The Ribosome as a Brownian Ratchet Machine

doi:10.1017/CBO9781139003704.011

Chapter 9 - The Ribosome as a Brownian Ratchet Machine

Published online by Cambridge University Press: 05 January 2012

Alexander S. Spirin and

Alexei V. Finkelstein

Edited by

Joachim Frank

Show author details

Joachim Frank: Affiliation:
Columbia University, New York

Book contents

Get access

Summary

Ribosomes are ribonucleoprotein nanoparticles responsible for the synthesis of all proteins in living cells. The function of a ribosome is to translate the genetic information encoded in the nucleotide sequence of mRNA into the amino acid sequence of a protein. During this process, the ribosome performs the unidirectional driving of a single mRNA chain and numerous mRNA-bound tRNA macromolecules through itself. In this process, the free energies of the transpeptidation reaction and GTP hydrolysis are consumed. Thus, the translating ribosome can be considered as a conveying protein-synthesizing molecular machine (Spirin 2002, 2004, 2009a; Frank & Gonzalez 2010). The purpose of this chapter is to analyze the conveying mechanism of this machine.

Subdivision of the Ribosome into Two Unequal Subunits

At first approximation, the ribosome can be described as a compact, almost spherical body with linear dimensions of 25 to 35 nm (reviewed in Spirin 1999, pp. 50–51). Detailed structural analyses reveal the highly complex, asymmetric quaternary structure of the ribosome (Ban et al. 2000; Wimberly et al. 2000; Harms et al. 2001; Yusupov et al. 2001; Ramakrishnan 2002; Gao et al. 2003; Schuwirth et al. 2005; Selmer et al. 2006).

Type: Chapter
Information: Molecular Machines in Biology
Workshop of the Cell
, pp. 158 - 190

DOI: https://doi.org/10.1017/CBO9781139003704.011 [Opens in a new window]

Publisher: Cambridge University Press

Print publication year: 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abel, KJurnak, F 1996 A complex profile of protein elongation: translating chemical energy into molecular movementStructure 4 229CrossRef Google Scholar PubMed

Abel, KYoder, MDHilgenfeld, RJurnak, F 1996 An alpha to beta conformational switch in EF-TuStructure 4 1153CrossRef Google Scholar PubMed

Agirrezabala, XLei, JBrunelle, JLOrtiz-Meoz, RFGreen, RFrank, J 2008 Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosomeMolecular Cell 32 190CrossRef Google Scholar PubMed

Agrawal, RKHeagle, ABPenczek, PGrassucci, RAFrank, J 1999 EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosomeNature Structural Biology 6 643CrossRef Google Scholar PubMed

Agrawal, RKPenczek, PGrassucci, RAFrank, J 1998 Visualization of elongation factor G on the 70S ribosome: the mechanism of translocationProceeding of the National Academy of Sciences of the USA 95 6134CrossRef Google Scholar PubMed

Ait-Haddou, RHerzog, W 2003 Brownian ratchet models of molecular motorsCell Biochemistry and Biophysics 38 191CrossRef Google Scholar PubMed

Aitken, CEPuglisi, JD 2010 Following the intersubunit conformation of the ribosome during translation in real timeNature Structural and Molecular Biology 17 793CrossRef Google Scholar

Astumian, RDDerényi, I 1998 Fluctuation driven transport and models of molecular motors and pumpsEuropean Biophysics Journal 27 474CrossRef Google Scholar PubMed

Ban, NNissen, PHansen, JMoore, PBSteitz, TA 2000 The complete atomic structure of the large ribosomal subunit at 2.4 A resolutionScience 289 905CrossRef Google Scholar PubMed

Baranov, VIBelitsina, NVSpirin, AS 1979 The use of columns with matrix-bound polyuridylic acid for isolation of translating ribosomesMethods in Enzymology 59 382CrossRef Google Scholar PubMed

Belitsina, NVGlukhova, MASpirin, AS 1975 Translocation in ribosomes by attachment-detachment of elongation factor G without GTP cleavage: Evidence from a column-bound ribosome systemFEBS Letters 54 35CrossRef Google Scholar PubMed

