Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

Proceedings of the National Academy of Sciences of the United States of America

Volumn 100, Issue 16, 2003, Pages 9319-9323

  Tama, Florence ^a   Valle, Mikel ^b   Frankt, Joachim ^b,c   Brooks III, Charles L ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

Dynamical transitions; Molecular machines; Ratchet like reorganization; Translocation

Indexed keywords

TRANSFER RNA;

ARTICLE; CELL ORGANELLE; CRYOELECTRON MICROSCOPY; CYTOSKELETON; DYNAMICS; MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN TRANSPORT; RIBOSOME; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CRYOELECTRON MICROSCOPY; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MODELS, STATISTICAL; RIBOSOMES; THERMUS THERMOPHILUS;

EID: 0042424707     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.1632476100     Document Type: Article

References (37)

1. Wilson, K. S. & Noller, H. F. (1998) Cell 92, 337-349.
2. Agrawal, R. K., Heagle, A. B., Penczek, P., Grassucci, R. A. & Frank, J. (1999) Nat. Struct. Biol. 6, 643-647.
3. Stark, H., Rodnina, M. V., Wieden, H. J., van Heel, M. & Wintermeyer, W. (2000) Cell 100, 301-309.
4. Frank, J. & Agrawal, R. K. (2000) Nature 406, 318-322.
5. Agrawal, R. K., Penczek, P., Grassucci, R. A., Burkhardt, N., Nierhaus, K. H. & Frank, J. (1999) J. Biol. Chem. 274, 8723-8729.
6. Gomez-Lorenzo, M. G., Spahn, C. M., Agrawal, R. K., Grassucci, R. A., Penczek, P., Chakraburtty, K., Ballesta, J. P., Lavandera, J. L., Garcia-Bustos, J. F. & Frank, J. (2000) EMBO J. 19, 2710-2718.
7. Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F. & Yonath, A. (2001) Cell 107, 679-688.
8. Carter, A. P., Clemons, W. M., Jr., Brodersen, D. E., Morgan-Warren, R. J., Hartsch, T., Wimberly, B. T. & Ramakrishnan, V. (2001) Science 291, 498-501.
9. Ramakrishnan, V. (2002) Cell 108, 557-572.
10. Gabashvili, I. S., Agrawal, R. K., Grassucci, R., Squires, C. L., Dahlberg, A. E. & Frank, J. (1999) EMBO J. 18, 6501-6507.
11. Gabashvili, I. S., Gregory, S. T., Valle, M., Grassucci, R., Worbs, M., Wahl, M. C., Dahlberg, A. E. & Frank, J. (2001) Mol. Cell 8, 181-188.
12. Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. (2000) Science 289, 905-920.
13. Wimberly, B. T., Brodersen, D. E., Clemons, W. M., Jr., Morgan-Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch, T. & Ramakrishnan, V. (2000) Nature 407, 327-339.
14. Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. & Noller, H. F. (2001) Science 292, 883-896.
15. Brooks, B. R. & Karplus, M. (1983) Proc. Natl. Acad. Sci. USA 80, 6571-6575.
16. Go, N., Noguti, T. & Nishikawa, T. (1983) Proc. Natl. Acad. Sci. USA 80, 3696-3700.
17. Tama, F. & Sanejouand, Y. H. (2001) Protein Eng. 14, 1-6.
18. Tirion, M. M. (1996) Phys. Rev. Lett. 77, 1905-1908.
19. Jernigan, R. L., Demirel, M. C. & Bahar, I. (1999) Int. J. Quantum Chem. 75, 301-312.
20. Bahar, I. & Jernigan, R. L. (1998) J. Mol. Biol. 281, 871-884.
21. Tama, F. & Brooks, C. L., III. (2002) J. Mol. Biol. 318, 733-747.
22. Bahar, I. (1999) Rev. Chem. Eng. 15, 319-347.
23. Tama, F., Wriggers, W. & Brooks, C. L., III. (2002) J. Mol. Biol. 321, 297-305.
24. Ming, D., Kong, Y., Lambert, M. A., Huang, Z. & Ma, J. (2002) Proc. Natl. Acad. Sci. USA 99, 8620-8625.
25. Lodmell, J. S. & Dahlberg, A. E. (1997) Science 277, 1262-1267.
26. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000) Nucleic Acids Res. 28, 235-242.
27. Bahar, I., Atilgan, A. R. & Erman, B. (1997) Fold. Des. 2, 173-181.
28. Durand, P., Trinquier, G. & Sanejouand, Y. H. (1994) Biopolymers 34, 759-771.
29. Tama, F., Gadea, F. X., Marques, O. & Sanejouand, Y. H. (2000) Proteins 41, 1-7.
30. Brooks, C. L., III, Karplus, M. & Pettitt, B. M. (1988) Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics (Wiley, New York).
31. Jernigan, R. L., Bahar, I., Covell, D. G., Atilgan, A. R., Erman, B. & Flatow, D. T. (2000) J. Biomol. Struct. Dyn. 18, 9-55.
32. Cate, J. H., Yusupov, M. M., Yusupova, G. Z., Earnest, T. N. & Noller, H. F. (1999) Science 285, 2095-2104.
33. Gabashvili, I. S., Agrawal, R. K., Spahn, C. M., Grassucci, R. A., Svergun, D. I., Frank, J. & Penczek, P. (2000) Cell 100, 537-549.
34. Frank, J., Verschoor, A., Li, Y., Zhu, J., Lata, R. K., Radermacher, M., Penczek, P., Grassucci, R., Agrawal, R. K. & Srivastava, S. (1995) Biochem. Cell Biol. 73, 757-765.
35. Agrawal, R. K., Penczek, P., Grassucci, R. A., Li, Y., Leith, A., Nierhaus, K. H. & Frank, J. (1996) Science 271, 1000-1002.
36. Humphrey, W., Dalke, A. & Schulten, K. (1996) J. Mol. Graphics 14, 33-38.
37. Valle, M., Zavialov, J., Sengupta, J., Rawat, U., Ehrenberg, M. & Frank, J. (2003) Cell, in press.