1ibk › Citations

Recognition of cognate transfer RNA by the 30S ribosomal subunit.

Ogle JM, Brodersen DE, Clemons WM, Tarry MJ, Carter AP, Ramakrishnan V
Science 292 897-902 (2001)
Related entries: 1ibl, 1ibm

Cited: 736 times
EuropePMC logo PMID: 11340196

Abstract

Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.

Reviews - 1ibk mentioned but not cited (4)

  1. Fidelity at the molecular level: lessons from protein synthesis. Zaher HS, Green R. Cell 136 746-762 (2009)
  2. Targeting Antibiotic Resistance. Chellat MF, Raguž L, Riedl R. Angew Chem Int Ed Engl 55 6600-6626 (2016)
  3. Suppression of premature termination codons as a therapeutic approach. Keeling KM, Wang D, Conard SE, Bedwell DM. Crit Rev Biochem Mol Biol 47 444-463 (2012)
  4. Molecular Insights into Determinants of Translational Readthrough and Implications for Nonsense Suppression Approaches. Lombardi S, Testa MF, Pinotti M, Branchini A. Int J Mol Sci 21 E9449 (2020)

Articles - 1ibk mentioned but not cited (7)

  1. The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results. Rosenbaum G, Alkire RW, Evans G, Rotella FJ, Lazarski K, Zhang RG, Ginell SL, Duke N, Naday I, Lazarz J, Molitsky MJ, Keefe L, Gonczy J, Rock L, Sanishvili R, Walsh MA, Westbrook E, Joachimiak A. J Synchrotron Radiat 13 30-45 (2006)
  2. Structural insights into cognate versus near-cognate discrimination during decoding. Agirrezabala X, Schreiner E, Trabuco LG, Lei J, Ortiz-Meoz RF, Schulten K, Green R, Frank J. EMBO J 30 1497-1507 (2011)
  3. POPSCOMP: an automated interaction analysis of biomolecular complexes. Kleinjung J, Fraternali F. Nucleic Acids Res 33 W342-6 (2005)
  4. Molecular dynamics study of the ribosomal A-site. Romanowska J, Setny P, Trylska J. J Phys Chem B 112 15227-15243 (2008)
  5. Ribosomal dynamics inferred from variations in experimental measurements. Gabashvili IS, Whirl-Carrillo M, Bada M, Banatao DR, Altman RB. RNA 9 1301-1307 (2003)
  6. The DARC site: a database of aligned ribosomal complexes. Jarasch A, Dziuk P, Becker T, Armache JP, Hauser A, Wilson DN, Beckmann R. Nucleic Acids Res 40 D495-500 (2012)
  7. Use of a fluorescence assay to determine relative affinities of semisynthetic aminoglycosides to small RNAs representing bacterial and mitochondrial A sites. Waduge P, Sati GC, Crich D, Chow CS. Bioorg Med Chem 27 115121 (2019)


Reviews citing this publication (155)

  1. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, Will CL, Lührmann R. Cell 136 701-718 (2009)
  2. The noncoding RNA revolution-trashing old rules to forge new ones. Cech TR, Steitz JA. Cell 157 77-94 (2014)
  3. Aminoglycoside modifying enzymes. Ramirez MS, Tolmasky ME. Drug Resist Updat 13 151-171 (2010)
  4. Ribosome structure and the mechanism of translation. Ramakrishnan V. Cell 108 557-572 (2002)
  5. What recent ribosome structures have revealed about the mechanism of translation. Schmeing TM, Ramakrishnan V. Nature 461 1234-1242 (2009)
  6. Structural insights into translational fidelity. Ogle JM, Ramakrishnan V. Annu Rev Biochem 74 129-177 (2005)
  7. Ribosome-targeting antibiotics and mechanisms of bacterial resistance. Wilson DN. Nat Rev Microbiol 12 35-48 (2014)
  8. tRNA's wobble decoding of the genome: 40 years of modification. Agris PF, Vendeix FA, Graham WD. J Mol Biol 366 1-13 (2007)
  9. The molecular mechanics of eukaryotic translation. Kapp LD, Lorsch JR. Annu Rev Biochem 73 657-704 (2004)
  10. Nucleic acid recognition by OB-fold proteins. Theobald DL, Mitton-Fry RM, Wuttke DS. Annu Rev Biophys Biomol Struct 32 115-133 (2003)
  11. Initiation of protein synthesis in bacteria. Laursen BS, Sørensen HP, Mortensen KK, Sperling-Petersen HU. Microbiol Mol Biol Rev 69 101-123 (2005)
  12. Versatility of aminoglycosides and prospects for their future. Vakulenko SB, Mobashery S. Clin Microbiol Rev 16 430-450 (2003)
  13. Non-canonical translation in RNA viruses. Firth AE, Brierley I. J Gen Virol 93 1385-1409 (2012)
  14. The bacterial ribosome as a target for antibiotics. Poehlsgaard J, Douthwaite S. Nat Rev Microbiol 3 870-881 (2005)
  15. A structural understanding of the dynamic ribosome machine. Steitz TA. Nat Rev Mol Cell Biol 9 242-253 (2008)
  16. Insights into the decoding mechanism from recent ribosome structures. Ogle JM, Carter AP, Ramakrishnan V. Trends Biochem Sci 28 259-266 (2003)
  17. The accuracy of ribosomal RNA comparative structure models. Gutell RR, Lee JC, Cannone JJ. Curr Opin Struct Biol 12 301-310 (2002)
  18. The elongation, termination, and recycling phases of translation in eukaryotes. Dever TE, Green R. Cold Spring Harb Perspect Biol 4 a013706 (2012)
  19. The A-Z of bacterial translation inhibitors. Wilson DN. Crit Rev Biochem Mol Biol 44 393-433 (2009)
  20. Structural basis of the translational elongation cycle. Voorhees RM, Ramakrishnan V. Annu Rev Biochem 82 203-236 (2013)
  21. Analysis of RNA motifs. Leontis NB, Westhof E. Curr Opin Struct Biol 13 300-308 (2003)
  22. Pseudouridine synthases. Hamma T, Ferré-D'Amaré AR. Chem Biol 13 1125-1135 (2006)
  23. RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Steitz TA, Moore PB. Trends Biochem Sci 28 411-418 (2003)
  24. Structure and dynamics of a processive Brownian motor: the translating ribosome. Frank J, Gonzalez RL. Annu Rev Biochem 79 381-412 (2010)
  25. Mechanisms and implications of programmed translational frameshifting. Dinman JD. Wiley Interdiscip Rev RNA 3 661-673 (2012)
  26. An integrated, structure- and energy-based view of the genetic code. Grosjean H, Westhof E. Nucleic Acids Res 44 8020-8040 (2016)
  27. Why nature really chose phosphate. Kamerlin SC, Sharma PK, Prasad RB, Warshel A. Q Rev Biophys 46 1-132 (2013)
  28. The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting. Plant EP, Jacobs KL, Harger JW, Meskauskas A, Jacobs JL, Baxter JL, Petrov AN, Dinman JD. RNA 9 168-174 (2003)
  29. The function and synthesis of ribosomes. Lafontaine DL, Tollervey D. Nat Rev Mol Cell Biol 2 514-520 (2001)
  30. RNA as a drug target: the case of aminoglycosides. Vicens Q, Westhof E. Chembiochem 4 1018-1023 (2003)
  31. Recognition and selection of tRNA in translation. Rodnina MV, Gromadski KB, Kothe U, Wieden HJ. FEBS Lett 579 938-942 (2005)
  32. Translocation of tRNA during protein synthesis. Noller HF, Yusupov MM, Yusupova GZ, Baucom A, Cate JH. FEBS Lett 514 11-16 (2002)
  33. Structure and Function of the Mitochondrial Ribosome. Greber BJ, Ban N. Annu Rev Biochem 85 103-132 (2016)
  34. Antibiotics and the ribosome. Tenson T, Mankin A. Mol Microbiol 59 1664-1677 (2006)
  35. Structural dynamics of the ribosome. Korostelev A, Ermolenko DN, Noller HF. Curr Opin Chem Biol 12 674-683 (2008)
  36. The involvement of RNA in ribosome function. Moore PB, Steitz TA. Nature 418 229-235 (2002)
  37. Ataluren as an agent for therapeutic nonsense suppression. Peltz SW, Morsy M, Welch EM, Jacobson A. Annu Rev Med 64 407-425 (2013)
  38. A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Atkins JF, Björk GR. Microbiol Mol Biol Rev 73 178-210 (2009)
  39. Hierarchy of RNA functional dynamics. Mustoe AM, Brooks CL, Al-Hashimi HM. Annu Rev Biochem 83 441-466 (2014)
  40. The structural basis of large ribosomal subunit function. Moore PB, Steitz TA. Annu Rev Biochem 72 813-850 (2003)
  41. Translation at the single-molecule level. Marshall RA, Aitken CE, Dorywalska M, Puglisi JD. Annu Rev Biochem 77 177-203 (2008)
  42. Aminoglycoside-induced translational read-through in disease: overcoming nonsense mutations by pharmacogenetic therapy. Zingman LV, Park S, Olson TM, Alekseev AE, Terzic A. Clin Pharmacol Ther 81 99-103 (2007)
  43. Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design. Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Annu Rev Biochem 87 451-478 (2018)
  44. Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures. Vicens Q, Westhof E. Biopolymers 70 42-57 (2003)
  45. Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu. Agirrezabala X, Frank J. Q Rev Biophys 42 159-200 (2009)
  46. Evolutionary optimization of speed and accuracy of decoding on the ribosome. Wohlgemuth I, Pohl C, Mittelstaet J, Konevega AL, Rodnina MV. Philos Trans R Soc Lond B Biol Sci 366 2979-2986 (2011)
  47. The ribosome in action: Tuning of translational efficiency and protein folding. Rodnina MV. Protein Sci 25 1390-1406 (2016)
  48. Translation in Prokaryotes. Rodnina MV. Cold Spring Harb Perspect Biol 10 a032664 (2018)
  49. Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases. Hainrichson M, Nudelman I, Baasov T. Org Biomol Chem 6 227-239 (2008)
  50. Stealth and mimicry by deadly bacterial toxins. Yates SP, Jørgensen R, Andersen GR, Merrill AR. Trends Biochem Sci 31 123-133 (2006)
  51. Ribosomal translocation: one step closer to the molecular mechanism. Shoji S, Walker SE, Fredrick K. ACS Chem Biol 4 93-107 (2009)
  52. The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer. Frank J, Sengupta J, Gao H, Li W, Valle M, Zavialov A, Ehrenberg M. FEBS Lett 579 959-962 (2005)
  53. Antibiotics that target protein synthesis. McCoy LS, Xie Y, Tor Y. Wiley Interdiscip Rev RNA 2 209-232 (2011)
  54. The social life of ribosomal proteins. Brodersen DE, Nissen P. FEBS J 272 2098-2108 (2005)
  55. Species-specific antibiotic-ribosome interactions: implications for drug development. Wilson DN, Harms JM, Nierhaus KH, Schlünzen F, Fucini P. Biol Chem 386 1239-1252 (2005)
  56. IRES-induced conformational changes in the ribosome and the mechanism of translation initiation by internal ribosomal entry. Hellen CU. Biochim Biophys Acta 1789 558-570 (2009)
  57. Ribosome structure and dynamics during translocation and termination. Dunkle JA, Cate JH. Annu Rev Biophys 39 227-244 (2010)
  58. Rate and accuracy of bacterial protein synthesis revisited. Johansson M, Lovmar M, Ehrenberg M. Curr Opin Microbiol 11 141-147 (2008)
  59. Structural aspects of translation termination on the ribosome. Korostelev AA. RNA 17 1409-1421 (2011)
  60. The driving force for molecular evolution of translation. Noller HF. RNA 10 1833-1837 (2004)
  61. The ribosome in focus: new structures bring new insights. Korostelev A, Noller HF. Trends Biochem Sci 32 434-441 (2007)
  62. Translation Elongation and Recoding in Eukaryotes. Dever TE, Dinman JD, Green R. Cold Spring Harb Perspect Biol 10 a032649 (2018)
  63. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function. Väre VY, Eruysal ER, Narendran A, Sarachan KL, Agris PF. Biomolecules 7 E29 (2017)
  64. Targeting Nonsense Mutations in Diseases with Translational Read-Through-Inducing Drugs (TRIDs). Nagel-Wolfrum K, Möller F, Penner I, Baasov T, Wolfrum U. BioDrugs 30 49-74 (2016)
  65. How should we think about the ribosome? Moore PB. Annu Rev Biophys 41 1-19 (2012)
  66. Improving on nature: antibiotics that target the ribosome. Sutcliffe JA. Curr Opin Microbiol 8 534-542 (2005)
  67. Pseudouridines and pseudouridine synthases of the ribosome. Ofengand J, Malhotra A, Remme J, Gutgsell NS, Del Campo M, Jean-Charles S, Peil L, Kaya Y. Cold Spring Harb Symp Quant Biol 66 147-159 (2001)
  68. Ribosome-based quality control of mRNA and nascent peptides. Simms CL, Thomas EN, Zaher HS. Wiley Interdiscip Rev RNA 8 (2017)
  69. Chemical and functional diversity of small molecule ligands for RNA. Hermann T. Biopolymers 70 4-18 (2003)
  70. Structure-based drug design meets the ribosome. Franceschi F, Duffy EM. Biochem Pharmacol 71 1016-1025 (2006)
  71. Bacterial transfer RNAs. Shepherd J, Ibba M. FEMS Microbiol Rev 39 280-300 (2015)
  72. Ribosome as a molecular machine. Spirin AS. FEBS Lett 514 2-10 (2002)
  73. EF-G and EF4: translocation and back-translocation on the bacterial ribosome. Yamamoto H, Qin Y, Achenbach J, Li C, Kijek J, Spahn CM, Nierhaus KH. Nat Rev Microbiol 12 89-100 (2014)
  74. New structural insights into the decoding mechanism: translation infidelity via a G·U pair with Watson-Crick geometry. Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G. FEBS Lett 587 1848-1857 (2013)