Belitsina, NVGlukhova, MASpirin, AS 1976 Stepwise elongation factor G-promoted elongation of polypeptides on the ribosome without GTP cleavageJournal of Molecular Biology 108 609CrossRef Google Scholar PubMed

Belitsina, NVSpirin, AS 1970 Studies on the structure of ribosomes. IV. Participation of aminoacyl-transfer RNA and peptidyl-transfer RNA in the association of ribosomal subparticlesJournal of Molecular Biology 52 45CrossRef Google Scholar PubMed

Belitsina, NVSpirin, AS 1979 Ribosomal translocation assayed by the matrix-bound poly(uridylic acid) column techniqueEuropean Journal of Biochemistry 94 315CrossRef Google Scholar PubMed

Belitsina, NVTnalina, GZSpirin, AS 1981 Template-free ribosomal synthesis of polylysine from lysyl-tRNAFEBS Letters 131 289CrossRef Google Scholar PubMed

Belitsina, NVTnalina, GZSpirin, AS 1982 Template-free ribosomal synthesis of polypeptides from aminoacyl-tRNAsBioSystems 15 233CrossRef Google Scholar PubMed

Berchtold, HReshetnikova, LReiser, COSchirmer, NKSprinzl, MHilgenfeld, R 1993 Crystal structure of active elongation factor Tu reveals major domain rearrangementsNature 365 126CrossRef Google Scholar PubMed

Berk, VZhang, WPai, RDCate, JHD 2006 Structural basis for mRNA and tRNA positioning on the ribosomeProceeding of the National Academy of Sciences of the USA 103 15830CrossRef Google Scholar PubMed

Bieling, PBeringer, MAdio, SRodnina, MV 2006 Peptide bond formation does not involve acid-base catalysis by ribosomal residuesNature Structural and Molecular Biology 13 423CrossRef Google Scholar

Blanchard, SCGonzalez, RLKim, HDChu, SPuglisi, JD 2004 tRNA selection and kinetic proofreading inNature Structural and Molecular Biology 11 1008CrossRef Google Scholar

Blanchard, SCKim, HDGonzalez, RLPuglisi, JDChu, S 2004 tRNA dynamics on the ribosome during translationProceeding of the National Academy of Sciences of the USA 101 12893CrossRef Google Scholar PubMed

Bretscher, MS 1968 Translocation in protein synthesis: a hybrid structure modelNature 218 675CrossRef Google Scholar PubMed

Chetverin, ABSpirin, AS 1982 Bioenergetics and protein synthesisBiochimica et Biophysica Acta 683 153CrossRef Google Scholar PubMed

Connell, SRTakemoto, CWilson, DNWang, HMurayama, KTerada, TShirouzu, MRost, MSchüler, MGiesebrecht, JDabrowski, MMielke, TFucini, PYokoyama, SSpahn, CM 2007 Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factorsMolecular Cell 25 751CrossRef Google Scholar PubMed

Cordova, NJErmentrout, BOster, GF 1992 Dynamics of single-motor molecules: the thermal ratchet modelProceeding of the National Academy of Sciences of the USA 89 339CrossRef Google Scholar PubMed

Cornish, PVErmolenko, DNNoller, HFHa, T 2008 Spontaneous intersubunit rotation in single ribosomesMolecular Cell 30 578CrossRef Google Scholar PubMed

Cornish, PVErmolenko, DNStaple, DWHoang, LHickerson, RPNoller, HFHa, T 2009 Following movement of the L1 stalk between three functional states in single ribosomesProceeding of the National Academy of Sciences of the USA 106 2571CrossRef Google Scholar PubMed

Cukras, ARSouthworth, DRBrunelle, JLCulver, GMGreen, R 2003 Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complexMolecular Cell 12 321CrossRef Google Scholar PubMed

Ermolenko, DNMajumdar, ZKHickerson, RPSpiegel, PCClegg, RMNoller, HF 2007 Observation of intersubunit movement of the ribosome in solution using FRETJournal of Molecular Biology 370 530CrossRef Google Scholar PubMed

Ermolenko, DNSpiegel, PCMajumdar, ZKHickerson, RPClegg, RMNoller, HF 2007 The antibiotic viomycin traps the ribosome in an intermediate state of translocationNature Structural and Molecular Biology 14 493CrossRef Google Scholar

