메뉴 건너뛰기




Volumn 19, Issue 1, 2009, Pages 103-109

Single-molecule observations of ribosome function

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSFER RNA;

EID: 60349097663     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2009.01.002     Document Type: Review
Times cited : (72)

References (53)
  • 1
    • 34250377197 scopus 로고    scopus 로고
    • The weird and wonderful world of bacterial ribosome regulation
    • Wilson D.N., and Nierhaus K.H. The weird and wonderful world of bacterial ribosome regulation. Crit Rev Biochem Mol Biol 42 (2007) 187-219
    • (2007) Crit Rev Biochem Mol Biol , vol.42 , pp. 187-219
    • Wilson, D.N.1    Nierhaus, K.H.2
  • 2
    • 34548395468 scopus 로고    scopus 로고
    • The ribosome in focus: new structures bring new insights
    • Korostelev A., and Noller H.F. The ribosome in focus: new structures bring new insights. Trends Biochem Sci 32 (2007) 434-441
    • (2007) Trends Biochem Sci , vol.32 , pp. 434-441
    • Korostelev, A.1    Noller, H.F.2
  • 3
    • 49349091280 scopus 로고    scopus 로고
    • What we have learned from ribosome structures
    • Ramakrishnan V. What we have learned from ribosome structures. Biochem Soc Trans 36 (2008) 567-574
    • (2008) Biochem Soc Trans , vol.36 , pp. 567-574
    • Ramakrishnan, V.1
  • 4
    • 39749138785 scopus 로고    scopus 로고
    • A structural understanding of the dynamic ribosome machine
    • Steitz T.A. A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol 9 (2008) 242-253
    • (2008) Nat Rev Mol Cell Biol , vol.9 , pp. 242-253
    • Steitz, T.A.1
  • 5
    • 33646495214 scopus 로고    scopus 로고
    • Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps
    • Mitra K., and Frank J. Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu Rev Biophys Biomol Struct 35 (2006) 299-317
    • (2006) Annu Rev Biophys Biomol Struct , vol.35 , pp. 299-317
    • Mitra, K.1    Frank, J.2
  • 6
    • 42249103513 scopus 로고    scopus 로고
    • A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET
    • Munro J.B., Vaiana A., Sanbonmatsu K.Y., and Blanchard S.C. A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET. Biopolymers 89 (2008) 565-577
    • (2008) Biopolymers , vol.89 , pp. 565-577
    • Munro, J.B.1    Vaiana, A.2    Sanbonmatsu, K.Y.3    Blanchard, S.C.4
  • 7
    • 34347383962 scopus 로고    scopus 로고
    • Insights into protein biosynthesis from structures of bacterial ribosomes
    • An excellent review summarizing many of the key degrees of freedom observed in the ribosome through structural investigations.
    • Berk V., and Cate J.H. Insights into protein biosynthesis from structures of bacterial ribosomes. Curr Opin Struct Biol 17 (2007) 302-309. An excellent review summarizing many of the key degrees of freedom observed in the ribosome through structural investigations.
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 302-309
    • Berk, V.1    Cate, J.H.2
  • 11
    • 33847350189 scopus 로고    scopus 로고
    • Single molecule FRET for the study on structural dynamics of biomolecules
    • Sugawa M., Arai Y., Iwane A.H., Ishii Y., and Yanagida T. Single molecule FRET for the study on structural dynamics of biomolecules. Biosystems 88 (2007) 243-250
    • (2007) Biosystems , vol.88 , pp. 243-250
    • Sugawa, M.1    Arai, Y.2    Iwane, A.H.3    Ishii, Y.4    Yanagida, T.5
  • 15
    • 44449087047 scopus 로고    scopus 로고
    • Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy
    • ••]
    • ••]
    • (2008) Nat Methods , vol.5 , pp. 491-505
    • Neuman, K.C.1    Nagy, A.2
  • 16
    • 47249110711 scopus 로고    scopus 로고
    • Translation at the single-molecule level
    • Excellent discussions of the basic precepts and foundations of single-molecule science and detailed descriptions of its application to specific biological systems. The article of Marshall et al. thoroughly covers the history and findings of single-molecule and optical trapping methods applied to investigations of translation.
    • Marshall R.A., Aitken C.E., Dorywalska M., and Puglisi J.D. Translation at the single-molecule level. Annu Rev Biochem 77 (2008) 177-203. Excellent discussions of the basic precepts and foundations of single-molecule science and detailed descriptions of its application to specific biological systems. The article of Marshall et al. thoroughly covers the history and findings of single-molecule and optical trapping methods applied to investigations of translation.
