi request reprint mRNA helicase activity of the ribosome
    Seyedtaghi Takyar
    Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Cell 120:49-58. 2005

Collaborators

Detail Information

Publications41

  1. ncbi request reprint RNA structure: reading the ribosome
    Harry F Noller
    Center for Molecular Biology of RNA, Department of Molecular, Cell, and Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Science 309:1508-14. 2005
    ....
  2. pmc Spontaneous intersubunit rotation in single ribosomes
    Peter V Cornish
    Department of Physics, University of Illinois, 1110 West Green Street, Urbana, IL 61801, USA
    Mol Cell 30:578-88. 2008
    ..Our results provide direct evidence that the intersubunit rotation that underlies ribosomal translocation is thermally driven...
  3. ncbi request reprint The 30S ribosomal P site: a function of 16S rRNA
    Harry F Noller
    Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz, CA 95064, USA
    FEBS Lett 579:855-8. 2005
    ..Deletion of these tails now shows that the 16S rRNA contacts alone are sufficient to support protein synthesis in living cells...
  4. pmc Crystal structure of a translation termination complex formed with release factor RF2
    Andrei Korostelev
    Center for Molecular Biology of RNA and Departments of Molecular, Cell and Developmental Biology and Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 105:19684-9. 2008
    ..We show that when the H-bonding capability of the main-chain N-H of the conserved glutamine is eliminated by substitution with proline, peptidyl-tRNA esterase activity is abolished, consistent with its proposed role in catalysis...
  5. ncbi request reprint Structural basis for translation termination on the 70S ribosome
    Martin Laurberg
    Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Nature 454:852-7. 2008
    ..Unexpectedly, the main-chain amide group of Gln 230 in the universally conserved GGQ motif of the factor is positioned to contribute directly to peptidyl-tRNA hydrolysis...
  6. pmc Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome
    Jie Zhou
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, CA 95064, USA
    RNA 18:230-40. 2012
    ..The rotational movements in the ribosome induced by RF3, and its distinctly different binding orientation to the sarcin-ricin loop of 23S rRNA, raise interesting implications for the mechanism of action of EF-G in translocation...
  7. pmc Creating ribosomes with an all-RNA 30S subunit P site
    Lee Hoang
    Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 101:12439-43. 2004
    ....
  8. pmc Recognition of the amber UAG stop codon by release factor RF1
    Andrei Korostelev
    Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, UCSC, Santa Cruz, CA, USA
    EMBO J 29:2577-85. 2010
    ..These findings are consistent with our proposal that structural rearrangements of RF1 and RF2 are critical to accurate translation termination...
  9. pmc Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome
    Andrei Korostelev
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95060, USA
    Proc Natl Acad Sci U S A 104:16840-3. 2007
    ..The bulged U723 in helix 23a interacts with the minor groove of the SD helix at the C1539.G-10 base pair, explaining its selective conservation in bacteria and archaea...
  10. ncbi request reprint mRNA helicase activity of the ribosome
    Seyedtaghi Takyar
    Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Cell 120:49-58. 2005
    ..Mutation of residues in proteins S3 and S4 that line the entry to the tunnel impairs helicase activity. We conclude that the ribosome itself is an mRNA helicase and that proteins S3 and S4 may play a role in its processivity...
  11. ncbi request reprint The antibiotic viomycin traps the ribosome in an intermediate state of translocation
    Dmitri N Ermolenko
    Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
    Nat Struct Mol Biol 14:493-7. 2007
    ....
  12. ncbi request reprint Observation of intersubunit movement of the ribosome in solution using FRET
    Dmitri N Ermolenko
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    J Mol Biol 370:530-40. 2007
    ....
  13. pmc Crystal structure of the 70S ribosome bound with the Q253P mutant form of release factor RF2
    Natalia Santos
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    Structure 21:1258-63. 2013
    ..This rules out proline-induced misfolding and further supports the proposal that catalytic activity requires interaction of the Gln-253 backbone amide with the 3' end of peptidyl-tRNA. ..
  14. pmc Rotation of the head of the 30S ribosomal subunit during mRNA translocation
    Zhuojun Guo
    Center for Molecular Biology of RNA and Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 109:20391-4. 2012
    ..The rate of quenching of pyrene-labeled mRNA is consistent with coupling of mRNA translocation to head rotation...