Ermolenko, DNNoller, HF 2011 mRNA translocation occurs during the second step of ribosomal intersubunit rotationNature Structural & Molecular Biology 18 457CrossRef Google Scholar PubMed

Fei, JBronson, JEHofman, JMSrinivas, RLWiggins, CHGonzalez, RL 2009 Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translationProceeding of the National Academy of Sciences of the USA 106 15702CrossRef Google Scholar PubMed

Fei, JKosuri, PMacDougall, DDGonzalez, RL 2008 Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongationMolecular Cell 30 348CrossRef Google Scholar PubMed

Feynman, RLeighton, RSands, M 1963 The Feynman Lectures on Physics1Addison-Wesley Publishing CompanyInc., Reading, MAGoogle Scholar

Finkelstein, AVPtitsyn, OB 2002 Protein PhysicsAcademic PressLondonGoogle Scholar

Fischer, NKonevega, ALWintermeyer, WRodnina, MVStark, H 2010 Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopyNature 466 329CrossRef Google Scholar PubMed

Fourmy, DYoshizawa, SPuglisi, JD 1998 Paromomycin binding induces a local conformational change in the A-site of 16 S rRNAJournal of Molecular Biology 277 333CrossRef Google Scholar PubMed

Frank, JAgrawal, RK 2000 A ratchet-like inter-subunit reorganization of the ribosome during translocationNature 406 318CrossRef Google Scholar PubMed

Frank, JGao, HSengupta, JGao, NTaylor, DJ 2007 The process of mRNA-tRNA translocationProceeding of the National Academy of Sciences of the USA 104 19671CrossRef Google Scholar PubMed

Frank, JGonzalez, RL 2010 Structure and dynamics of a processive Brownian motor: The translating ribosomeAnnual Review of Biochemistry 79 CrossRef Google Scholar PubMed

Fredrick, KNoller, HF 2003 Catalysis of ribosomal translocation by sparsomycinScience 300 1159CrossRef Google Scholar PubMed

Gabashvili, ISAgrawal, RKSpahn, CMGrassucci, RASvergun, DIFrank, JPenczek, P 2000 ‘Solution structure of the E. coli 70S ribosome at 11.5 A resolutionCell 100 537CrossRef Google Scholar

Gao, HSengupta, JValle, MKorostelev, AEswar, NStagg, SMVan Roey, PAgrawal, RKHarvey, SCSali, AChapman, MSFrank, J 2003 Study of the structural dynamics of the E coli 70S ribosome using real-space refinementCell 113 789CrossRef Google Scholar

Gao, YGSelmer, MDunham, CMWeixlbaumer, AKelley, ACRamakrishnan, V 2009 The structure of the ribosome with elongation factor G trapped in the posttranslocational stateScience 326 694CrossRef Google Scholar PubMed

Gavrilova, LPKostiashkina, OEKoteliansky, VERutkevitch, NMSpirin, AS 1976 Factor-free (“non-enzymic”) and factor-dependent systems of translation of polyuridylic acid by ribosomesJournal of Molecular Biology 101 537CrossRef Google Scholar PubMed

Gavrilova, LPKoteliansky, VESpirin, AS 1974 Ribosomal protein S12 and “non-enzymatic” translocationFEBS Letters 45 324CrossRef Google Scholar PubMed

Gavrilova, LPPerminova, INSpirin, AS 1981 Elongation factor Tu can reduce translation errors in poly(U)-directed cell-free systemsJournal of Molecular Biology 149 69CrossRef Google Scholar PubMed

Gavrilova, LPSpirin, AS 1971 Stimulation of “non-enzymic” translocation in ribosomes by ρ-chloromercuribenzoateFEBS Letters 17 324CrossRef Google Scholar

Gavrilova, LPSpirin, AS 1972 A modification of the 30S ribosomal subparticle is responsible for stimulation of “non-enzymatic” translocation by -chloromercuribenzoateFEBS Letters 22 91CrossRef Google Scholar

Gavrilova, LPSpirin, AS 1974 Nonenzymatic” translationMethods in Enzymology 30 452CrossRef Google Scholar PubMed

