1pn7 › Citations

Locking and unlocking of ribosomal motions.

Valle M, Zavialov A, Sengupta J, Rawat U, Ehrenberg M, Frank J
Cell 114 123-34 (2003)
Related entries: 1pn6, 1pn8

Cited: 426 times
EuropePMC logo PMID: 12859903

Abstract

During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the direction of the mRNA movement. By means of cryo-electron microscopy we observe that this rotation is accompanied by a 20 A movement of the L1 stalk of the 50S subunit, implying that this region is involved in the translocation of deacylated tRNAs from the P to the E site. These ribosomal motions can occur only when the P-site tRNA is deacylated. Prior to peptidyl-transfer to the A-site tRNA or peptide removal, the presence of the charged P-site tRNA locks the ribosome and prohibits both of these motions.

Reviews citing this publication (79)

  1. What recent ribosome structures have revealed about the mechanism of translation. Schmeing TM, Ramakrishnan V. Nature 461 1234-1242 (2009)
  2. A structural understanding of the dynamic ribosome machine. Steitz TA. Nat Rev Mol Cell Biol 9 242-253 (2008)
  3. Functional complexity and regulation through RNA dynamics. Dethoff EA, Chugh J, Mustoe AM, Al-Hashimi HM. Nature 482 322-330 (2012)
  4. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Nucleic Acids Res 44 7007-7078 (2016)
  5. Strategies for RNA folding and assembly. Schroeder R, Barta A, Semrad K. Nat Rev Mol Cell Biol 5 908-919 (2004)
  6. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. Chem Rev 118 4177-4338 (2018)
  7. Frameshifting RNA pseudoknots: structure and mechanism. Giedroc DP, Cornish PV. Virus Res 139 193-208 (2009)
  8. Structural basis of the translational elongation cycle. Voorhees RM, Ramakrishnan V. Annu Rev Biochem 82 203-236 (2013)
  9. Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Tama F, Brooks CL. Annu Rev Biophys Biomol Struct 35 115-133 (2006)
  10. Viral IRES RNA structures and ribosome interactions. Kieft JS. Trends Biochem Sci 33 274-283 (2008)
  11. Structural and mechanistic insights into hepatitis C viral translation initiation. Fraser CS, Doudna JA. Nat Rev Microbiol 5 29-38 (2007)
  12. Structure and dynamics of a processive Brownian motor: the translating ribosome. Frank J, Gonzalez RL. Annu Rev Biochem 79 381-412 (2010)
  13. The structure and function of the eukaryotic ribosome. Wilson DN, Doudna Cate JH. Cold Spring Harb Perspect Biol 4 a011536 (2012)
  14. The small subunit processome in ribosome biogenesis—progress and prospects. Phipps KR, Charette J, Baserga SJ. Wiley Interdiscip Rev RNA 2 1-21 (2011)
  15. Hierarchy of RNA functional dynamics. Mustoe AM, Brooks CL, Al-Hashimi HM. Annu Rev Biochem 83 441-466 (2014)
  16. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. Penczek PA, Frank J, Spahn CM. J Struct Biol 154 184-194 (2006)
  17. Structural dynamics of the ribosome. Korostelev A, Ermolenko DN, Noller HF. Curr Opin Chem Biol 12 674-683 (2008)
  18. Navigating the ribosome's metastable energy landscape. Munro JB, Sanbonmatsu KY, Spahn CM, Blanchard SC. Trends Biochem Sci 34 390-400 (2009)
  19. The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation. Rodnina MV, Wintermeyer W. Biochem Soc Trans 39 658-662 (2011)
  20. Translation at the single-molecule level. Marshall RA, Aitken CE, Dorywalska M, Puglisi JD. Annu Rev Biochem 77 177-203 (2008)
  21. Protein acetylation in prokaryotes. Jones JD, O'Connor CD. Proteomics 11 3012-3022 (2011)
  22. Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Mitra K, Frank J. Annu Rev Biophys Biomol Struct 35 299-317 (2006)
  23. 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)
  24. Structural analysis of macromolecular assemblies by electron microscopy. Orlova EV, Saibil HR. Chem Rev 111 7710-7748 (2011)
  25. Peptide release on the ribosome: mechanism and implications for translational control. Youngman EM, McDonald ME, Green R. Annu Rev Microbiol 62 353-373 (2008)
  26. Ribosomal translocation: one step closer to the molecular mechanism. Shoji S, Walker SE, Fredrick K. ACS Chem Biol 4 93-107 (2009)
  27. Ribosome structure and dynamics during translocation and termination. Dunkle JA, Cate JH. Annu Rev Biophys 39 227-244 (2010)
  28. The ribosome in focus: new structures bring new insights. Korostelev A, Noller HF. Trends Biochem Sci 32 434-441 (2007)
  29. Bacterial Protein Synthesis as a Target for Antibiotic Inhibition. Arenz S, Wilson DN. Cold Spring Harb Perspect Med 6 a025361 (2016)
  30. Elongation factors on the ribosome. Nilsson J, Nissen P. Curr Opin Struct Biol 15 349-354 (2005)
  31. Single-molecule observations of ribosome function. Blanchard SC. Curr Opin Struct Biol 19 103-109 (2009)
  32. Intersubunit Bridges of the Bacterial Ribosome. Liu Q, Liu Q, Fredrick K. J Mol Biol 428 2146-2164 (2016)
  33. Unraveling the dynamics of ribosome translocation. Chen J, Tsai A, O'Leary SE, Petrov A, Puglisi JD. Curr Opin Struct Biol 22 804-814 (2012)
  34. 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)
  35. Single ribosome dynamics and the mechanism of translation. Aitken CE, Petrov A, Puglisi JD. Annu Rev Biophys 39 491-513 (2010)
  36. A structural view on the mechanism of the ribosome-catalyzed peptide bond formation. Simonović M, Steitz TA. Biochim Biophys Acta 1789 612-623 (2009)
  37. Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs. Haebel PW, Gutmann S, Ban N. Curr Opin Struct Biol 14 58-65 (2004)
  38. 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)
  39. Structural insights into ribosome translocation. Ling C, Ermolenko DN. Wiley Interdiscip Rev RNA 7 620-636 (2016)
  40. A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET. Munro JB, Vaiana A, Sanbonmatsu KY, Blanchard SC. Biopolymers 89 565-577 (2008)
  41. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Goh BC, Hadden JA, Bernardi RC, Singharoy A, McGreevy R, Rudack T, Cassidy CK, Schulten K. Annu Rev Biophys 45 253-278 (2016)
  42. Dynamics of the translational machinery. Petrov A, Kornberg G, O'Leary S, Tsai A, Uemura S, Puglisi JD. Curr Opin Struct Biol 21 137-145 (2011)
  43. Ribosomal proteins: structure, function, and evolution. Korobeinikova AV, Garber MB, Gongadze GM. Biochemistry (Mosc) 77 562-574 (2012)
  44. The future is hybrid. Steven AC, Baumeister W. J Struct Biol 163 186-195 (2008)
  45. Structure determination of macromolecular assemblies by single-particle analysis of cryo-electron micrographs. Orlova EV, Saibil HR. Curr Opin Struct Biol 14 584-590 (2004)
  46. Three-dimensional electron microscopy at molecular resolution. Subramaniam S, Milne JL. Annu Rev Biophys Biomol Struct 33 141-155 (2004)
  47. Building functional modules from molecular interactions. Hofmann KP, Spahn CM, Heinrich R, Heinemann U. Trends Biochem Sci 31 497-508 (2006)
  48. How can elongation factors EF-G and EF-Tu discriminate the functional state of the ribosome using the same binding site? Sergiev PV, Bogdanov AA, Dontsova OA. FEBS Lett 579 5439-5442 (2005)
  49. Intermediate states during mRNA-tRNA translocation. Frank J. Curr Opin Struct Biol 22 778-785 (2012)
  50. Insights into protein biosynthesis from structures of bacterial ribosomes. Berk V, Cate JH. Curr Opin Struct Biol 17 302-309 (2007)
  51. Two promising future developments of cryo-EM: capturing short-lived states and mapping a continuum of states of a macromolecule. Chen B, Frank J. Microscopy (Oxf) 65 69-79 (2016)
  52. 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)
  53. Structural basis for protein synthesis: snapshots of the ribosome in motion. Noeske J, Cate JH. Curr Opin Struct Biol 22 743-749 (2012)
  54. Synchronous tRNA movements during translocation on the ribosome are orchestrated by elongation factor G and GTP hydrolysis. Holtkamp W, Wintermeyer W, Rodnina MV. Bioessays 36 908-918 (2014)
  55. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Ray S, Widom JR, Walter NG. Chem Rev 118 4120-4155 (2018)
  56. RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes. Pfingsten JS, Kieft JS. RNA 14 1255-1263 (2008)