    • (2008) Annu Rev Biochem , vol.77 , pp. 177-203
    • Marshall, R.A.1    Aitken, C.E.2    Dorywalska, M.3    Puglisi, J.D.4
  • 17
    • 38049178477 scopus 로고    scopus 로고
    • The process of mRNA-tRNA translocation
    • An excellent review of the process of translocation on the ribosome and the changing view of dynamic processes in the ribosome during protein synthesis.
    • Frank J., Gao H., Sengupta J., Gao N., and Taylor D.J. The process of mRNA-tRNA translocation. Proc Natl Acad Sci U S A 104 (2007) 19671-19678. An excellent review of the process of translocation on the ribosome and the changing view of dynamic processes in the ribosome during protein synthesis.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 19671-19678
    • Frank, J.1    Gao, H.2    Sengupta, J.3    Gao, N.4    Taylor, D.J.5
  • 18
    • 41649087227 scopus 로고    scopus 로고
    • Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections
    • Elad N., Clare D.K., Saibil H.R., and Orlova E.V. Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections. J Struct Biol 162 (2008) 108-120
    • (2008) J Struct Biol , vol.162 , pp. 108-120
    • Elad, N.1    Clare, D.K.2    Saibil, H.R.3    Orlova, E.V.4
  • 19
    • 33646042904 scopus 로고    scopus 로고
    • A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation
    • Penczek P.A., Frank J., and Spahn C.M. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J Struct Biol 154 (2006) 184-194
    • (2006) J Struct Biol , vol.154 , pp. 184-194
    • Penczek, P.A.1    Frank, J.2    Spahn, C.M.3
  • 21
    • 34547892257 scopus 로고    scopus 로고
    • Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic 'fingerprinting'
    • Liu S., Bokinsky G., Walter N.G., and Zhuang X. Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic 'fingerprinting'. Proc Natl Acad Sci U S A 104 (2007) 12634-12639
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 12634-12639
    • Liu, S.1    Bokinsky, G.2    Walter, N.G.3    Zhuang, X.4
  • 23
    • 36549020733 scopus 로고    scopus 로고
    • Fluctuations of transfer RNAs between classical and hybrid states
    • Kim H.D., Puglisi J.D., and Chu S. Fluctuations of transfer RNAs between classical and hybrid states. Biophys J 93 (2007) 3575-3582
    • (2007) Biophys J , vol.93 , pp. 3575-3582
    • Kim, H.D.1    Puglisi, J.D.2    Chu, S.3
  • 24
    • 0037461492 scopus 로고    scopus 로고
    • Single-molecule approach to dispersed kinetics and dynamic disorder: Probing conformational fluctuation and enzymatic dynamics
    • A seminal article addressing intrinsic heterogeneities present in biological systems.
    • Xie X.S. Single-molecule approach to dispersed kinetics and dynamic disorder: Probing conformational fluctuation and enzymatic dynamics. J Chem Phys 117 (2002) 11024-11032. A seminal article addressing intrinsic heterogeneities present in biological systems.
    • (2002) J Chem Phys , vol.117 , pp. 11024-11032
    • Xie, X.S.1
  • 25
    • 0347004715 scopus 로고    scopus 로고
    • Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme
    • Xie Z., Srividya N., Sosnick T.R., Pan T., and Scherer N.F. Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme. Proc Natl Acad Sci U S A 101 (2004) 534-539
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 534-539
    • Xie, Z.1    Srividya, N.2    Sosnick, T.R.3    Pan, T.4    Scherer, N.F.5
  • 26
    • 33644767158 scopus 로고    scopus 로고
    • Single-molecule FRET study of denaturant induced unfolding of RNase H
    • Kuzmenkina E.V., Heyes C.D., and Nienhaus G.U. Single-molecule FRET study of denaturant induced unfolding of RNase H. J Mol Biol 357 (2006) 313-324
    • (2006) J Mol Biol , vol.357 , pp. 313-324
    • Kuzmenkina, E.V.1    Heyes, C.D.2    Nienhaus, G.U.3
  • 27
    • 33744797914 scopus 로고    scopus 로고
    • Conformational heterogeneity in RNA polymerase observed by single-pair FRET microscopy
    • Coban O., Lamb D.C., Zaychikov E., Heumann H., and Nienhaus G.U. Conformational heterogeneity in RNA polymerase observed by single-pair FRET microscopy. Biophys J 90 (2006) 4605-4617
    • (2006) Biophys J , vol.90 , pp. 4605-4617
    • Coban, O.1    Lamb, D.C.2    Zaychikov, E.3    Heumann, H.4    Nienhaus, G.U.5
