Simulating activity of the bacterial ribosome

Quarterly Reviews of Biophysics

Volumn 42, Issue 4, 2009, Pages 301-316

  Trylska, Joanna ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT;

ARTICLE; BACTERIUM; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DRUG EFFECT; MOTION; PHYSIOLOGY; RIBOSOME; STATIC ELECTRICITY; ULTRASTRUCTURE;

ANTI-BACTERIAL AGENTS; BACTERIA; COMPUTER SIMULATION; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOTION; RIBOSOMES; STATIC ELECTRICITY;

BACTERIA (MICROORGANISMS);

EID: 77952343336     PISSN: 00335835     EISSN: 14698994     Source Type: Journal    
DOI: 10.1017/S0033583510000028     Document Type: Article

References (70)

1. ALEKSANDROV, A. & SIMONSON, T. (2008). Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site. Journal of the American Chemical Society 130, 1114-1115.
2. BAKER, N. A. (2004). Poisson-Boltzmann methods for biomolecular electrostatics. Numerical Computer Methods, Pt D 383, 94-118.
3. BAKER, N.A., SEPT, D., JOSEPH, S., HOLST, M.J. & MCCAMMON, J. A. (2001). Electrostatics of nanosys-tems: application to microtubules and the ribosome. Proceedings of the National Academy of Sciences USA 98, 10037-10041.
4. BAN, N., NISSEN, P., HANSEN, J., MOORE, P. B. & STEITZ, T. A. (2000). The complete atomic structure of the large ribosomal subunit at 2-4 angstrom resolution. Science 289, 905-920.
5. BASHAN, A. & YONATH, A. (2008). Correlating ribosome function with high-resolution structures. Trends in Microbiology 16, 326-335.
6. BERNSTEIN, F. C, KOETZLE, T. F., WILLIAMS, G.J. B., MEYER, E. F., BRICE, M. D., RODGERS, J. R.
7. KENNARD, O., SHIMANOUCHI, T. & TASUMI, M. (1977). Protein Data Bank-Computer-based archival file for macromolecular structures. Journal of Molecular Biology 112, 535-542.
8. BOROVINSKAYA, M.A., SHOJI, S., FREDRICK, K. & CATE, J. H. D. (2008). Structural basis for hygromycin B inhibition of protein biosynthesis. RNA 14, 1590-1599.
9. CARTER, A.P., CLEMONS, W.M., BRODERSEN, D.E., MORGAN-WARREN, R.J., WIMBERLY, B.T. & RAMAKRISHNAN, V. (2000). Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407, 340-348.
10. CHACON, P., TAMA, F. & WRIGGERS, W. (2003). Mega-Dalton biomolecular motion captured from electron microscopy reconstructions. Journal of Molecular Biology 326, 485-492.
11. DLUGOSZ, M. & TRYLSKA, J. (2009). Aminoglycoside association pathways with the 30S ribosomal subunit. Journal of Physical Chemistry B 113, 7322-7330.
12. ELCOCK, A. H. (2006). Molecular Simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome. Plos Computational Biology 2, 824-841.
13. FRANK, J. (2003). Electron microscopy of functional ribosome complexes. Biopolymers 68, 223-233.
14. FRANK, J. & AGRAWAL, R. K. (2000). A ratchet-like inter-subunit reorganization of the ribosome during trans-location. Nature 406, 318-322.
15. GABASHVILI, I. S., AGRAWAL, R. K., GRASSUCCI, R., SQUIRES, C. L., DAHLBERG, A. E. & FRANK, J. (1999). Major rearrangements in the 70S ribosomal 3D structure caused by a conformational switch in 16S ribosomal RNA. EMBO Journal 18, 6501-6507.
16. GAVRILOVA, L.P., KOSTIASHKINA, O.E., KOTELIANSKY, V. E., RUTKEVITCH, N. M. & SPIRIN, A. S. (1976). Factor-free (non-enzymic) and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribo-somes. Journal of Molecular Biology 101, 537-552.
17. GO, N. (1983). Theoretical-studies of protein folding. Annual Review of Biophysics and Bioengineering 12, 183-210.
18. HAMACHER, K., TRYLSKA, J. & MCCAMMON, J. A. (2006). Dependency map of proteins in the small ribosomal subunit. Plos Computational Biology 2, 80-87.
19. HARMS, J., SCHLUENZEN, F., ZARIVACH, R., BASHAN, A., GAT, S., AGMON, I., BARTELS, H., FRANCESCHI, F. & YONATH, A. (2001). High resolution structure of the large ribosomal subunit from a mesophilic Eubacterium. Cell 107, 679-688.
20. HELD, W.A., BALLOU, B., MIZUSHIM, S. & NOMURA, M. (1974). Assembly mapping of 30 S ribosomal-proteins from Escherichia coli-further studies. Journal of Biological Chemistry 249, 3103-3111.
21. HERMANN, T. (2005). Drugs targeting the ribosome. Current Opinion in Structural Biology 15, 355-366.