  75. Molecular recognition of RNA: challenges for modelling interactions and plasticity. Fulle S, Gohlke H. J Mol Recognit 23 220-231 (2010)
  76. The search and its outcome: high-resolution structures of ribosomal particles from mesophilic, thermophilic, and halophilic bacteria at various functional states. Yonath A. Annu Rev Biophys Biomol Struct 31 257-273 (2002)
  77. Ribosome dynamics during decoding. Rodnina MV, Fischer N, Maracci C, Stark H. Philos Trans R Soc Lond B Biol Sci 372 20160182 (2017)
  78. A structural view on the mechanism of the ribosome-catalyzed peptide bond formation. Simonović M, Steitz TA. Biochim Biophys Acta 1789 612-623 (2009)
  79. Towards the discovery of drug-like RNA ligands? Foloppe N, Matassova N, Aboul-Ela F. Drug Discov Today 11 1019-1027 (2006)
  80. RNA triplexes: from structural principles to biological and biotech applications. Devi G, Zhou Y, Zhong Z, Toh DF, Chen G. Wiley Interdiscip Rev RNA 6 111-128 (2015)
  81. Review: Translational GTPases. Maracci C, Rodnina MV. Biopolymers 105 463-475 (2016)
  82. The roles of RNA in the synthesis of protein. Moore PB, Steitz TA. Cold Spring Harb Perspect Biol 3 a003780 (2011)
  83. Ribosomal RNA guanine-(N2)-methyltransferases and their targets. Sergiev PV, Bogdanov AA, Dontsova OA. Nucleic Acids Res 35 2295-2301 (2007)
  84. Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism. Westhof E, Yusupov M, Yusupova G. F1000Prime Rep 6 19 (2014)
  85. tRNA mimicry in translation termination and beyond. Nakamura Y, Ito K. Wiley Interdiscip Rev RNA 2 647-668 (2011)
  86. Translational recoding: canonical translation mechanisms reinterpreted. Rodnina MV, Korniy N, Klimova M, Karki P, Peng BZ, Senyushkina T, Belardinelli R, Maracci C, Wohlgemuth I, Samatova E, Peske F. Nucleic Acids Res 48 1056-1067 (2020)
  87. Modifications of aminoglycoside antibiotics targeting RNA. Zhou J, Wang G, Zhang LH, Ye XS. Med Res Rev 27 279-316 (2007)
  88. Ribosomal proteins: structure, function, and evolution. Korobeinikova AV, Garber MB, Gongadze GM. Biochemistry (Mosc) 77 562-574 (2012)
  89. Building functional modules from molecular interactions. Hofmann KP, Spahn CM, Heinrich R, Heinemann U. Trends Biochem Sci 31 497-508 (2006)
  90. Structural aspects of mitochondrial translational apparatus. Agrawal RK, Sharma MR. Curr Opin Struct Biol 22 797-803 (2012)
  91. Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders. Bednářová A, Hanna M, Durham I, VanCleave T, England A, Chaudhuri A, Krishnan N. Front Mol Neurosci 10 135 (2017)
  92. Mistranslation of the genetic code. Moghal A, Mohler K, Ibba M. FEBS Lett 588 4305-4310 (2014)
  93. Ribosome structural dynamics in translocation: yet another functional role for ribosomal RNA. Noller HF, Lancaster L, Mohan S, Zhou J. Q Rev Biophys 50 e12 (2017)
  94. After the ribosome structure: how does translocation work? Joseph S. RNA 9 160-164 (2003)
  95. How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation. Choi J, Grosely R, Prabhakar A, Lapointe CP, Wang J, Puglisi JD. Annu Rev Biochem 87 421-449 (2018)
  96. Structural dynamics of ribosomal RNA during decoding on the ribosome. Rodnina MV, Daviter T, Gromadski K, Wintermeyer W. Biochimie 84 745-754 (2002)
  97. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Thamban Chandrika N, Garneau-Tsodikova S. Chem Soc Rev 47 1189-1249 (2018)
  98. Crystal structures of 70S ribosomes bound to release factors RF1, RF2 and RF3. Zhou J, Korostelev A, Lancaster L, Noller HF. Curr Opin Struct Biol 22 733-742 (2012)
  99. Antibiotic resistance by enzyme inactivation: from mechanisms to solutions. De Pascale G, Wright GD. Chembiochem 11 1325-1334 (2010)
  100. Single-molecule analysis of translational dynamics. Petrov A, Chen J, O'Leary S, Tsai A, Puglisi JD. Cold Spring Harb Perspect Biol 4 a011551 (2012)
  101. The 30S ribosomal P site: a function of 16S rRNA. Noller HF, Hoang L, Fredrick K. FEBS Lett 579 855-858 (2005)
  102. Molecular recognition and catalysis in translation termination complexes. Klaholz BP. Trends Biochem Sci 36 282-292 (2011)
  103. Toward an understanding of the structural basis of translation. Frank J. Genome Biol 4 237 (2003)
  104. Convergent evolution of AUA decoding in bacteria and archaea. Suzuki T, Numata T. RNA Biol 11 1586-1596 (2014)
  105. Elements of ribosomal drug resistance and specificity. Blaha GM, Polikanov YS, Steitz TA. Curr Opin Struct Biol 22 750-758 (2012)
  106. Phosphoryl transfer by aminoglycoside 3'-phosphotransferases and manifestation of antibiotic resistance. Kim C, Mobashery S. Bioorg Chem 33 149-158 (2005)
  107. Roles of ribosomal proteins in the functioning of translational machinery of eukaryotes. Graifer D, Karpova G. Biochimie 109 1-17 (2015)
  108. Colicins and their potential in cancer treatment. Lancaster LE, Wintermeyer W, Rodnina MV. Blood Cells Mol Dis 38 15-18 (2007)
  109. Nature as a source of inspiration for cationic lipid synthesis. Labas R, Beilvert F, Barteau B, David S, Chèvre R, Pitard B. Genetica 138 153-168 (2010)
  110. RNA reactions one molecule at a time. Tinoco I, Chen G, Qu X. Cold Spring Harb Perspect Biol 2 a003624 (2010)
  111. The mechanics of ribosomal translocation. Achenbach J, Nierhaus KH. Biochimie 114 80-89 (2015)
  112. Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions. Zheng C, Black KA, Dos Santos PC. Biomolecules 7 E33 (2017)
  113. Genetic approaches to studying protein synthesis: effects of mutations at Psi516 and A535 in Escherichia coli 16S rRNA. Lee K, Holland-Staley CA, Cunningham PR. J Nutr 131 2994S-3004S (2001)
  114. Meanderings of the mRNA through the ribosome. Culver GM. Structure 9 751-758 (2001)
  115. Ribosome Rescue Pathways in Bacteria. Müller C, Crowe-McAuliffe C, Wilson DN. Front Microbiol 12 652980 (2021)
  116. The multiple flavors of GoU pairs in RNA. Westhof E, Yusupov M, Yusupova G. J Mol Recognit 32 e2782 (2019)
  117. Two distinct conformations of the conserved RNA-rich decoding center of the small ribosomal subunit are recognized by tRNAs and release factors. Youngman EM, Cochella L, Brunelle JL, He S, Green R. Cold Spring Harb Symp Quant Biol 71 545-549 (2006)
  118. Functional interactions by transfer RNAs in the ribosome. Khade P, Joseph S. FEBS Lett 584 420-426 (2010)
  119. Structural Insights into tRNA Dynamics on the Ribosome. Agirrezabala X, Valle M. Int J Mol Sci 16 9866-9895 (2015)
  120. Unboxing the T-box riboswitches-A glimpse into multivalent and multimodal RNA-RNA interactions. Zhang J. Wiley Interdiscip Rev RNA 11 e1600 (2020)
  121. Clinical potential of ataluren in the treatment of Duchenne muscular dystrophy. Namgoong JH, Bertoni C. Degener Neurol Neuromuscul Dis 6 37-48 (2016)
  122. New Insights into Ribosome Structure and Function. Jobe A, Liu Z, Gutierrez-Vargas C, Frank J. Cold Spring Harb Perspect Biol 11 a032615 (2019)
  123. Structural and functional topography of the human ribosome. Graifer D, Karpova G. Acta Biochim Biophys Sin (Shanghai) 44 281-299 (2012)
  124. Transfer RNAs: diversity in form and function. Berg MD, Brandl CJ. RNA Biol 18 316-339 (2021)
  125. Unique posttranslational modifications in eukaryotic translation factors and their roles in protozoan parasite viability and pathogenesis. Mittal N, Subramanian G, Bütikofer P, Madhubala R. Mol Biochem Parasitol 187 21-31 (2013)
  126. Substrate-Induced Formation of Ribosomal Decoding Center for Accurate and Rapid Genetic Code Translation. Pavlov MY, Ehrenberg M. Annu Rev Biophys 47 525-548 (2018)
  127. Aminoacyl-tRNA synthesis in archaea: different but not unique. Praetorius-Ibba M, Ibba M. Mol Microbiol 48 631-637 (2003)
  128. Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination. Prabhakar A, Choi J, Wang J, Petrov A, Puglisi JD. Protein Sci 26 1352-1362 (2017)
  129. Extensions, Extra Factors, and Extreme Complexity: Ribosomal Structures Provide Insights into Eukaryotic Translation. Weisser M, Ban N. Cold Spring Harb Perspect Biol 11 a032367 (2019)
  130. Hydroxylation and translational adaptation to stress: some answers lie beyond the STOP codon. Katz MJ, Gándara L, De Lella Ezcurra AL, Wappner P. Cell Mol Life Sci 73 1881-1893 (2016)
  131. Molecular Mechanisms and Determinants of Innovative Correction Approaches in Coagulation Factor Deficiencies. Balestra D, Branchini A. Int J Mol Sci 20 E3036 (2019)
  132. A recent intermezzo at the Ribosome Club. Pavlov MY, Liljas A, Ehrenberg M. Philos Trans R Soc Lond B Biol Sci 372 20160185 (2017)
  133. Interaction of rRNA with mRNA and tRNA in Translating Mammalian Ribosome: Functional Implications in Health and Disease. Bastide A, David A. Biomolecules 8 E100 (2018)
  134. Relating Structure and Dynamics in RNA Biology. Larsen KP, Choi J, Prabhakar A, Puglisi EV, Puglisi JD. Cold Spring Harb Perspect Biol 11 a032474 (2019)
  135. Ribosomal translocation: sparsomycin pushes the button. Southworth DR, Green R. Curr Biol 13 R652-4 (2003)
  136. Self-Referential Encoding on Modules of Anticodon Pairs-Roots of the Biological Flow System. Cardoso Guimarães R. Life (Basel) 7 E16 (2017)
  137. The parable of the caveman and the Ferrari: protein synthesis and the RNA world. Noller HF. Philos Trans R Soc Lond B Biol Sci 372 20160187 (2017)
  138. Biochemical aspects of bacterial strategies for handling the incomplete translation processes. Shimizu Y. Front Microbiol 5 170 (2014)
  139. Fluorescent analysis of bioactive molecules in single cells based on microfluidic chips. Fan Y, Dong D, Li Q, Si H, Pei H, Li L, Tang B. Lab Chip 18 1151-1173 (2018)
  140. From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery. Agirrezabala X, Frank J. Hum Genomics 4 226-237 (2010)
  141. Mitonuclear Interactions in the Maintenance of Mitochondrial Integrity. Karakaidos P, Rampias T. Life (Basel) 10 E173 (2020)
  142. The SmpB C-terminal tail helps tmRNA to recognize and enter stalled ribosomes. Miller MR, Buskirk AR. Front Microbiol 5 462 (2014)
  143. The Structural Dynamics of Translation. Korostelev AA. Annu Rev Biochem 91 245-267 (2022)
  144. The importance of codon-anticodon interactions in translation elongation. Saint-Léger A, Ribas de Pouplana L. Biochimie 114 72-79 (2015)
  145. Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays. Koh HR, Wang X, Myong S. Methods 105 109-118 (2016)
  146. Aminoglycoside interactions with RNAs and nucleases. Kirsebom LA, Virtanen A, Mikkelsen NE. Handb Exp Pharmacol 73-96 (2006)
  147. An RNA-centric historical narrative around the Protein Data Bank. Westhof E, Leontis NB. J Biol Chem 296 100555 (2021)
  148. Conservation of Archaeal C/D Box sRNA-Guided RNA Modifications. Breuer R, Gomes-Filho JV, Randau L. Front Microbiol 12 654029 (2021)
  149. Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii. Fages-Lartaud M, Hundvin K, Hohmann-Marriott MF. Plant J 112 919-945 (2022)
  150. Genetic Code Engineering by Natural and Unnatural Base Pair Systems for the Site-Specific Incorporation of Non-Standard Amino Acids Into Proteins. Kimoto M, Hirao I. Front Mol Biosci 9 851646 (2022)
  151. Non-AUG translation initiation in mammals. Andreev DE, Loughran G, Fedorova AD, Mikhaylova MS, Shatsky IN, Baranov PV. Genome Biol 23 111 (2022)
  152. Diversity and Similarity of Termination and Ribosome Rescue in Bacterial, Mitochondrial, and Cytoplasmic Translation. Korostelev AA. Biochemistry (Mosc) 86 1107-1121 (2021)
  153. Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons. Gamper H, Masuda I, Hou YM. J Mol Biol 434 167440 (2022)
  154. Our current understanding of the toxicity of altered mito-ribosomal fidelity during mitochondrial protein synthesis: What can it tell us about human disease? Vila-Sanjurjo A, Mallo N, Atkins JF, Elson JL, Smith PM. Front Physiol 14 1082953 (2023)
  155. Tuberactinomycin antibiotics: Biosynthesis, anti-mycobacterial action, and mechanisms of resistance. Laughlin ZT, Conn GL. Front Microbiol 13 961921 (2022)