  57. Single-Particle Reconstruction of Biological Molecules-Story in a Sample (Nobel Lecture). Frank J. Angew Chem Int Ed Engl 57 10826-10841 (2018)
  58. Toward an understanding of the structural basis of translation. Frank J. Genome Biol 4 237 (2003)
  59. 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)
  60. Frameshifting dynamics. Tinoco I, Kim HK, Yan S. Biopolymers 99 1147-1166 (2013)
  61. The mechanics of ribosomal translocation. Achenbach J, Nierhaus KH. Biochimie 114 80-89 (2015)
  62. The translation elongation cycle-capturing multiple states by cryo-electron microscopy. Frank J. Philos Trans R Soc Lond B Biol Sci 372 20160180 (2017)
  63. Single-Molecule Fluorescence Applied to Translation. Prabhakar A, Puglisi EV, Puglisi JD. Cold Spring Harb Perspect Biol 11 a032714 (2019)
  64. The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches. Gerovac M, Vogel J, Smirnov A. Front Mol Biosci 8 661448 (2021)
  65. Introduction to 3D reconstruction of macromolecules using single particle electron microscopy. Llorca O. Acta Pharmacol Sin 26 1153-1164 (2005)
  66. The mechanics of translocation: a molecular "spring-and-ratchet" system. Moran SJ, Flanagan JF, Namy O, Stuart DI, Brierley I, Gilbert RJ. Structure 16 664-672 (2008)
  67. Structural Insights into tRNA Dynamics on the Ribosome. Agirrezabala X, Valle M. Int J Mol Sci 16 9866-9895 (2015)
  68. Simulating activity of the bacterial ribosome. Trylska J. Q Rev Biophys 42 301-316 (2009)
  69. Ribosomal tunnel and translation regulation. Bogdanov AA, Sumbatyan NV, Shishkina AV, Karpenko VV, Korshunova GA. Biochemistry (Mosc) 75 1501-1516 (2010)
  70. Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome. Valle M. Eur Biophys J 40 589-597 (2011)
  71. 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)
  72. Frozen in time: analyzing molecular dynamics with time-resolved cryo-EM. Amann SJ, Keihsler D, Bodrug T, Brown NG, Haselbach D. Structure 31 4-19 (2023)
  73. Quantitative studies of ribosome conformational dynamics. Fraser CS, Doudna JA. Q Rev Biophys 40 163-189 (2007)
  74. The mechanism of translation. Frank J. F1000Res 6 198 (2017)
  75. Functional Importance of Mobile Ribosomal Proteins. Chang KC, Wen JD, Yang LW. Biomed Res Int 2015 539238 (2015)
  76. Mechanisms of ribosome recycling in bacteria and mitochondria: a structural perspective. Seely SM, Gagnon MG. RNA Biol 19 662-677 (2022)
  77. Ribosome as a Translocase and Helicase. Bao C, Ermolenko DN. Biochemistry (Mosc) 86 992-1002 (2021)
  78. The energetics of subunit rotation in the ribosome. Hassan A, Byju S, Whitford PC. Biophys Rev 13 1029-1037 (2021)
  79. Two "Edges" in Our Knowledge on the Functions of Ribosomal Proteins: The Revealed Contributions of Their Regions to Translation Mechanisms and the Issues of Their Extracellular Transport by Exosomes. Ochkasova A, Arbuzov G, Malygin A, Graifer D. Int J Mol Sci 24 11458 (2023)

Articles citing this publication (347)

  1. 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)
  2. tRNA dynamics on the ribosome during translation. Blanchard SC, Kim HD, Gonzalez RL, Puglisi JD, Chu S. Proc Natl Acad Sci U S A 101 12893-12898 (2004)
  3. 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)
  4. Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. Spahn CM, Gomez-Lorenzo MG, Grassucci RA, Jørgensen R, Andersen GR, Beckmann R, Penczek PA, Ballesta JP, Frank J. EMBO J 23 1008-1019 (2004)
  5. Structure of the human 80S ribosome. Khatter H, Myasnikov AG, Natchiar SK, Klaholz BP. Nature 520 640-645 (2015)
  6. Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JH. Science 332 981-984 (2011)
  7. Spontaneous intersubunit rotation in single ribosomes. Cornish PV, Ermolenko DN, Noller HF, Ha T. Mol Cell 30 578-588 (2008)
  8. Crystal structure of the eukaryotic ribosome. Ben-Shem A, Jenner L, Yusupova G, Yusupov M. Science 330 1203-1209 (2010)
  9. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Ratje AH, Loerke J, Mikolajka A, Brünner M, Hildebrand PW, Starosta AL, Dönhöfer A, Connell SR, Fucini P, Mielke T, Whitford PC, Onuchic JN, Yu Y, Sanbonmatsu KY, Hartmann RK, Penczek PA, Wilson DN, Spahn CM. Nature 468 713-716 (2010)
  10. Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. Fischer N, Konevega AL, Wintermeyer W, Rodnina MV, Stark H. Nature 466 329-333 (2010)
  11. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Scheres SH, Gao H, Valle M, Herman GT, Eggermont PP, Frank J, Carazo JM. Nat Methods 4 27-29 (2007)
  12. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH. Nat Struct Mol Biol 14 727-732 (2007)
  13. Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Fei J, Kosuri P, MacDougall DD, Gonzalez RL. Mol Cell 30 348-359 (2008)
  14. 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)
  15. 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)
  16. Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor. Spahn CM, Jan E, Mulder A, Grassucci RA, Sarnow P, Frank J. Cell 118 465-475 (2004)
  17. The ribosome uses two active mechanisms to unwind messenger RNA during translation. Qu X, Wen JD, Lancaster L, Noller HF, Bustamante C, Tinoco I. Nature 475 118-121 (2011)
  18. The cryo-EM structure of a translation initiation complex from Escherichia coli. Allen GS, Zavialov A, Gursky R, Ehrenberg M, Frank J. Cell 121 703-712 (2005)
  19. 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)
  20. Structures of the ribosome in intermediate states of ratcheting. Zhang W, Dunkle JA, Cate JH. Science 325 1014-1017 (2009)
  21. Elongation factor G bound to the ribosome in an intermediate state of translocation. Tourigny DS, Fernández IS, Kelley AC, Ramakrishnan V. Science 340 1235490 (2013)
  22. Kinetically competent intermediates in the translocation step of protein synthesis. Pan D, Kirillov SV, Cooperman BS. Mol Cell 25 519-529 (2007)
  23. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. Tama F, Miyashita O, Brooks CL. J Struct Biol 147 315-326 (2004)
  24. The native 3D organization of bacterial polysomes. Brandt F, Etchells SA, Ortiz JO, Elcock AH, Hartl FU, Baumeister W. Cell 136 261-271 (2009)
  25. Observation of intersubunit movement of the ribosome in solution using FRET. Ermolenko DN, Majumdar ZK, Hickerson RP, Spiegel PC, Clegg RM, Noller HF. J Mol Biol 370 530-540 (2007)
  26. Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits. Lebaron S, Schneider C, van Nues RW, Swiatkowska A, Walsh D, Böttcher B, Granneman S, Watkins NJ, Tollervey D. Nat Struct Mol Biol 19 744-753 (2012)
  27. 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)
  28. Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Blaha G, Stanley RE, Steitz TA. Science 325 966-970 (2009)
  29. Capreomycin binds across the ribosomal subunit interface using tlyA-encoded 2'-O-methylations in 16S and 23S rRNAs. Johansen SK, Maus CE, Plikaytis BB, Douthwaite S. Mol Cell 23 173-182 (2006)
  30. 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)
  31. Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES. Boehringer D, Thermann R, Ostareck-Lederer A, Lewis JD, Stark H. Structure 13 1695-1706 (2005)
  32. Structure of the ribosome-bound cricket paralysis virus IRES RNA. Schüler M, Connell SR, Lescoute A, Giesebrecht J, Dabrowski M, Schroeer B, Mielke T, Penczek PA, Westhof E, Spahn CM. Nat Struct Mol Biol 13 1092-1096 (2006)
  33. Following movement of the L1 stalk between three functional states in single ribosomes. Cornish PV, Ermolenko DN, Staple DW, Hoang L, Hickerson RP, Noller HF, Ha T. Proc Natl Acad Sci U S A 106 2571-2576 (2009)
  34. Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Connell SR, Takemoto C, Wilson DN, Wang H, Murayama K, Terada T, Shirouzu M, Rost M, Schüler M, Giesebrecht J, Dabrowski M, Mielke T, Fucini P, Yokoyama S, Spahn CM. Mol Cell 25 751-764 (2007)
  35. 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)
  36. Structure of ratcheted ribosomes with tRNAs in hybrid states. Julián P, Konevega AL, Scheres SH, Lázaro M, Gil D, Wintermeyer W, Rodnina MV, Valle M. Proc Natl Acad Sci U S A 105 16924-16927 (2008)