  • 28
    • 33746747438 scopus 로고    scopus 로고
    • Analysis of single-molecule FRET trajectories using hidden markov modeling
    • McKinney S.A., Joo C., and Ha T. Analysis of single-molecule FRET trajectories using hidden markov modeling. Biophys J 91 (2006) 1941-1951
    • (2006) Biophys J , vol.91 , pp. 1941-1951
    • McKinney, S.A.1    Joo, C.2    Ha, T.3
  • 29
    • 33646937406 scopus 로고    scopus 로고
    • Single-molecule fluorescence studies of protein folding and conformational dynamics
    • Michalet X., Weiss S., and Jager M. Single-molecule fluorescence studies of protein folding and conformational dynamics. Chem Rev 106 (2006) 1785-1813
    • (2006) Chem Rev , vol.106 , pp. 1785-1813
    • Michalet, X.1    Weiss, S.2    Jager, M.3
  • 30
    • 33746675190 scopus 로고    scopus 로고
    • Single-molecule experiments in biological physics: methods and applications
    • Ritort F. Single-molecule experiments in biological physics: methods and applications. J Phys: Condens Matter 18 (2006) R531
    • (2006) J Phys: Condens Matter , vol.18
    • Ritort, F.1
  • 31
    • 0018863379 scopus 로고
    • Characterisation of a new, fully active fluorescent derivative of E. coli tRNA Phe
    • Plumbridge J.A., Baumert H.G., Ehrenberg M., and Rigler R. Characterisation of a new, fully active fluorescent derivative of E. coli tRNA Phe. Nucleic Acids Res 8 (1980) 827-843
    • (1980) Nucleic Acids Res , vol.8 , pp. 827-843
    • Plumbridge, J.A.1    Baumert, H.G.2    Ehrenberg, M.3    Rigler, R.4
  • 32
    • 0029049551 scopus 로고
    • Macromolecular arrangement in the aminoacyl-tRNA.elongation factor Tu.GTP ternary complex. A fluorescence energy transfer study
    • Watson B.S., Hazlett T.L., Eccleston J.F., Davis C., Jameson D.M., and Johnson A.E. Macromolecular arrangement in the aminoacyl-tRNA.elongation factor Tu.GTP ternary complex. A fluorescence energy transfer study. Biochemistry 34 (1995) 7904-7912
    • (1995) Biochemistry , vol.34 , pp. 7904-7912
    • Watson, B.S.1    Hazlett, T.L.2    Eccleston, J.F.3    Davis, C.4    Jameson, D.M.5    Johnson, A.E.6
  • 33
    • 44449125068 scopus 로고    scopus 로고
    • Spontaneous intersubunit rotation in single ribosomes
    • Cornish P.V., Ermolenko D.N., Noller H.F., and Ha T. Spontaneous intersubunit rotation in single ribosomes. Mol Cell 30 (2008) 578-588
    • (2008) Mol Cell , vol.30 , pp. 578-588
    • Cornish, P.V.1    Ermolenko, D.N.2    Noller, H.F.3    Ha, T.4
  • 34
    • 42949126723 scopus 로고    scopus 로고
    • Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation
    • Fei J., Kosuri P., MacDougall D.D., and Gonzalez Jr. R.L. Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol Cell 30 (2008) 348-359
    • (2008) Mol Cell , vol.30 , pp. 348-359
    • Fei, J.1    Kosuri, P.2    MacDougall, D.D.3    Gonzalez Jr., R.L.4
  • 35
    • 33847051154 scopus 로고    scopus 로고
    • Identification of two distinct hybrid state intermediates on the ribosome
    • smFRET investigations of tRNA dynamics on the ribosome and the identification of two distinct hybrid states dynamically sampled in pre-translocation complexes.
    • Munro J.B., Altman R.B., O'Connor N., and Blanchard S.C. Identification of two distinct hybrid state intermediates on the ribosome. Mol Cell 25 (2007) 505-517. smFRET investigations of tRNA dynamics on the ribosome and the identification of two distinct hybrid states dynamically sampled in pre-translocation complexes.
    • (2007) Mol Cell , vol.25 , pp. 505-517
    • Munro, J.B.1    Altman, R.B.2    O'Connor, N.3    Blanchard, S.C.4
  • 37
    • 36549043024 scopus 로고    scopus 로고
    • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    • A concise summary of recent experimental data shedding light on the intrinsically dynamic nature of biological molecules and the implications of these insights to enzyme function.
    • Bahar I., Chennubhotla C., and Tobi D. Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr Opin Struct Biol 17 (2007) 633-640. A concise summary of recent experimental data shedding light on the intrinsically dynamic nature of biological molecules and the implications of these insights to enzyme function.