Articles citing this publication (570)

  1. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Schlünzen F, Zarivach R, Harms J, Bashan A, Tocilj A, Albrecht R, Yonath A, Franceschi F. Nature 413 814-821 (2001)
  2. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V. Cell 111 721-732 (2002)
  3. The path of messenger RNA through the ribosome. Yusupova GZ, Yusupov MM, Cate JH, Noller HF. Cell 106 233-241 (2001)
  4. rRNA modifications and ribosome function. Decatur WA, Fournier MJ. Trends Biochem Sci 27 344-351 (2002)
  5. Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J. Cell 107 373-386 (2001)
  6. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Korostelev A, Trakhanov S, Laurberg M, Noller HF. Cell 126 1065-1077 (2006)
  7. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Gao YG, Selmer M, Dunham CM, Weixlbaumer A, Kelley AC, Ramakrishnan V. Science 326 694-699 (2009)
  8. The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Schmeing TM, Voorhees RM, Kelley AC, Gao YG, Murphy FV, Weir JR, Ramakrishnan V. Science 326 688-694 (2009)
  9. tRNA selection and kinetic proofreading in translation. Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD. Nat Struct Mol Biol 11 1008-1014 (2004)
  10. The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. Klein DJ, Moore PB, Steitz TA. J Mol Biol 340 141-177 (2004)
  11. The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. Kramer EB, Farabaugh PJ. RNA 13 87-96 (2007)
  12. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA. Brodersen DE, Clemons WM, Carter AP, Wimberly BT, Ramakrishnan V. J Mol Biol 316 725-768 (2002)
  13. Crystal structure of the eukaryotic ribosome. Ben-Shem A, Jenner L, Yusupova G, Yusupov M. Science 330 1203-1209 (2010)
  14. SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses. Banerjee AK, Blanco MR, Bruce EA, Honson DD, Chen LM, Chow A, Bhat P, Ollikainen N, Quinodoz SA, Loney C, Thai J, Miller ZD, Lin AE, Schmidt MM, Stewart DG, Goldfarb D, De Lorenzo G, Rihn SJ, Voorhees RM, Botten JW, Majumdar D, Guttman M. Cell 183 1325-1339.e21 (2020)
  15. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Gromadski KB, Rodnina MV. Mol Cell 13 191-200 (2004)
  16. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Valle M, Zavialov A, Li W, Stagg SM, Sengupta J, Nielsen RC, Nissen P, Harvey SC, Ehrenberg M, Frank J. Nat Struct Biol 10 899-906 (2003)
  17. The mechanism for activation of GTP hydrolysis on the ribosome. Voorhees RM, Schmeing TM, Kelley AC, Ramakrishnan V. Science 330 835-838 (2010)
  18. Structural basis for translation termination on the 70S ribosome. Laurberg M, Asahara H, Korostelev A, Zhu J, Trakhanov S, Noller HF. Nature 454 852-857 (2008)
  19. An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation. Savelsbergh A, Katunin VI, Mohr D, Peske F, Rodnina MV, Wintermeyer W. Mol Cell 11 1517-1523 (2003)
  20. Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Vicens Q, Westhof E. Structure 9 647-658 (2001)
  21. Study of the structural dynamics of the E coli 70S ribosome using real-space refinement. Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J. Cell 113 789-801 (2003)
  22. Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome. Greber BJ, Bieri P, Leibundgut M, Leitner A, Aebersold R, Boehringer D, Ban N. Science 348 303-308 (2015)
  23. The role of modifications in codon discrimination by tRNA(Lys)UUU. Murphy FV, Ramakrishnan V, Malkiewicz A, Agris PF. Nat Struct Mol Biol 11 1186-1191 (2004)
  24. A new understanding of the decoding principle on the ribosome. Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G. Nature 484 256-259 (2012)
  25. Identification of two distinct hybrid state intermediates on the ribosome. Munro JB, Altman RB, O'Connor N, Blanchard SC. Mol Cell 25 505-517 (2007)
  26. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Jenner LB, Demeshkina N, Yusupova G, Yusupov M. Nat Struct Mol Biol 17 555-560 (2010)
  27. Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. François B, Russell RJ, Murray JB, Aboul-ela F, Masquida B, Vicens Q, Westhof E. Nucleic Acids Res 33 5677-5690 (2005)
  28. Insights into translational termination from the structure of RF2 bound to the ribosome. Weixlbaumer A, Jin H, Neubauer C, Voorhees RM, Petry S, Kelley AC, Ramakrishnan V. Science 322 953-956 (2008)
  29. Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. Ma J, Campbell A, Karlin S. J Bacteriol 184 5733-5745 (2002)
  30. Plasmid-mediated high-level resistance to aminoglycosides in Enterobacteriaceae due to 16S rRNA methylation. Galimand M, Courvalin P, Lambert T. Antimicrob Agents Chemother 47 2565-2571 (2003)
  31. Structural basis for messenger RNA movement on the ribosome. Yusupova G, Jenner L, Rees B, Moras D, Yusupov M. Nature 444 391-394 (2006)
  32. Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Agirrezabala X, Lei J, Brunelle JL, Ortiz-Meoz RF, Green R, Frank J. Mol Cell 32 190-197 (2008)
  33. Translational selection and yeast proteome evolution. Akashi H. Genetics 164 1291-1303 (2003)
  34. An active role for tRNA in decoding beyond codon:anticodon pairing. Cochella L, Green R. Science 308 1178-1180 (2005)
  35. Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates. Strunk BS, Loucks CR, Su M, Vashisth H, Cheng S, Schilling J, Brooks CL, Karbstein K, Skiniotis G. Science 333 1449-1453 (2011)
  36. Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. Gillespie JJ, Johnston JS, Cannone JJ, Gutell RR. Insect Mol Biol 15 657-686 (2006)
  37. Simulating movement of tRNA into the ribosome during decoding. Sanbonmatsu KY, Joseph S, Tung CS. Proc Natl Acad Sci U S A 102 15854-15859 (2005)
  38. Crystal structure of a translation termination complex formed with release factor RF2. Korostelev A, Asahara H, Lancaster L, Laurberg M, Hirschi A, Zhu J, Trakhanov S, Scott WG, Noller HF. Proc Natl Acad Sci U S A 105 19684-19689 (2008)
  39. The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE. Neubauer C, Gao YG, Andersen KR, Dunham CM, Kelley AC, Hentschel J, Gerdes K, Ramakrishnan V, Brodersen DE. Cell 139 1084-1095 (2009)
  40. The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Qin Y, Polacek N, Vesper O, Staub E, Einfeldt E, Wilson DN, Nierhaus KH. Cell 127 721-733 (2006)
  41. Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. Agris PF. EMBO Rep 9 629-635 (2008)
  42. Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome. Fernández IS, Bai XC, Murshudov G, Scheres SH, Ramakrishnan V. Cell 157 823-831 (2014)
  43. The process of mRNA-tRNA translocation. Frank J, Gao H, Sengupta J, Gao N, Taylor DJ. Proc Natl Acad Sci U S A 104 19671-19678 (2007)
  44. Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease. Yasukawa T, Suzuki T, Ishii N, Ohta S, Watanabe K. EMBO J 20 4794-4802 (2001)
  45. Interaction of translation initiation factor 3 with the 30S ribosomal subunit. Dallas A, Noller HF. Mol Cell 8 855-864 (2001)
  46. RNA helicase Prp43 and its co-factor Pfa1 promote 20 to 18 S rRNA processing catalyzed by the endonuclease Nob1. Pertschy B, Schneider C, Gnädig M, Schäfer T, Tollervey D, Hurt E. J Biol Chem 284 35079-35091 (2009)
  47. Specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48S translation initiation complex. Pisarev AV, Kolupaeva VG, Pisareva VP, Merrick WC, Hellen CU, Pestova TV. Genes Dev 20 624-636 (2006)
  48. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Ivanov IP, Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV. Nucleic Acids Res 39 4220-4234 (2011)
  49. Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation. Peske F, Savelsbergh A, Katunin VI, Rodnina MV, Wintermeyer W. J Mol Biol 343 1183-1194 (2004)
  50. A hierarchical model for evolution of 23S ribosomal RNA. Bokov K, Steinberg SV. Nature 457 977-980 (2009)
  51. GTPase activation of elongation factor EF-Tu by the ribosome during decoding. Schuette JC, Murphy FV, Kelley AC, Weir JR, Giesebrecht J, Connell SR, Loerke J, Mielke T, Zhang W, Penczek PA, Ramakrishnan V, Spahn CM. EMBO J 28 755-765 (2009)
  52. Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. Taylor DJ, Nilsson J, Merrill AR, Andersen GR, Nissen P, Frank J. EMBO J 26 2421-2431 (2007)
  53. Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Weixlbaumer A, Murphy FV, Dziergowska A, Malkiewicz A, Vendeix FA, Agris PF, Ramakrishnan V. Nat Struct Mol Biol 14 498-502 (2007)
  54. Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing. Liang XH, Liu Q, Fournier MJ. RNA 15 1716-1728 (2009)
  55. Structure of the mammalian 80S ribosome at 8.7 A resolution. Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW. Structure 16 535-548 (2008)
  56. How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation. Zhou J, Lancaster L, Donohue JP, Noller HF. Science 345 1188-1191 (2014)
  57. Features of ribosome-peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression. Cruz-Vera LR, Rajagopal S, Squires C, Yanofsky C. Mol Cell 19 333-343 (2005)
  58. Molecular mechanisms of antibiotic resistance. Wright GD. Chem Commun (Camb) 47 4055-4061 (2011)
  59. Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Murphy FV, Ramakrishnan V. Nat Struct Mol Biol 11 1251-1252 (2004)
  60. Structural rearrangements of the ribosome at the tRNA proofreading step. Jenner L, Demeshkina N, Yusupova G, Yusupov M. Nat Struct Mol Biol 17 1072-1078 (2010)
  61. The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome. Stanley RE, Blaha G, Grodzicki RL, Strickler MD, Steitz TA. Nat Struct Mol Biol 17 289-293 (2010)
  62. tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome. Grundy FJ, Winkler WC, Henkin TM. Proc Natl Acad Sci U S A 99 11121-11126 (2002)
  63. A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity. Gromadski KB, Daviter T, Rodnina MV. Mol Cell 21 369-377 (2006)
  64. Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide. Vicens Q, Westhof E. J Mol Biol 326 1175-1188 (2003)
  65. A late-acting quality control process for mature eukaryotic rRNAs. LaRiviere FJ, Cole SE, Ferullo DJ, Moore MJ. Mol Cell 24 619-626 (2006)
  66. Modeling a minimal ribosome based on comparative sequence analysis. Mears JA, Cannone JJ, Stagg SM, Gutell RR, Agrawal RK, Harvey SC. J Mol Biol 321 215-234 (2002)
  67. Unusual base pairing during the decoding of a stop codon by the ribosome. Fernández IS, Ng CL, Kelley AC, Wu G, Yu YT, Ramakrishnan V. Nature 500 107-110 (2013)
  68. History of the ribosome and the origin of translation. Petrov AS, Gulen B, Norris AM, Kovacs NA, Bernier CR, Lanier KA, Fox GE, Harvey SC, Wartell RM, Hud NV, Williams LD. Proc Natl Acad Sci U S A 112 15396-15401 (2015)
  69. An active role for the ribosome in determining the fate of oxidized mRNA. Simms CL, Hudson BH, Mosior JW, Rangwala AS, Zaher HS. Cell Rep 9 1256-1264 (2014)
  70. Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry. Jørgensen R, Merrill AR, Yates SP, Marquez VE, Schwan AL, Boesen T, Andersen GR. Nature 436 979-984 (2005)
  71. Assembly of the 30S ribosomal subunit. Culver GM. Biopolymers 68 234-249 (2003)
  72. Highly conserved NIKS tetrapeptide is functionally essential in eukaryotic translation termination factor eRF1. Frolova L, Seit-Nebi A, Kisselev L. RNA 8 129-136 (2002)
  73. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Duarte CM, Wadley LM, Pyle AM. Nucleic Acids Res 31 4755-4761 (2003)
  74. How mutations in tRNA distant from the anticodon affect the fidelity of decoding. Schmeing TM, Voorhees RM, Kelley AC, Ramakrishnan V. Nat Struct Mol Biol 18 432-436 (2011)
  75. Irreversible chemical steps control intersubunit dynamics during translation. Marshall RA, Dorywalska M, Puglisi JD. Proc Natl Acad Sci U S A 105 15364-15369 (2008)
  76. Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex. Cukras AR, Southworth DR, Brunelle JL, Culver GM, Green R. Mol Cell 12 321-328 (2003)
  77. The molecular basis for A-site mutations conferring aminoglycoside resistance: relationship between ribosomal susceptibility and X-ray crystal structures. Pfister P, Hobbie S, Vicens Q, Böttger EC, Westhof E. Chembiochem 4 1078-1088 (2003)
  78. A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition. Bayfield MA, Dahlberg AE, Schulmeister U, Dorner S, Barta A. Proc Natl Acad Sci U S A 98 10096-10101 (2001)
  79. Intersubunit movement is required for ribosomal translocation. Horan LH, Noller HF. Proc Natl Acad Sci U S A 104 4881-4885 (2007)
  80. eIF3j is located in the decoding center of the human 40S ribosomal subunit. Fraser CS, Berry KE, Hershey JW, Doudna JA. Mol Cell 26 811-819 (2007)
  81. Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes. Shao S, Murray J, Brown A, Taunton J, Ramakrishnan V, Hegde RS. Cell 167 1229-1240.e15 (2016)
  82. Deletion of a conserved, central ribosomal intersubunit RNA bridge. Ali IK, Lancaster L, Feinberg J, Joseph S, Noller HF. Mol Cell 23 865-874 (2006)
  83. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. Rozov A, Demeshkina N, Khusainov I, Westhof E, Yusupov M, Yusupova G. Nat Commun 7 10457 (2016)
  84. Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions. Konevega AL, Soboleva NG, Makhno VI, Semenkov YP, Wintermeyer W, Rodnina MV, Katunin VI. RNA 10 90-101 (2004)
  85. Discrimination between defects in elongation fidelity and termination efficiency provides mechanistic insights into translational readthrough. Salas-Marco J, Bedwell DM. J Mol Biol 348 801-815 (2005)
  86. New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. Piekna-Przybylska D, Decatur WA, Fournier MJ. RNA 13 305-312 (2007)
  87. Structural basis for hygromycin B inhibition of protein biosynthesis. Borovinskaya MA, Shoji S, Fredrick K, Cate JH. RNA 14 1590-1599 (2008)
  88. Accurate translocation of mRNA by the ribosome requires a peptidyl group or its analog on the tRNA moving into the 30S P site. Fredrick K, Noller HF. Mol Cell 9 1125-1131 (2002)
  89. Human tRNA(Lys3)(UUU) is pre-structured by natural modifications for cognate and wobble codon binding through keto-enol tautomerism. Vendeix FA, Murphy FV, Cantara WA, Leszczyńska G, Gustilo EM, Sproat B, Malkiewicz A, Agris PF. J Mol Biol 416 467-485 (2012)
  90. Decoding in the absence of a codon by tmRNA and SmpB in the ribosome. Neubauer C, Gillet R, Kelley AC, Ramakrishnan V. Science 335 1366-1369 (2012)
  91. Ensemble cryo-EM elucidates the mechanism of translation fidelity. Loveland AB, Demo G, Grigorieff N, Korostelev AA. Nature 546 113-117 (2017)
  92. Mutational analysis of S12 protein and implications for the accuracy of decoding by the ribosome. Sharma D, Cukras AR, Rogers EJ, Southworth DR, Green R. J Mol Biol 374 1065-1076 (2007)
  93. The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation. Schluenzen F, Takemoto C, Wilson DN, Kaminishi T, Harms JM, Hanawa-Suetsugu K, Szaflarski W, Kawazoe M, Shirouzu M, Nierhaus KH, Yokoyama S, Fucini P. Nat Struct Mol Biol 13 871-878 (2006)
  94. Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution. Correll CC, Swinger K. RNA 9 355-363 (2003)
  95. The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors. Schmitt E, Blanquet S, Mechulam Y. EMBO J 21 1821-1832 (2002)
  96. Three-dimensional structures of translating ribosomes by Cryo-EM. Gilbert RJ, Fucini P, Connell S, Fuller SD, Nierhaus KH, Robinson CV, Dobson CM, Stuart DI. Mol Cell 14 57-66 (2004)
  97. Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection. Johansson M, Zhang J, Ehrenberg M. Proc Natl Acad Sci U S A 109 131-136 (2012)
  98. Inactivation of ribosomal protein genes in Bacillus subtilis reveals importance of each ribosomal protein for cell proliferation and cell differentiation. Akanuma G, Nanamiya H, Natori Y, Yano K, Suzuki S, Omata S, Ishizuka M, Sekine Y, Kawamura F. J Bacteriol 194 6282-6291 (2012)
  99. Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome. Gromadski KB, Rodnina MV. Nat Struct Mol Biol 11 316-322 (2004)
  100. The role of fluctuations in tRNA selection by the ribosome. Lee TH, Blanchard SC, Kim HD, Puglisi JD, Chu S. Proc Natl Acad Sci U S A 104 13661-13665 (2007)
  101. Uniform binding of aminoacylated transfer RNAs to the ribosomal A and P sites. Fahlman RP, Dale T, Uhlenbeck OC. Mol Cell 16 799-805 (2004)
  102. Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes. Nishiyama T, Yamamoto H, Shibuya N, Hatakeyama Y, Hachimori A, Uchiumi T, Nakashima N. Nucleic Acids Res 31 2434-2442 (2003)
  103. Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors. Geary C, Baudrey S, Jaeger L. Nucleic Acids Res 36 1138-1152 (2008)
  104. Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit. Schmeing TM, Moore PB, Steitz TA. RNA 9 1345-1352 (2003)
  105. Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome. Zhou J, Lancaster L, Trakhanov S, Noller HF. RNA 18 230-240 (2012)