  37. Control of ribosomal subunit rotation by elongation factor G. Pulk A, Cate JH. Science 340 1235970 (2013)
  38. 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)
  39. 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)
  40. Ribosome-dependent activation of stringent control. Brown A, Fernández IS, Gordiyenko Y, Ramakrishnan V. Nature 534 277-280 (2016)
  41. Comprehensive molecular structure of the eukaryotic ribosome. Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, Sali A, Harvey SC, Frank J. Structure 17 1591-1604 (2009)
  42. Dynamic pathways of -1 translational frameshifting. Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD. Nature 512 328-332 (2014)
  43. tRNA-mRNA mimicry drives translation initiation from a viral IRES. Costantino DA, Pfingsten JS, Rambo RP, Kieft JS. Nat Struct Mol Biol 15 57-64 (2008)
  44. Reinitiation and other unconventional posttermination events during eukaryotic translation. Skabkin MA, Skabkina OV, Hellen CU, Pestova TV. Mol Cell 51 249-264 (2013)
  45. Dissecting the ribosomal inhibition mechanisms of edeine and pactamycin: the universally conserved residues G693 and C795 regulate P-site RNA binding. Dinos G, Wilson DN, Teraoka Y, Szaflarski W, Fucini P, Kalpaxis D, Nierhaus KH. Mol Cell 13 113-124 (2004)
  46. 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)
  47. Evolution of the ribosome at atomic resolution. Petrov AS, Bernier CR, Hsiao C, Norris AM, Kovacs NA, Waterbury CC, Stepanov VG, Harvey SC, Fox GE, Wartell RM, Hud NV, Williams LD. Proc Natl Acad Sci U S A 111 10251-10256 (2014)
  48. Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G. Zavialov AV, Hauryliuk VV, Ehrenberg M. Mol Cell 18 675-686 (2005)
  49. Peptidyl-tRNA regulates the GTPase activity of translation factors. Zavialov AV, Ehrenberg M. Cell 114 113-122 (2003)
  50. iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates. Lopéz-Blanco JR, Chacón P. J Struct Biol 184 261-270 (2013)
  51. The antibiotic viomycin traps the ribosome in an intermediate state of translocation. Ermolenko DN, Spiegel PC, Majumdar ZK, Hickerson RP, Clegg RM, Noller HF. Nat Struct Mol Biol 14 493-497 (2007)
  52. Trajectories of the ribosome as a Brownian nanomachine. Dashti A, Schwander P, Langlois R, Fung R, Li W, Hosseinizadeh A, Liao HY, Pallesen J, Sharma G, Stupina VA, Simon AE, Dinman JD, Frank J, Ourmazd A. Proc Natl Acad Sci U S A 111 17492-17497 (2014)
  53. Coordinated conformational and compositional dynamics drive ribosome translocation. Chen J, Petrov A, Tsai A, O'Leary SE, Puglisi JD. Nat Struct Mol Biol 20 718-727 (2013)
  54. Structure of the ribosome with elongation factor G trapped in the pretranslocation state. Brilot AF, Korostelev AA, Ermolenko DN, Grigorieff N. Proc Natl Acad Sci U S A 110 20994-20999 (2013)
  55. mRNA translocation occurs during the second step of ribosomal intersubunit rotation. Ermolenko DN, Noller HF. Nat Struct Mol Biol 18 457-462 (2011)
  56. Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation. Ramrath DJ, Lancaster L, Sprink T, Mielke T, Loerke J, Noller HF, Spahn CM. Proc Natl Acad Sci U S A 110 20964-20969 (2013)
  57. Divergent tRNA-like element supports initiation, elongation, and termination of protein biosynthesis. Jan E, Kinzy TG, Sarnow P. Proc Natl Acad Sci U S A 100 15410-15415 (2003)
  58. Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome. Spiegel PC, Ermolenko DN, Noller HF. RNA 13 1473-1482 (2007)
  59. Structure of eEF3 and the mechanism of transfer RNA release from the E-site. Andersen CB, Becker T, Blau M, Anand M, Halic M, Balar B, Mielke T, Boesen T, Pedersen JS, Spahn CM, Kinzy TG, Andersen GR, Beckmann R. Nature 443 663-668 (2006)
  60. The hybrid state of tRNA binding is an authentic translation elongation intermediate. Dorner S, Brunelle JL, Sharma D, Green R. Nat Struct Mol Biol 13 234-241 (2006)
  61. Energy barriers and driving forces in tRNA translocation through the ribosome. Bock LV, Blau C, Schröder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC, Grubmüller H. Nat Struct Mol Biol 20 1390-1396 (2013)
  62. RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. Gao H, Zhou Z, Rawat U, Huang C, Bouakaz L, Wang C, Cheng Z, Liu Y, Zavialov A, Gursky R, Sanyal S, Ehrenberg M, Frank J, Song H. Cell 129 929-941 (2007)
  63. Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Fei J, Bronson JE, Hofman JM, Srinivas RL, Wiggins CH, Gonzalez RL. Proc Natl Acad Sci U S A 106 15702-15707 (2009)
  64. Rotation of the head of the 30S ribosomal subunit during mRNA translocation. Guo Z, Noller HF. Proc Natl Acad Sci U S A 109 20391-20394 (2012)
  65. A steric block in translation caused by the antibiotic spectinomycin. Borovinskaya MA, Shoji S, Holton JM, Fredrick K, Cate JHD. ACS Chem Biol 2 545-552 (2007)
  66. 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)
  67. The ribosomal stalk binds to translation factors IF2, EF-Tu, EF-G and RF3 via a conserved region of the L12 C-terminal domain. Helgstrand M, Mandava CS, Mulder FA, Liljas A, Sanyal S, Akke M. J Mol Biol 365 468-479 (2007)
  68. Allosteric control of the ribosome by small-molecule antibiotics. Wang L, Pulk A, Wasserman MR, Feldman MB, Altman RB, Cate JH, Blanchard SC. Nat Struct Mol Biol 19 957-963 (2012)
  69. Conformational changes of elongation factor G on the ribosome during tRNA translocation. Lin J, Gagnon MG, Bulkley D, Steitz TA. Cell 160 219-227 (2015)
  70. Spontaneous formation of the unlocked state of the ribosome is a multistep process. Munro JB, Altman RB, Tung CS, Cate JH, Sanbonmatsu KY, Blanchard SC. Proc Natl Acad Sci U S A 107 709-714 (2010)
  71. Intersubunit movement is required for ribosomal translocation. Horan LH, Noller HF. Proc Natl Acad Sci U S A 104 4881-4885 (2007)
  72. Estimation of variance in single-particle reconstruction using the bootstrap technique. Penczek PA, Yang C, Frank J, Spahn CM. J Struct Biol 154 168-183 (2006)
  73. Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Gao N, Zavialov AV, Li W, Sengupta J, Valle M, Gursky RP, Ehrenberg M, Frank J. Mol Cell 18 663-674 (2005)
  74. Role and timing of GTP binding and hydrolysis during EF-G-dependent tRNA translocation on the ribosome. Wilden B, Savelsbergh A, Rodnina MV, Wintermeyer W. Proc Natl Acad Sci U S A 103 13670-13675 (2006)
  75. Structure and dynamics of the mammalian ribosomal pretranslocation complex. Budkevich T, Giesebrecht J, Altman RB, Munro JB, Mielke T, Nierhaus KH, Blanchard SC, Spahn CM. Mol Cell 44 214-224 (2011)
  76. Control of phosphate release from elongation factor G by ribosomal protein L7/12. Savelsbergh A, Mohr D, Kothe U, Wintermeyer W, Rodnina MV. EMBO J 24 4316-4323 (2005)
  77. Exploring global motions and correlations in the ribosome. Trylska J, Tozzini V, McCammon JA. Biophys J 89 1455-1463 (2005)
  78. A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation. Kim HK, Liu F, Fei J, Bustamante C, Gonzalez RL, Tinoco I. Proc Natl Acad Sci U S A 111 5538-5543 (2014)
  79. Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM. Frank J, Ourmazd A. Methods 100 61-67 (2016)
  80. The Cryo-EM structure of a complete 30S translation initiation complex from Escherichia coli. Julián P, Milon P, Agirrezabala X, Lasso G, Gil D, Rodnina MV, Valle M. PLoS Biol 9 e1001095 (2011)
  81. Structural basis for hygromycin B inhibition of protein biosynthesis. Borovinskaya MA, Shoji S, Fredrick K, Cate JH. RNA 14 1590-1599 (2008)
  82. Fluctuations of transfer RNAs between classical and hybrid states. Kim HD, Puglisi JD, Chu S. Biophys J 93 3575-3582 (2007)
  83. Correlated conformational events in EF-G and the ribosome regulate translocation. Munro JB, Wasserman MR, Altman RB, Wang L, Blanchard SC. Nat Struct Mol Biol 17 1470-1477 (2010)
  84. X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit. Wilson DN, Schluenzen F, Harms JM, Yoshida T, Ohkubo T, Albrecht R, Buerger J, Kobayashi Y, Fucini P. EMBO J 24 251-260 (2005)
  85. 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)