Girshovich, ASBochkareva, ESVasiliev, VD 1986 Localization of elongation factor Tu on the ribosomeFEBS Letters 197 1CrossRef Google Scholar PubMed

Girshovich, ASKurtskhalia, TVOvchinnikov, YuAVasiliev, VD 1981 Localization of the elongation factor G on Escherichia coli ribosomeFEBS Letters 130 54CrossRef Google Scholar PubMed

Gomez-Lorenzo, MGSpahn, CMAgrawal, RKGrassucci, RAPenczek, PAChakraburtty, KBallesta, JPLavandera, JLGarcia-Bustos, JFFrank, J 2000 Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 A resolutionThe EMBO Journal 19 2710CrossRef Google Scholar PubMed

Gongadze, GMGudkov, ATBushuev, VNSepetov, NF 1984 The attachment of elongation factor G to the ribosome changes intramolecular mobility of protein L7/L12Doklady Akademii Nauk SSSR 279 230Google Scholar

Gonzalez, RLChu, SPuglisi, JD 2007 Thiostrepton inhibition of tRNA delivery to the ribosomeRNA 13 2091CrossRef Google Scholar PubMed

Gottesman, ME 1967 Reaction of ribosome-bound peptidyl transfer ribonucleic acid with aminoacyl transfer ribonucleic acid or puromycinThe Journal of Biological Chemistry 242 5564Google Scholar PubMed

Gudkov, ATGongadze, GMBushuev, VNOkon, MS 1982 Proton nuclear magnetic resonance study of the ribosomal protein L7/L12 in situFEBS Letters 138 229CrossRef Google Scholar PubMed

Gumbart, JTrabuco, LGSchreiner, EVilla, ESchulten, K 2009 Regulation of the protein-conducting channel by a bound ribosomeStructure 17 1453CrossRef Google Scholar PubMed

Hansen, JLSchmeing, TMMoore, PBSteitz, TA 2002 Structural insights into peptide bond formationProceeding of the National Academy of Sciences of the USA 99 11670CrossRef Google Scholar PubMed

Harms, JSchluenzen, FZarivach, RBashan, AGat, SAgmon, IBartels, HFranceschi, FYonath, A 2001 High resolution structure of the large ribosomal subunit from a mesophilic eubacteriumCell 107 679CrossRef Google Scholar PubMed

Horan, LHNoller, HF 2007 Intersubunit movement is required for ribosomal translocationProceeding of the National Academy of Sciences of the USA 104 4881CrossRef Google Scholar PubMed

Julián, PKonevega, ALScheres, SHLázaro, MGil, DWintermeyer, WRodnina, MVValle, M 2008 Structure of ratcheted ribosomes with tRNAs in hybrid statesProceeding of the National Academy of Sciences of the USA 105 16924CrossRef Google Scholar PubMed

Kaji, AKaji, H 1963 Specific interaction of soluble RNA and polyribonucleic acid induced polysomesBiochemical and Biophysical Research Communications 13 186CrossRef Google Scholar

Kakhniashvili, DGSpirin, AS 1977 ‘Dependence of factor-free and factor-promoted translation systems on temperature. Absence of effects of the elongation factors and GTP on the activation energyDoklady Akademii Nauk SSSR 234 958Google Scholar

Kaltschmidt, EWittmann, HG 1970 ‘Ribosomal proteins. XII. Number of proteins in small and large ribosomal subunits of as determined by two-dimensional gel electrophoresisProceeding of the National Academy of Sciences of the USA 67 1276CrossRef Google Scholar PubMed

Kim, HDPuglisi, JDChu, S 2007 Fluctuations of transfer RNAs between classical and hybrid statesBiophysical Journal 93 3575CrossRef Google Scholar PubMed

Kjeldgaard, MNissen, PThirup, SNyborg, J 1993 The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformationStructure 1 35CrossRef Google Scholar PubMed

Korostelev, ANoller, HF 2007 Analysis of structural dynamics in the ribosome by TLS crystallographic refinementJournal of Molecular Biology 373 1058CrossRef Google Scholar PubMed

Korostelev, ATrakhanov, SLaurberg, MNoller, HF 2006 Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangementsCell 126 1065CrossRef Google Scholar PubMed