  106. Different aa-tRNAs are selected uniformly on the ribosome. Ledoux S, Uhlenbeck OC. Mol Cell 31 114-123 (2008)
  107. Ribosome•RelA structures reveal the mechanism of stringent response activation. Loveland AB, Bah E, Madireddy R, Zhang Y, Brilot AF, Grigorieff N, Korostelev AA. Elife 5 e17029 (2016)
  108. Specificity of RNA-RNA helix recognition. Battle DJ, Doudna JA. Proc Natl Acad Sci U S A 99 11676-11681 (2002)
  109. Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. Guy MP, Podyma BM, Preston MA, Shaheen HH, Krivos KL, Limbach PA, Hopper AK, Phizicky EM. RNA 18 1921-1933 (2012)
  110. A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation. Sundermeier TR, Dulebohn DP, Cho HJ, Karzai AW. Proc Natl Acad Sci U S A 102 2316-2321 (2005)
  111. Structural aspects of RbfA action during small ribosomal subunit assembly. Datta PP, Wilson DN, Kawazoe M, Swami NK, Kaminishi T, Sharma MR, Booth TM, Takemoto C, Fucini P, Yokoyama S, Agrawal RK. Mol Cell 28 434-445 (2007)
  112. Tracing the evolution of RNA structure in ribosomes. Caetano-Anollés G. Nucleic Acids Res 30 2575-2587 (2002)
  113. Idiosyncratic tuning of tRNAs to achieve uniform ribosome binding. Olejniczak M, Dale T, Fahlman RP, Uhlenbeck OC. Nat Struct Mol Biol 12 788-793 (2005)
  114. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Hoang C, Chen J, Vizthum CA, Kandel JM, Hamilton CS, Mueller EG, Ferré-D'Amaré AR. Mol Cell 24 535-545 (2006)
  115. Eukaryotic ribosomal RNA determinants of aminoglycoside resistance and their role in translational fidelity. Fan-Minogue H, Bedwell DM. RNA 14 148-157 (2008)
  116. GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Marshall RA, Aitken CE, Puglisi JD. Mol Cell 35 37-47 (2009)
  117. Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis. Zhang G, Ignatova Z. PLoS One 4 e5036 (2009)
  118. Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons. Takai K, Yokoyama S. Nucleic Acids Res 31 6383-6391 (2003)
  119. Self-assembled lamellar complexes of siRNA with lipidic aminoglycoside derivatives promote efficient siRNA delivery and interference. Desigaux L, Sainlos M, Lambert O, Chevre R, Letrou-Bonneval E, Vigneron JP, Lehn P, Lehn JM, Pitard B. Proc Natl Acad Sci U S A 104 16534-16539 (2007)
  120. Aminoglycoside interactions and impacts on the eukaryotic ribosome. Prokhorova I, Altman RB, Djumagulov M, Shrestha JP, Urzhumtsev A, Ferguson A, Chang CT, Yusupov M, Blanchard SC, Yusupova G. Proc Natl Acad Sci U S A 114 E10899-E10908 (2017)
  121. Mitochondrial deafness alleles confer misreading of the genetic code. Hobbie SN, Bruell CM, Akshay S, Kalapala SK, Shcherbakov D, Böttger EC. Proc Natl Acad Sci U S A 105 3244-3249 (2008)
  122. Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function. Demirci H, Murphy F, Belardinelli R, Kelley AC, Ramakrishnan V, Gregory ST, Dahlberg AE, Jogl G. RNA 16 2319-2324 (2010)
  123. Optimization of speed and accuracy of decoding in translation. Wohlgemuth I, Pohl C, Rodnina MV. EMBO J 29 3701-3709 (2010)
  124. Engineering the rRNA decoding site of eukaryotic cytosolic ribosomes in bacteria. Hobbie SN, Kalapala SK, Akshay S, Bruell C, Schmidt S, Dabow S, Vasella A, Sander P, Böttger EC. Nucleic Acids Res 35 6086-6093 (2007)
  125. Structural insights into the translational infidelity mechanism. Rozov A, Demeshkina N, Westhof E, Yusupov M, Yusupova G. Nat Commun 6 7251 (2015)
  126. Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome. Abeyrathne PD, Koh CS, Grant T, Grigorieff N, Korostelev AA. Elife 5 e14874 (2016)
  127. Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure. Lim VI, Curran JF. RNA 7 942-957 (2001)
  128. Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding. Stahl G, McCarty GP, Farabaugh PJ. Trends Biochem Sci 27 178-183 (2002)
  129. The protein synthesis inhibitors, oxazolidinones and chloramphenicol, cause extensive translational inaccuracy in vivo. Thompson J, O'Connor M, Mills JA, Dahlberg AE. J Mol Biol 322 273-279 (2002)
  130. Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex. Lynch SR, Gonzalez RL, Puglisi JD. Structure 11 43-53 (2003)
  131. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias. Shah P, Gilchrist MA. PLoS Genet 6 e1001128 (2010)
  132. Exploring the substrate promiscuity of drug-modifying enzymes for the chemoenzymatic generation of N-acylated aminoglycosides. Green KD, Chen W, Houghton JL, Fridman M, Garneau-Tsodikova S. Chembiochem 11 119-126 (2010)
  133. Human ribosomal protein L13a is dispensable for canonical ribosome function but indispensable for efficient rRNA methylation. Chaudhuri S, Vyas K, Kapasi P, Komar AA, Dinman JD, Barik S, Mazumder B. RNA 13 2224-2237 (2007)
  134. Measurement of internal movements within the 30 S ribosomal subunit using Förster resonance energy transfer. Hickerson R, Majumdar ZK, Baucom A, Clegg RM, Noller HF. J Mol Biol 354 459-472 (2005)
  135. Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations. Réblová K, Lankas F, Rázga F, Krasovska MV, Koca J, Sponer J. Biopolymers 82 504-520 (2006)
  136. A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation. Connell SR, Topf M, Qin Y, Wilson DN, Mielke T, Fucini P, Nierhaus KH, Spahn CM. Nat Struct Mol Biol 15 910-915 (2008)
  137. A structural basis for streptomycin-induced misreading of the genetic code. Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G. Nat Commun 4 1355 (2013)
  138. RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes. Grosjean H, Gaspin C, Marck C, Decatur WA, de Crécy-Lagard V. BMC Genomics 9 470 (2008)
  139. The crystal structure of the eukaryotic 40S ribosomal subunit in complex with eIF1 and eIF1A. Weisser M, Voigts-Hoffmann F, Rabl J, Leibundgut M, Ban N. Nat Struct Mol Biol 20 1015-1017 (2013)
  140. Interaction of helix D of elongation factor Tu with helices 4 and 5 of protein L7/12 on the ribosome. Kothe U, Wieden HJ, Mohr D, Rodnina MV. J Mol Biol 336 1011-1021 (2004)
  141. Structural transitions induced by the interaction between tRNA(Gly) and the Bacillus subtilis glyQS T box leader RNA. Yousef MR, Grundy FJ, Henkin TM. J Mol Biol 349 273-287 (2005)
  142. The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery. Wadley LM, Pyle AM. Nucleic Acids Res 32 6650-6659 (2004)
  143. A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS. McMahon M, Contreras A, Holm M, Uechi T, Forester CM, Pang X, Jackson C, Calvert ME, Chen B, Quigley DA, Luk JM, Kelley RK, Gordan JD, Gill RM, Blanchard SC, Ruggero D. Elife 8 e48847 (2019)
  144. Stop codon recognition by release factors induces structural rearrangement of the ribosomal decoding center that is productive for peptide release. Youngman EM, He SL, Nikstad LJ, Green R. Mol Cell 28 533-543 (2007)
  145. Structural characterization of ribosome recruitment and translocation by type IV IRES. Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernández IS. Elife 5 e13567 (2016)
  146. The ribosome as a conveying thermal ratchet machine. Spirin AS. J Biol Chem 284 21103-21119 (2009)
  147. The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons. Näsvall SJ, Chen P, Björk GR. RNA 13 2151-2164 (2007)
  148. Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome. Adamczyk AJ, Warshel A. Proc Natl Acad Sci U S A 108 9827-9832 (2011)
  149. Eukaryotic rpL10 drives ribosomal rotation. Sulima SO, Gülay SP, Anjos M, Patchett S, Meskauskas A, Johnson AW, Dinman JD. Nucleic Acids Res 42 2049-2063 (2014)
  150. Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape. Novozhilov AS, Wolf YI, Koonin EV. Biol Direct 2 24 (2007)
  151. Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome. Cochella L, Brunelle JL, Green R. Nat Struct Mol Biol 14 30-36 (2007)
  152. Evolution of protein synthesis from an RNA world. Noller HF. Cold Spring Harb Perspect Biol 4 a003681 (2012)
  153. Protein mistranslation protects bacteria against oxidative stress. Fan Y, Wu J, Ung MH, De Lay N, Cheng C, Ling J. Nucleic Acids Res 43 1740-1748 (2015)
  154. The pathway to GTPase activation of elongation factor SelB on the ribosome. Fischer N, Neumann P, Bock LV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schröder GF, Grubmüller H, Ficner R, Rodnina MV, Stark H. Nature 540 80-85 (2016)
  155. Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site. François B, Szychowski J, Adhikari SS, Pachamuthu K, Swayze EE, Griffey RH, Migawa MT, Westhof E, Hanessian S. Angew Chem Int Ed Engl 43 6735-6738 (2004)
  156. FRET enabled real time detection of RNA-small molecule binding. Xie Y, Dix AV, Tor Y. J Am Chem Soc 131 17605-17614 (2009)
  157. Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center. Koh CS, Brilot AF, Grigorieff N, Korostelev AA. Proc Natl Acad Sci U S A 111 9139-9144 (2014)
  158. Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in Escherichia coli. Abdi NM, Fredrick K. RNA 11 1624-1632 (2005)
  159. Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae. Plant EP, Nguyen P, Russ JR, Pittman YR, Nguyen T, Quesinberry JT, Kinzy TG, Dinman JD. PLoS One 2 e517 (2007)
  160. Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG. Brock JE, Pourshahian S, Giliberti J, Limbach PA, Janssen GR. RNA 14 2159-2169 (2008)
  161. The real-time path of translation factor IF3 onto and off the ribosome. Fabbretti A, Pon CL, Hennelly SP, Hill WE, Lodmell JS, Gualerzi CO. Mol Cell 25 285-296 (2007)
  162. Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site. Kondo J, Urzhumtsev A, Westhof E. Nucleic Acids Res 34 676-685 (2006)
  163. Characterization of the Bacillus subtilis GTPase YloQ and its role in ribosome function. Campbell TL, Daigle DM, Brown ED. Biochem J 389 843-852 (2005)
  164. Modified nucleotides in tRNA(Lys) and tRNA(Val) are important for translocation. Phelps SS, Malkiewicz A, Agris PF, Joseph S. J Mol Biol 338 439-444 (2004)
  165. Mutagenesis of 16S rRNA C1409-G1491 base-pair differentiates between 6'OH and 6'NH3+ aminoglycosides. Pfister P, Hobbie S, Brüll C, Corti N, Vasella A, Westhof E, Böttger EC. J Mol Biol 346 467-475 (2005)
  166. The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE protein are essential for its tRNA modifying function. Yim L, Martínez-Vicente M, Villarroya M, Aguado C, Knecht E, Armengod ME. J Biol Chem 278 28378-28387 (2003)
  167. AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices. Elgavish T, Cannone JJ, Lee JC, Harvey SC, Gutell RR. J Mol Biol 310 735-753 (2001)
  168. Expanded use of sense codons is regulated by modified cytidines in tRNA. Cantara WA, Murphy FV, Demirci H, Agris PF. Proc Natl Acad Sci U S A 110 10964-10969 (2013)
  169. The ribosome-recycling step: consensus or controversy? Hirokawa G, Demeshkina N, Iwakura N, Kaji H, Kaji A. Trends Biochem Sci 31 143-149 (2006)
  170. Thermodynamics of nucleic acid "shape readout" by an aminosugar. Xi H, Davis E, Ranjan N, Xue L, Hyde-Volpe D, Arya DP. Biochemistry 50 9088-9113 (2011)
  171. Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Klosterman PS, Hendrix DK, Tamura M, Holbrook SR, Brenner SE. Nucleic Acids Res 32 2342-2352 (2004)
  172. Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs. Sanbonmatsu KY, Joseph S. J Mol Biol 328 33-47 (2003)
  173. Yeast eIF4B binds to the head of the 40S ribosomal subunit and promotes mRNA recruitment through its N-terminal and internal repeat domains. Walker SE, Zhou F, Mitchell SF, Larson VS, Valasek L, Hinnebusch AG, Lorsch JR. RNA 19 191-207 (2013)
  174. Amino acid starvation and colicin D treatment induce A-site mRNA cleavage in Escherichia coli. Garza-Sánchez F, Gin JG, Hayes CS. J Mol Biol 378 505-519 (2008)
  175. Mechanism of tetracycline resistance by ribosomal protection protein Tet(O). Li W, Atkinson GC, Thakor NS, Allas U, Lu CC, Chan KY, Tenson T, Schulten K, Wilson KS, Hauryliuk V, Frank J. Nat Commun 4 1477 (2013)
  176. Stochastic gating and drug-ribosome interactions. Vaiana AC, Sanbonmatsu KY. J Mol Biol 386 648-661 (2009)
  177. A Ribosomopathy Reveals Decoding Defective Ribosomes Driving Human Dysmorphism. Paolini NA, Attwood M, Sondalle SB, Vieira CMDS, van Adrichem AM, di Summa FM, O'Donohue MF, Gleizes PE, Rachuri S, Briggs JW, Fischer R, Ratcliffe PJ, Wlodarski MW, Houtkooper RH, von Lindern M, Kuijpers TW, Dinman JD, Baserga SJ, Cockman ME, MacInnes AW. Am J Hum Genet 100 506-522 (2017)
  178. Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops. Maehigashi T, Dunkle JA, Miles SJ, Dunham CM. Proc Natl Acad Sci U S A 111 12740-12745 (2014)
  179. The impact of aminoglycosides on the dynamics of translation elongation. Tsai A, Uemura S, Johansson M, Puglisi EV, Marshall RA, Aitken CE, Korlach J, Ehrenberg M, Puglisi JD. Cell Rep 3 497-508 (2013)
  180. Codon reading by tRNAAla with modified uridine in the wobble position. Kothe U, Rodnina MV. Mol Cell 25 167-174 (2007)
  181. Compensatory evolution reveals functional interactions between ribosomal proteins S12, L14 and L19. Maisnier-Patin S, Paulander W, Pennhag A, Andersson DI. J Mol Biol 366 207-215 (2007)
  182. Defining the basis for the specificity of aminoglycoside-rRNA recognition: a comparative study of drug binding to the A sites of Escherichia coli and human rRNA. Kaul M, Barbieri CM, Pilch DS. J Mol Biol 346 119-134 (2005)
  183. Differential selectivity of natural and synthetic aminoglycosides towards the eukaryotic and prokaryotic decoding A sites. Kondo J, Hainrichson M, Nudelman I, Shallom-Shezifi D, Barbieri CM, Pilch DS, Westhof E, Baasov T. Chembiochem 8 1700-1709 (2007)
  184. EFG-independent translocation of the mRNA:tRNA complex is promoted by modification of the ribosome with thiol-specific reagents. Southworth DR, Brunelle JL, Green R. J Mol Biol 324 611-623 (2002)
  185. Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction. Rozov A, Khusainov I, El Omari K, Duman R, Mykhaylyk V, Yusupov M, Westhof E, Wagner A, Yusupova G. Nat Commun 10 2519 (2019)
  186. Missense suppressor mutations in 16S rRNA reveal the importance of helices h8 and h14 in aminoacyl-tRNA selection. McClory SP, Leisring JM, Qin D, Fredrick K. RNA 16 1925-1934 (2010)
  187. Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex. Han Q, Zhao Q, Fish S, Simonsen KB, Vourloumis D, Froelich JM, Wall D, Hermann T. Angew Chem Int Ed Engl 44 2694-2700 (2005)
  188. Motion of transfer RNA from the A/T state into the A-site using docking and simulations. Caulfield T, Devkota B. Proteins 80 2489-2500 (2012)
  189. Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation. Phelps SS, Jerinic O, Joseph S. Mol Cell 10 799-807 (2002)
  190. YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity. Feng S, Chen Y, Kamada K, Wang H, Tang K, Wang M, Gao YG. Nucleic Acids Res 41 9549-9556 (2013)
  191. Zinc depletion induces ribosome hibernation in mycobacteria. Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK. Proc Natl Acad Sci U S A 115 8191-8196 (2018)
  192. Electron microscopy of functional ribosome complexes. Frank J. Biopolymers 68 223-233 (2003)
  193. Principles of stop-codon reading on the ribosome. Sund J, Andér M, Aqvist J. Nature 465 947-950 (2010)
  194. Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs. Licznar P, Mejlhede N, Prère MF, Wills N, Gesteland RF, Atkins JF, Fayet O. EMBO J 22 4770-4778 (2003)
  195. RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. Yu AM, Choi YH, Tu MJ. Pharmacol Rev 72 862-898 (2020)
  196. Variable and conserved elements of human ribosomes surrounding the mRNA at the decoding and upstream sites. Graifer D, Molotkov M, Styazhkina V, Demeshkina N, Bulygin K, Eremina A, Ivanov A, Laletina E, Ven'yaminova A, Karpova G. Nucleic Acids Res 32 3282-3293 (2004)
  197. An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation. Harding HP, Lackey JG, Hsu HC, Zhang Y, Deng J, Xu RM, Damha MJ, Ron D. RNA 14 225-232 (2008)
  198. Error-prone and error-restrictive mutations affecting ribosomal protein S12. Agarwal D, Gregory ST, O'Connor M. J Mol Biol 410 1-9 (2011)
  199. Increased selectivity toward cytoplasmic versus mitochondrial ribosome confers improved efficiency of synthetic aminoglycosides in fixing damaged genes: a strategy for treatment of genetic diseases caused by nonsense mutations. Kandasamy J, Atia-Glikin D, Shulman E, Shapira K, Shavit M, Belakhov V, Baasov T. J Med Chem 55 10630-10643 (2012)
  200. Inhibition of human tyrosyl-DNA phosphodiesterase by aminoglycoside antibiotics and ribosome inhibitors. Liao Z, Thibaut L, Jobson A, Pommier Y. Mol Pharmacol 70 366-372 (2006)
  201. Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM. Li W, Agirrezabala X, Lei J, Bouakaz L, Brunelle JL, Ortiz-Meoz RF, Green R, Sanyal S, Ehrenberg M, Frank J. EMBO J 27 3322-3331 (2008)