  86. Following the intersubunit conformation of the ribosome during translation in real time. Aitken CE, Puglisi JD. Nat Struct Mol Biol 17 793-800 (2010)
  87. 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)
  88. Structure of EF-G-ribosome complex in a pretranslocation state. Chen Y, Feng S, Kumar V, Ero R, Gao YG. Nat Struct Mol Biol 20 1077-1084 (2013)
  89. The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. Trabuco LG, Schreiner E, Eargle J, Cornish P, Ha T, Luthey-Schulten Z, Schulten K. J Mol Biol 402 741-760 (2010)
  90. Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations. Orzechowski M, Tama F. Biophys J 95 5692-5705 (2008)
  91. 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)
  92. GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Marshall RA, Aitken CE, Puglisi JD. Mol Cell 35 37-47 (2009)
  93. Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM. Datta PP, Sharma MR, Qi L, Frank J, Agrawal RK. Mol Cell 20 723-731 (2005)
  94. EF-G-independent reactivity of a pre-translocation-state ribosome complex with the aminoacyl tRNA substrate puromycin supports an intermediate (hybrid) state of tRNA binding. Sharma D, Southworth DR, Green R. RNA 10 102-113 (2004)
  95. GTP hydrolysis by EF-G synchronizes tRNA movement on small and large ribosomal subunits. Holtkamp W, Cunha CE, Peske F, Konevega AL, Wintermeyer W, Rodnina MV. EMBO J 33 1073-1085 (2014)
  96. Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset. Gao H, Valle M, Ehrenberg M, Frank J. J Struct Biol 147 283-290 (2004)
  97. A fast dynamic mode of the EF-G-bound ribosome. Munro JB, Altman RB, Tung CS, Sanbonmatsu KY, Blanchard SC. EMBO J 29 770-781 (2010)
  98. Aminoglycoside activity observed on single pre-translocation ribosome complexes. Feldman MB, Terry DS, Altman RB, Blanchard SC. Nat Chem Biol 6 54-62 (2010)
  99. Role of hybrid tRNA-binding states in ribosomal translocation. Walker SE, Shoji S, Pan D, Cooperman BS, Fredrick K. Proc Natl Acad Sci U S A 105 9192-9197 (2008)
  100. HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions. Zhang Y, Mandava CS, Cao W, Li X, Zhang D, Li N, Zhang Y, Zhang X, Qin Y, Mi K, Lei J, Sanyal S, Gao N. Nat Struct Mol Biol 22 906-913 (2015)
  101. Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3. Jin H, Kelley AC, Ramakrishnan V. Proc Natl Acad Sci U S A 108 15798-15803 (2011)
  102. Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements. Mitra K, Schaffitzel C, Fabiola F, Chapman MS, Ban N, Frank J. Mol Cell 22 533-543 (2006)
  103. Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases. Rázga F, Koca J, Sponer J, Leontis NB. Biophys J 88 3466-3485 (2005)
  104. 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)
  105. RNA chaperone activity of large ribosomal subunit proteins from Escherichia coli. Semrad K, Green R, Schroeder R. RNA 10 1855-1860 (2004)
  106. Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy. Chen B, Kaledhonkar S, Sun M, Shen B, Lu Z, Barnard D, Lu TM, Gonzalez RL, Frank J. Structure 23 1097-1105 (2015)
  107. A role for the 30S subunit E site in maintenance of the translational reading frame. Devaraj A, Shoji S, Holbrook ED, Fredrick K. RNA 15 255-265 (2009)
  108. Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit. Sengupta J, Bussiere C, Pallesen J, West M, Johnson AW, Frank J. J Cell Biol 189 1079-1086 (2010)
  109. Crystal structure of a mutant elongation factor G trapped with a GTP analogue. Hansson S, Singh R, Gudkov AT, Liljas A, Logan DT. FEBS Lett 579 4492-4497 (2005)
  110. 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)
  111. The ribosome as a conveying thermal ratchet machine. Spirin AS. J Biol Chem 284 21103-21119 (2009)
  112. 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)
  113. EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics. Chen B, Boël G, Hashem Y, Ning W, Fei J, Wang C, Gonzalez RL, Hunt JF, Frank J. Nat Struct Mol Biol 21 152-159 (2014)
  114. SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles. Elmlund D, Elmlund H. J Struct Biol 180 420-427 (2012)
  115. 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)
  116. The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift. Léger M, Dulude D, Steinberg SV, Brakier-Gingras L. Nucleic Acids Res 35 5581-5592 (2007)
  117. Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling. Sternberg SH, Fei J, Prywes N, McGrath KA, Gonzalez RL. Nat Struct Mol Biol 16 861-868 (2009)
  118. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. Whitford PC, Blanchard SC, Cate JH, Sanbonmatsu KY. PLoS Comput Biol 9 e1003003 (2013)
  119. Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections. Elad N, Clare DK, Saibil HR, Orlova EV. J Struct Biol 162 108-120 (2008)
  120. Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis. Zhang W, Kimmel M, Spahn CM, Penczek PA. Structure 16 1770-1776 (2008)
  121. The structure of LepA, the ribosomal back translocase. Evans RN, Blaha G, Bailey S, Steitz TA. Proc Natl Acad Sci U S A 105 4673-4678 (2008)
  122. Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis. Shi X, Khade PK, Sanbonmatsu KY, Joseph S. J Mol Biol 419 125-138 (2012)
  123. 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)
  124. Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states. Tan D, Li Q, Zhang MJ, Liu C, Ma C, Zhang P, Ding YH, Fan SB, Tao L, Yang B, Li X, Ma S, Liu J, Feng B, Liu X, Wang HW, He SM, Gao N, Ye K, Dong MQ, Lei X. Elife 5 e12509 (2016)
  125. 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)
  126. Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules. Baxter WT, Grassucci RA, Gao H, Frank J. J Struct Biol 166 126-132 (2009)
  127. Guanine-nucleotide exchange on ribosome-bound elongation factor G initiates the translocation of tRNAs. Zavialov AV, Hauryliuk VV, Ehrenberg M. J Biol 4 9 (2005)
  128. The A-site finger in 23 S rRNA acts as a functional attenuator for translocation. Komoda T, Sato NS, Phelps SS, Namba N, Joseph S, Suzuki T. J Biol Chem 281 32303-32309 (2006)
  129. Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes. Jin Q, Sorzano CO, de la Rosa-Trevín JM, Bilbao-Castro JR, Núñez-Ramírez R, Llorca O, Tama F, Jonić S. Structure 22 496-506 (2014)
  130. Cryo-EM structure of the mammalian eukaryotic release factor eRF1-eRF3-associated termination complex. Taylor D, Unbehaun A, Li W, Das S, Lei J, Liao HY, Grassucci RA, Pestova TV, Frank J. Proc Natl Acad Sci U S A 109 18413-18418 (2012)
  131. Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing. Unbehaun A, Marintchev A, Lomakin IB, Didenko T, Wagner G, Hellen CU, Pestova TV. EMBO J 26 3109-3123 (2007)
  132. Structural insights into fusidic acid resistance and sensitivity in EF-G. Hansson S, Singh R, Gudkov AT, Liljas A, Logan DT. J Mol Biol 348 939-949 (2005)
  133. Allosteric vs. spontaneous exit-site (E-site) tRNA dissociation early in protein synthesis. Chen C, Stevens B, Kaur J, Smilansky Z, Cooperman BS, Goldman YE. Proc Natl Acad Sci U S A 108 16980-16985 (2011)
  134. Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit. Li N, Chen Y, Guo Q, Zhang Y, Yuan Y, Ma C, Deng H, Lei J, Gao N. Nucleic Acids Res 41 7073-7083 (2013)
  135. Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis. Fei J, Richard AC, Bronson JE, Gonzalez RL. Nat Struct Mol Biol 18 1043-1051 (2011)
  136. tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Flis J, Holm M, Rundlet EJ, Loerke J, Hilal T, Dabrowski M, Bürger J, Mielke T, Blanchard SC, Spahn CMT, Budkevich TV. Cell Rep 25 2676-2688.e7 (2018)
  137. Function of the ribosomal E-site: a mutagenesis study. Sergiev PV, Lesnyak DV, Kiparisov SV, Burakovsky DE, Leonov AA, Bogdanov AA, Brimacombe R, Dontsova OA. Nucleic Acids Res 33 6048-6056 (2005)
  138. Rapid ribosomal translocation depends on the conserved 18-55 base pair in P-site transfer RNA. Pan D, Kirillov S, Zhang CM, Hou YM, Cooperman BS. Nat Struct Mol Biol 13 354-359 (2006)
  139. tmRNA-SmpB: a journey to the centre of the bacterial ribosome. Weis F, Bron P, Giudice E, Rolland JP, Thomas D, Felden B, Gillet R. EMBO J 29 3810-3818 (2010)