Lee, THBlanchard, SCKim, HDPuglisi, JDChu, S 2007 The role of fluctuations in tRNA selection by the ribosomeProceeding of the National Academy of Sciences of the USA 104 13661CrossRef Google Scholar PubMed

Lim, VISpirin, AS 1986 Stereochemical analysis of ribosomal transpeptidation: Conformation of nascent peptideJournal of Molecular Biology 188 565CrossRef Google Scholar PubMed

Lodish, HFJacobsen, M 1972 ‘Regulation of hemoglobin synthesis. Equal rates of translation and termination of α- and β-globin chainsThe Journal of Biological Chemistry 247 3622Google Scholar

Marshall, RADorywalska, MPuglisi, JD 2008 Irreversible chemical steps control intersubunit dynamics during translationProceeding of the National Academy of Sciences of the USA 105 15364CrossRef Google Scholar PubMed

Moazed, DNoller, HF 1986 Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probesCell 47 985CrossRef Google Scholar PubMed

Moazed, DNoller, HF 1989 Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sitesCell 57 585CrossRef Google Scholar PubMed

Moazed, DNoller, HF 1989 Intermediate states in the movement of transfer RNA in the ribosomeNature 342 142CrossRef Google Scholar PubMed

Moazed, DRobertson, JMNoller, HF 1988 Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNANature 334 362CrossRef Google Scholar PubMed

Munro, JBAltman, RBO’Connor, NBlanchard, SC 2007 Identification of two distinct hybrid state intermediates on the ribosomeMolecular Cell 25 505CrossRef Google Scholar PubMed

Nakamoto, TConway, TWAllende, JESpyrides, GILipmann, F 1963 ‘Formation of peptide bonds. I. Peptide formation from aminoacyl-sRNACold Spring Harbor Symposia on Quantitative Biology 28 227CrossRef Google Scholar

Nishiyama, MHiguchi, HIshii, YTaniguchi, YYanagida, T 2003 Single molecule processes on the stepwise movement of ATP-driven molecular motorsBioSystems 71 1CrossRef Google Scholar PubMed

Nissen, PHansen, JBan, NMoore, PBSteitz, TA 2000 The structural basis of ribosome activity in peptide bond synthesisScience 289 920CrossRef Google Scholar PubMed

Nyborg, JKjeldgaard, M 1996 Elongation in bacterial protein synthesisCurrent Opinion in Biotechnology 7 369CrossRef Google Scholar

Nyborg, JLiljas, A 1998 Protein biosynthesis: structural studies of the elongation cycleFEBS Letters 430 1CrossRef Google Scholar PubMed

Ogle, JMBrodersen, DEClemons, WMTarry, MJCarter, APRamakrishnan, V 2001 Recognition of cognate transfer RNA by the 30S ribosomal subunitScience 292 897CrossRef Google Scholar PubMed

Ogle, JMMurphy, FVTarry, MJRamakrishnan, V 2002 Selection of tRNA by the ribosome requires a transition from an open to a closed formCell 111 721CrossRef Google Scholar PubMed

Pan, DKirillov, SVCooperman, BS 2007 Kinetically competent intermediates in the translocation step of protein synthesisMolecular Cell 25 519CrossRef Google Scholar PubMed

Pape, TWintermeyer, WRodnina, M 1999 Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosomeThe EMBO Journal 18 3800CrossRef Google Scholar PubMed

Perutz, MF 1970 Stereochemistry of cooperative effects in haemoglobinNature 228 726CrossRef Google Scholar PubMed

Pestka, S 1968 ‘Studies on the formation of transfer ribonucleic acid-ribosome complexes. 3. The formation of peptide bonds by ribosomes in the absence of supernatant enzymesThe Journal of Biological Chemistry 243 2810Google Scholar PubMed

Pestka, S 1969 ‘Studies on the formation of transfer ribonucleic acid-ribosome complexes. VI. Oligopeptide synthesis and translocation on ribosomes in the presence and absence of soluble transfer factorsThe Journal of Biological Chemistry 244 1533Google Scholar PubMed