  202. The ribosome prohibits the G•U wobble geometry at the first position of the codon-anticodon helix. Rozov A, Westhof E, Yusupov M, Yusupova G. Nucleic Acids Res 44 6434-6441 (2016)
  203. 30S ribosomal subunit assembly is a target for inhibition by aminoglycosides in Escherichia coli. Mehta R, Champney WS. Antimicrob Agents Chemother 46 1546-1549 (2002)
  204. Messenger RNA interactions in the decoding center control the rate of translocation. Khade PK, Joseph S. Nat Struct Mol Biol 18 1300-1302 (2011)
  205. Ribosome reactivation by replacement of damaged proteins. Pulk A, Liiv A, Peil L, Maiväli U, Nierhaus K, Remme J. Mol Microbiol 75 801-814 (2010)
  206. Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome. Zhang J, Ieong KW, Johansson M, Ehrenberg M. Proc Natl Acad Sci U S A 112 9602-9607 (2015)
  207. Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin. Kondo J, François B, Urzhumtsev A, Westhof E. Angew Chem Int Ed Engl 45 3310-3314 (2006)
  208. New features of the ribosome and ribosomal inhibitors: non-enzymatic recycling, misreading and back-translocation. Szaflarski W, Vesper O, Teraoka Y, Plitta B, Wilson DN, Nierhaus KH. J Mol Biol 380 193-205 (2008)
  209. The Pseudomonas aeruginosa membranes: a target for a new amphiphilic aminoglycoside derivative? Ouberai M, El Garch F, Bussiere A, Riou M, Alsteens D, Lins L, Baussanne I, Dufrêne YF, Brasseur R, Decout JL, Mingeot-Leclercq MP. Biochim Biophys Acta 1808 1716-1727 (2011)
  210. Defect in the formation of 70S ribosomes caused by lack of ribosomal protein L34 can be suppressed by magnesium. Akanuma G, Kobayashi A, Suzuki S, Kawamura F, Shiwa Y, Watanabe S, Yoshikawa H, Hanai R, Ishizuka M. J Bacteriol 196 3820-3830 (2014)
  211. Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA. Christian EL, Kaye NM, Harris ME. EMBO J 21 2253-2262 (2002)
  212. Functional annotation of class I lysyl-tRNA synthetase phylogeny indicates a limited role for gene transfer. Ambrogelly A, Korencic D, Ibba M. J Bacteriol 184 4594-4600 (2002)
  213. Functional conformations of the L11-ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations. Li W, Sengupta J, Rath BK, Frank J. RNA 12 1240-1253 (2006)
  214. L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy. Jonker HR, Ilin S, Grimm SK, Wöhnert J, Schwalbe H. Nucleic Acids Res 35 441-454 (2007)
  215. Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit. Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V. RNA 13 817-823 (2007)
  216. Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin. Shalev-Benami M, Zhang Y, Rozenberg H, Nobe Y, Taoka M, Matzov D, Zimmerman E, Bashan A, Isobe T, Jaffe CL, Yonath A, Skiniotis G. Nat Commun 8 1589 (2017)
  217. Determinants of the rate of mRNA translocation in bacterial protein synthesis. Borg A, Ehrenberg M. J Mol Biol 427 1835-1847 (2015)
  218. EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon-anticodon duplex. Liu G, Song G, Zhang D, Zhang D, Li Z, Lyu Z, Dong J, Achenbach J, Gong W, Zhao XS, Nierhaus KH, Qin Y. Nat Struct Mol Biol 21 817-824 (2014)
  219. Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2. Scarlett DJ, McCaughan KK, Wilson DN, Tate WP. J Biol Chem 278 15095-15104 (2003)
  220. Multiple defects in translation associated with altered ribosomal protein L4. O'Connor M, Gregory ST, Dahlberg AE. Nucleic Acids Res 32 5750-5756 (2004)
  221. Ribozyme-catalysed RNA synthesis using triplet building blocks. Attwater J, Raguram A, Morgunov AS, Gianni E, Holliger P. Elife 7 e35255 (2018)
  222. Structural and evolutionary classification of G/U wobble basepairs in the ribosome. Mokdad A, Krasovska MV, Sponer J, Leontis NB. Nucleic Acids Res 34 1326-1341 (2006)
  223. The ribosome moves: RNA mechanics and translocation. Noller HF, Lancaster L, Zhou J, Mohan S. Nat Struct Mol Biol 24 1021-1027 (2017)
  224. Free energy calculation of modified base-pair formation in explicit solvent: A predictive model. Vendeix FA, Munoz AM, Agris PF. RNA 15 2278-2287 (2009)
  225. Gentamicin B1 is a minor gentamicin component with major nonsense mutation suppression activity. Baradaran-Heravi A, Niesser J, Balgi AD, Choi K, Zimmerman C, South AP, Anderson HJ, Strynadka NC, Bally MB, Roberge M. Proc Natl Acad Sci U S A 114 3479-3484 (2017)
  226. Novel 2,5-dideoxystreptamine derivatives targeting the ribosomal decoding site RNA. Vourloumis D, Takahashi M, Winters GC, Simonsen KB, Ayida BK, Barluenga S, Qamar S, Shandrick S, Zhao Q, Hermann T. Bioorg Med Chem Lett 12 3367-3372 (2002)
  227. Automated segmentation of molecular subunits in electron cryomicroscopy density maps. Baker ML, Yu Z, Chiu W, Bajaj C. J Struct Biol 156 432-441 (2006)
  228. Binding of tobramycin leads to conformational changes in yeast tRNA(Asp) and inhibition of aminoacylation. Walter F, Pütz J, Giegé R, Westhof E. EMBO J 21 760-768 (2002)
  229. Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome. Gagnon MG, Lin J, Bulkley D, Steitz TA. Science 345 684-687 (2014)
  230. Letter Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon. Lehmann J, Libchaber A. RNA 14 1264-1269 (2008)
  231. Maintenance of the correct open reading frame by the ribosome. Hansen TM, Baranov PV, Ivanov IP, Ivanov IP, Gesteland RF, Atkins JF. EMBO Rep 4 499-504 (2003)
  232. Polypeptide release at sense and noncognate stop codons by localized charge-exchange alterations in translational release factors. Uno M, Ito K, Nakamura Y. Proc Natl Acad Sci U S A 99 1819-1824 (2002)
  233. Ribosome hijacking: a role for small protein B during trans-translation. Nonin-Lecomte S, Germain-Amiot N, Gillet R, Hallier M, Ponchon L, Dardel F, Felden B. EMBO Rep 10 160-165 (2009)
  234. S16 throws a conformational switch during assembly of 30S 5' domain. Ramaswamy P, Woodson SA. Nat Struct Mol Biol 16 438-445 (2009)
  235. Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA. Dunkle JA, Vinal K, Desai PM, Zelinskaya N, Savic M, West DM, Conn GL, Dunham CM. Proc Natl Acad Sci U S A 111 6275-6280 (2014)
  236. The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions. Lee JC, Gutell RR, Russell R. J Mol Biol 360 978-988 (2006)
  237. The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit. Lancaster L, Lambert NJ, Maklan EJ, Horan LH, Noller HF. RNA 14 1999-2012 (2008)
  238. A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1. Léger M, Sidani S, Brakier-Gingras L. RNA 10 1225-1235 (2004)
  239. Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes. Soung GY, Miller JL, Koc H, Koc EC. J Proteome Res 8 3390-3402 (2009)
  240. Novel paromamine derivatives exploring shallow-groove recognition of ribosomal-decoding-site RNA. Simonsen KB, Ayida BK, Vourloumis D, Takahashi M, Winters GC, Barluenga S, Qamar S, Shandrick S, Zhao Q, Hermann T. Chembiochem 3 1223-1228 (2002)
  241. A functional interaction between ribosomal proteins S7 and S11 within the bacterial ribosome. Robert F, Brakier-Gingras L. J Biol Chem 278 44913-44920 (2003)
  242. Abbreviated Pathway for Biosynthesis of 2-Thiouridine in Bacillus subtilis. Black KA, Dos Santos PC. J Bacteriol 197 1952-1962 (2015)
  243. Multiple Cis-acting elements modulate programmed -1 ribosomal frameshifting in Pea enation mosaic virus. Gao F, Simon AE. Nucleic Acids Res 44 878-895 (2016)
  244. A structure-based strategy to identify new molecular scaffolds targeting the bacterial ribosomal A-site. Foloppe N, Chen IJ, Davis B, Hold A, Morley D, Howes R. Bioorg Med Chem 12 935-947 (2004)
  245. Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading. Loveland AB, Demo G, Korostelev AA. Nature 584 640-645 (2020)
  246. Delayed rRNA processing results in significant ribosome biogenesis and functional defects. Meskauskas A, Baxter JL, Carr EA, Yasenchak J, Gallagher JE, Baserga SJ, Dinman JD. Mol Cell Biol 23 1602-1613 (2003)
  247. Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides. Zhou Y, Kierzek E, Loo ZP, Antonio M, Yau YH, Chuah YW, Geifman-Shochat S, Kierzek R, Chen G. Nucleic Acids Res 41 6664-6673 (2013)
  248. Role of 16S rRNA Helix 44 in Ribosomal Resistance to Hygromycin B. Pfister P, Risch M, Brodersen DE, Böttger EC. Antimicrob Agents Chemother 47 1496-1502 (2003)
  249. Selectively guanidinylated aminoglycosides as antibiotics. Fair RJ, Hensler ME, Thienphrapa W, Dam QN, Nizet V, Tor Y. ChemMedChem 7 1237-1244 (2012)
  250. The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome. Voorhees RM, Mandal D, Neubauer C, Köhrer C, RajBhandary UL, Ramakrishnan V. Nat Struct Mol Biol 20 641-643 (2013)
  251. Analysis of structural dynamics in the ribosome by TLS crystallographic refinement. Korostelev A, Noller HF. J Mol Biol 373 1058-1070 (2007)
  252. Deducing the kinetics of protein synthesis in vivo from the transition rates measured in vitro. Rudorf S, Thommen M, Rodnina MV, Lipowsky R. PLoS Comput Biol 10 e1003909 (2014)
  253. Historical Article From the structure and function of the ribosome to new antibiotics (Nobel Lecture). Steitz TA. Angew Chem Int Ed Engl 49 4381-4398 (2010)
  254. O6-Methylguanosine leads to position-dependent effects on ribosome speed and fidelity. Hudson BH, Zaher HS. RNA 21 1648-1659 (2015)
  255. Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3. Ng CL, Lang K, Meenan NA, Sharma A, Kelley AC, Kleanthous C, Ramakrishnan V. Nat Struct Mol Biol 17 1241-1246 (2010)
  256. The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates. Kondo J, Westhof E. Nucleic Acids Res 36 2654-2666 (2008)
  257. Fluorescent HIV-1 Dimerization Initiation Site: design, properties, and use for ligand discovery. Tam VK, Kwong D, Tor Y. J Am Chem Soc 129 3257-3266 (2007)
  258. Molecular dynamics simulations of human tRNA Lys,3 UUU: the role of modified bases in mRNA recognition. McCrate NE, Varner ME, Kim KI, Nagan MC. Nucleic Acids Res 34 5361-5368 (2006)
  259. Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair. Mathews DH, Case DA. J Mol Biol 357 1683-1693 (2006)
  260. Steric complementarity in the decoding center is important for tRNA selection by the ribosome. Khade PK, Shi X, Joseph S. J Mol Biol 425 3778-3789 (2013)
  261. Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Li S, Su Z, Lehmann J, Stamatopoulou V, Giarimoglou N, Henderson FE, Fan L, Pintilie GD, Zhang K, Chen M, Ludtke SJ, Wang YX, Stathopoulos C, Chiu W, Zhang J. Nat Struct Mol Biol 26 1094-1105 (2019)
  262. Historical Article Unraveling the structure of the ribosome (Nobel Lecture). Ramakrishnan V. Angew Chem Int Ed Engl 49 4355-4380 (2010)
  263. When Proteins Start to Make Sense: Fine-tuning Aminoglycosides for PTC Suppression Therapy. Shalev M, Baasov T. Medchemcomm 5 1092-1105 (2014)
  264. Binding of ribosome recycling factor to ribosomes, comparison with tRNA. Hirokawa G, Kiel MC, Muto A, Kawai G, Igarashi K, Kaji H, Kaji A. J Biol Chem 277 35847-35852 (2002)
  265. Cryo-EM structure of the large subunit of the spinach chloroplast ribosome. Ahmed T, Yin Z, Bhushan S. Sci Rep 6 35793 (2016)
  266. Crystal structure of 70S ribosome with both cognate tRNAs in the E and P sites representing an authentic elongation complex. Feng S, Chen Y, Gao YG. PLoS One 8 e58829 (2013)
  267. Defining the mRNA recognition signature of a bacterial toxin protein. Schureck MA, Dunkle JA, Maehigashi T, Miles SJ, Dunham CM. Proc Natl Acad Sci U S A 112 13862-13867 (2015)
  268. Development of antibiotic-overproducing strains by site-directed mutagenesis of the rpsL gene in Streptomyces lividans. Okamoto-Hosoya Y, Okamoto S, Ochi K. Appl Environ Microbiol 69 4256-4259 (2003)
  269. Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation on the ribosome. Matassova AB, Rodnina MV, Wintermeyer W. RNA 7 1879-1885 (2001)
  270. Identification of the molecular attributes required for aminoglycoside activity against Leishmania. Shalev M, Kondo J, Kopelyanskiy D, Jaffe CL, Adir N, Baasov T. Proc Natl Acad Sci U S A 110 13333-13338 (2013)
  271. Novel acyclic deoxystreptamine mimetics targeting the ribosomal decoding site. Vourloumis D, Winters GC, Takahashi M, Simonsen KB, Ayida BK, Shandrick S, Zhao Q, Hermann T. Chembiochem 4 879-885 (2003)
  272. The ribosomal grip of the peptidyl-tRNA is critical for reading frame maintenance. Näsvall SJ, Nilsson K, Björk GR. J Mol Biol 385 350-367 (2009)
  273. A structural model for the assembly of the 30S subunit of the ribosome. Stagg SM, Mears JA, Harvey SC. J Mol Biol 328 49-61 (2003)
  274. Effects of Escherichia coli ribosomal protein S12 mutations on cell-free protein synthesis. Chumpolkulwong N, Hori-Takemoto C, Hosaka T, Inaoka T, Kigawa T, Shirouzu M, Ochi K, Yokoyama S. Eur J Biochem 271 1127-1134 (2004)
  275. Functional studies of the 900 tetraloop capping helix 27 of 16S ribosomal RNA. Bélanger F, Léger M, Saraiya AA, Cunningham PR, Brakier-Gingras L. J Mol Biol 320 979-989 (2002)
  276. Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site. Murray JB, Meroueh SO, Russell RJ, Lentzen G, Haddad J, Mobashery S. Chem Biol 13 129-138 (2006)
  277. The role of upstream sequences in selecting the reading frame on tmRNA. Miller MR, Healey DW, Robison SG, Dewey JD, Buskirk AR. BMC Biol 6 29 (2008)
  278. tRNA anticodon shifts in eukaryotic genomes. Rogers HH, Griffiths-Jones S. RNA 20 269-281 (2014)
  279. A signal relay between ribosomal protein S12 and elongation factor EF-Tu during decoding of mRNA. Gregory ST, Carr JF, Dahlberg AE. RNA 15 208-214 (2009)
  280. Aminoglycoside-hybrid ligands targeting the ribosomal decoding site. Vourloumis D, Winters GC, Simonsen KB, Takahashi M, Ayida BK, Shandrick S, Zhao Q, Han Q, Hermann T. Chembiochem 6 58-65 (2005)
  281. Anticodon-dependent conservation of bacterial tRNA gene sequences. Saks ME, Conery JS. RNA 13 651-660 (2007)
  282. Characterization of GE82832, a peptide inhibitor of translocation interacting with bacterial 30S ribosomal subunits. Brandi L, Fabbretti A, Di Stefano M, Lazzarini A, Abbondi M, Gualerzi CO. RNA 12 1262-1270 (2006)
  283. Colicin E3 cleavage of 16S rRNA impairs decoding and accelerates tRNA translocation on Escherichia coli ribosomes. Lancaster LE, Savelsbergh A, Kleanthous C, Wintermeyer W, Rodnina MV. Mol Microbiol 69 390-401 (2008)
  284. Crystal structure of the bacterial ribosomal decoding site complexed with a synthetic doubly functionalized paromomycin derivative: a new specific binding mode to an a-minor motif enhances in vitro antibacterial activity. Kondo J, Pachamuthu K, François B, Szychowski J, Hanessian S, Westhof E. ChemMedChem 2 1631-1638 (2007)
  285. Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome. Ishida H, Hayward S. Biophys J 95 5962-5973 (2008)
  286. Rational design of azepane-glycoside antibiotics targeting the bacterial ribosome. Barluenga S, Simonsen KB, Littlefield ES, Ayida BK, Vourloumis D, Winters GC, Takahashi M, Shandrick S, Zhao Q, Han Q, Hermann T. Bioorg Med Chem Lett 14 713-718 (2004)
  287. Recurring RNA structural motifs underlie the mechanics of L1 stalk movement. Mohan S, Noller HF. Nat Commun 8 14285 (2017)
  288. Ribosome engineering to promote new crystal forms. Selmer M, Gao YG, Weixlbaumer A, Ramakrishnan V. Acta Crystallogr D Biol Crystallogr 68 578-583 (2012)
  289. Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids. Walberer BJ, Cheng AC, Frankel AD. J Mol Biol 327 767-780 (2003)
  290. The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions. Amarantos I, Zarkadis IK, Kalpaxis DL. Nucleic Acids Res 30 2832-2843 (2002)
  291. The role of SmpB and the ribosomal decoding center in licensing tmRNA entry into stalled ribosomes. Miller MR, Liu Z, Cazier DJ, Gebhard GM, Herron SR, Zaher HS, Green R, Buskirk AR. RNA 17 1727-1736 (2011)
  292. Use of 2-aminopurine as a fluorescent tool for characterizing antibiotic recognition of the bacterial rRNA A-site. Barbieri CM, Kaul M, Pilch DS. Tetrahedron 63 3567-6574 (2007)
  293. Visualization of codon-dependent conformational rearrangements during translation termination. He SL, Green R. Nat Struct Mol Biol 17 465-470 (2010)
  294. C/D box sRNA-guided 2'-O-methylation patterns of archaeal rRNA molecules. Dennis PP, Tripp V, Lui L, Lowe T, Randau L. BMC Genomics 16 632 (2015)
  295. Codon-anticodon interaction at the P site is a prerequisite for tRNA interaction with the small ribosomal subunit. Schäfer MA, Tastan AO, Patzke S, Blaha G, Spahn CM, Wilson DN, Nierhaus KH. J Biol Chem 277 19095-19105 (2002)
  296. Potential for interdependent development of tRNA determinants for aminoacylation and ribosome decoding. Liu C, Gamper H, Liu H, Cooperman BS, Hou YM. Nat Commun 2 329 (2011)
  297. Ribosome-small-subunit-dependent GTPase interacts with tRNA-binding sites on the ribosome. Kimura T, Takagi K, Hirata Y, Hase Y, Muto A, Himeno H. J Mol Biol 381 467-477 (2008)