  140. A time-resolved investigation of ribosomal subunit association. Hennelly SP, Antoun A, Ehrenberg M, Gualerzi CO, Knight W, Lodmell JS, Hill WE. J Mol Biol 346 1243-1258 (2005)
  141. Accessibility of 18S rRNA in human 40S subunits and 80S ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics. Shenvi CL, Dong KC, Friedman EM, Hanson JA, Cate JH. RNA 11 1898-1908 (2005)
  142. An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome. Rakauskaite R, Dinman JD. Mol Cell Biol 26 8992-9002 (2006)
  143. The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. Kurkcuoglu O, Doruker P, Sen TZ, Kloczkowski A, Jernigan RL. Phys Biol 5 046005 (2008)
  144. Coarse-grained force field for the nucleosome from self-consistent multiscaling. Voltz K, Trylska J, Tozzini V, Kurkal-Siebert V, Langowski J, Smith J. J Comput Chem 29 1429-1439 (2008)
  145. Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements. Kavran JM, Steitz TA. J Mol Biol 371 1047-1059 (2007)
  146. Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions. Wasserman MR, Pulk A, Zhou Z, Altman RB, Zinder JC, Green KD, Garneau-Tsodikova S, Cate JH, Blanchard SC. Nat Commun 6 7896 (2015)
  147. Kinetics of Spontaneous and EF-G-Accelerated Rotation of Ribosomal Subunits. Sharma H, Adio S, Senyushkina T, Belardinelli R, Peske F, Rodnina MV. Cell Rep 16 2187-2196 (2016)
  148. RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics. Rázga F, Zacharias M, Réblová K, Koca J, Sponer J. Structure 14 825-835 (2006)
  149. Definition of bases in 23S rRNA essential for ribosomal subunit association. Maiväli U, Remme J. RNA 10 600-604 (2004)
  150. Determinants of the rate of mRNA translocation in bacterial protein synthesis. Borg A, Ehrenberg M. J Mol Biol 427 1835-1847 (2015)
  151. Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies. Velazquez-Muriel JA, Valle M, Santamaría-Pang A, Kakadiaris IA, Carazo JM. Structure 14 1115-1126 (2006)
  152. Infectious bursal disease virus capsid assembly and maturation by structural rearrangements of a transient molecular switch. Luque D, Saugar I, Rodríguez JF, Verdaguer N, Garriga D, Martín CS, Velázquez-Muriel JA, Trus BL, Carrascosa JL, Castón JR. J Virol 81 6869-6878 (2007)
  153. Mrpl36 is important for generation of assembly competent proteins during mitochondrial translation. Prestele M, Vogel F, Reichert AS, Herrmann JM, Ott M. Mol Biol Cell 20 2615-2625 (2009)
  154. Ribosome motions modulate electrostatic properties. Trylska J, Konecny R, Tama F, Brooks CL, McCammon JA. Biopolymers 74 423-431 (2004)
  155. Class-1 release factor eRF1 promotes GTP binding by class-2 release factor eRF3. Hauryliuk V, Zavialov A, Kisselev L, Ehrenberg M. Biochimie 88 747-757 (2006)
  156. Modular domains of the Dicistroviridae intergenic internal ribosome entry site. Jang CJ, Jan E. RNA 16 1182-1195 (2010)
  157. Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data. Caulfield TR, Devkota B, Rollins GC. J Biophys 2011 219515 (2011)
  158. 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)
  159. Progression of the ribosome recycling factor through the ribosome dissociates the two ribosomal subunits. Barat C, Datta PP, Raj VS, Sharma MR, Kaji H, Kaji A, Agrawal RK. Mol Cell 27 250-261 (2007)
  160. 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)
  161. Structural insights into initial and intermediate steps of the ribosome-recycling process. Yokoyama T, Shaikh TR, Iwakura N, Kaji H, Kaji A, Agrawal RK. EMBO J 31 1836-1846 (2012)
  162. 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)
  163. Conserved element of the dicistrovirus IGR IRES that mimics an E-site tRNA/ribosome interaction mediates multiple functions. Jang CJ, Lo MC, Jan E. J Mol Biol 387 42-58 (2009)
  164. Near-critical behavior of aminoacyl-tRNA pools in E. coli at rate-limiting supply of amino acids. Elf J, Ehrenberg M. Biophys J 88 132-146 (2005)
  165. Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation. Nguyen K, Whitford PC. Nat Commun 7 10586 (2016)
  166. Destabilization of the P site codon-anticodon helix results from movement of tRNA into the P/E hybrid state within the ribosome. McGarry KG, Walker SE, Wang H, Fredrick K. Mol Cell 20 613-622 (2005)
  167. Unsupervised classification of single particles by cluster tracking in multi-dimensional space. Fu J, Gao H, Frank J. J Struct Biol 157 226-239 (2007)
  168. Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding. García-Ortega L, Alvarez-García E, Gavilanes JG, Martínez-del-Pozo A, Joseph S. Nucleic Acids Res 38 4108-4119 (2010)
  169. Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes. Soung GY, Miller JL, Koc H, Koc EC. J Proteome Res 8 3390-3402 (2009)
  170. Interactions of translational factor EF-G with the bacterial ribosome before and after mRNA translocation. Wilson KS, Nechifor R. J Mol Biol 337 15-30 (2004)
  171. Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits. Gao N, Zavialov AV, Ehrenberg M, Frank J. J Mol Biol 374 1345-1358 (2007)
  172. Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Réblová K, Sponer J, Lankas F. Nucleic Acids Res 40 6290-6303 (2012)
  173. Conformational changes in switch I of EF-G drive its directional cycling on and off the ribosome. Ticu C, Nechifor R, Nguyen B, Desrosiers M, Wilson KS. EMBO J 28 2053-2065 (2009)
  174. Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation. Fu J, Munro JB, Blanchard SC, Frank J. Proc Natl Acad Sci U S A 108 4817-4821 (2011)
  175. Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P. Biophys J 97 1178-1187 (2009)
  176. Following movement of domain IV of elongation factor G during ribosomal translocation. Salsi E, Farah E, Dann J, Ermolenko DN. Proc Natl Acad Sci U S A 111 15060-15065 (2014)
  177. Insights into the molecular determinants of EF-G catalyzed translocation. Wang L, Altman RB, Blanchard SC. RNA 17 2189-2200 (2011)
  178. Recognition of guanosine by dissimilar tRNA methyltransferases. Sakaguchi R, Giessing A, Dai Q, Lahoud G, Liutkeviciute Z, Klimasauskas S, Piccirilli J, Kirpekar F, Hou YM. RNA 18 1687-1701 (2012)
  179. The ribosome uses cooperative conformational changes to maximize and regulate the efficiency of translation. Ning W, Fei J, Gonzalez RL. Proc Natl Acad Sci U S A 111 12073-12078 (2014)
  180. Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit. Petrov AN, Meskauskas A, Roshwalb SC, Dinman JD. Nucleic Acids Res 36 6187-6198 (2008)
  181. Dynamics of ribosomes and release factors during translation termination in E. coli. Adio S, Sharma H, Senyushkina T, Karki P, Maracci C, Wohlgemuth I, Holtkamp W, Peske F, Rodnina MV. Elife 7 e34252 (2018)
  182. Fusidic acid targets elongation factor G in several stages of translocation on the bacterial ribosome. Borg A, Holm M, Shiroyama I, Hauryliuk V, Pavlov M, Sanyal S, Ehrenberg M. J Biol Chem 290 3440-3454 (2015)
  183. Molecular dynamics of EF-G during translocation. Li W, Trabuco LG, Schulten K, Frank J. Proteins 79 1478-1486 (2011)
  184. The pretranslocation ribosome is targeted by GTP-bound EF-G in partially activated form. Hauryliuk V, Mitkevich VA, Eliseeva NA, Petrushanko IY, Ehrenberg M, Makarov AA. Proc Natl Acad Sci U S A 105 15678-15683 (2008)
  185. The ribosomal A-site finger is crucial for binding and activation of the stringent factor RelA. Kudrin P, Dzhygyr I, Ishiguro K, Beljantseva J, Maksimova E, Oliveira SRA, Varik V, Payoe R, Konevega AL, Tenson T, Suzuki T, Hauryliuk V. Nucleic Acids Res 46 1973-1983 (2018)
  186. Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation. Kapp LD, Kolitz SE, Lorsch JR. RNA 12 751-764 (2006)
  187. Analysis of structural dynamics in the ribosome by TLS crystallographic refinement. Korostelev A, Noller HF. J Mol Biol 373 1058-1070 (2007)
  188. Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions. Chen J, Coakley A, O'Connor M, Petrov A, O'Leary SE, Atkins JF, Puglisi JD. Cell 163 1267-1280 (2015)
  189. Functional interactions between the G' subdomain of bacterial translation factor EF-G and ribosomal protein L7/L12. Nechifor R, Murataliev M, Wilson KS. J Biol Chem 282 36998-37005 (2007)