Pestova, TVLorsh, JRHellen, CUT 2007 The mechanism of translation initiation in eukaryotesTranslational Control in Biology and MedicineMathews, MBSonenberg, NHershey, JWBCold Spring Harbor Laboratory PressPlainview, NY87Google Scholar

Polekhina, GThirup, SKjeldgaard, MNissen, PLippmann, CNyborg, J 1996 Helix unwinding in the effector region of elongation factor EF-Tu-GDPStructure 4 1141CrossRef Google Scholar PubMed

Purich, DL 2001 Enzyme catalysis: a new definition accounting for noncovalent substrate- and product-like statesTrends in Biochemical Sciences 26 417CrossRef Google Scholar PubMed

Ramakrishnan, V 2002 Ribosome structure and the mechanism of translationCell 108 557CrossRef Google Scholar

Riddle, DLCarbon, J 1973 Frameshift suppression: A nucleotide addition in the anticodon of a glycine transfer RNANature New Biology 242 230CrossRef Google Scholar PubMed

Robertson, JMWintermeyer, W 1987 ‘Mechanism of ribosomal translocation. tRNA binds transiently to an exit site before leaving the ribosome during translocationJournal of Molecular Biology 196 525CrossRef Google Scholar

Rodnina, MVGromadski, KBKothe, UWieden, H-J 2005 Recognition and selection of tRNA in translationFEBS Letters 579 938CrossRef Google Scholar PubMed

Rodnina, MVPape, TFricke, RKuhn, LWintermeyer, W 1996 Initial binding of the elongation factor Tu.GTP.aminoacyl-tRNA complex preceding codon recognition on the ribosomeThe Journal of Biological Chemistry 271 646CrossRef Google Scholar PubMed

Rodnina, MVWintermeyer, W 2001 Ribosome fidelity: tRNA discrimination, proofreading and inducedTrends in Biochemical Sciences 26 124CrossRef Google Scholar PubMed

Schmeing, TMHuang, KSKitchen, DEStrobel, SASteitz, TA 2005 Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA in the peptidyl transferaseMolecular Cell 20 437CrossRef Google Scholar

Schmeing, TMHuang, KSStrobel, SASteitz, TA 2005 An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNANature 438 520CrossRef Google Scholar PubMed

Schmeing, TMVoorhees, RMKelley, ACGao, YGMurphy, FVWeir, JRRamakrishnan, V 2009 The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNAScience 326 688CrossRef Google Scholar PubMed

Schuette, JCMurphy, FVKelley, ACWeir, JRGiesebrecht, JConnell, SRLoerke, JMielke, TZhang, WPenczek, PARamakrishnan, VSpahn, CM 2009 GTPase activation of elongation factor EF-Tu by the ribosome during decodingThe EMBO Journal 28 755CrossRef Google Scholar PubMed

Schuwirth, BSBorovinskaya, MAHau, CWZhang, WVila-Sanjurjo, AHolton, JMCate, JH 2005 Structures of the bacterial ribosome at 3.5 A resolutionScience 310 827CrossRef Google Scholar PubMed

Selmer, MDunham, CMMurphy, FVWeixlbaumer, APetry, SKelley, ACWeir, JRRamakrishnan, V 2006 Structure of the 70S ribosome complexed with mRNA and tRNAScience 313 1935CrossRef Google Scholar PubMed

Semenkov, YPRodnina, MVWintermeyer, W 1996 The “allosteric three-site model” of elongation cannot be confirmed in a well-defined ribosome system from Proceeding of the National Academy of Sciences of the USA 93 12183CrossRef Google Scholar

Serdyuk, INBaranov, VITsalkova, TGulyamova, DPavlov, MSpirin, ASMay, R 1992 Structural dynamics of translating ribosomesBiochimie 74 299CrossRef Google Scholar PubMed

Serdyuk, INSpirin, AS 1986 Structural dynamics of the translating ribosomesStructure, Function, and Genetics of RibosomesHardesty, BKramer, GSpringer-Verlag New York IncNew York425CrossRef Google Scholar

Smoluchowski, M von 1912 Experimentell nachweisbare, der Ublichen Thermodynamik widersprechende MolekularphenomenePhysikalische Zeitschrift 13 1069Google Scholar