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 633-640
    • Bahar, I.1    Chennubhotla, C.2    Tobi, D.3
  • 38
    • 0346362324 scopus 로고    scopus 로고
    • 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 D.R., and Green R. 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. RNA 10 (2004) 102-113
    • (2004) RNA , vol.10 , pp. 102-113
    • Sharma, D.1    Southworth, D.R.2    Green, R.3
  • 39
    • 33847024820 scopus 로고    scopus 로고
    • Kinetically competent intermediates in the translocation step of protein synthesis
    • Pan D., Kirillov S., and Cooperman B.S. Kinetically competent intermediates in the translocation step of protein synthesis. Mol Cell 25 (2007) 519-529
    • (2007) Mol Cell , vol.25 , pp. 519-529
    • Pan, D.1    Kirillov, S.2    Cooperman, B.S.3
  • 41
    • 0024458904 scopus 로고
    • Intermediate states in the movement of transfer RNA in the ribosome
    • Moazed D., and Noller H.F. Intermediate states in the movement of transfer RNA in the ribosome. Nature 342 (1989) 142-148
    • (1989) Nature , vol.342 , pp. 142-148
    • Moazed, D.1    Noller, H.F.2
  • 44
    • 55949134736 scopus 로고    scopus 로고
    • Structure of ratcheted ribosomes with tRNAs in hybrid states
    • Articles describing the first structural characterization of tRNA hybrid states on the pre-translocation ribosome using cryo-EM and particle sorting methods.
    • Julian P., Konevega A.L., Scheres S.H.W., Lazaro M., Gil D., Wintermeyer W., Rodnina M., and Valle M. Structure of ratcheted ribosomes with tRNAs in hybrid states. PNAS 105 (2008) 16924-16927. Articles describing the first structural characterization of tRNA hybrid states on the pre-translocation ribosome using cryo-EM and particle sorting methods.
    • (2008) PNAS , vol.105 , pp. 16924-16927
    • Julian, P.1    Konevega, A.L.2    Scheres, S.H.W.3    Lazaro, M.4    Gil, D.5    Wintermeyer, W.6    Rodnina, M.7    Valle, M.8
  • 45
    • 0034691576 scopus 로고    scopus 로고
    • A ratchet-like inter-subunit reorganization of the ribosome during translocation
    • Frank J., and Agrawal R.K. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406 (2000) 318-322
    • (2000) Nature , vol.406 , pp. 318-322
    • Frank, J.1    Agrawal, R.K.2
  • 46
    • 33644798018 scopus 로고    scopus 로고
    • The hybrid state of tRNA binding is an authentic translation elongation intermediate
    • Dorner S., Brunelle J.L., Sharma D., and Green R. The hybrid state of tRNA binding is an authentic translation elongation intermediate. Nat Struct Mol Biol 13 (2006) 234-241
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 234-241
    • Dorner, S.1    Brunelle, J.L.2    Sharma, D.3    Green, R.4
  • 47
    • 55749099506 scopus 로고    scopus 로고
    • Irreversible chemical steps control intersubunit dynamics during translation
    • Marshall R.A., Dorywalska M., and Puglisi J.D. Irreversible chemical steps control intersubunit dynamics during translation. Proc Natl Acad Sci U S A 105 (2008) 15364-15369
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 15364-15369
    • Marshall, R.A.1    Dorywalska, M.2    Puglisi, J.D.3
  • 49
    • 52949141857 scopus 로고    scopus 로고
    • Molecular signatures of ribosomal evolution
    • A first-of-its-kind article presenting comparative analyses of ribosomal RNA and ribosomal protein sequences from diverse species representing the three domains of life, discussing these findings in the context of potential convergent and divergent ribosome functions.
    • Roberts E., Sethi A., Montoya J., Woese C.R., and Luthey-Schulten Z. Molecular signatures of ribosomal evolution. Proc Natl Acad Sci U S A 105 (2008) 13953-13958. A first-of-its-kind article presenting comparative analyses of ribosomal RNA and ribosomal protein sequences from diverse species representing the three domains of life, discussing these findings in the context of potential convergent and divergent ribosome functions.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 13953-13958
    • Roberts, E.1    Sethi, A.2    Montoya, J.3    Woese, C.R.4    Luthey-Schulten, Z.5
  • 52
    • 33645465733 scopus 로고    scopus 로고
    • Antibiotics and the ribosome
    • Tenson T., and Mankin A. Antibiotics and the ribosome. Mol Microbiol 59 (2006) 1664-1677
    • (2006) Mol Microbiol , vol.59 , pp. 1664-1677
    • Tenson, T.1    Mankin, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.