  190. The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation. Bulkley D, Brandi L, Polikanov YS, Fabbretti A, O'Connor M, Gualerzi CO, Steitz TA. Cell Rep 6 357-365 (2014)
  191. Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data. Li W, Frank J. Proc Natl Acad Sci U S A 104 16540-16545 (2007)
  192. Cofactor dependent conformational switching of GTPases. Hauryliuk V, Hansson S, Ehrenberg M. Biophys J 95 1704-1715 (2008)
  193. Contribution of intersubunit bridges to the energy barrier of ribosomal translocation. Liu Q, Liu Q, Fredrick K. Nucleic Acids Res 41 565-574 (2013)
  194. Post-termination Ribosome Intermediate Acts as the Gateway to Ribosome Recycling. Prabhakar A, Capece MC, Petrov A, Choi J, Puglisi JD. Cell Rep 20 161-172 (2017)
  195. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. Ahmed A, Whitford PC, Sanbonmatsu KY, Tama F. J Struct Biol 177 561-570 (2012)
  196. Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Réblová K, Rázga F, Li W, Gao H, Frank J, Sponer J. Nucleic Acids Res 38 1325-1340 (2010)
  197. Recurring RNA structural motifs underlie the mechanics of L1 stalk movement. Mohan S, Noller HF. Nat Commun 8 14285 (2017)
  198. A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding. Rhodin MH, Dinman JD. Nucleic Acids Res 38 8377-8389 (2010)
  199. Functional epitopes at the ribosome subunit interface. Rackham O, Wang K, Chin JW. Nat Chem Biol 2 254-258 (2006)
  200. Ribosome recycling factor disassembles the post-termination ribosomal complex independent of the ribosomal translocase activity of elongation factor G. Fujiwara T, Ito K, Yamami T, Nakamura Y. Mol Microbiol 53 517-528 (2004)
  201. The conserved A-site finger of the 23S rRNA: just one of the intersubunit bridges or a part of the allosteric communication pathway? Sergiev PV, Kiparisov SV, Burakovsky DE, Lesnyak DV, Leonov AA, Bogdanov AA, Dontsova OA. J Mol Biol 353 116-123 (2005)
  202. mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding. Bao C, Loerch S, Ling C, Korostelev AA, Grigorieff N, Ermolenko DN. Elife 9 e55799 (2020)
  203. A chemical genomic screen in Saccharomyces cerevisiae reveals a role for diphthamidation of translation elongation factor 2 in inhibition of protein synthesis by sordarin. Botet J, Rodríguez-Mateos M, Ballesta JP, Revuelta JL, Remacha M. Antimicrob Agents Chemother 52 1623-1629 (2008)
  204. An extensive network of information flow through the B1b/c intersubunit bridge of the yeast ribosome. Rhodin MH, Dinman JD. PLoS One 6 e20048 (2011)
  205. Complete kinetic mechanism for recycling of the bacterial ribosome. Borg A, Pavlov M, Ehrenberg M. RNA 22 10-21 (2016)
  206. Dynamics of the context-specific translation arrest by chloramphenicol and linezolid. Choi J, Marks J, Zhang J, Chen DH, Wang J, Vázquez-Laslop N, Mankin AS, Puglisi JD. Nat Chem Biol 16 310-317 (2020)
  207. 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)
  208. Initiation factor 2 stabilizes the ribosome in a semirotated conformation. Ling C, Ermolenko DN. Proc Natl Acad Sci U S A 112 15874-15879 (2015)
  209. Interaction of the HIV-1 frameshift signal with the ribosome. Mazauric MH, Seol Y, Yoshizawa S, Visscher K, Fourmy D. Nucleic Acids Res 37 7654-7664 (2009)
  210. Single-molecule study of ribosome hierarchic dynamics at the peptidyl transferase center. Altuntop ME, Ly CT, Wang Y. Biophys J 99 3002-3009 (2010)
  211. 5S rRNA: Structure and Function from Head to Toe. Dinman JD. Int J Biomed Sci 1 2-7 (2005)
  212. Contribution of ribosomal residues to P-site tRNA binding. Shoji S, Abdi NM, Bundschuh R, Fredrick K. Nucleic Acids Res 37 4033-4042 (2009)
  213. Movement of elongation factor G between compact and extended conformations. Salsi E, Farah E, Netter Z, Dann J, Ermolenko DN. J Mol Biol 427 454-467 (2015)
  214. Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome. Ishida H, Hayward S. Biophys J 95 5962-5973 (2008)
  215. A small protein unique to bacteria organizes rRNA tertiary structure over an extensive region of the 50 S ribosomal subunit. Maeder C, Draper DE. J Mol Biol 354 436-446 (2005)
  216. EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome. Zhang D, Yan K, Liu G, Song G, Luo J, Shi Y, Cheng E, Wu S, Jiang T, Lou J, Gao N, Qin Y. Nat Struct Mol Biol 23 125-131 (2016)
  217. Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures. Matsumoto A, Ishida H. Structure 17 1605-1613 (2009)
  218. Mechanism of elongation factor-G-mediated fusidic acid resistance and fitness compensation in Staphylococcus aureus. Koripella RK, Chen Y, Peisker K, Koh CS, Selmer M, Sanyal S. J Biol Chem 287 30257-30267 (2012)
  219. Structural analysis of 70S ribosomes by cross-linking/mass spectrometry reveals conformational plasticity. Tüting C, Iacobucci C, Ihling CH, Kastritis PL, Sinz A. Sci Rep 10 12618 (2020)
  220. Structure and function of FusB: an elongation factor G-binding fusidic acid resistance protein active in ribosomal translocation and recycling. Guo X, Peisker K, Bäckbro K, Chen Y, Koripella RK, Mandava CS, Sanyal S, Selmer M. Open Biol 2 120016 (2012)
  221. Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation. Ermolenko DN, Cornish PV, Ha T, Noller HF. RNA 19 158-166 (2013)
  222. Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Rázga F, Koca J, Mokdad A, Sponer J. Nucleic Acids Res 35 4007-4017 (2007)
  223. Elongation factor P: Function and effects on bacterial fitness. Doerfel LK, Rodnina MV. Biopolymers 99 837-845 (2013)
  224. Sordarin derivatives induce a novel conformation of the yeast ribosome translocation factor eEF2. Søe R, Mosley RT, Justice M, Nielsen-Kahn J, Shastry M, Merrill AR, Andersen GR. J Biol Chem 282 657-666 (2007)
  225. Crosslinking of translation factor EF-G to proteins of the bacterial ribosome before and after translocation. Nechifor R, Wilson KS. J Mol Biol 368 1412-1425 (2007)
  226. Genetic evidence against the 16S ribosomal RNA helix 27 conformational switch model. Rodriguez-Correa D, Dahlberg AE. RNA 10 28-33 (2004)
  227. Identification of nucleotides in E. coli 16S rRNA essential for ribosome subunit association. Pulk A, Maiväli U, Remme J. RNA 12 790-796 (2006)
  228. Model of ribosome translation and mRNA unwinding. Xie P. Eur Biophys J 42 347-354 (2013)
  229. Model of the toxic complex of anthrax: responsive conformational changes in both the lethal factor and the protective antigen heptamer. Tama F, Ren G, Brooks CL, Mitra AK. Protein Sci 15 2190-2200 (2006)
  230. Phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis. Miller JL, Cimen H, Koc H, Koc EC. J Proteome Res 8 4789-4798 (2009)
  231. Uniting Native Capillary Electrophoresis and Multistage Ultraviolet Photodissociation Mass Spectrometry for Online Separation and Characterization of Escherichia coli Ribosomal Proteins and Protein Complexes. Mehaffey MR, Xia Q, Brodbelt JS. Anal Chem 92 15202-15211 (2020)
  232. Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy. Sengupta J, Nilsson J, Gursky R, Kjeldgaard M, Nissen P, Frank J. J Mol Biol 382 179-187 (2008)
  233. A conserved base-pair between tRNA and 23 S rRNA in the peptidyl transferase center is important for peptide release. Feinberg JS, Joseph S. J Mol Biol 364 1010-1020 (2006)
  234. 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)
  235. Inhibition of antiassociation activity of translation initiation factor 3 by paromomycin. Hirokawa G, Kaji H, Kaji A. Antimicrob Agents Chemother 51 175-180 (2007)
  236. Shine-Dalgarno interaction prevents incorporation of noncognate amino acids at the codon following the AUG. Di Giacco V, Márquez V, Qin Y, Pech M, Triana-Alonso FJ, Wilson DN, Nierhaus KH. Proc Natl Acad Sci U S A 105 10715-10720 (2008)
  237. Structural basis for ribosome recycling by RRF and tRNA. Zhou D, Tanzawa T, Lin J, Gagnon MG. Nat Struct Mol Biol 27 25-32 (2020)
  238. Structural diversity in bacterial ribosomes: mycobacterial 70S ribosome structure reveals novel features. Shasmal M, Sengupta J. PLoS One 7 e31742 (2012)