22. HONIG, B. & NICHOLLS, A. (1995). Classical electrostatics in biology and chemistry. Science 268, 1144-1149.
23. HUMPHREY, W., DALKE, A. & SCHULTEN, K. (1996). VMD: visual molecular dynamics. Journal of Molecular Graphics 14, 33-38.
24. ISHIDA, H. & HAYWARD, S. (2008). Path of nascent poly-peptide in exit tunnel revealed by molecular dynamics simulation of ribosome. Biophysical Journal 95, 5962-5973.
25. JENNI, S. & BAN, N. (2003). The chemistry of protein synthesis and voyage through the ribosomal tunnel. Current Opinion in Structural Biology 13, 212-219.
26. KIRMIZIALTIN, S., GANESAN, V. & MAKAROV, D. E. (2004). Translocation of a beta-hairpin-forming peptide through a cylindrical tunnel. Journal of Chemical Physics 121, 10268-10277.
27. KLEIN, D. J., MOORE, P. B. & STEITZ, T. A. (2004). The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. Journal of Molecular Biology 340, 141-177.
28. KOROSTELEV, A., ERMOLENKO, D.N. & NOLLER, H.F. (2008). Structural dynamics of the ribosome. Current Opinion in Chemical Biology 12, 674-683.
29. KURKCUOGLU, O., DORUKER, P., SEN, T. Z., KLOCZKOWSKI, A. & JERNIGAN, R. L. (2008). The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. Physical Biology 5, 46005.
30. KURKCUOGLU, O., KURKCUOGLU, Z., DORUKER, P. & JERNIGAN, R. L. (2009). Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins 75, 837-845.
31. LILJAS, A. (2004). Structural Aspects of Protein Synthesis. Singapore: World Scientific Publishing Co. Pte. Ltd.
32. LU, J. L. & DEUTSCH, C. (2005). Folding zones inside the ribosomal exit tunnel. Nature Structural & Molecular Biology 12, 1123-1129.
33. MA, C. S., BAKER, N. A., JOSEPH, S. & MCCAMMON, J. A. (2002). Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. Journal of the American Chemical Society 124, 1438-1442.
34. MALHOTRA, A., TAN, R. K. Z. & HARVEY, S. C. (1994). Modeling large RNAs and ribonucleoprotein-particles using molecular mechanics techniques. Biophysical Journal 66, 1777-1795.
35. MEROUEH, S. O. & MOBASHERY, S. (2007). Conformational transition in the aminoacyl t-RNA site of the bacterial ribosome both in the presence and absence of an ami-noglycoside antibiotic. Chemical Biology & Drug Design 69, 291-297.
36. MITRA, K., SCHAFFITZEL, C., FABIOLA, F., CHAPMAN, M. S., BAN, N. & FRANK, J. (2006). Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements. Molecular Cell 22, 533-543.
37. MUNRO, J.B., VAIANA, A., SANBONMATSU, K.Y. & BLANCHARD, S. C. (2008). A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET. Biopolymers 89, 565-577.
38. NAKATOGAWA, H. & ITO, K. (2002). The ribosomal exit tunnel functions as a discriminating gate. Cell 108, 629-636.
39. POEHLSGAARD, J. & DOUTHWAITE, S. (2005). The bacterial ribosome as a target for antibiotics. Nature Reviews Microbiology 3, 870-881.
40. POWERS, T., DAUBRESSE, G. & NOLLER, H. F. (1993). Dynamics of in-vitro assembly of 16-S ribosomal-RNA into 30-S ribosomal-subunits. Journal ofMolecular Biology 232, 362-374.
41. QIN, S. B. & ZHOU, H. X. (2009). Dissection of the high rate constant for the binding of a ribotoxin to the ribosome. Proceedings of the National Academy of Sciences USA 106, 6974-6979.
42. QIZHI CUI, R. Z-K. TAN, HARVEY, S. C. & CASE, D. A. (2006). Low-resolution molecular dynamics simulations of the 30S ribosomal subunit. Multiscale Modeling and Simulation 5, 1248-1263.
43. REBLOVA, K., LANKAS, F., RAZGA, F., KRASOVSKA, M. V., KOCA, J. & SPONER, J. (2006). Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations. Biopolymers 82, 504-520.
44. RODNINA, M. V., BERINGER, M. & WINTERMEYER, W. (2006). Mechanism of peptide bond formation on the ribosome. Quarterly Reviews of Biophysics 39, 203-225. (Pubitemid 44950378)
45. ROMANOWSKA, J., SETNY, P. & TRYLSKA, J. (2008). Molecular dynamics study of the ribosomal A-site. Journal of Physical Chemistry B 112, 15227-15243.
46. SANBONMATSU, K. Y. (2006). Energy landscape of the ribosomal decoding center. Biochimie 88, 1053-1059.
47. SANBONMATSU, K. Y., JOSEPH, S. & TUNG, C. S. (2005). Simulating movement of tRNA into the ribosome during decoding. Proceedings of the National Academy of Sciences USA 102, 15854-15859.