  15. pmc Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation
    Jie Zhou
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Science 340:1236086. 2013
    ..These findings provide new insights into the molecular mechanism of ribosomal translocation. ..
  16. pmc Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome
    P Clint Spiegel
    Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz 95064, USA
    RNA 13:1473-82. 2007
    ..Our results show that binding of EF-G in the presence of GDPNP or GDP.fusidic acid stabilizes the ribosomal intermediate hybrid state, but that complete translocation is supported only by EF-G.GTP or EF-G.GDPNP...
  17. ncbi request reprint Measurement of internal movements within the 30 S ribosomal subunit using Förster resonance energy transfer
    Robyn Hickerson
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA
    J Mol Biol 354:459-72. 2005
    ....
  18. ncbi request reprint Deletion of a conserved, central ribosomal intersubunit RNA bridge
    Iraj K Ali
    Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Mol Cell 23:865-74. 2006
    ..However, Deltah69 50S subunits are unable to associate with 30S subunits in the absence of tRNA, are defective in RF1-catalyzed peptide release, and can be recycled in the absence of RRF...
  19. ncbi request reprint Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements
    Andrei Korostelev
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Cell 126:1065-77. 2006
    ..Differences between the conformations of vacant and tRNA-bound 70S ribosomes suggest an induced fit of the ribosome structure in response to tRNA binding, including significant changes in the peptidyl-transferase catalytic site...
  20. pmc Multistart simulated annealing refinement of the crystal structure of the 70S ribosome
    Andrei Korostelev
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 106:18195-200. 2009
    ..8 and 3.7 A resolution. Our analysis suggests that results obtained from cross-crystal averaging are inherently biased toward the higher-resolution dataset...
  21. pmc Crystal structures of 70S ribosomes bound to release factors RF1, RF2 and RF3
    Jie Zhou
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    Curr Opin Struct Biol 22:733-42. 2012
    ..While structures alone do not tell us how these complicated molecular assemblies work, is it nevertheless clear that it will not be possible to understand their mechanisms without detailed structural information...
  22. ncbi request reprint Following the dynamics of changes in solvent accessibility of 16 S and 23 S rRNA during ribosomal subunit association using synchrotron-generated hydroxyl radicals
    Thuylinh Nguyenle
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, 95064, USA
    J Mol Biol 359:1235-48. 2006
    ..The rates individually measured for the inter-subunit contacts are comparable within experimental error. The application of this approach to the study of ribosome dynamics during the translation cycle is discussed...
  23. ncbi request reprint Catalysis of ribosomal translocation by sparsomycin
    Kurt Fredrick
    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA
    Science 300:1159-62. 2003
    ..These findings directly implicate the peptidyl transferase center of the 50S subunit in the mechanism of translocation, a process involving large-scale movement of tRNA and mRNA in the 30S subunit, some 70 angstroms away...
  24. pmc mRNA translocation occurs during the second step of ribosomal intersubunit rotation
    Dmitri N Ermolenko
    Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California, USA
    Nat Struct Mol Biol 18:457-62. 2011
    ..We compared the rates of these movements and found that mRNA translocation occurs during the second, clockwise rotation event, corresponding to the transition from the hybrid state to the classical state...
  25. pmc Analysis of structural dynamics in the ribosome by TLS crystallographic refinement
    Andrei Korostelev
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    J Mol Biol 373:1058-70. 2007
    ....
  26. pmc Structural dynamics of the ribosome
    Andrei Korostelev
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Curr Opin Chem Biol 12:674-83. 2008
    ..In spite of much progress, our understanding of the mechanics of translation is now beset with countless new questions, reflecting the vast molecular architecture of the ribosome itself...
  27. pmc The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit
    Laura Lancaster
    Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    RNA 14:1999-2012. 2008
    ..Our results reveal an influence of the SRL on the higher-order structure of the 50S subunit, with implications for its role in translation...
  28. pmc Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome
    Jianyu Zhu
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 108:1839-44. 2011
    ..These structures suggest how relatively small structured RNAs can manipulate complex biological machines...
