Ribosomal dynamics inferred from variations in experimental measurements

RNA

Volumn 9, Issue 11, 2003, Pages 1301-1307

  Gabashvili, Irene S ^a,b   Whirl Carrillo, Michelle ^a   Bada, Michael ^a   Banatao, D Rey ^a   Altman, Russ B ^a  

^a STANFORD UNIVERSITY   (United States)

^b HEWLETT PACKARD LABORATORIES   (United States)

Author keywords

Distance measures; Dynamics; Ribosome; Structure

Indexed keywords

RIBOSOME RNA; RNA; RNA 16S; RNA 5S; TRANSFER RNA;

ARTICLE; CRYSTAL STRUCTURE; MEASUREMENT; MOLECULAR DYNAMICS; PRIORITY JOURNAL; RIBOSOME; RNA STRUCTURE; RNA TRANSPORT; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RIBOSOMES; RNA, RIBOSOMAL;

EID: 0142147363     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5141503     Document Type: Article

References (36)

1. Agrawal, R.K., Lata, R.K., and Frank, J. 1999. Conformational variability in Escherichia coli 70S ribosome as revealed by 3D cryoelectron microscopy. Int. J. Biochem. Cell Biol. 31: 243-254.
2. Bada, M.A. and Altman, R.B. 2000. Computational modeling of structural experimental data. Methods Enzymol. 317: 470-491.
3. Ban, N., Nissen, P., Hansen, J., Moore, P.B., and Steitz, T.A. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 Å. resolution. Science 289: 905-920.
4. Bayfield, M.A., Dahlberg, A.E., Schulmeister, U., Dorner, S., and Barta, A. 2001. A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition. Proc. Natl. Acad. Sci. 98: 10096-10101.
5. Brodersen, D.E., Clemons Jr., W.M., Carter, A.P., Wimberly, B.T., and Ramakrishnan, V. 2002. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: Structure of the proteins and their interactions with 16S RNA. Mol. Biol. 316: 725-768.
6. Chen, R.O., Felciano, R., and Altman, R.B. 1997. RIBOWEB: Linking structural computations to a knowledge base of published experimental data. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5: 84-87.
7. Edwards, A.M., Kus, B., Jansen, R., Greenbaum, D., Greenblat, J., and Gerstein, M. 2002. Bridging structural biology and genomics: Assessing protein interaction data with known complexes. Trends Genet. 18: 529-536.
8. Frank, J. and Agrawal, R.K. 2000. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406: 318-322.
9. Gabashvili, I.S., Agrawal, R.K., Grassucci, R., Squires, C.L., Dahlberg, A.E., and Frank, J. 1999. Major rearrangements in the 70S ribosomal 3D structure caused by a conformational switch in 16S ribosomal RNA. EMBO J. 18: 6501-6507.
10. Gabashvili, I.S., Agrawal, R.K., Spahn, C.M., Grassucci, R.A., Svergun, D.I., Frank, J., and Penczek, P. 2000. Solution structure of the E. coli 70S ribosome at 11.5 Å resolution. Cell 100: 537-549.
11. Gao, H., Sengupta, J., Valle, M., Korostelev, M., Esawr, N., Stagg, S.M., Van Roey, P., Agrawal, R.K., Harvey, S.C., Sali, A., et al. 2003. Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement. Cell 113: 789-780.
12. Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. 2001. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 207: 679-688.
13. Huang, C.C., Couch, G.S., Pettersen, E.F., and Ferrin, T.E. 1996. Chimera: An extensible molecular modeling application constructed using standard components. Pac. Symp. Biocomput. 1: 724-730.
14. Jansen, R., Greenbaum, D., and Gerstein, M. 2002. Relating whole-genome expression data with protein-protein interactions. Genome Res. 12: 37-46.
15. Klaholz, B.P., Pape, T., Zavialov, A.V., Myasnikov, A.G., Orlova, E.V., Vestergaard, B., Ehrenberg, M., and van Heel, M. 2003. Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature 421: 90-94.