Southworth, DRBrunelle, JLGreen, R 2002 EFG-independent translocation of the mRNA:tRNA complex is promoted by modification of the ribosome with thiol-specific reagentsJournal of Molecular Biology 324 611CrossRef Google Scholar PubMed

Spahn, CMGomez-Lorenzo, MGGrassucci, RAJorgensen, RAndersen, GRBeckmann, RPenczek, PABallesta, JPFrank, J 2004 Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocationThe EMBO Journal 23 1008CrossRef Google Scholar PubMed

Spiegel, PCErmolenko, DNNoller, HF 2007 Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosomeRNA 13 1473CrossRef Google Scholar PubMed

Spirin, AS 1968 On the mechanism of the ribosome working: Subunits locking-unlocking hypothesisDoklady Akademii Nauk SSSR 179 1467Google Scholar

Spirin, AS 1968 ‘How does the ribosome work? A hypothesis based on the two subunit construction of the ribosomeCurrents in Modern Biology 2 115Google Scholar

Spirin, AS 1969 A model of the functioning ribosome: Locking and unlocking of the ribosome subparticlesCold Spring Harbor Symposia on Quantitative Biology 34 197CrossRef Google Scholar PubMed

Spirin, AS 1978 Energetics of the ribosomeProgress in Nucleic Acid Research and Molecular BiologyCohn, WEAcademic Press, IncNew York-London39Google Scholar

Spirin, AS 1984 Testing the classical two-tRNA-site model for the ribosomal elongation cycleFEBS Letters 165 280CrossRef Google Scholar PubMed

Spirin, AS 1985 Ribosomal translocation: Facts and modelsProgress in Nucleic Acid Research and Molecular BiologyCohn, WEAcademic Press, IncNew York-London75Google Scholar

Spirin, AS 1988 Energetics and dynamics of the protein-synthesizing machineryThe Roots of Modern BiochemistryKleinkauf, Hvon Dören, HJaenicke, LWalter de Gruyter & CoBerlin511Google Scholar

Spirin, AS 1999 RibosomesKluwer Academic PublishersPlenum PressNew YorkCrossRef Google Scholar

Spirin, AS 2002 Ribosome as a molecular machineFEBS Letters 514 2CrossRef Google Scholar PubMed

Spirin, AS 2004 The ribosome as an RNA-based molecular machineRNA Biology 1 3CrossRef Google Scholar PubMed

Spirin, AS 2009 The ribosome as a conveying thermal ratchet machineThe Journal of Biological Chemistry 284 21103CrossRef Google Scholar PubMed

Spirin, AS 2009 How does a scanning ribosomal particle move along the 5′-untranslated region of eukaryotic mRNA? Brownian ratchet modelBiochemistry 48 10688CrossRef Google Scholar PubMed

Spirin, ASBaranov, VIPolubesov, GSSerdyuk, INMay, RP 1987 Translocation makes the ribosome less compactJournal of Molecular Biology 194 119CrossRef Google Scholar PubMed

Spirin, ASBelitsina, NVYusupova, GZ 1988 Ribosomal synthesis of polypeptides from aminoacyl-tRNA without polynucleotide templateMethods in Enzymology 164 631CrossRef Google Scholar PubMed

Spirin, ASKostiashkina, OEJonak, J 1976 Contribution of the elongation factors to resistance of ribosomes against inhibitors: Comparison of the inhibitor effects on the factor-dependent and factor-free translation systemsJournal of Molecular Biology 101 553CrossRef Google Scholar

Stark, HRodnina, MVWieden, HJvan Heel, MWintermeyer, W 2000 Large scale movement of elongation factor G and extensive conformational change of the ribosome during translocationCell 100 301CrossRef Google Scholar PubMed

Stark, HRodnina, MVWieden, HJZemlin, FWintermeyer, Wvan Heel, M 2002 Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complexNature Structural Biology 9 849Google Scholar PubMed

Taylor, DJNilsson, JMerrill, ARAndersen, GRNissen, PFrank, J 2007 Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocationThe EMBO Journal 26 2421CrossRef Google Scholar PubMed

Trabuco, LGVilla, EMitra, KFrank, JSchulten, K 2008 Flexible fitting of atomic structures into electron microscopy maps using molecular dynamicsStructure 16 673CrossRef Google Scholar PubMed