  239. 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)
  240. A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases. Wang L, Yang F, Zhang D, Chen Z, Xu RM, Nierhaus KH, Gong W, Qin Y. Nat Struct Mol Biol 19 403-410 (2012)
  241. Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding. Sharma AK, Chowdhury D. Phys Biol 8 026005 (2011)
  242. Following the dynamics of changes in solvent accessibility of 16 S and 23 S rRNA during ribosomal subunit association using synchrotron-generated hydroxyl radicals. Nguyenle T, Laurberg M, Brenowitz M, Noller HF. J Mol Biol 359 1235-1248 (2006)
  243. G-ribo: a new structural motif in ribosomal RNA. Steinberg SV, Boutorine YI. RNA 13 549-554 (2007)
  244. 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)
  245. The Intersubunit Bridge B1b of the Bacterial Ribosome Facilitates Initiation of Protein Synthesis and Maintenance of Translational Fidelity. Lilleorg S, Reier K, Remme J, Liiv A. J Mol Biol 429 1067-1080 (2017)
  246. The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry. Sanz-García E, Stewart AB, Belnap DM. J Struct Biol 171 216-222 (2010)
  247. Thermodynamics of GTP and GDP binding to bacterial initiation factor 2 suggests two types of structural transitions. Hauryliuk V, Mitkevich VA, Draycheva A, Tankov S, Shyp V, Ermakov A, Kulikova AA, Makarov AA, Ehrenberg M. J Mol Biol 394 621-626 (2009)
  248. A pathway for the transmission of allosteric signals in the ribosome through a network of RNA tertiary interactions. Chan YL, Dresios J, Wool IG. J Mol Biol 355 1014-1025 (2006)
  249. Heterogeneity of single molecule FRET signals reveals multiple active ribosome subpopulations. Wang Y, Xiao M, Li Y. Proteins 82 1-9 (2014)
  250. Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL. Venditti V, Niccolai N, Butcher SE. Nucleic Acids Res 36 e20 (2008)
  251. Mutations in conserved helix 69 of 23S rRNA of Thermus thermophilus that affect capreomycin resistance but not posttranscriptional modifications. Monshupanee T, Gregory ST, Douthwaite S, Chungjatupornchai W, Dahlberg AE. J Bacteriol 190 7754-7761 (2008)
  252. 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)
  253. Aminoglycoside activity observed on single pre-translocation ribosome complexes. Feldman MB, Terry DS, Altman RB, Blanchard SC. Nat Chem Biol 6 244 (2010)
  254. Brownian dynamics study of the association between the 70S ribosome and elongation factor G. Długosz M, Huber GA, McCammon JA, Trylska J. Biopolymers 95 616-627 (2011)
  255. Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation. Bock LV, Blau C, Vaiana AC, Grubmüller H. Nucleic Acids Res 43 6747-6760 (2015)
  256. Footprinting analysis of BWYV pseudoknot-ribosome complexes. Mazauric MH, Leroy JL, Visscher K, Yoshizawa S, Fourmy D. RNA 15 1775-1786 (2009)
  257. Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometry. Yamamoto T, Shimizu Y, Ueda T, Shiro Y. J Biol Chem 285 5646-5652 (2010)
  258. A model for co-translational translocation: ribosome-regulated nascent polypeptide translocation at the protein-conducting channel. Mitra K, Frank J. FEBS Lett 580 3353-3360 (2006)
  259. Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data. Ahmed A, Tama F. J Struct Biol 182 67-77 (2013)
  260. EF-G catalyzed translocation dynamics in the presence of ribosomal frameshifting stimulatory signals. Kim HK, Tinoco I. Nucleic Acids Res 45 2865-2874 (2017)
  261. FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps. Saha M, Morais MC. Bioinformatics 28 3265-3273 (2012)
  262. Intrinsic molecular properties of the protein-protein bridge facilitate ratchet-like motion of the ribosome. Shasmal M, Chakraborty B, Sengupta J. Biochem Biophys Res Commun 399 192-197 (2010)
  263. Methylated 23S rRNA nucleotide m2G1835 of Escherichia coli ribosome facilitates subunit association. Osterman IA, Sergiev PV, Tsvetkov PO, Makarov AA, Bogdanov AA, Dontsova OA. Biochimie 93 725-729 (2011)
  264. 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)
  265. 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)
  266. Searching for a wrench to throw into the splicing machine. Jurica MS. Nat Chem Biol 4 3-6 (2008)
  267. Structural basis of signal sequence surveillance and selection by the SRP-FtsY complex. von Loeffelholz O, Knoops K, Ariosa A, Zhang X, Karuppasamy M, Huard K, Schoehn G, Berger I, Shan SO, Schaffitzel C. Nat Struct Mol Biol 20 604-610 (2013)
  268. 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)
  269. Comparison of fungal 80 S ribosomes by cryo-EM reveals diversity in structure and conformation of rRNA expansion segments. Nilsson J, Sengupta J, Gursky R, Nissen P, Frank J. J Mol Biol 369 429-438 (2007)
  270. Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations. Ishida H, Matsumoto A. PLoS One 9 e101951 (2014)
  271. Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA. Saraiya AA, Lamichhane TN, Chow CS, SantaLucia J, Cunningham PR. J Mol Biol 376 645-657 (2008)
  272. Ribosomal dynamics inferred from variations in experimental measurements. Gabashvili IS, Whirl-Carrillo M, Bada M, Banatao DR, Altman RB. RNA 9 1301-1307 (2003)
  273. Ribosomal elongation cycle: energetic, kinetic and stereochemical aspects. Lim VI, Curran JF, Garber MB. J Mol Biol 351 470-480 (2005)
  274. The Peptidyl Transferase Center: a Window to the Past. Tirumalai MR, Rivas M, Tran Q, Fox GE. Microbiol Mol Biol Rev 85 e0010421 (2021)
  275. An explanation of biphasic characters of mRNA translocation in the ribosome. Xie P. Biosystems 118 1-7 (2014)
  276. Bayesian-Estimated Hierarchical HMMs Enable Robust Analysis of Single-Molecule Kinetic Heterogeneity. Hon J, Gonzalez RL. Biophys J 116 1790-1802 (2019)
  277. Damped-dynamics flexible fitting. Kovacs JA, Yeager M, Abagyan R. Biophys J 95 3192-3207 (2008)
  278. High-resolution crystal structure of the isolated ribosomal L1 stalk. Tishchenko S, Gabdulkhakov A, Nevskaya N, Sarskikh A, Kostareva O, Nikonova E, Sycheva A, Moshkovskii S, Garber M, Nikonov S. Acta Crystallogr D Biol Crystallogr 68 1051-1057 (2012)
  279. 5S rRNA: Structure and Function from Head to Toe. Dontsova OA, Dinman JD. Int J Biomed Sci 1 1-7 (2005)
  280. Quantitative Connection between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome. Thompson CDK, Sharma AK, Frank J, Gonzalez RL, Chowdhury D. J Phys Chem B 119 10888-10901 (2015)
  281. Stabilization of eukaryotic ribosomal termination complexes by deacylated tRNA. Susorov D, Mikhailova T, Ivanov A, Sokolova E, Alkalaeva E. Nucleic Acids Res 43 3332-3343 (2015)
  282. The identification of the determinants of the cyclic, sequential binding of elongation factors tu and g to the ribosome. Yu H, Chan YL, Wool IG. J Mol Biol 386 802-813 (2009)
  283. A central interdomain protein joint in elongation factor G regulates antibiotic sensitivity, GTP hydrolysis, and ribosome translocation. Ticu C, Murataliev M, Nechifor R, Wilson KS. J Biol Chem 286 21697-21705 (2011)
  284. MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures. Saha M, Levitt M, Chiu W. Bioinformatics 26 i301-9 (2010)
  285. Role of the ribosomal protein L27 revealed by single-molecule FRET study. Wang Y, Xiao M. Protein Sci 21 1696-1704 (2012)
  286. Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine. Koh CS, Madireddy R, Beane TJ, Zamore PD, Korostelev AA. Sci Rep 7 969 (2017)
  287. A dynamical model of programmed -1 ribosomal frameshifting. Xie P. J Theor Biol 336 119-131 (2013)
  288. Comment A library of RNA bridges. Gao N, Frank J. Nat Chem Biol 2 231-232 (2006)
  289. A steric gate controls P/E hybrid-state formation of tRNA on the ribosome. Levi M, Walak K, Wang A, Mohanty U, Whitford PC. Nat Commun 11 5706 (2020)
  290. Conserved but nonessential interaction of SRP RNA with translation factor EF-G. Sagar MB, Lucast L, Doudna JA. RNA 10 772-778 (2004)
  291. Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex. Xie P. Int J Mol Sci 16 23723-23744 (2015)
  292. Dynamics of forward and backward translocation of mRNA in the ribosome. Xie P. PLoS One 8 e70789 (2013)
