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Genomes and Genes | Harry F NollerSummaryAffiliation: University of California Country: USA Publications
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Publications
RNA structure: reading the ribosomeHarry 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....
Spontaneous intersubunit rotation in single ribosomesPeter 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...- The 30S ribosomal P site: a function of 16S rRNAHarry 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... - Crystal structure of a translation termination complex formed with release factor RF2Andrei 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... 
Structural basis for translation termination on the 70S ribosomeMartin 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...- Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosomeJie 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... - Creating ribosomes with an all-RNA 30S subunit P siteLee 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.... - Recognition of the amber UAG stop codon by release factor RF1Andrei 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... - Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosomeAndrei 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... - mRNA helicase activity of the ribosomeSeyedtaghi 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... - The antibiotic viomycin traps the ribosome in an intermediate state of translocationDmitri 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.... - Observation of intersubunit movement of the ribosome in solution using FRETDmitri 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.... - Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangementsAndrei 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... - Deletion of a conserved, central ribosomal intersubunit RNA bridgeIraj 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... - Measurement of internal movements within the 30 S ribosomal subunit using Förster resonance energy transferRobyn 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.... - Multistart simulated annealing refinement of the crystal structure of the 70S ribosomeAndrei 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... - Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosomeP 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... - Following the dynamics of changes in solvent accessibility of 16 S and 23 S rRNA during ribosomal subunit association using synchrotron-generated hydroxyl radicalsThuylinh 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... - Catalysis of ribosomal translocation by sparsomycinKurt 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... - Analysis of structural dynamics in the ribosome by TLS crystallographic refinementAndrei 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.... - Structural dynamics of the ribosomeAndrei 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... - The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunitLaura 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... - mRNA translocation occurs during the second step of ribosomal intersubunit rotationDmitri 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... - Intersubunit movement is required for ribosomal translocationLucas 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... - The ribosome in focus: new structures bring new insightsAndrei 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... - Involvement of 16S rRNA nucleotides G1338 and A1339 in discrimination of initiator tRNALaura 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... - Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosomeJianyu 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... - Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probingLaura 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... - Detecting the coevolution of biosequences--an example of RNA interaction predictionChen 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... - Crystal structures of 70S ribosomes bound to release factors RF1, RF2 and RF3Jie 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... - Evolution of protein synthesis from an RNA worldHarry 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... - Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chipMikhail 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... - A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNAMonika Martick
Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
Nature 454:899-902. 2008.... - Accurate translocation of mRNA by the ribosome requires a peptidyl group or its analog on the tRNA moving into the 30S P siteKurt 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... - The driving force for molecular evolution of translationHarry 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... - Translocation of tRNA during protein synthesisHarry 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... - Following translation by single ribosomes one codon at a timeJin 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... - Measurements of internal distance changes of the 30S ribosome using FRET with multiple donor-acceptor pairs: quantitative spectroscopic methodsZigurts 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...