Trobro, SAqvist, J 2005 Mechanism of peptide bond synthesis on the ribosomeProceeding of the National Academy of Sciences of the USA 102 12395CrossRef Google Scholar PubMed

Uemura, SAitken, CEKorlach, JFlusberg, BATurner, SWPuglisi, JD 2010 Real-time tRNA transit on single translating ribosomes at codon resolutionNature 464 1012CrossRef Google Scholar PubMed

Vale, RD 2003 Myosin V motor proteins: marching stepwise towards a mechanismThe Journal of Cell Biology 163 445CrossRef Google Scholar PubMed

Vale, RDOosawa, F 1990 Protein motors and Maxwell's demons: Does mechanochemical transduction involve a thermal ratchet?Advances in Biophysics 26 97CrossRef Google Scholar PubMed

Valle, MSengupta, JSwami, NKGrassucci, RABurkhardt, NNierhaus, KHAgrawal, RKFrank, J 2002 Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation processThe EMBO Journal 21 3557CrossRef Google Scholar PubMed

Valle, MZavialov, AVSengupta, JRawat, UEhrenberg, MFrank, J 2003 Locking and unlocking of ribosomal motionsCell 114 123CrossRef Google Scholar PubMed

Valle, MZavialov, ALi, WStagg, SMSengupta, JNielsen, RCNissen, PHarvey, SCEhrenberg, MFrank, J 2003 Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopyNature Structural Biology 10 899CrossRef Google Scholar PubMed

Vasiliev, VDSelivanova, OMKoteliansky, VE 1978 Specific self-packing of the ribosomal 16S RNAFEBS Letters 95 273CrossRef Google Scholar

Vasiliev, VDSerdyuk, INGudkov, ATSpirin, AS 1986 Self-organization of ribosomal RNAStructure, Function, and Genetics of RibosomesHardesty, BKramer, GSpringer-VerlagNew York128CrossRef Google Scholar

Vasiliev, VDZalite, OM 1980 Specific compact self-packing of the ribosomal 23S RNAFEBS Letters 121 101CrossRef Google Scholar

Villa, ESengupta, JTrabuco, LGLeBarron, JBaxter, WTShaikh, TRGrassucci, RANissen, PEhrenberg, MSchulten, KAFrank, J 2009 Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysisProceeding of the National Academy of Sciences of the USA 106 1063CrossRef Google Scholar PubMed

Voorhees, RMWeixlbaumer, ALoakes, DKelley, ACRamakrishnan, V 2009 Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosomeNature Structural & Molecular Biology 16 528CrossRef Google Scholar PubMed

Wimberly, BTBrodersen, DEClemons, WMMorgan-Warren, RJCarter, APVonrhein, CHartsch, TRamakrishnan, V 2000 Structure of the 30S ribosomal subunitNature 407 327Google Scholar PubMed

Wintermeyer, WRobertson, JM 1982 Transient kinetics of transfer ribonucleic acid binding to ther ribosomal A and P sites: observation of a common intermediate complexBiochemistry 21 2246CrossRef Google Scholar

Yarus, MValle, MFrank, J 2003 A twisted tRNA intermediate sets the threshold for decodingRNA 9 384CrossRef Google Scholar PubMed

Yusupov, MMYusupova, GZBaucom, ALieberman, KEarnest, TNCate, JHNoller, HF 2001 Crystal structure of the ribosome at 5.5 A resolutionScience 292 883CrossRef Google Scholar PubMed

Yusupova, GJenner, LRees, BMoras, DYusupov, M 2006 Structural basis for messenger RNA movement on the ribosomeNature 444 391CrossRef Google Scholar PubMed

Yusupova, GZYusupov, MMCate, JHNoller, HF 2001 The path of messenger RNA through the ribosomeCell 106 233CrossRef Google Scholar PubMed

Zhang, WDunkle, JACate, JH 2009 Structures of the ribosome in intermediate states of ratchetingScience 325 1014CrossRef Google Scholar PubMed

Book contents

Chapter 9 - The Ribosome as a Brownian Ratchet Machine

Summary

Access options

References

Save book to Kindle

Save book to Dropbox

Save book to Google Drive