48. SANBONMATSU, K. Y. & TUNG, C. S. (2007). High performance computing in biology: multimillion atom simulations of nanoscale systems. Journal of Structural Biology 157, 470-480.
49. SCHLICK, T. (2002). Molecular Modeling and Simulation, Springer-Verlag.
50. SCHLUENZEN, F., TOCILJ, A., ZARIVACH, R., HARMS, J., GLUEHMANN, M., JANELL, D., BASHAN, A., BARTELS, H., AGMON, I., FRANCESCHI, F. & YONATH, A. (2000). Structure of functionally activated small ribosomal subunit at 3-3 angstrom resolution. Cell 102, 615-623.
51. SOUTHWORTH, D. R., BRUNELLE, J. L. & GREEN, R. (2002). EFG-independent translocation of the mRNA: tRNA complex is promoted by modification of the ribosome with thiol-specific reagents. Journal of Molecular Biology 324, 611-623.
52. STAGG, S. M., MEARS, J. A. & HARVEY, S. C. (2003). A structural model for the assembly of the 30 S subunit of the ribosome. Journal ofMolecular Biology 328, 49-61.
53. TALKINGTON, M. W. T., SIUZDAK, G. & WILLIAMSON, J. R. (2005). An assembly landscape for the 30S ribosomal subunit. Nature 438, 628-632.
54. TAMA, F., VALLE, M., FRANK, J. & BROOKS, C. L. (2003). Dynamic reorganization of the functionally active ribo-some explored by normal mode analysis and cryo-elec-tron microscopy. Proceedings of the National Academy of Sciences USA 100, 9319-9323.
55. TENSON, T. & EHRENBERG, M. (2002). Regulatory nascent peptides in the ribosomal tunnel. Cell 108, 591-594.
56. TRYLSKA, J., KONECNY, R., TAMA, F., BROOKS, C.L. & MCCAMMON, J. A. (2004). Ribosome motions modulate electrostatic properties. Biopolymers 74, 423-431.
57. TRYLSKA, J., MCCAMMON, J. A. & BROOKS, C. L. (2005a). Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. Journal of the American Chemical Society 127, 11125-11133.
58. TRYLSKA, J., TOZZINI, V. & MCCAMMON, J. A. (2005b). Exploring global motions and correlations in the ribo-some. Biophysical Journal 89, 1455-1463.
59. TUNG, C. S. & SANBONMATSU, K. Y. (2004). Atomic model of the Thermus thermophilus 70S ribosome developed in silico. Biophysical Journal 87, 2714-2722.
60. VAIANA, A. C. & SANBONMATSU, K. Y. (2009). Stochastic gating and drug-ribosome interactions. Journal of Molecular Biology 386, 648-661.
61. VALLE, M., ZAVIALOV, A., SENGUPTA, J., RAWAT, U., EHRENBERG, M. & FRANK, J. (2003). Locking and unlocking of ribosomal motions. Cell 114, 123-134.
62. VOSS, N. R., GERSTEIN, M., STEITZ, T. A. & MOORE, P. B. (2006). The geometry of the ribosomal polypeptide exit tunnel. Journal of Molecular Biology 360, 893-906.
63. WANG, Y. M., RADER, A. J., BAHAR, I. & JERNIGAN, R. L. (2004). Global ribosome motions revealed with elastic network model. Journal of Structural Biology 147, 302-314.
64. WILLIAMSON, J. R. (2008). Biophysical studies of bacterial ribosome assembly. Current Opinion in Structural Biology 18, 299-304.
65. WILSON, D. N. & NIERHAUS, K. H. (2003). The ribosome through the looking glass. Angewandte Chemie-International Edition 42, 3464-3486.
66. WIMBERLY, B. T., BRODERSEN, D. E., CLEMONS, W. M., MORGAN-WARREN, R. J., CARTER, A. P., VONRHEIN, C., HARTSCH, T. & RAMAKRISHNAN, V. (2000). Structure of the 30S ribosomal subunit. Nature 407, 327-339.
67. YAN, A. M., WANG, Y. M., KLOCZKOWSKI, A. & JERNIGAN, R. L. (2008). Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome. Journal of Chemical Theory and Computation 4, 1757-1767.
68. YANG, G., TRYLSKA, J., TOR, Y. & MCCAMMON, J. A. (2006). Binding of aminoglycosidic antibiotics to the oligonu-cleotide A-site model and 30S ribosomal subunit: Poisson-Boltzmann model, thermal denaturation, and fluorescence studies. Journal of Medicinal Chemistry 49, 5478-5490.
69. YUSUPOV, M. M., YUSUPOVA, G. Z., BAUCOM, A., LIEBERMAN, K., EARNEST, T. N., CATE, J. H. D. & NOLLER, H. F. (2001). Crystal structure of the ribosome at 5-5 angstrom resolution. Science 292, 883-896.
70. ZIV, G., HARAN, G. & THIRUMALAI, D. (2005). Ribosome exit tunnel can entropically stabilize alpha-helices. Proceedings of the National Academy of Sciences USA 102, 18956-18961.