  298. The central role of protein S12 in organizing the structure of the decoding site of the ribosome. Demirci H, Wang L, Murphy FV, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST. RNA 19 1791-1801 (2013)
  299. The role of the mitochondrial ribosome in human disease: searching for mutations in 12S mitochondrial rRNA with high disruptive potential. Smith PM, Elson JL, Greaves LC, Wortmann SB, Rodenburg RJ, Lightowlers RN, Chrzanowska-Lightowlers ZM, Taylor RW, Vila-Sanjurjo A. Hum Mol Genet 23 949-967 (2014)
  300. Altered patterns of global protein synthesis and translational fidelity in RPS15-mutated chronic lymphocytic leukemia. Bretones G, Álvarez MG, Arango JR, Rodríguez D, Nadeu F, Prado MA, Valdés-Mas R, Puente DA, Paulo JA, Delgado J, Villamor N, López-Guillermo A, Finley DJ, Gygi SP, Campo E, Quesada V, López-Otín C. Blood 132 2375-2388 (2018)
  301. Apramycin recognition by the human ribosomal decoding site. Hermann T, Tereshko V, Skripkin E, Patel DJ. Blood Cells Mol Dis 38 193-198 (2007)
  302. Distinctive contributions of the ribosomal P-site elements m2G966, m5C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli. Arora S, Bhamidimarri SP, Bhattacharyya M, Govindan A, Weber MH, Vishveshwara S, Varshney U. Nucleic Acids Res 41 4963-4975 (2013)
  303. Fluorescently labeled ribosomes as a tool for analyzing antibiotic binding. Llano-Sotelo B, Hickerson RP, Lancaster L, Noller HF, Mankin AS. RNA 15 1597-1604 (2009)
  304. Position-dependent effects of regioisomeric methylated adenine and guanine ribonucleosides on translation. You C, Dai X, Wang Y. Nucleic Acids Res 45 9059-9067 (2017)
  305. Ribosomal protein S12 and aminoglycoside antibiotics modulate A-site mRNA cleavage and transfer-messenger RNA activity in Escherichia coli. Holberger LE, Hayes CS. J Biol Chem 284 32188-32200 (2009)
  306. Selection of peptides that target the aminoacyl-tRNA site of bacterial 16S ribosomal RNA. Li M, Duc AC, Klosi E, Pattabiraman S, Spaller MR, Chow CS. Biochemistry 48 8299-8311 (2009)
  307. Slow formation of stable complexes during coincubation of minimal rRNA and ribosomal protein S4. Mayerle M, Bellur DL, Woodson SA. J Mol Biol 412 453-465 (2011)
  308. Specificity of the ribosomal A site for aminoacyl-tRNAs. Dale T, Fahlman RP, Olejniczak M, Uhlenbeck OC. Nucleic Acids Res 37 1202-1210 (2009)
  309. The tetracycline resistance protein Tet(o) perturbs the conformation of the ribosomal decoding centre. Connell SR, Trieber CA, Stelzl U, Einfeldt E, Taylor DE, Nierhaus KH. Mol Microbiol 45 1463-1472 (2002)
  310. Thermodynamic control of -1 programmed ribosomal frameshifting. Bock LV, Caliskan N, Korniy N, Peske F, Rodnina MV, Grubmüller H. Nat Commun 10 4598 (2019)
  311. ASC1 and RPS3: new actors in 18S nonfunctional rRNA decay. Limoncelli KA, Merrikh CN, Moore MJ. RNA 23 1946-1960 (2017)
  312. A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme. Bouchard P, Legault P. RNA 20 1451-1464 (2014)
  313. Cleavage of RNA oligonucleotides by aminoglycosides. Belousoff MJ, Graham B, Spiccia L, Tor Y. Org Biomol Chem 7 30-33 (2009)
  314. Critical residues for cofactor binding and catalytic activity in the aminoglycoside resistance methyltransferase Sgm. Savic M, Ilic-Tomic T, Macmaster R, Vasiljevic B, Conn GL. J Bacteriol 190 5855-5861 (2008)
  315. Erythromycin, roxithromycin, and clarithromycin: use of slow-binding kinetics to compare their in vitro interaction with a bacterial ribosomal complex active in peptide bond formation. Dinos GP, Connell SR, Nierhaus KH, Kalpaxis DL. Mol Pharmacol 63 617-623 (2003)
  316. Functional compatibility of elongation factors between mammalian mitochondrial and bacterial ribosomes: characterization of GTPase activity and translation elongation by hybrid ribosomes bearing heterologous L7/12 proteins. Terasaki M, Suzuki T, Hanada T, Watanabe K. J Mol Biol 336 331-342 (2004)
  317. Genetic evidence against the 16S ribosomal RNA helix 27 conformational switch model. Rodriguez-Correa D, Dahlberg AE. RNA 10 28-33 (2004)
  318. Structural basis for selective targeting of leishmanial ribosomes: aminoglycoside derivatives as promising therapeutics. Shalev M, Rozenberg H, Smolkin B, Nasereddin A, Kopelyanskiy D, Belakhov V, Schrepfer T, Schacht J, Jaffe CL, Adir N, Baasov T. Nucleic Acids Res 43 8601-8613 (2015)
  319. Structural insights into translational recoding by frameshift suppressor tRNASufJ. Fagan CE, Maehigashi T, Dunkle JA, Miles SJ, Dunham CM. RNA 20 1944-1954 (2014)
  320. Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform. Tzani I, Ivanov IP, Ivanov IP, Andreev DE, Dmitriev RI, Dean KA, Baranov PV, Atkins JF, Loughran G. Open Biol 6 150203 (2016)
  321. Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions. Hoernes TP, Faserl K, Juen MA, Kremser J, Gasser C, Fuchs E, Shi X, Siewert A, Lindner H, Kreutz C, Micura R, Joseph S, Höbartner C, Westhof E, Hüttenhofer A, Erlacher MD. Nat Commun 9 4865 (2018)
  322. A single mutation in the IF3 N-terminal domain perturbs the fidelity of translation initiation at three levels. Maar D, Liveris D, Sussman JK, Ringquist S, Moll I, Heredia N, Kil A, Bläsi U, Schwartz I, Simons RW. J Mol Biol 383 937-944 (2008)
  323. Accuracy modulating mutations of the ribosomal protein S4-S5 interface do not necessarily destabilize the rps4-rps5 protein-protein interaction. Vallabhaneni H, Farabaugh PJ. RNA 15 1100-1109 (2009)
  324. Bases in 16S rRNA important for subunit association, tRNA binding, and translocation. Shi X, Chiu K, Ghosh S, Joseph S. Biochemistry 48 6772-6782 (2009)
  325. Functional role of methylation of G518 of the 16S rRNA 530 loop by GidB in Mycobacterium tuberculosis. Wong SY, Javid B, Addepalli B, Piszczek G, Strader MB, Limbach PA, Barry CE. Antimicrob Agents Chemother 57 6311-6318 (2013)
  326. Helix 69 is key for uniformity during substrate selection on the ribosome. Ortiz-Meoz RF, Green R. J Biol Chem 286 25604-25610 (2011)
  327. Identification of compounds that decrease the fidelity of start codon recognition by the eukaryotic translational machinery. Takacs JE, Neary TB, Ingolia NT, Saini AK, Martin-Marcos P, Pelletier J, Hinnebusch AG, Lorsch JR. RNA 17 439-452 (2011)
  328. Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis. Zhang Z, Sanbonmatsu KY, Voth GA. J Am Chem Soc 133 16828-16838 (2011)
  329. Piperidine glycosides targeting the ribosomal decoding site. Simonsen KB, Ayida BK, Vourloumis D, Winters GC, Takahashi M, Shandrick S, Zhao Q, Hermann T. Chembiochem 4 886-890 (2003)
  330. Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons. Parisien M, Yi C, Pan T. RNA 18 355-367 (2012)
  331. Ribosomes lacking protein S20 are defective in mRNA binding and subunit association. Tobin C, Mandava CS, Ehrenberg M, Andersson DI, Sanyal S. J Mol Biol 397 767-776 (2010)
  332. Study of the functional interaction of the 900 Tetraloop of 16S ribosomal RNA with helix 24 within the bacterial ribosome. Bélanger F, Gagnon MG, Steinberg SV, Cunningham PR, Brakier-Gingras L. J Mol Biol 338 683-693 (2004)
  333. Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria. Rozov A, Wolff P, Grosjean H, Yusupov M, Yusupova G, Westhof E. Nucleic Acids Res 46 7425-7435 (2018)
  334. The ribosome as an optimal decoder: a lesson in molecular recognition. Savir Y, Tlusty T. Cell 153 471-479 (2013)
  335. Conformation of 4.5S RNA in the signal recognition particle and on the 30S ribosomal subunit. Gu SQ, Jöckel J, Beinker P, Warnecke J, Semenkov YP, Rodnina MV, Wintermeyer W. RNA 11 1374-1384 (2005)
  336. Elongation factor 4 remodels the A-site tRNA on the ribosome. Gagnon MG, Lin J, Steitz TA. Proc Natl Acad Sci U S A 113 4994-4999 (2016)
  337. Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. Zeng X, Chugh J, Casiano-Negroni A, Al-Hashimi HM, Brooks CL. J Mol Biol 426 3201-3213 (2014)
  338. In vitro read-through of phenylalanine hydroxylase (PAH) nonsense mutations using aminoglycosides: a potential therapy for phenylketonuria. Ho G, Reichardt J, Christodoulou J. J Inherit Metab Dis 36 955-959 (2013)
  339. Inhibition of antiassociation activity of translation initiation factor 3 by paromomycin. Hirokawa G, Kaji H, Kaji A. Antimicrob Agents Chemother 51 175-180 (2007)
  340. Mapping of the second tetracycline binding site on the ribosomal small subunit of E.coli. Anokhina MM, Barta A, Nierhaus KH, Spiridonova VA, Kopylov AM. Nucleic Acids Res 32 2594-2597 (2004)
  341. Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement. Gao H, Frank J. Structure 13 401-406 (2005)
  342. Monitoring translation with modified mRNAs strategically labeled with isomorphic fluorescent guanosine mimetics. Liu W, Shin D, Tor Y, Cooperman BS. ACS Chem Biol 8 2017-2023 (2013)
  343. New codons for efficient production of unnatural proteins in a semisynthetic organism. Fischer EC, Hashimoto K, Zhang Y, Feldman AW, Dien VT, Karadeema RJ, Adhikary R, Ledbetter MP, Krishnamurthy R, Romesberg FE. Nat Chem Biol 16 570-576 (2020)
  344. Rapid synthesis, RNA binding, and antibacterial screening of a peptidic-aminosugar (PA) library. Jiang L, Watkins D, Jin Y, Gong C, King A, Washington AZ, Green KD, Garneau-Tsodikova S, Oyelere AK, Arya DP. ACS Chem Biol 10 1278-1289 (2015)
  345. Ribosomal crystallography: from poorly diffracting microcrystals to high-resolution structures. Gluehmann M, Zarivach R, Bashan A, Harms J, Schluenzen F, Bartels H, Agmon I, Rosenblum G, Pioletti M, Auerbach T, Avila H, Hansen HA, Franceschi F, Yonath A. Methods 25 292-302 (2001)
  346. Role of pseudouridine in structural rearrangements of helix 69 during bacterial ribosome assembly. Sakakibara Y, Chow CS. ACS Chem Biol 7 871-878 (2012)
  347. Rsp5 ubiquitin ligase modulates translation accuracy in yeast Saccharomyces cerevisiae. Kwapisz M, Cholbinski P, Hopper AK, Rousset JP, Zoladek T. RNA 11 1710-1718 (2005)
  348. Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif. McLaughlin WA, Berman HM. J Mol Biol 330 43-55 (2003)
  349. Structural insights into substrate recognition by the Neurospora Varkud satellite ribozyme: importance of U-turns at the kissing-loop junction. Bouchard P, Legault P. Biochemistry 53 258-269 (2014)
  350. The N-terminal extension of Escherichia coli ribosomal protein L20 is important for ribosome assembly, but dispensable for translational feedback control. Guillier M, Allemand F, Graffe M, Raibaud S, Dardel F, Springer M, Chiaruttini C. RNA 11 728-738 (2005)
  351. Translocation of a tRNA with an extended anticodon through the ribosome. Phelps SS, Gaudin C, Yoshizawa S, Benitez C, Fourmy D, Joseph S. J Mol Biol 360 610-622 (2006)
  352. A minimum structure of aminoglycosides that causes an initiation shift of trans-translation. Konno T, Takahashi T, Kurita D, Muto A, Himeno H. Nucleic Acids Res 32 4119-4126 (2004)
  353. A structural basis for the antibiotic resistance conferred by an A1408G mutation in 16S rRNA and for the antiprotozoal activity of aminoglycosides. Kondo J. Angew Chem Int Ed Engl 51 465-468 (2012)
  354. Antibiotic selectivity for prokaryotic vs. eukaryotic decoding sites. Xie Y, Dix AV, Tor Y. Chem Commun (Camb) 46 5542-5544 (2010)
  355. Conformational transition in the aminoacyl t-RNA site of the bacterial ribosome both in the presence and absence of an aminoglycoside antibiotic. Meroueh SO, Mobashery S. Chem Biol Drug Des 69 291-297 (2007)
  356. Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit. Simonović M, Steitz TA. Proc Natl Acad Sci U S A 105 500-505 (2008)
  357. Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A. Fislage M, Zhang J, Brown ZP, Mandava CS, Sanyal S, Ehrenberg M, Frank J. Nucleic Acids Res 46 5861-5874 (2018)
  358. Crystal structure of the Thermus thermophilus 16 S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine. Demirci H, Gregory ST, Dahlberg AE, Jogl G. J Biol Chem 283 26548-26556 (2008)
  359. Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state. Athavale SS, Gossett JJ, Hsiao C, Bowman JC, O'Neill E, Hershkovitz E, Preeprem T, Hud NV, Wartell RM, Harvey SC, Williams LD. RNA 18 752-758 (2012)
  360. Evolving Mistranslating tRNAs Through a Phenotypically Ambivalent Intermediate in Saccharomyces cerevisiae. Berg MD, Hoffman KS, Genereaux J, Mian S, Trussler RS, Haniford DB, O'Donoghue P, Brandl CJ. Genetics 206 1865-1879 (2017)
  361. G-ribo: a new structural motif in ribosomal RNA. Steinberg SV, Boutorine YI. RNA 13 549-554 (2007)
  362. Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study. Panecka J, Mura C, Trylska J. PLoS One 9 e111811 (2014)
  363. Kinetic basis for global loss of fidelity arising from mismatches in the P-site codon:anticodon helix. Zaher HS, Green R. RNA 16 1980-1989 (2010)
  364. SMMRNA: a database of small molecule modulators of RNA. Mehta A, Sonam S, Gouri I, Loharch S, Sharma DK, Parkesh R. Nucleic Acids Res 42 D132-41 (2014)
  365. Structural basis of early translocation events on the ribosome. Rundlet EJ, Holm M, Schacherl M, Natchiar SK, Altman RB, Spahn CMT, Myasnikov AG, Blanchard SC. Nature 595 741-745 (2021)
  366. Structural signatures of antibiotic binding sites on the ribosome. David-Eden H, Mankin AS, Mandel-Gutfreund Y. Nucleic Acids Res 38 5982-5994 (2010)
  367. Structure based hypothesis of a mitochondrial ribosome rescue mechanism. Huynen MA, Duarte I, Chrzanowska-Lightowlers ZM, Nabuurs SB. Biol Direct 7 14 (2012)
  368. Structure-toxicity relationship of aminoglycosides: correlation of 2'-amine basicity with acute toxicity in pseudo-disaccharide scaffolds. Chen L, Hainrichson M, Bourdetsky D, Mor A, Yaron S, Baasov T. Bioorg Med Chem 16 8940-8951 (2008)
  369. Studying aminoglycoside modification by the acetyltransferase class of resistance-causing enzymes via microarray. Barrett OJ, Pushechnikov A, Wu M, Disney MD. Carbohydr Res 343 2924-2931 (2008)
  370. The effective number of codons for individual amino acids: some codons are more optimal than others. Fuglsang A. Gene 320 185-190 (2003)
  371. Why base tautomerization does not cause errors in mRNA decoding on the ribosome. Satpati P, Åqvist J. Nucleic Acids Res 42 12876-12884 (2014)
  372. tRNA slippage at the tmRNA resume codon. Trimble MJ, Minnicus A, Williams KP. RNA 10 805-812 (2004)
  373. A functional relationship between helix 1 and the 900 tetraloop of 16S ribosomal RNA within the bacterial ribosome. Bélanger F, Théberge-Julien G, Cunningham PR, Brakier-Gingras L. RNA 11 906-913 (2005)
  374. Accuracy of genetic code translation and its orthogonal corruption by aminoglycosides and Mg2+ ions. Zhang J, Pavlov MY, Ehrenberg M. Nucleic Acids Res 46 1362-1374 (2018)
  375. An unusual mechanism for EF-Tu activation during tmRNA-mediated ribosome rescue. Miller MR, Buskirk AR. RNA 20 228-235 (2014)
  376. Codon-specific effects of tRNA anticodon loop modifications on translational misreading errors in the yeast Saccharomyces cerevisiae. Joshi K, Bhatt MJ, Farabaugh PJ. Nucleic Acids Res 46 10331-10339 (2018)
  377. Defining the molecular forces that determine the impact of neomycin on bacterial protein synthesis: importance of the 2'-amino functionality. Barbieri CM, Kaul M, Bozza-Hingos M, Zhao F, Tor Y, Hermann T, Pilch DS. Antimicrob Agents Chemother 51 1760-1769 (2007)
  378. Development of K562 cell clones expressing beta-globin mRNA carrying the beta039 thalassaemia mutation for the screening of correctors of stop-codon mutations. Salvatori F, Cantale V, Breveglieri G, Zuccato C, Finotti A, Bianchi N, Borgatti M, Feriotto G, Destro F, Canella A, Breda L, Rivella S, Gambari R. Biotechnol Appl Biochem 54 41-52 (2009)
  379. Distinct functional classes of ram mutations in 16S rRNA. McClory SP, Devaraj A, Fredrick K. RNA 20 496-504 (2014)
  380. Incomplete homogenization of 18 S ribosomal DNA coding regions in Arabidopsis thaliana. Mentewab AB, Jacobsen MJ, Flowers RA. BMC Res Notes 4 93 (2011)
  381. Novel aminoglycoside 2''-phosphotransferase identified in a gram-negative pathogen. Toth M, Frase H, Antunes NT, Vakulenko SB. Antimicrob Agents Chemother 57 452-457 (2013)
  382. Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA. Simonović M, Steitz TA. RNA 14 2372-2378 (2008)
  383. Polyamines accelerate codon recognition by transfer RNAs on the ribosome. Hetrick B, Khade PK, Lee K, Stephen J, Thomas A, Joseph S. Biochemistry 49 7179-7189 (2010)
  384. Quantitative analysis of deoxynucleotide substitutions in the codon-anticodon helix. Fahlman RP, Olejniczak M, Uhlenbeck OC. J Mol Biol 355 887-892 (2006)
  385. Selection of small peptides, inhibitors of translation. Llano-Sotelo B, Klepacki D, Mankin AS. J Mol Biol 391 813-819 (2009)
  386. Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy. Li W, Hoffman DW. Protein Sci 10 2426-2438 (2001)
