Role of large thermal fluctuations and magnesium ions in t-RNA selectivity of the ribosome

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

Volumn 108, Issue 10, 2011, Pages 3947-3951

  Guo, Zuojun ^a   Gibson, Meghan ^a   Sitha, Sanyasi ^a   Chu, Steven ^b,c   Mohanty, Udayan ^a  

^a BOSTON COLLEGE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c U S DEPARTMENT OF ENERGY   (United States)

Author keywords

Biomolecular machinery; Magnesium binding sites; Rare events

Indexed keywords

GUANOSINE TRIPHOSPHATASE; MAGNESIUM ION; TRANSFER RNA;

ARTICLE; BINDING SITE; CONCEPTUAL FRAMEWORK; ENZYME ACTIVATION; ENZYME BINDING; ENZYME STABILITY; ENZYME STRUCTURE; PRIORITY JOURNAL; PROTEIN MOTIF; RIBOSOME;

BINDING SITES; CATIONS, DIVALENT; GTP PHOSPHOHYDROLASES; MAGNESIUM; PEPTIDE ELONGATION FACTOR TU; RIBOSOMES; RNA, TRANSFER;

EID: 79952745560     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1100671108     Document Type: Article

References (39)

1. Schrodinger E (1944) What is life? (Cambridge University Press, Cambridge).
2. Chu S (2010) Is life based on the laws of physics. Visions of Discovery: New Light on Physics, Cosmology, and Consciousness, eds RY Chiao, ML Cohen, AJ Leggett, WD Phillips, and CL Harper, Jr (Cambridge University Press, Cambridge), pp 452-470.
3. Zhuang X, et al. (2002) Correlating structural dynamics and function in single ribozyme molecules. Science 296:1473-1476. (Pubitemid 34553093)
4. Nahas M, et al. (2004) Observation of internal cleavage and ligation reactions of a ribozyme. Nat Struct Mol Biol 11:1107-1113. (Pubitemid 39453340)
5. Blanchard SC, Kim HD, Gonzalez RL, Jr, Puglisi JD, Chu S (2004) tRNA dynamics on ribosome. Proc Nat Acad Sci USA 101:12893-12898.
6. Blanchard SC, Gonzalez RL, Jr, Kim HD, Chu S, Puglisi JD (2004) tRNA selection and kinetic proofreading in translation. Nat Struct Biol 11:1008-1014. (Pubitemid 39315306)
7. Lee TH, Blanchard SC, Kim HD, Puglisi JD, Chu S (2007) The role of fluctuations in tRNA selection by the ribosome. Proc Natl Acad Sci USA 104:13661-13665. (Pubitemid 350003377)
8. Gonzalez RL, Jr, Chu S, Puglisi JD (2007) Thiostrepton inhibition of tRNA delivery to the ribosome. RNA 13:2091-2097.
9. Valle M, et al. (2003) Incorporation of aminoacytl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat Struct Mol Biol 10:899-906. (Pubitemid 37386098)
10. Olge JM, Murphy FV, Tarry MJ, Ramakrsihnan V (2002) Selection of the ribosome requires a transition from an open to a closed form. Cell 111:721-732. (Pubitemid 35446316)
11. Haran T, Mohanty U (2009) The unique structure of A-tracts and intrinsic DNA bending. Q Rev Biophys 42:41-81.
12. Strauss JK, Maher LJ, 3rd (1994) DNA bending by asymmetric phosphate neutralization. Science 266:1829-1834.
13. Woodson SA (2005) Metal ions and RNA folding: a high charged topic with a dynamic future. Curr Opin Chem Biol 9:104-109.
14. Pyle AM (2002) Metal ions in the structure and function of RNA. J Biol Inorg Chem 7:679-690.
15. Schultes E, Spasic A, Mohanty U, Bartel D (2005) Collapse of randomly generated RNA sequences. Nat Struct Biol 12:1130-1136. (Pubitemid 41746785)
16. Kimes BW, Morris DR (1973) Cations and ribosome structure. II. Effects of the 50S subunit of substituting polyamines for magnesium ion. Biochemistry 12:442-449.
17. Chao FC (1957) Dissociation of macromolecular ribonucleoprotein of yeast. Arch Biochem Biophys 70:426-431.
18. Goldberg A (1966) Magnesium binding by Escherichia coli ribosome. J Mol Biol 16:633-673.
19. McCarthy BJ (1962) Effects of magnesium starvation on ribosome content of Escherichia coli. Biochim Biophys Acta 55:850-888.
20. Zamir A, Miskin R, Vogel Z, Elson D (1974) The inactivation and reactivation of Escherichia coli ribosomes. Method Enzymol 30:406-426.
21. Selmer M, et al. (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313:1935-1942. (Pubitemid 44497996)
22. Schuwirth BS, et al. (2005) Structure of the bacterial ribosome at 3.5 Å resolution. Science 310:827-834. (Pubitemid 41567336)
23. Klein DJ, Moore PJ, Steitz TA (2004) The contribution of metal ions to the structural stability of the large ribosomal subunit. RNA 10:1366-1379. (Pubitemid 39122107)
24. Onsager L, Machlup S (1953) Fluctuations and irreversible processes. Phys Rev 91:1505-1512.
25. Oppenheim I, Shuler KE, Weiss GH (1977) Stochastic process in chemical physics: the master equation (MIT Press, Cambridge).
26. Varadhan SRS (2008) Large deviations. Ann Probab 36:397-419.
27. Freidlin MI, Wentzell AD (1988) Random perturbations of dynamical systems (Springer, New York), 2nd ed.
28. Bühler O (2007) Large deviation theory and extreme waves. Proc. 15th Aha Huliko'a Hawaiian Winter Workshop Proceedings 1-9.
29. Maestro (version 9.0), Jaguar (version 7.6), and Qsite (version 5.5), (Schrödinger, LLC, NY).
30. Friesner RA, Dunietz BD (2001) Larges-scale ab initio quantum chemical calculations on biological systems. Acc Chem Res 34:351-358. (Pubitemid 32816456)
31. Slater NB (1959) Theory of unimolecular reactions (Methuen, London).
32. Wolynes PG (1981) Quantum theory of activated events in condensed phases. Phys Rev Lett 47:968-971.
33. Wang J, Wolynes PG (1999) Intermittency of activated events in single molecules: the reaction diffusion description. J Chem Phys 110:4812-4819. (Pubitemid 129615748)
34. Wang J, Wolynes PG (1996) Instantons and the fluctuating path description of reactions in complex environments. J Phys Chem 100:1129-1136. (Pubitemid 126835005)
35. Whitford PC, et al. (2010) Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA 16:1196-1204.
36. Mohanty U, Spasic A (2008) Counterion condensation in nucleic acid. Adv Chem Phys 139:139-176.
37. Manning GS (1978) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys 11:179-246.
38. Petrov AS, Lamm G, Pack GR (2005) Calculation of the binding free energy for magnesium-RNA interactions. Biopolymers 77:137-154. (Pubitemid 40278855)
39. Fogolari F, Brigo A, Molinari H (2002) The Poisson-Boltzmann equation for electrostatics: a tool for structural biology. J Mol Recognit 15:377-392. (Pubitemid 36101029)