  293. Kinetics of CrPV and HCV IRES-mediated eukaryotic translation using single-molecule fluorescence microscopy. Bugaud O, Barbier N, Chommy H, Fiszman N, Le Gall A, Dulin D, Saguy M, Westbrook N, Perronet K, Namy O. RNA 23 1626-1635 (2017)
  294. Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation. Bao C, Zhu M, Nykonchuk I, Wakabayashi H, Mathews DH, Ermolenko DN. Nat Commun 13 988 (2022)
  295. The Ribosome Comes Alive. Frank J. Isr J Chem 50 95-98 (2010)
  296. Dynamics of tRNA translocation, mRNA translocation and tRNA dissociation during ribosome translation through mRNA secondary structures. Xie P. Eur Biophys J 43 229-240 (2014)
  297. Interaction strengths between the ribosome and tRNA at various steps of translocation. Liu CY, Qureshi MT, Lee TH. Biophys J 100 2201-2208 (2011)
  298. Intramolecular movements in EF-G, trapped at different stages in its GTP hydrolytic cycle, probed by FRET. Nguyen B, Ticu C, Wilson KS. J Mol Biol 397 1245-1260 (2010)
  299. L27-tRNA interaction revealed by mutagenesis and pH titration. Xiao M, Wang Y. Biophys Chem 167 8-15 (2012)
  300. 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)
  301. rRNA mutations that inhibit transfer-messenger RNA activity on stalled ribosomes. Crandall J, Rodriguez-Lopez M, Pfeiffer M, Mortensen B, Buskirk A. J Bacteriol 192 553-559 (2010)
  302. 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)
  303. Analysis of ribosomal inter-subunit sites as targets for complementary oligonucleotides. Thoduka SG, Zaleski PA, Dąbrowska Z, Równicki M, Stróżecka J, Górska A, Olejniczak M, Trylska J. Biopolymers 107 (2017)
  304. Dynamic relationships between ribosomal conformational and RNA positional changes during ribosomal translocation. Xie P. Heliyon 2 e00214 (2016)
  305. Dynamics of +1 ribosomal frameshifting. Xie P. Math Biosci 249 44-51 (2014)
  306. Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis. Kürkçüoğlu Ö. Turk J Biol 42 392-404 (2018)
  307. Proteomic analysis of the influence of Cu(2+) on the crystal protein production of Bacillus thuringiensis X022. Liu X, Zuo M, Wang T, Sun Y, Liu S, Hu S, He H, Yang Q, Rang J, Quan M, Xia L, Ding X. Microb Cell Fact 14 153 (2015)
  308. Recycling of the posttermination complexes of Mycobacterium smegmatis and Escherichia coli ribosomes using heterologous factors. Seshadri A, Singh NS, Singh NS, Varshney U. J Mol Biol 401 854-865 (2010)
  309. Structural features of the tmRNA-ribosome interaction. Bugaeva EY, Surkov S, Golovin AV, Ofverstedt LG, Skoglund U, Isaksson LA, Bogdanov AA, Shpanchenko OV, Dontsova OA. RNA 15 2312-2320 (2009)
  310. Transcriptional Profiling and Molecular Characterization of the yccT Mutant Link: A Novel STY1099 Protein with the Peroxide Stress Response and Cell Division of Salmonella enterica Serovar Enteritidis. Vidovic S, Liu X, An R, Mendoza KM, Abrahante JE, Johny AK, Reed KM. Biology (Basel) 8 E86 (2019)
  311. News Translocation at work. Achenbach J, Nierhaus KH. Nat Struct Mol Biol 20 1019-1022 (2013)
  312. Translocation dynamics of tRNA-mRNA in the ribosome. Xie P. Biophys Chem 180-181 22-28 (2013)
  313. Biphasic character of ribosomal translocation and non-Michaelis-Menten kinetics of translation. Xie P. Phys Rev E Stat Nonlin Soft Matter Phys 90 062703 (2014)
  314. 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)
  315. Displaying 3D data on RNA secondary structures: coloRNA. LeBarron J, Mitra K, Frank J. J Struct Biol 157 262-270 (2007)
  316. Model of EF4-induced ribosomal state transitions and mRNA translocation. Xie P. Phys Biol 11 046007 (2014)
  317. Molecular dynamics of ribosomal elongation factors G and Tu. Kulczycka K, Długosz M, Trylska J. Eur Biophys J 40 289-303 (2011)
  318. The central part of the 5.8 S rRNA is differently arranged in programmed and free human ribosomes. Graifer D, Molotkov M, Eremina A, Ven'yaminova A, Repkova M, Karpova G. Biochem J 387 139-145 (2005)
  319. The ribosome's energy landscape: Recent insights from computation. Whitford PC. Biophys Rev 7 301-310 (2015)
  320. Limited proteolysis analysis of the ribosome is affected by subunit association. Hamburg DM, Suh MJ, Limbach PA. Biopolymers 91 410-422 (2009)
  321. Model of ribosomal translocation coupled with intra- and inter-subunit rotations. Xie P. Biochem Biophys Rep 2 87-93 (2015)
  322. RNA-protein distance patterns in ribosomes reveal the mechanism of translational attenuation. Yu D, Zhang C, Qin P, Cornish PV, Xu D. Sci China Life Sci 57 1131-1139 (2014)
  323. tmRNA on its way through the ribosome: two steps of resume, and what next? Fu J, Hashem Y, Wower J, Frank J. RNA Biol 8 586-590 (2011)
  324. Another burst of smoke: atomic resolution structures of RF3 bound to the ribosome. McDonald ME, Green R. RNA 18 605-609 (2012)
  325. Comparing FRET Pairs that Report on Intersubunit Rotation in Bacterial Ribosomes. Das A, Bao C, Ermolenko DN. J Mol Biol 435 168185 (2023)
  326. Druggable differences: Targeting mechanistic differences between trans-translation and translation for selective antibiotic action. Srinivas P, Keiler KC, Dunham CM. Bioessays 44 e2200046 (2022)
  327. Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting. Nishima W, Girodat D, Holm M, Rundlet EJ, Alejo JL, Fischer K, Blanchard SC, Sanbonmatsu KY. Nucleic Acids Res 50 8302-8320 (2022)
  328. Mass fractal dimension of the ribosome and implication of its dynamic characteristics. Lee CY. Phys Rev E Stat Nonlin Soft Matter Phys 73 042901 (2006)
  329. Mechanism of translation based on intersubunit complementarities of ribosomal RNAs and tRNAs. Nagano K, Nagano N. J Theor Biol 245 644-668 (2007)
  330. Modeling of ribosome dynamics on a ds-mRNA under an external load. Shakiba B, Dayeri M, Mohammad-Rafiee F. J Chem Phys 145 025101 (2016)
  331. Modes of action of ADP-ribosylated elongation factor 2 in inhibiting the polypeptide elongation cycle: a modeling study. Chen KC, Xie H, Cai Y. PLoS One 8 e66446 (2013)
  332. Comment Protein synthesis: Translocation in slow motion. Ehrenberg M. Nature 466 325-326 (2010)
  333. Sordarin bound eEF2 unlocks spontaneous forward and reverse translocation on CrPV IRES. Ou Z, Petrov A. Nucleic Acids Res 51 6999-7013 (2023)
  334. A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.). Yanagisawa T, Ishii R, Hikida Y, Fukunaga R, Sengoku T, Sekine S, Yokoyama S. J Struct Funct Genomics 16 25-41 (2015)
  335. A thermal ratchet model of tRNA-mRNA translocation by the ribosome. Xie P. Biosystems 96 19-28 (2009)
  336. Dynamic analysis of ribosome by a movie made from many three-dimensional electron-microscopy density maps. Matsumoto A. Biophys Physicobiol 16 108-113 (2019)
  337. EF4 reveals the energy barrier for tRNA back-translocation in the peptidyl transferase center. Song G, Qin Y. RNA Biol 13 934-939 (2016)
  338. Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis. Majumdar S, Emmerich A, Krakovka S, Mandava CS, Svärd SG, Sanyal S. Nucleic Acids Res 51 3436-3451 (2023)
  339. Interplay between Inter-Subunit Rotation of the Ribosome and Binding of Translational GTPases. Das A, Adiletta N, Ermolenko DN. Int J Mol Sci 24 6878 (2023)
  340. Model of the pathway of -1 frameshifting: Long pausing. Xie P. Biochem Biophys Rep 5 408-424 (2016)
  341. Movement in ribosome translocation. Fraser CS, Hershey JW. J Biol 4 8 (2005)
  342. Partial spontaneous intersubunit rotations in pretranslocation ribosomes. Huang T, Choi J, Prabhakar A, Puglisi JD, Petrov A. Proc Natl Acad Sci U S A 120 e2114979120 (2023)
  343. 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)
  344. 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)
  345. The dynamics of subunit rotation in a eukaryotic ribosome. Freitas FC, Fuchs G, de Oliveira RJ, Whitford PC. Biophysica 1 204-221 (2021)
  346. Comment The ins and outs of protein synthesis. Cate JH. Structure 13 1584-1585 (2005)
  347. Translocation: lights, camera, and action. Shi X, Joseph S. Nat Struct Mol Biol 23 367-368 (2016)


Quick links