Ribosomal elongation cycle: Energetic, kinetic and stereochemical aspects

Journal of Molecular Biology

Volumn 351, Issue 3, 2005, Pages 470-480

  Lim, Valery I ^a   Curran, James F ^b   Garber, Maria B ^c  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b WAKE FOREST UNIVERSITY   (United States)

^c INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

Hydrogen and cation ligand bonds; Kinetic barriers; Kinetic traps; Ribosomal cycle; Translation

Indexed keywords

ELONGATION FACTOR G; ELONGATION FACTOR TU; GAMMA GLUTAMYLTRANSFERASE; GUANOSINE TRIPHOSPHATE;

ARTICLE; CATALYSIS; CELL KINETICS; CHEMICAL BOND; CONFORMATIONAL TRANSITION; DISSOCIATION; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; LIGAND BINDING; MACROMOLECULE; METAL BINDING; MITOCHONDRIAL ENERGY TRANSFER; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN HYDROLYSIS; RNA ANALYSIS; RNA STRUCTURE; RNA SYNTHESIS; RNA TRANSLATION; RNA TRANSPORT; STEREOCHEMISTRY; STRUCTURE ACTIVITY RELATION;

EID: 22544455065     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.06.019     Document Type: Article

References (50)

1. A. Liljas, and M.B. Garber Ribosomal proteins and elongation factors Curr. Opin. Struct. Biol. 5 1995 721 727
2. R.K. Agrawal, P. Penczek, R.A. Grassucci, and J. Frank Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation Proc. Natl Acad. Sci. USA 95 1998 6134 6138
3. K.S. Wilson, and H.F. Noller Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing Cell 92 1998 131 139
4. L.B. Blyn, L.M. Risen, R.H. Griffey, and D.E. Draper The RNA-binding domain of ribosomal protein L11 recognizes an rRNA tertiary structure stabilized by both thiostrepton and magnesium ion Nucl. Acids Res. 28 2000 1778 1784
5. M.M. Yusupov, G.Z. Yusupova, A. Baucom, K. Lieberman, T.N. Earnest, J.H. Cate, and H.F. Noller Crystal structure of the ribosome at 5.5 Å resolution Science 292 2001 883 896
6. L.L. Kisselev Polypeptide release factors in prokaryotes and eukaryotes: same function, different structure Structure 10 2002 8 9
7. P.B. Moore, and T.A. Steitz The involvement of RNA in ribosome function Nature 418 2002 229 235
8. V. Ramakrishnan Ribosome structure and the mechanism of translation Cell 108 2002 557 572
9. H. Stark, M.V. Rodnina, H-J. Wieden, F. Zemlin, W. Wintermeyer, and M. van Heel Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex Nature Struct. Biol. 9 2002 849 854
10. D.N. Wilson, G. Blaha, S.R. Connell, P.V. Ivanov, H. Jenke, and U. Stelzl Protein synthesis at atomic resolution: mechanistics of translation in the light of highly resolved structures for the ribosome Curr. Protein Pept. Sci. 3 2002 1 53
11. A. Bashan, I. Agmon, R. Zarivach, F. Schluenzen, J. Harms, and R. Berisio Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression Mol. Cell 11 2003 91 102
12. C. Woese Molecular mechanics of translation: a reciprocating ratchet mechanism Nature 226 1970 817 820
13. M.V. Rodnina, and W. Wintermeyer Ribosome fidelity: tRNA discrimination, proofreading and induced fit Trends Biochem. Sci. 26 2001 124 130
14. J.M. Ogle, I.V. Murphy, M.J. Tarry, and V. Ramakrishnan Selection of tRNA by the ribosome requires a transition from an open to a closed form Cell 111 2002 721 732
15. B.P. Klaholz, T. Pape, A.V. Zavialov, A.G. Myasnikov, E.V. Orlova, and B. Vestergaard Structure of the Escherichia coli ribosomal termination complex with release factor 2 Nature 421 2003 90 94
16. U.B.S. Rawat, A.V. Zavialov, J. Sengupta, M. Valle, R.A. Grassucci, and J. Linde A cryo-electron microscopic study of ribosome-bound termination factor RF2 Nature 421 2003 87 90
17. M. Valle, A. Zavialov, J. Sengupta, U. Rawat, and M. Ehrenberg Locking and unlocking of ribosomal motions Cell 114 2003 123 134
18. W. Saenger Principles of Nucleic Acid Structure 1984 Springer New York
19. H.A. Scheraga Calculations of conformations of polypeptides Advan. Phys. Org. Chem. 6 1968 103 183
20. L. Pauling, and P. Pauling Chemistry 1975 WH Freeman & Company San-Francisco
21. J.D. Watson Molecular Biology of the Gene 1976 WB Benjamin, Inc Menlo Park, CA
22. D. Chandler Hydrophobicity: two faces of water Nature 417 2002 491