  387. Structure of Pseudomonas aeruginosa ribosomes from an aminoglycoside-resistant clinical isolate. Halfon Y, Jimenez-Fernandez A, La Rosa R, Espinosa Portero R, Krogh Johansen H, Matzov D, Eyal Z, Bashan A, Zimmerman E, Belousoff M, Molin S, Yonath A. Proc Natl Acad Sci U S A 116 22275-22281 (2019)
  388. A mechanism for light-induced translation of the rbcL mRNA encoding the large subunit of ribulose-1,5-bisphosphate carboxylase in barley chloroplasts. Kim J, Mullet JE. Plant Cell Physiol 44 491-499 (2003)
  389. Base pairs and pseudo pairs observed in RNA-ligand complexes. Kondo J, Westhof E. J Mol Recognit 23 241-252 (2010)
  390. Codon-Anticodon Recognition in the Bacillus subtilis glyQS T Box Riboswitch: RNA-DEPENDENT CODON SELECTION OUTSIDE THE RIBOSOME. Caserta E, Liu LC, Grundy FJ, Henkin TM. J Biol Chem 290 23336-23347 (2015)
  391. Distortion of tRNA upon near-cognate codon recognition on the ribosome. Mittelstaet J, Konevega AL, Rodnina MV. J Biol Chem 286 8158-8164 (2011)
  392. Eukaryote-specific motif of ribosomal protein S15 neighbors A site codon during elongation and termination of translation. Khairulina J, Graifer D, Bulygin K, Ven'yaminova A, Frolova L, Karpova G. Biochimie 92 820-825 (2010)
  393. High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove. Suddala KC, Zhang J. Nat Struct Mol Biol 26 1114-1122 (2019)
  394. How does tmRNA move through the ribosome? Ivanov PV, Zvereva MI, Shpanchenko OV, Dontsova OA, Bogdanov AA, Aglyamova GV, Lim VI, Teraoka Y, Nierhaus KH. FEBS Lett 514 55-59 (2002)
  395. On the interaction of colicin E3 with the ribosome. Zarivach R, Ben-Zeev E, Wu N, Auerbach T, Bashan A, Jakes K, Dickman K, Kosmidis A, Schluenzen F, Yonath A, Eisenstein M, Shoham M. Biochimie 84 447-454 (2002)
  396. Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation. Garcia-Ortega L, Stephen J, Joseph S. Mol Cell 32 292-299 (2008)
  397. Ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of P-site tRNA are not essential for EF-G catalyzed translocation. Feinberg JS, Joseph S. RNA 12 580-588 (2006)
  398. Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators. Battaglia RA, Grigg JC, Ke A. Nat Struct Mol Biol 26 1106-1113 (2019)
  399. Tobramycin Variants with Enhanced Ribosome-Targeting Activity. Fosso MY, Zhu H, Green KD, Garneau-Tsodikova S, Fredrick K. Chembiochem 16 1565-1570 (2015)
  400. Wobble modification defect suppresses translational activity of tRNAs with MERRF and MELAS mutations. Yasukawa T, Suzuki T, Ohta S, Watanabe K. Mitochondrion 2 129-141 (2002)
  401. A model for the study of ligand binding to the ribosomal RNA helix h44. Dibrov SM, Parsons J, Hermann T. Nucleic Acids Res 38 4458-4465 (2010)
  402. A new way to see RNA. Keating KS, Humphris EL, Pyle AM. Q Rev Biophys 44 433-466 (2011)
  403. Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection. Morse JC, Girodat D, Burnett BJ, Holm M, Altman RB, Sanbonmatsu KY, Wieden HJ, Blanchard SC. Proc Natl Acad Sci U S A 117 3610-3620 (2020)
  404. Emergence of a code in the polymerization of amino acids along RNA templates. Lehmann J, Cibils M, Libchaber A. PLoS One 4 e5773 (2009)
  405. On dichotomic classes and bijections of the genetic code. Fimmel E, Danielli A, Strüngmann L. J Theor Biol 336 221-230 (2013)
  406. Progress toward Eukaryotic Semisynthetic Organisms: Translation of Unnatural Codons. Zhou AX, Sheng K, Feldman AW, Romesberg FE. J Am Chem Soc 141 20166-20170 (2019)
  407. Ribosomal elongation cycle: energetic, kinetic and stereochemical aspects. Lim VI, Curran JF, Garber MB. J Mol Biol 351 470-480 (2005)
  408. Ribosomal small subunit domains radiate from a central core. Gulen B, Petrov AS, Okafor CD, Vander Wood D, O'Neill EB, Hud NV, Williams LD. Sci Rep 6 20885 (2016)
  409. Sequence-specific bacterial growth inhibition by peptide nucleic acid targeted to the mRNA binding site of 16S rRNA. Hatamoto M, Nakai K, Ohashi A, Imachi H. Appl Microbiol Biotechnol 84 1161-1168 (2009)
  410. Synthesis and evaluation of novel bacterial rRNA-binding benzimidazoles by mass spectrometry. He Y, Yang J, Wu B, Robinson D, Sprankle K, Kung PP, Lowery K, Mohan V, Hofstadler S, Swayze EE, Griffey R. Bioorg Med Chem Lett 14 695-699 (2004)
  411. Comment The how and Y of cold shock. Wilson DN, Nierhaus KH. Nat Struct Mol Biol 11 1026-1028 (2004)
  412. The molecular choreography of protein synthesis: translational control, regulation, and pathways. Chen J, Choi J, O'Leary SE, Prabhakar A, Petrov A, Grosely R, Puglisi EV, Puglisi JD. Q Rev Biophys 49 e11 (2016)
  413. Comment Wobble during decoding: more than third-position promiscuity. Cochella L, Green R. Nat Struct Mol Biol 11 1160-1162 (2004)
  414. Energetic tuning by tRNA modifications ensures correct decoding of isoleucine and methionine on the ribosome. Satpati P, Bauer P, Aqvist J. Chemistry 20 10271-10275 (2014)
  415. Functional elucidation of a key contact between tRNA and the large ribosomal subunit rRNA during decoding. Ortiz-Meoz RF, Green R. RNA 16 2002-2013 (2010)
  416. Internucleotide movements during formation of 16 S rRNA-rRNA photocrosslinks and their connection to the 30 S subunit conformational dynamics. Huggins W, Ghosh SK, Nanda K, Wollenzien P. J Mol Biol 354 358-374 (2005)
  417. Magnesium Suppresses Defects in the Formation of 70S Ribosomes as Well as in Sporulation Caused by Lack of Several Individual Ribosomal Proteins. Akanuma G, Yamazaki K, Yagishi Y, Iizuka Y, Ishizuka M, Kawamura F, Kato-Yamada Y. J Bacteriol 200 e00212-18 (2018)
  418. Motifs in nucleic acids: molecular mechanics restraints for base pairing and base stacking. Harvey SC, Wang C, Teletchea S, Lavery R. J Comput Chem 24 1-9 (2003)
  419. Prolactin-induced changes in protein expression in human pancreatic islets. Labriola L, Ferreira GB, Montor WR, Demasi MA, Pimenta DC, Lojudice FH, Genzini T, Goldberg AC, Eliaschewitz FG, Sogayar MC. Mol Cell Endocrinol 264 16-27 (2007)
  420. Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP. Carbone CE, Loveland AB, Gamper HB, Hou YM, Demo G, Korostelev AA. Nat Commun 12 7236 (2021)
  421. Uptake of fluorescent gentamicin by peripheral vestibular cells after systemic administration. Liu J, Kachelmeier A, Dai C, Li H, Steyger PS. PLoS One 10 e0120612 (2015)
  422. mRNA bound to the 30S subunit is a HigB toxin substrate. Schureck MA, Maehigashi T, Miles SJ, Marquez J, Dunham CM. RNA 22 1261-1270 (2016)
  423. 30S Subunit-dependent activation of the Sorangium cellulosum So ce56 aminoglycoside resistance-conferring 16S rRNA methyltransferase Kmr. Savic M, Sunita S, Zelinskaya N, Desai PM, Macmaster R, Vinal K, Conn GL. Antimicrob Agents Chemother 59 2807-2816 (2015)
  424. Analysis of recognition of transfer-messenger RNA by the ribosomal decoding center. Lim VI, Garber MB. J Mol Biol 346 395-398 (2005)
  425. Association of aminoglycosidic antibiotics with the ribosomal A-site studied with Brownian dynamics. Długosz M, Antosiewicz JM, Trylska J. J Chem Theory Comput 4 549-559 (2008)
  426. Increased fidelity of protein synthesis extends lifespan. Martinez-Miguel VE, Lujan C, Espie-Caullet T, Martinez-Martinez D, Moore S, Backes C, Gonzalez S, Galimov ER, Brown AEX, Halic M, Tomita K, Rallis C, von der Haar T, Cabreiro F, Bjedov I. Cell Metab 33 2288-2300.e12 (2021)
  427. Comment A tipping point for mistranslation and disease. Schimmel P, Guo M. Nat Struct Mol Biol 16 348-349 (2009)
  428. An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch. Krepl M, Vögele J, Kruse H, Duchardt-Ferner E, Wöhnert J, Sponer J. Nucleic Acids Res 46 6528-6543 (2018)
  429. Disruption of rimP-SC, encoding a ribosome assembly cofactor, markedly enhances the production of several antibiotics in Streptomyces coelicolor. Pan Y, Lu C, Dong H, Yu L, Liu G, Tan H. Microb Cell Fact 12 65 (2013)
  430. In vivo involvement of mutated initiation factor IF1 in gene expression control at the translational level. Croitoru VV, Bucheli-Witschel M, Isaksson LA. FEBS Lett 579 995-1000 (2005)
  431. Involvement of helix 34 of 16 S rRNA in decoding and translocation on the ribosome. Kubarenko A, Sergiev P, Wintermeyer W, Dontsova O, Rodnina MV. J Biol Chem 281 35235-35244 (2006)
  432. Mutations in 16S rRNA that suppress cold-sensitive initiation factor 1 affect ribosomal subunit association. Belotserkovsky JM, Dabbs ER, Isaksson LA. FEBS J 278 3508-3517 (2011)
  433. Potential key bases of ribosomal RNA to kingdom-specific spectra of antibiotic susceptibility and the possible archaeal origin of eukaryotes. Xie Q, Wang Y, Lin J, Qin Y, Wang Y, Bu W. PLoS One 7 e29468 (2012)
  434. Ribosome Structure Reveals Preservation of Active Sites in the Presence of a P-Site Wobble Mismatch. Svidritskiy E, Korostelev AA. Structure 23 2155-2161 (2015)
  435. Role of the ribosomal P-site elements of m²G966, m⁵C967, and the S9 C-terminal tail in maintenance of the reading frame during translational elongation in Escherichia coli. Arora S, Bhamidimarri SP, Weber MH, Varshney U. J Bacteriol 195 3524-3530 (2013)
  436. Structural analysis of base substitutions in Thermus thermophilus 16S rRNA conferring streptomycin resistance. Demirci H, Murphy FV, Murphy EL, Connetti JL, Dahlberg AE, Jogl G, Gregory ST. Antimicrob Agents Chemother 58 4308-4317 (2014)
  437. The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors. Macé K, Giudice E, Chat S, Gillet R. Nucleic Acids Res 46 3211-3217 (2018)
  438. Translation error clusters induced by aminoglycoside antibiotics. Wohlgemuth I, Garofalo R, Samatova E, Günenç AN, Lenz C, Urlaub H, Rodnina MV. Nat Commun 12 1830 (2021)
  439. A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA. Kanazawa H, Baba F, Koganei M, Kondo J. Nucleic Acids Res 45 12529-12535 (2017)
  440. A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea. Jüttner M, Weiß M, Ostheimer N, Reglin C, Kern M, Knüppel R, Ferreira-Cerca S. Nucleic Acids Res 48 2073-2090 (2020)
  441. Atomic mutagenesis at the ribosomal decoding site. Schrode P, Huter P, Clementi N, Erlacher M. RNA Biol 14 104-112 (2017)
  442. Classification of the possible pairs between the first anticodon and the third codon positions based on a simple model assuming two geometries with which the pairing effectively potentiates the decoding complex. Takai K. J Theor Biol 242 564-580 (2006)
  443. Designed spiro-bicyclic analogues targeting the ribosomal decoding center. Cottin T, Pyrkotis C, Stathakis CI, Mavridis I, Katsoulis IA, Anastasopoulou P, Kythreoti G, Zografos AL, Nahmias VR, Papakyriakou A, Vourloumis D. Chembiochem 12 71-87 (2011)
  444. Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases. Mosquera-Rendón J, Cárdenas-Brito S, Pineda JD, Corredor M, Benítez-Páez A. BMC Res Notes 7 440 (2014)
  445. Hypothesis: emergence of translation as a result of RNA helicase evolution. Zenkin N. J Mol Evol 74 249-256 (2012)
  446. Molecular Dynamics Investigation of a Mechanism of Allosteric Signal Transmission in Ribosomes. Makarov GI, Golovin AV, Sumbatyan NV, Bogdanov AA. Biochemistry (Mosc) 80 1047-1056 (2015)
  447. Novel Escherichia coli RF1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins Kid and RelE. Diago-Navarro E, Mora L, Buckingham RH, Díaz-Orejas R, Lemonnier M. Mol Microbiol 71 66-78 (2009)
  448. Roles of specific aminoglycoside-ribosome interactions in the inhibition of translation. Ying L, Zhu H, Shoji S, Fredrick K. RNA 25 247-254 (2019)
  449. Testing constraints on rRNA bases that make nonsequence-specific contacts with the codon-anticodon complex in the ribosomal A site. Taliaferro DL, Farabaugh PJ. RNA 13 1279-1286 (2007)
  450. The origin of life: look up and look down. Peters JW, Williams LD. Astrobiology 12 1087-1092 (2012)
  451. Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature. O'Sullivan ME, Poitevin F, Sierra RG, Gati C, Dao EH, Rao Y, Aksit F, Ciftci H, Corsepius N, Greenhouse R, Hayes B, Hunter MS, Liang M, McGurk A, Mbgam P, Obrinsky T, Pardo-Avila F, Seaberg MH, Cheng AG, Ricci AJ, DeMirci H. Nucleic Acids Res 46 9793-9804 (2018)
  452. Codon-dependent tRNA fluctuations monitored with fluorescence polarization. Mishra PP, Qureshi MT, Ren W, Lee TH. Biophys J 99 3849-3858 (2010)
  453. Decoding on the ribosome depends on the structure of the mRNA phosphodiester backbone. Keedy HE, Thomas EN, Zaher HS. Proc Natl Acad Sci U S A 115 E6731-E6740 (2018)
  454. Group I intron renders differential susceptibility of Candida albicans to Bleomycin. Jayaguru P, Raghunathan M. Mol Biol Rep 34 11-17 (2007)
  455. Letter How does the ribosome sense a cognate tRNA? Noller HF. J Mol Biol 425 3776-3777 (2013)
  456. Interaction strengths between the ribosome and tRNA at various steps of translocation. Liu CY, Qureshi MT, Lee TH. Biophys J 100 2201-2208 (2011)
  457. Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies. Dudek M, Romanowska J, Wituła T, Trylska J. Biochimie 102 188-202 (2014)
  458. Mechanistic characterization of UDP-glucuronic acid 4-epimerase. Borg AJE, Dennig A, Weber H, Nidetzky B. FEBS J 288 1163-1178 (2021)
  459. Morphological variation of individual Escherichia coli 30S ribosomal subunits in vitro and in situ, as revealed by cryo-electron tomography. Zhao Q, Ofverstedt LG, Skoglund U, Isaksson LA. Exp Cell Res 297 495-507 (2004)
  460. Non-bridging phosphate oxygen atoms within the tRNA anticodon stem-loop are essential for ribosomal A site binding and translocation. Phelps SS, Joseph S. J Mol Biol 349 288-301 (2005)
  461. On models of the genetic code generated by binary dichotomic algorithms. Gumbel M, Fimmel E, Danielli A, Strüngmann L. Biosystems 128 9-18 (2015)
  462. Plant defensin antibacterial mode of action against Pseudomonas species. Sathoff AE, Lewenza S, Samac DA. BMC Microbiol 20 173 (2020)
  463. RNA aptamers directed against release factor 1 from Thermus thermophilus. Szkaradkiewicz K, Nanninga M, Nesper-Brock M, Gerrits M, Erdmann VA, Sprinzl M. FEBS Lett 514 90-95 (2002)
  464. Singly modified amikacin and tobramycin derivatives show increased rRNA A-site binding and higher potency against resistant bacteria. Fair RJ, McCoy LS, Hensler ME, Aguilar B, Nizet V, Tor Y. ChemMedChem 9 2164-2171 (2014)
  465. Synthesis and antibacterial activity of novel neamine derivatives. Minowa N, Akiyama Y, Hiraiwa Y, Maebashi K, Usui T, Ikeda D. Bioorg Med Chem Lett 16 6351-6354 (2006)
  466. The new classification scheme of the genetic code, its early evolution, and tRNA usage. Nikolajewa S, Friedel M, Beyer A, Wilhelm T. J Bioinform Comput Biol 4 609-620 (2006)
  467. Two nucleotide substitutions in the A-site of yeast 18S rRNA affect translation and differentiate the interaction of ribosomes with aminoglycoside antibiotics. Tselika S, Konstantinidis TC, Synetos D. Biochimie 90 908-917 (2008)
  468. A 16S rRNA-tRNA product containing a nucleotide phototrimer and specific for tRNA in the P/E hybrid state in the Escherichia coli ribosome. Huggins W, Wollenzien P. Nucleic Acids Res 32 6548-6556 (2004)
  469. A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine. Vangaveti S, Cantara WA, Spears JL, DeMirci H, Murphy FV, Ranganathan SV, Sarachan KL, Agris PF. J Mol Biol 432 913-929 (2020)
  470. Analysis of invariant sequences in 266 complete genomes. Goto N, Kurokawa K, Yasunaga T. Gene 401 172-180 (2007)
  471. Another look at mutations in ribosomal protein S4 lends strong support to the domain closure model. Fredrick K. J Bacteriol 197 1014-1016 (2015)
  472. Characterization of the 16S-23S internal transcribed spacer among 34 higher plants: suitability for interspecific plastid transformation. McNutt PM, Dehart MJ, Matej LA. Plant Cell Rep 26 47-60 (2007)
  473. Configuration of wobble base pairs having pyrimidines as anticodon wobble bases: significance for codon degeneracy. Das G, Lyngdoh RH. J Biomol Struct Dyn 32 1500-1520 (2014)
  474. Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site. Panecka J, Šponer J, Trylska J. Biochimie 112 96-110 (2015)
  475. Evaluation of RNA-binding specificity of aminoglycosides with DNA microarrays. Liang FS, Greenberg WA, Hammond JA, Hoffmann J, Head SR, Wong CH. Proc Natl Acad Sci U S A 103 12311-12316 (2006)
  476. Evolution of the Standard Genetic Code. Yarus M. J Mol Evol 89 19-44 (2021)
  477. Prediction of the structure of the complex between the 30S ribosomal subunit and colicin E3 via weighted-geometric docking. Ben-Zeev E, Zarivach R, Shoham M, Yonath A, Eisenstein M. J Biomol Struct Dyn 20 669-676 (2003)
  478. Real-time measurements of aminoglycoside effects on protein synthesis in live cells. Aguirre Rivera J, Larsson J, Volkov IL, Seefeldt AC, Sanyal S, Johansson M. Proc Natl Acad Sci U S A 118 e2013315118 (2021)
  479. Ribosomal ambiguity made less ambiguous. Moore PB. Proc Natl Acad Sci U S A 110 9627-9628 (2013)