  29. ncbi request reprint Involvement of 16S rRNA nucleotides G1338 and A1339 in discrimination of initiator tRNA
    Laura Lancaster
    Department of Molecular, Cell and Developmental Biology and The Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Mol Cell 20:623-32. 2005
    ..Moreover, our findings indicate that discrimination also involves recognition of at least one additional feature of the tRNA(fMet) anticodon stem loop...
  30. pmc Intersubunit movement is required for ribosomal translocation
    Lucas H Horan
    Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 104:4881-5. 2007
    ..These findings show that intersubunit movement is required for ribosomal translocation, accounting for the universal two-subunit architecture of ribosomes...
  31. ncbi request reprint Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing
    Laura Lancaster
    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Cell 111:129-40. 2002
    ..Surprisingly, the orientation of RRF in the ribosome differs markedly from any of those previously observed for tRNA, suggesting that structural mimicry does not necessarily reflect functional mimicry...
  32. ncbi request reprint The ribosome in focus: new structures bring new insights
    Andrei Korostelev
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Trends Biochem Sci 32:434-41. 2007
    ..Clues to the structural dynamics of translation are suggested by conformational changes that occur in both tRNA and the ribosome upon complex formation...
  33. ncbi request reprint Detecting the coevolution of biosequences--an example of RNA interaction prediction
    Chen Hsiang Yeang
    Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, USA
    Mol Biol Evol 24:2119-31. 2007
    ..The results on RNA data suggest a general model of coevolution might be applied to other types of interactions between protein, DNA, and RNA molecules...
  34. pmc Evolution of protein synthesis from an RNA world
    Harry F Noller
    Center for Molecular Biology of RNA and Department of Molecular, Cell, and Developmental Biology, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Cold Spring Harb Perspect Biol 4:a003681. 2012
    ..This process involved homodimeric "duplicator RNAs," resembling the anticodon arms of tRNAs, which directed ligation of trinucleotides in response to an RNA template...
  35. doi request reprint Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip
    Mikhail I Rudenko
    School of Engineering, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA
    Biosens Bioelectron 29:34-9. 2011
    ..The incorporation of nanopores into a larger optofluidic chip system opens possibilities for electrical and optical studies of single ribosomes in well-defined and rapidly variable chemical environments...
  36. ncbi request reprint Translocation of tRNA during protein synthesis
    Harry F Noller
    Center for Molecular Biology of RNA and Department of Molecular, Cellular and Developmental Biology, Sinsheimer Laboratories, UCSC, Santa Cruz, CA 95064, USA
    FEBS Lett 514:11-6. 2002
    ..We highlight several key questions regarding the mechanism of translocation, and discuss possible mechanistic models in light of the recent crystal structures of the ribosome and its subunits...
  37. pmc The driving force for molecular evolution of translation
    Harry F Noller
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    RNA 10:1833-7. 2004
    ..Observed examples of substantial structural rearrangements in RNA that are induced by binding of peptides and other small molecules support this possibility...
  38. ncbi request reprint Accurate translocation of mRNA by the ribosome requires a peptidyl group or its analog on the tRNA moving into the 30S P site
    Kurt Fredrick
    Center for Molecular Biology of RNA, Sinsheimer Laboraties, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Mol Cell 9:1125-31. 2002
    ..If aminoacyl-tRNA is translocated, an intermediate level of translocational accuracy is observed. Thus, translocational accuracy depends on the acylation state of the tRNA entering the 30S P site...
  39. pmc A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA
    Monika Martick
    Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
    Nature 454:899-902. 2008
    ....
  40. pmc Following translation by single ribosomes one codon at a time
    Jin Der Wen
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 452:598-603. 2008
    ..Translocation and RNA unwinding are strictly coupled ribosomal functions...
  41. ncbi request reprint Measurements of internal distance changes of the 30S ribosome using FRET with multiple donor-acceptor pairs: quantitative spectroscopic methods
    Zigurts K Majumdar
    Laboratory for Fluorescence Dynamics, Department of Physics, University of Illinois at Urbana Champaign, IL 61801, USA
    J Mol Biol 351:1123-45. 2005
    ..Here, we explain the spectroscopic methods we have used, which should be of general interest in studies that aim at obtaining quantitative distance information from FRET...