Single-molecule study of viomycin's inhibition mechanism on ribosome translocation

Biochemistry

Volumn 49, Issue 45, 2010, Pages 9732-9738

  Ly, Cindy T ^a   Altuntop, Mediha E ^a   Wang, Yuhong ^a  

^a University of Houston   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYBRID STATE; INHIBITION MECHANISMS; LOCAL DYNAMICS; RIBOSOMAL PROTEINS; SINGLE-MOLECULE; SINGLE-MOLECULE STUDIES;

ANTIBIOTICS;

DYNAMICS;

RIBOSOMAL PROTEIN L27; RIBOSOME PROTEIN; TRANSFER RNA; UNCLASSIFIED DRUG; VIOMYCIN;

ARTICLE; DRUG BINDING; DRUG INHIBITION; DRUG MECHANISM; FLUORESCENCE RESONANCE ENERGY TRANSFER; HYBRID; PRIORITY JOURNAL; RIBOSOME;

BIOLOGICAL TRANSPORT; FLUORESCENCE RESONANCE ENERGY TRANSFER; OLIGOPEPTIDES; PEPTIDE ELONGATION FACTOR G; PROTEIN BIOSYNTHESIS; PROTEIN TRANSPORT; RIBOSOMES; RNA, MESSENGER; RNA, TRANSFER; TRANSLOCATION, GENETIC; VIOMYCIN;

EID: 78149443288     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101029g     Document Type: Article

References (30)

1. Simonovic, M. and Steitz, T. A. (2009) A structural view on the mechanism of the ribosome-catalyzed peptide bond formation Biochim. Biophys. Acta 1789, 612-623
2. Schmeing, T. M. and Ramakrishnan, V. (2009) What recent ribosome structures have revealed about the mechanism of translation Nature 461, 1234-1242
3. Moazed, D. and Noller, H. F. (1989) Intermediate states in the movement of transfer RNA in the ribosome Nature 342, 142-148
4. Dorner, S., Brunelle, J. L., Sharma, D., and Green, R. (2006) The hybrid state of tRNA binding is an authentic translation elongation intermediate Nat. Struct. Mol. Biol. 13, 234-241
5. Bretscher, M. S. (1968) Translocation in protein synthesis: a hybrid structure model Nature 218, 675-677
6. Sharma, D., Southworth, D. R., and Green, R. (2004) 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, 102-113
7. Peske, F., Savelsbergh, A., Katunin, V. I., Rodnina, M. V., and Wintermeyer, W. (2004) Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation J. Mol. Biol. 343, 1183-1194
8. Semenkov, Y. P., Shapkina, T. G., and Kirillov, S. V. (1992) Puromycin reaction of the A-site bound peptidyl-tRNA Biochimie 74, 411-417
9. Pan, D., Kirillov, S. V., and Cooperman, B. S. (2007) Kinetically competent intermediates in the translocation step of protein synthesis Mol. Cell 25, 519-529
10. Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M., and Frank, J. (2003) Locking and unlocking of ribosomal motions Cell 114, 123-134
11. Frank, J. and Agrawal, R. K. (2000) A ratchet-like inter-subunit reorganization of the ribosome during translocation Nature 406, 318-322
12. Julian, P., Konevega, A. L., Scheres, S. H., Lazaro, M., Gil, D., Wintermeyer, W., Rodnina, M. V., and Valle, M. (2008) Structure of ratcheted ribosomes with tRNAs in hybrid states Proc. Natl. Acad. Sci. U.S.A. 105, 16924-16927
13. Agirrezabala, X., Lei, J., Brunelle, J. L., Ortiz-Meoz, R. F., Green, R., and Frank, J. (2008) Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome Mol. Cell 32, 190-197
14. Ermolenko, D. N., Spiegel, P. C., Majumdar, Z. K., Hickerson, R. P., Clegg, R. M., and Noller, H. F. (2007) The antibiotic viomycin traps the ribosome in an intermediate state of translocation Nat. Struct. Mol. Biol. 14, 493-497
15. Frank, J., Gao, H., Sengupta, J., Gao, N., and Taylor, D. J. (2007) The process of mRNA-tRNA translocation Proc. Natl. Acad. Sci. U.S.A. 104, 19671-19678
16. Horan, L. H. and Noller, H. F. (2007) Intersubunit movement is required for ribosomal translocation Proc. Natl. Acad. Sci. U.S.A. 104, 4881-4885
17. Munro, J. B., Altman, R. B., Tung, C. S., Cate, J. H., Sanbonmatsu, K. Y., and Blanchard, S. C. (2009) Spontaneous formation of the unlocked state of the ribosome is a multistep process, Proc. Natl. Acad. Sci. U.S.A.
18. Modolell, J. and Vazquez (1977) The inhibition of ribosomal translocation by viomycin Eur. J. Biochem. 81, 491-497
19. Shoji, S., Walker, S. E., and Fredrick, K. (2006) Reverse translocation of tRNA in the ribosome Mol. Cell 24, 931-942
20. Yamada, T., Mizugichi, Y., Nierhaus, K. H., and Wittmann, H. G. (1978) Resistance to viomycin conferred by RNA of either ribosomal subunit Nature 275, 460-461
21. Stanley, R. E., Blaha, G., Grodzicki, R. L., Strickler, M. D., and Steitz, T. A. (2010) The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome Nat. Struct. Mol. Biol. 17, 289-293
22. Cornish, P. V., Ermolenko, D. N., Noller, H. F., and Ha, T. (2008) Spontaneous intersubunit rotation in single ribosomes Mol. Cell 30, 578-588
23. Kim, H. D., Puglisi, J. D., and Chu, S. (2007) Fluctuations of transfer RNAs between classical and hybrid states Biophys. J. 93, 3575-3582
24. Feldman, M. B., Terry, D. S., Altman, R. B., and Blanchard, S. C. (2010) Aminoglycoside activity observed on single pre-translocation ribosome complexes Nat. Chem. Biol. 6, 244
25. Frank, J. and Gonzalez, R. L., Jr. (2010) Structure and dynamics of a processive Brownian motor: the translating ribosome, Annu. Rev. Biochem.
26. Altuntop, M. E., Ly, C. T., and Wang, Y. (2010) A single molecule study of ribosome's hierarchic dynamics at the peptidyl transferase center, Biophys. J. (in press).
27. Wang, Y., Qin, H., Kudaravalli, R. D., Kirillov, S. V., Dempsey, G. T., Pan, D., Cooperman, B. S., and Goldman, Y. E. (2007) Single-molecule structural dynamics of EF-G-ribosome interaction during translocation Biochemistry 46, 10767-10775
28. Rasnik, I., McKinney, S. A., and Ha, T. (2006) Nonblinking and long-lasting single-molecule fluorescence imaging Nat. Methods 3, 891-893
29. McKinney, S. A., Joo, C., and Ha, T. (2006) Analysis of single-molecule FRET trajectories using hidden Markov modeling Biophys. J. 91, 1941-1951
30. Fei, J., Kosuri, P., MacDougall, D. D., and Gonzalez, R. L., Jr. (2008) Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation Mol. Cell 30, 348-359