16. Lodmell, J.S. and Dahlberg, A.E. 1997. A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA. Science 277: 1262-1267.
17. Matadeen, R., Patwardhan, A., Gowen, B., Orlova, E.V., Pape, T., Cuff, M., Mueller, F., Brimacombe, R., and van Heel, M. 1999. The Escherichia coli large ribosomal subunit at 7.5 Å resolution. Structure Fold. Design 7: 1575-1583.
18. Matassova, N.B., Rodnina, M.V., and Wintermeyer, W. 2001. Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation on the ribosome. RNA 7: 1879-1885.
19. Noller, H.F. and Baucom, A. 2001. Structure of the 70 S ribosome: Implications for movement. Biochem. Soc. Trans. 30: 1159-1161.
20. Ogle, J.M., Murphy, F.V., Tarry, M.J., and Ramakrishnan, V. 2002. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111: 721-732.
21. Pioletti, M., Harms, J., Zarivach, R., Gluhmann, M., Avila, H., Bashan, A., Bartels, H., Auerbach, T., Jacobi, C., Hartsch, T., et al. 2001. Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J. 20: 1829-1839.
22. Polacek, N., Patzke, S., Nierhaus, K.H., and Barta, A. 2000. Periodic conformational changes in rRNA: Monitoring the dynamics of translating ribosomes. Mol. Cell 6: 159-171.
23. Ramakrishnan, V. 2002. Ribosome structure and the mechanism of translation. Cell 108: 557-572.
24. Rawat, U.B., Zavialov, A.V., Sengupta, J., Valle, M., Grassucci, R.A., Linde, J., Vestergaard, B., Ehrenberg, M., and Frank, J. 2003. A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421: 87-90.
25. Raychaudhuri, S., Sutphin, P.D., Stuart, J.M., and Altman, R.B. 2000. CLEAVER: Analyzing microarray data using known biological categories. SMI Rep. SMI-2000-0839.
26. Sanbonmatsu, K. and Joseph, S. 2003. Understanding discrimination by the ribosome: Stability testing and groove measurement of codon-anticodon pairs. J. Mol. Biol. 328: 33-47.
27. Schluenzen, F., Tocilj, A., Zarivach, R., Harms, J., Gluehmann, M., Janell, D., Bashan, A., Bartels, H., Agmon, I., Franceschi, F., et al. 2000. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell 102: 615-623.
28. Sergiev, P.V., Dontsova, O.A., and Bogdanov, A.A. 2001. Study of ribosome structure using the biochemical methods: Judgment day. Mol. Biol. (Mosk) 35: 559-583.
29. Sommer, I. and Brimacombe, R. 2001. Methods for refining interactively established models of ribosomal RNA towards a physicochemically plausible structure. J. Comp. Chem. 22: 407-417.
30. Stagg, S.M., Mears, J.A., and Harvey, S.C. 2003. A structural model for the assembly of the 30S subunit of the ribosome. J. Mol. Biol. 328: 49-61.
31. Stark, H., Rodnina, M.V., Wieden, H.J., van Heel, M., and Wintermeyer, W. 1999. Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation. Cell 100: 301-309.
32. Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M., and Frank, J. 2003. Locking and unlocking of ribosomal motions. Cell 114: 123-134.
33. Whirl-Carrillo, M., Gabashvili, I.S., Banatao, D.R., Bada, M., and Altman, R.B. 2002. Mining biochemical information: Lessons taught by the ribosome. RNA 8: 279-289.
34. Wimberly, B.T., Brodersen, D.E., Clemons Jr., W.M., Morgan-Warren, R.J., Carter, A.P., Vonrhein, C., Hartsch, T., and Ramakrishnan, V. 2000. Structure of the 30S ribosomal subunit. Nature 407: 327-339.
35. Yonath, A. 2002. The search and its outcome: High-resolution structures of ribosomal particles from mesophilic, thermophilic, and halophilic bacteria at various functional states. Annu. Rev. Biophys. Biomol. Struct. 31: 257-273.
36. Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H., and Noller, H.F. 2001. Crystal structure of the ribosome at 5.5 Å resolution. Science 292: 883-896.