  480. Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscoding. Hoffer ED, Maehigashi T, Fredrick K, Dunham CM. Nucleic Acids Res 47 1557-1563 (2019)
  481. Ribosome assembly defects subvert initiation Factor3 mediated scrutiny of bona fide start signal. Sharma H, Anand B. Nucleic Acids Res 47 11368-11386 (2019)
  482. Super-resolution force spectroscopy reveals ribosomal motion at sub-nucleotide steps. Jia H, Wang Y, Xu S. Chem Commun (Camb) 54 5883-5886 (2018)
  483. The cyclic phosphodiesterase CNP and RNA cyclase RtcA fine-tune noncanonical XBP1 splicing during ER stress. Unlu I, Lu Y, Wang X. J Biol Chem 293 19365-19376 (2018)
  484. Co-evolution of the genetic code and ribozyme replication. Stevenson DS. J Theor Biol 217 235-253 (2002)
  485. Correlation of the structure and conformational changes of selected fragments of plant small ribosomal RNA within the steps of polypeptide chain elongation. Bakowska-Zywicka K, Twardowski T. J Plant Physiol 164 496-504 (2007)
  486. DNA template dependent accuracy variation of nucleotide selection in transcription. Mellenius H, Ehrenberg M. PLoS One 10 e0119588 (2015)
  487. Displaying 3D data on RNA secondary structures: coloRNA. LeBarron J, Mitra K, Frank J. J Struct Biol 157 262-270 (2007)
  488. Effect of Cu(II) on the complex between kanamycin A and the bacterial ribosomal A site. Balenci D, Bernardi F, Cellai L, D'Amelio N, Gaggelli E, Gaggelli N, Molteni E, Valensin G. Chembiochem 9 114-123 (2008)
  489. Elongation Factor Tu Switch I Element is a Gate for Aminoacyl-tRNA Selection. Girodat D, Blanchard SC, Wieden HJ, Sanbonmatsu KY. J Mol Biol 432 3064-3077 (2020)
  490. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D'Amaré AR, Leung AK. Crystals (Basel) 11 952 (2021)
  491. Epistasis analysis of 16S rRNA ram mutations helps define the conformational dynamics of the ribosome that influence decoding. Ying L, Fredrick K. RNA 22 499-505 (2016)
  492. Flipping through the genetic code: new developments in discrimination between cognate and near-cognate tRNAs and the effect of antibiotics. Sanbonmatsu KY. J Mol Biol 426 3197-3200 (2014)
  493. Photolabile anticodon stem-loop analogs of tRNAPhe as probes of ribosomal structure and structural fluctuation at the decoding center. Druzina Z, Cooperman BS. RNA 10 1550-1562 (2004)
  494. Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA. Lambert MN, Hoerter JA, Pereira MJ, Walter NG. RNA 11 1688-1700 (2005)
  495. Structure of the 30S ribosomal decoding complex at ambient temperature. Dao EH, Poitevin F, Sierra RG, Gati C, Rao Y, Ciftci HI, Akşit F, McGurk A, Obrinski T, Mgbam P, Hayes B, De Lichtenberg C, Pardo-Avila F, Corsepius N, Zhang L, Seaberg MH, Hunter MS, Liang M, Koglin JE, Wakatsuki S, Demirci H. RNA 24 1667-1676 (2018)
  496. Structures of tmRNA and SmpB as they transit through the ribosome. Guyomar C, D'Urso G, Chat S, Giudice E, Gillet R. Nat Commun 12 4909 (2021)
  497. Tensor decomposition reveals concurrent evolutionary convergences and divergences and correlations with structural motifs in ribosomal RNA. Muralidhara C, Gross AM, Gutell RR, Alter O. PLoS One 6 e18768 (2011)
  498. The ribosome goes Nobel. Rodnina MV, Wintermeyer W. Trends Biochem Sci 35 1-5 (2010)
  499. The ribosome: lifting the veil from a fascinating organelle. Tate WP, Poole ES. Bioessays 26 582-588 (2004)
  500. Translational readthrough-promoting drugs enhance pseudoknot-mediated suppression of the stop codon at the Moloney murine leukemia virus gag–pol junction. Green L, Goff SP. J Gen Virol 96 3411-3421 (2015)
  501. Unnatural rigid scaffolds targeting the bacterial ribosome. Katsoulis IA, Pyrkotis C, Papakyriakou A, Kythreoti G, Zografos AL, Mavridis I, Nahmias VR, Anastasopoulou P, Vourloumis D. Chembiochem 10 1969-1972 (2009)
  502. tRNA/mRNA Mimicry by tmRNA and SmpB in Trans-Translation. Kurita D, Muto A, Himeno H. J Nucleic Acids 2011 130581 (2011)
  503. 2'-O-ribose methylation of transfer RNA promotes recovery from oxidative stress in Saccharomyces cerevisiae. Endres L, Rose RE, Doyle F, Rahn T, Lee B, Seaman J, McIntyre WD, Fabris D. PLoS One 15 e0229103 (2020)
  504. A hypothetical pathway from the RNA to the DNA world. Line MA. Orig Life Evol Biosph 35 395-400 (2005)
  505. Binding of a viral IRES to the 40S subunit occurs in two successive steps mediated by eS25. Walters B, Axhemi A, Jankowsky E, Thompson SR. Nucleic Acids Res 48 8063-8073 (2020)
  506. Comparative sequence and structure analysis of eIF1A and eIF1AD. Yu J, Marintchev A. BMC Struct Biol 18 11 (2018)
  507. Cultured bloodstream Trypanosoma brucei adapt to life without mitochondrial translation release factor 1. Procházková M, Panicucci B, Zíková A. Sci Rep 8 5135 (2018)
  508. Diverse effects of residues 74-78 in ribosomal protein S12 on decoding and antibiotic sensitivity. Agarwal D, O'Connor M. Biochem Biophys Res Commun 445 475-479 (2014)
  509. Fundamental amino acid mass distributions and entropy costs in proteomes. Lehmann J, Libchaber A, Greenbaum BD. J Theor Biol 410 119-124 (2016)
  510. Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression. Masuda I, Hwang JY, Christian T, Maharjan S, Mohammad F, Gamper H, Buskirk AR, Hou YM. Elife 10 e70619 (2021)
  511. Minimum sequence requirements for the binding of paromomycin to the rRNA decoding site A. Anderson PC, Mecozzi S. Biopolymers 86 95-111 (2007)
  512. Mutations of ribosomal protein S5 suppress a defect in late-30S ribosomal subunit biogenesis caused by lack of the RbfA biogenesis factor. Nord S, Bhatt MJ, Tükenmez H, Farabaugh PJ, Wikström PM. RNA 21 1454-1468 (2015)
  513. NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs. Qureshi NS, Matzel T, Cetiner EC, Schnieders R, Jonker HRA, Schwalbe H, Fürtig B. Nucleic Acids Res 49 7753-7764 (2021)
  514. Omics Analysis Reveals the Mechanism of Enhanced Recombinant Protein Production Under Simulated Microgravity. Huangfu J, Kim HS, Xu K, Ning X, Qin L, Li J, Li C. Front Bioeng Biotechnol 8 30 (2020)
  515. Resolving the elegant architecture of the ribosome. Puglisi JD. Mol Cell 36 720-723 (2009)
  516. Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position. Liu W, Shin D, Ng M, Sanbonmatsu KY, Tor Y, Cooperman BS. Molecules 22 E1427 (2017)
  517. Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics. Nicholson D, Edwards TA, O'Neill AJ, Ranson NA. Structure 28 1087-1100.e3 (2020)
  518. Synthesis of triazole-functionalized 2-DOS analogues and their evaluation as A-site binders. Anastasopoulou P, Kythreoti G, Cosmidis T, Pyrkotis C, Nahmias VR, Vourloumis D. Bioorg Med Chem Lett 24 1122-1126 (2014)
  519. Tertiary interactions between helices h13 and h44 in 16S RNA contribute to the fidelity of translation. Tran DK, Finley J, Vila-Sanjurjo A, Lale A, Sun Q, O'Connor M. FEBS J 278 4405-4412 (2011)
  520. The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins. Ponce de Leon M, de Miranda AB, Alvarez-Valin F, Carels N. Bioinform Biol Insights 8 93-108 (2014)
  521. Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase. Mellenius H, Ehrenberg M. Nucleic Acids Res 45 11582-11593 (2017)
  522. Trinucleotide duplex formation inside a confined nanospace under supercooled conditions. Arafune H, Yamaguchi A, Namekawa M, Sato Y, Itoh T, Yoshida R, Teramae N. Nat Commun 5 5151 (2014)
  523. Variation of the chemical reactivity of Thermus thermophilus HB8 ribosomal proteins as a function of pH. Running WE, Reilly JP. Proteomics 10 3669-3687 (2010)
  524. A tRNA-mimic Strategy to Explore the Role of G34 of tRNAGly in Translation and Codon Frameshifting. Janvier A, Despons L, Schaeffer L, Tidu A, Martin F, Eriani G. Int J Mol Sci 20 E3911 (2019)
  525. Accuracy mechanism of eukaryotic ribosome translocation. Djumagulov M, Demeshkina N, Jenner L, Rozov A, Yusupov M, Yusupova G. Nature 600 543-546 (2021)
  526. Another burst of smoke: atomic resolution structures of RF3 bound to the ribosome. McDonald ME, Green R. RNA 18 605-609 (2012)
  527. Arginine Methylation Regulates Ribosome CAR Function. Scopino K, Dalgarno C, Nachmanoff C, Krizanc D, Thayer KM, Weir MP. Int J Mol Sci 22 1335 (2021)
  528. Cryo-EM reconstruction of the human 40S ribosomal subunit at 2.15 Å resolution. Pellegrino S, Dent KC, Spikes T, Warren AJ. Nucleic Acids Res 51 4043-4054 (2023)
  529. Little Evidence the Standard Genetic Code Is Optimized for Resource Conservation. Rozhoňová H, Payne JL. Mol Biol Evol 38 5127-5133 (2021)
  530. Mechanism of translation based on intersubunit complementarities of ribosomal RNAs and tRNAs. Nagano K, Nagano N. J Theor Biol 245 644-668 (2007)
  531. Multiple e-Pharmacophore modeling to identify a single molecule that could target both streptomycin and paromomycin binding sites for 30S ribosomal subunit inhibition. C P A, Subhramanian S, Sizochenko N, Melge AR, Leszczynski J, Mohan CG. J Biomol Struct Dyn 37 1582-1596 (2019)
  532. Oligonucleotides Featuring a Covalently Mercurated 6-Phenylcarbazole Residue as High-Affinity Hybridization Probes for Thiopyrimidine-Containing Sequences. Kotammagari TK, Tähtinen P, Lönnberg T. Chemistry 28 e202202530 (2022)
  533. Pseudouridine modifications influence binding of aminoglycosides to helix 69 of bacterial ribosomes. Sakakibara Y, Chow CS. Org Biomol Chem 15 8535-8543 (2017)
  534. Structural Bases for the Fitness Cost of the Antibiotic-Resistance and Lethal Mutations at Position 1408 of 16S rRNA. Kondo J, Koganei M. Molecules 25 E159 (2019)
  535. Thermodynamics of the pseudo-knot in helix 18 of 16S ribosomal RNA. Wojciechowska M, Dudek M, Trylska J. Biopolymers 109 e23116 (2018)
  536. Twice exploration of tRNA +1 frameshifting in an elongation cycle of protein synthesis. Gamper H, Mao Y, Masuda I, McGuigan H, Blaha G, Wang Y, Xu S, Hou YM. Nucleic Acids Res 49 10046-10060 (2021)
  537. Unique anticodon loop conformation with the flipped-out wobble nucleotide in the crystal structure of unbound tRNAVal. Jeong H, Kim J. RNA 27 1330-1338 (2021)
  538. [Protein S3 fragments neighboring mRNA during elongation and translation termination on the human ribosome]. Khaĭrulina IuS, Molotkov MV, Bulygin KN, Graĭfer DM, Ven'yaminova AG, Frolova LIu, Stahl J, Karpova GG. Bioorg Khim 34 773-780 (2008)
  539. 30S subunit recognition and G1405 modification by the aminoglycoside-resistance 16S ribosomal RNA methyltransferase RmtC. Srinivas P, Nosrati M, Zelinskaya N, Dey D, Comstock LR, Dunham CM, Conn GL. Proc Natl Acad Sci U S A 120 e2304128120 (2023)
  540. A crescendo of competent coding (c3) contains the Standard Genetic Code. Yarus M. RNA 28 1337-1347 (2022)
  541. A role for circular code properties in translation. Giannerini S, Gonzalez DL, Goracci G, Danielli A. Sci Rep 11 9218 (2021)
  542. Acquisition of Streptomycin Resistance by Oxidative Stress Induced by Hydrogen Peroxide in Radiation-Resistant Bacterium Deinococcus geothermalis. Lee C, Ye Q, Shin E, Ting T, Lee SJ. Int J Mol Sci 23 9764 (2022)
  543. Agricultural diversification and intra-household dietary diversity: Panel data analysis of farm households in Bangladesh. Alam MJ, Begum IA, Mastura T, Kishore A, Woodhill J, Chatterjee K, Jackson T. PLoS One 18 e0287321 (2023)
  544. Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia. Hiregange DG, Rivalta A, Bose T, Breiner-Goldstein E, Samiya S, Cimicata G, Kulakova L, Zimmerman E, Bashan A, Herzberg O, Yonath A. Nucleic Acids Res 50 1770-1782 (2022)
  545. Evolution of Ribosomal Protein S14 Demonstrated by the Reconstruction of Chimeric Ribosomes in Bacillus subtilis. Akanuma G, Kawamura F, Watanabe S, Watanabe M, Okawa F, Natori Y, Nanamiya H, Asai K, Chibazakura T, Yoshikawa H, Soma A, Hishida T, Kato-Yamada Y. J Bacteriol 203 e00599-20 (2021)
  546. Fitting the standard genetic code into its triplet table. Yarus M. Proc Natl Acad Sci U S A 118 e2021103118 (2021)
  547. Genetic code degeneracy is established by the decoding center of the ribosome. Ye S, Lehmann J. Nucleic Acids Res 50 4113-4126 (2022)
  548. Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding. Girodat D, Wieden HJ, Blanchard SC, Sanbonmatsu KY. Nat Commun 14 5582 (2023)
  549. Hyperaccurate Ribosomes for Improved Genetic Code Reprogramming. Shakya B, Joyner OG, Hartman MCT. ACS Synth Biol 11 2193-2201 (2022)
  550. Insight into the mechanism of chemical modification of antibacterial agents by antibiotic resistance enzyme O-phosphotransferase-IIIA. Power BH, Smith N, Downer B, Alisaraie L. Chem Biol Drug Des 89 84-97 (2017)
  551. Modulation of translational decoding by m6A modification of mRNA. Jain S, Koziej L, Poulis P, Kaczmarczyk I, Gaik M, Rawski M, Ranjan N, Glatt S, Rodnina MV. Nat Commun 14 4784 (2023)
  552. Ordering events in a developing genetic code. Yarus M. RNA Biol 21 1-8 (2024)
  553. Overview of tRNA Modifications in Chloroplasts. Fages-Lartaud M, Hohmann-Marriott MF. Microorganisms 10 226 (2022)
  554. Quality control of protein synthesis in the early elongation stage. Nagao A, Nakanishi Y, Yamaguchi Y, Mishina Y, Karoji M, Toya T, Fujita T, Iwasaki S, Miyauchi K, Sakaguchi Y, Suzuki T. Nat Commun 14 2704 (2023)
  555. Real-time evidence for EF-G-induced dynamics of helix 44 in 16S rRNA. Tanner DR, Hedrick EG, Hill WE. J Mol Biol 422 45-57 (2012)
  556. Reconstruction of the rRNA Sequences of LUCA, with Bioinformatic Implication of the Local Similarities Shared by Them. Men Y, Lu G, Wang Y, Lin J, Xie Q. Biology (Basel) 11 837 (2022)
  557. Refinement of a low-resolution crystal structure to better understand erythromycin interactions on large ribosomal subunit. Wahab HA, Yam WK, Samian MR, Najimudin N. J Biomol Struct Dyn 26 131-146 (2008)
  558. Rigid spiroethers targeting the decoding center of the bacterial ribosome. Mavridis I, Kythreoti G, Koltsida K, Vourloumis D. Bioorg Med Chem 22 1329-1341 (2014)
  559. Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB. Tian Y, Zeng F, Raybarman A, Fatma S, Carruthers A, Li Q, Huang RH. Proc Natl Acad Sci U S A 119 e2202464119 (2022)
  560. Solution structure of an alternate conformation of helix27 from Escherichia coli16S rRNA. Spano MN, Walter NG. Biopolymers 95 653-668 (2011)
  561. Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in Staphylococcus aureus. Belinite M, Khusainov I, Soufari H, Marzi S, Romby P, Yusupov M, Hashem Y. Front Mol Biosci 8 738752 (2021)
  562. Streptothricin F is a bactericidal antibiotic effective against highly drug-resistant gram-negative bacteria that interacts with the 30S subunit of the 70S ribosome. Morgan CE, Kang YS, Green AB, Smith KP, Dowgiallo MG, Miller BC, Chiaraviglio L, Truelson KA, Zulauf KE, Rodriguez S, Kang AD, Manetsch R, Yu EW, Kirby JE. PLoS Biol 21 e3002091 (2023)
  563. Structural analysis of mitochondrial rRNA gene variants identified in patients with deafness. Vila-Sanjurjo A, Mallo N, Elson JL, Smith PM, Blakely EL, Taylor RW. Front Physiol 14 1163496 (2023)
  564. Structure of the actively translating plant 80S ribosome at 2.2 Å resolution. Smirnova J, Loerke J, Kleinau G, Schmidt A, Bürger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R. Nat Plants 9 987-1000 (2023)
  565. The Genetic Code Assembles via Division and Fusion, Basic Cellular Events. Yarus M. Life (Basel) 13 2069 (2023)
  566. The universally conserved nucleotides of the small subunit ribosomal RNAs. Noller HF, Donohue JP, Gutell RR. RNA 28 623-644 (2022)
  567. Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals. Fedorova AD, Kiniry SJ, Andreev DE, Mudge JM, Baranov PV. Nat Commun 13 7910 (2022)
  568. Two alternative conformations of mRNA in the human ribosome during elongation and termination of translation as revealed by EPR spectroscopy. Bulygin KN, Timofeev IO, Malygin AA, Graifer DM, Meschaninova MI, Venyaminova AG, Krumkacheva OA, Fedin MV, Yu Frolova L, Karpova GG, Bagryanskaya EG. Comput Struct Biotechnol J 19 4702-4710 (2021)
  569. Comment Zooming in on eukaryotic translation initiation. Liljas A. Nat Struct Mol Biol 20 1141-1142 (2013)
  570. [Template location on the human ribosome: environment of the mRNA nucleotide adjacent to the A-site codon on the 3'-side]. Demeshkina NA, Stiazhkina VA, Bulygin KN, Repkova MN, Ven'iaminova AG, Karpova GG. Bioorg Khim 31 295-302 (2005)


Related citations provided by authors (2)

  1. Structure of the 30S Ribosomal Subunit. Wimberly BT, Brodersen DE, Clemons Jr WM, Morgan-Warren R, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V Nature 407 327-339 (2000)
  2. Functional Insights from the Structure of the 30S Ribosomal Subunit and its Interactions with Antibiotics. Carter AP, Clemons Jr WM, Brodersen DE, Wimberly BT, Morgan-Warren R, Ramakrishnan V Nature 407 340-348 (2000)

Quick links