23. J.L. Finney Water? What's so special about it? Phil. Trans. Roy. Soc. ser. B 359 2004 1145 1165
24. A. Vila-Sunjurjo, W.K. Ridgeway, V. Seymaner, W. Zhang, S. Santoso, K. Yu, and J.H.D. Cate X-ray crystal structure of the wt and a hyper-accurate ribosome from Escherichia coli Proc. Natl Acad. Sci. USA 100 2003 8682 8686
25. V.I. Lim Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure J. Mol. Biol. 88 1974 857 872
26. V. Filimonov The thermodynamics of conformation transitions in polynucleotides H.-J. Hinz Thermodynamic Data for Biochemistry and Biotechnology 1986 Springer Berlin/Heidelberg/New York/Tokyo 377 401
27. T. Lazaridis, G. Archontis, and M. Karplus Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics Advan. Protein Chem. 47 1995 231 306
28. G.I. Makhatadze, and P.L. Privalov Energetics of protein structure Advan. Protein Chem. 47 1995 307 425
29. D.M. Taverna, and R.A. Goldstein Why are proteins marginally stable? Proteins: Struct. Funct. Genet. 46 2002 105 109
30. M. Kjeldgaard, and J. Nyborg Refined structure of elongation factor Tu from Escherichia coli J. Mol. Biol. 223 1992 721 742
31. H. Berchtold, L. Reshetnikova, C.O.A. Reisr, K. Schirmer, M. Sprinzl, and R. Hilgenfeld Crystal structure of active elongation factor Tu reveals major domain rearrangements Nature 365 1993 126 132
32. M. Kjeldgaard, P. Nissen, S. Thirup, and J. Nyborg The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation Structure 1 1993 35 50
33. M.S. VanLoock, R.K. Agrawal, I.S. Gabashvili, L. Qi, J. Frank, and S.C. Harvey Movement of the decoding region of the 16S ribosomal RNA accompanies tRNA translocation J. Mol. Biol. 304 2000 507 515
34. V.I. Lim, and J.F. Curran Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure RNA 7 2001 942 957
35. J.F. Atkins, D. Elseviers, and L. Gorini Low activity of β-galactosidase in frameshift mutants of Escherichia coli Proc. Natl Acad. Sci. USA 69 1972 1192 1195
36. J.M. Ogle, D.E. Brodersen, W.M. Clemons Jr, M.J. Tarry, A.P. Carter, and V. Ramakrishnan Recognition of cognate transfer RNA by the 30S ribosomal subunit Science 292 2001 897 902
37. Phe, EF-Tu, and a GTP analog Science 270 1995 1464 1472
38. H. Stark, M.V. Rodnina, J. Rinke-Appel, R. Brimacombe, W. Wintermeyer, and M. van Heel Visualization of elongation factor Tu on the Escherichia coli ribosome Nature 389 1997 403 406
39. D. Mohr, W. Wintermeyer, and M.V. Rodnina GTPase activation of elongation factor Tu and G on the ribosome Biochemistry 41 2002 12520 12528
40. T.M. Schmeing, A.C. Seila, J.L. Hansen, B. Freeborn, J.K. Soukup, and S.A. Scaringe A pre-translocational intermediate in protein synthesis observed in crystal of enzymatically active 50S subunits Nature Struct. Biol. 9 2002 225 230
41. S. Yoshizawa, D. Fourmy, and J.D. Puglisi Recognition of the codon-anticodon helix by ribosomal RNA Science 285 1999 1722 1725
42. M. Valle, R. Gillet, S. Kaur, A. Henne, V. Ramakrishnan, and J. Frank Visualizing tmRNA entry into a stalled ribosom Science 300 2003 127 130
43. V.I. Lim, and M.B. Garber Analysis of recognition of transfer-messenger RNA by the ribosomal decoding center J. Mol. Biol. 346 2005 395 398
44. J. Frank, and R.K. Agrawal A ratchet-like inter-subunit reorganization of the ribosome during translocation Nature 406 2000 318 322
45. M. Yarus, and J.F. Curran The translational context effect D.L. Hatfield B.J. Lee R.M. Pirtle Transfer RNA in Protein Synthesis 1992 CRC Press Boca Raton, FL 319 365
46. D. Smith, and M. Yarus tRNA-tRNA interactions within cellular ribosomes Proc. Natl Acad. Sci. USA 86 1989 4397 4401
47. A. Weijland, and A. Parmeggiany Why do two EF-Tu molecules act in the elongation cycle of protein biosynthesis? Trends Biochem. Sci. 19 1994 188 193
48. T. Pape, W. Wintermeyer, and M. Rodnina Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome EMBO J. 18 1999 3800 3807
49. S.C. Blanchard, R.L. Gonzalez Jr, H.D. Kim, S. Chu, and J.D. Puglisi tRNA selection and kinetic proofreading in translation Nature Struct. Mol. Biol. 11 2004 1008 1014
50. G.N. Ramachandran, and V. Sasisekharan Conformation of polypeptides and proteins Advan. Protein Chem. 28 1968 283 437