Mechanism of peptide bond synthesis on the ribosome

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

Volumn 102, Issue 35, 2005, Pages 12395-12400

  Trobro, Stefan ^a   Åqvist, Johan ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Catalytic mechanism; Computer simulation; Peptidyl transfer

Indexed keywords

ADENINE; AMINE; AMINOACYL TRANSFER RNA; DEOXYADENOSINE; LARGE SUBUNIT RIBOSOMAL RNA; OXYGEN; PEPTIDE TRANSFER RIBONUCLEIC ACID; SOLVENT; TRANSFER RNA; UNCLASSIFIED DRUG;

ACID BASE BALANCE; ARTICLE; CATALYSIS; CHEMICAL REACTION; CRYSTAL STRUCTURE; ENERGY; ENTROPY; GENETIC CONSERVATION; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTON TRANSPORT; REDUCTION; RIBOSOME; SIMULATION; SYNTHESIS;

BINDING SITES; BIOPHYSICS; CRYSTALLOGRAPHY, X-RAY; MACROMOLECULAR SUBSTANCES; MODELS, CHEMICAL; MODELS, MOLECULAR; PEPTIDE BIOSYNTHESIS; PEPTIDES; RIBOSOMES; RNA, TRANSFER, AMINO ACYL; THERMODYNAMICS;

EID: 24644461086     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0504043102     Document Type: Article

References (34)

1. Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. (2000) Science 289, 905-919.
2. 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.
3. Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F. & Yonath, A. (2001) Cell 107, 679-688.
4. Moore, P. B. & Steitz, T. A. (2003) RNA 9, 155-159.
5. Ramakrishnan, V. (2002) Cell 108, 557-572.
6. Bashan, A., Agmon, I., Zarivach, R., Schluenzen, F., Harms, J., Berisio, R., Bartels, H., Franceschi, F., Auerbach, T., Hansen, H. A. S., et al. (2003) Mol. Cell 11, 91-102.
7. Hansen, J. L., Schmeing, T. M., Moore, P. B. & Steitz, T. A. (2002) Proc. Natl. Acad. Sci. USA 99, 11670-11675.
8. Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. (2000) Science 289, 920-930.
9. Muth, G. W., Ortoleva-Donnelly, L. & Strobel, S. A. (2000) Science 289, 947-950.
10. Katunin, V. I., Muth, G. W., Strobel, S. A., Wintermeyer, W. & Rodnina, M. V. (2002) Mol. Cell 10, 339-346.
11. Warshel, A. (1991) Computer Modeling of Chemical Reactions in Enzymes and Solutions (Wiley Interscience, New York).
12. Aqvist, J. & Warshel, A. (1993) Chem. Rev. 93, 2523-2544.
13. Schmeing, T. M., Seila, A. C., Hansen, J. L., Freeborn, B., Soukup, J. K., Scaringe, S. A., Strobel, S. A., Moore, P. B. & Steitz, T. A. (2002) Nat. Struct. Biol. 9, 225-230.
14. Marelius, J., Kolmodin, K., Feierberg, I. & Aqvist, J. (1998) J. Mol. Graphics 16, 213-225.
15. MacKerell, A. D., Jr., Wiórkiewicz-Kuczera, J. & Karplus, M. (1995) J. Am. Chem. Soc. 117, 11946-11975.
16. Sievers, A., Beringer, M., Rodnina, M. V. & Wolfenden, R. (2004) Proc. Natl. Acad. Sci. USA 101, 7897-7901 and 12397-12398.
17. Lee, F. S. & Warshel, A. (1992) J. Chem. Phys. 97, 3100-3107.
18. Feierberg, I. & Aqvist, J. (2002) Theor. Chem. Acc. 108, 71-84.
19. Strajbl, M., Florian, J. & Warshel, A. (2000) J. Am. Chem. Soc. 122, 5354-5366.
20. Radzicka, A. & Wolfenden, R. (1996) J. Am. Chem. Soc. 118, 6105-6109.
21. Peter, C., Oostenbrink, C., van Dorp, A. & van Gunsteren, W. F. (2004) J. Chem. Phys. 120, 2652-2661.
22. Antonczak, S., Ruiz-López, M. F. & Rivail, J. L. (1994) J. Am. Chem. Soc. 116, 3912-3921.
23. Quiggle, K., Kumar, G., Ott, T. W., Ryu, E. K. & Chládek, S. (1981) Biochemistry 20, 3480-3485.
24. Weinger, J. S., Parnell, K. M., Dorner, S., Green, R. & Strobel, S. A. (2004) Nat. Struct. Biol. 11, 1101-1106.
25. Gordon, P. M., Fong, R., Deb, S. K., Li, N.-S., Schwans, J. P., Ye, J.-D. & Piccirilli, J. A. (2004) Chem. Biol. 11, 237-246.
26. Erlacher, M. D., Lang, K., Shankaran, N., Wotzel, B., Hüttenhofer, A., Micura, R., Mankin, A. S. & Polacek, N. (2005) Nucleic Acids Res. 33, 1618-1627.
27. Page, M. I. & Jencks, W. P. (1971) Proc. Natl. Acad. Sci. USA 68, 1678-1683.
28. Menger, F. M. (1985) Acc. Chem. Res. 18, 128-134.
29. Bruice, T. C. & Lightstone, F. C. (1999) Acc. Chem. Res. 32, 127-136.
30. Shurki, A., Strajbl, M., Villa, J. & Warshel, A. (2002) J. Am. Chem. Soc. 124, 4097-4107.
31. Armstrong, A. A. & Amzel, L. M. (2003) J. Am. Chem. Soc. 125, 14596-14602.
32. Shuman, C. F., Hämäläinen, M. & Danielson U. H. (2004) J. Mol. Recognit. 17, 106-119.
33. Villà, J. & Warshel, A. (2001) J. Phys. Chem. B 105, 7887-7907.
34. Cannon, W. R. & Benkovic, S. J. (1998) J. Biol. Chem. 273, 26257-26260.