Transfer RNAs: Electrostatic patterns and an early stage of recognition by synthetases and elongation factor EF-Tu

Biochemistry

Volumn 45, Issue 14, 2006, Pages 4481-4490

  Polozov, Robert V ^a   Montrel, Mikhail ^a   Ivanov, Victor V ^b,c   Melnikov, Yuri ^c   Sivozhelezov, Victor S ^d,e  

^a INSTITUTE OF THEORETICAL AND EXPERIMENTAL BIOPHYSICS   (Russian Federation)

^b JOINT INSTITUTE FOR NUCLEAR RESEARCH   (Russian Federation)

^c INTERNATIONAL SOLVAY INSTITUTES   (Belgium)

^d UNIVERSITY OF GENOA   (Italy)

^e INSTITUTE OF CELL BIOPHYSICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROSTATICS; ENZYMES; IONIZATION; PH EFFECTS; POISSON EQUATION; PROTONS;

ELECTROSTATIC PATTERNS; ELECTROSTATIC RECOGNITION; HISTIDINE RESIDUES; TRNA;

RNA;

AMINOACYL TRANSFER RNA; ELONGATION FACTOR TU; HISTIDINE; PHOSPHATE; SYNTHETASE; TRANSFER RNA;

ARTICLE; ELECTRICITY; ENERGY; IONIZATION; MOLECULAR RECOGNITION; PH; PRIORITY JOURNAL; PROTEIN RNA BINDING; RNA STRUCTURE; RNA TRANSLATION;

AMINO ACYL-TRNA SYNTHETASES; ELECTROSTATICS; MODELS, MOLECULAR; PEPTIDE ELONGATION FACTOR TU; RNA, TRANSFER; RNA, TRANSFER, AMINO ACYL;

EID: 33645678058     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0516733     Document Type: Article

References (37)

1. Koolman, J., and Rohm, K. H. (1998) Taschenatlas der Biochemie, Suttgart-New York, Georg Thieme Verlag, New York.
2. Rodnina, M. V., Gromadski, K. B., Kothe, U., and Wieden, H. J. (2005) Recognition and selection of tRNA in translation, FEBS Lett. 579, 938-942.
3. Wintermeyer, W., Peske, F., Beringer, M., Gromadski, K. B., Savelsbergh, A., and Rodnina, M. V. (2004) Mechanisms of elongation on the ribosome: dynamics of a macromolecular machine, Biochem. Soc. Trans. 32, 733-737.
4. Rodnina, M. V., Beringer, M., and Bieling, P. (2005) Ten remarks on peptide bond formation on the ribosome, Biochem. Soc. Trans. 33, 493-498.
5. Asahara, H., and Uhlenbeck, O. C. (2002) The tRNA specificity of Thermus thermophilus EF-Tu. Proc. Natl. Acad. Sci. U.S.A. 99, 3499-3504.
6. Ohlendorf, D. H., and Matthew, J. B. (1985) Electrostatics and flexibility in protein-DNA interactions, Adv. Biophys. 20, 137-151.
7. Fogolari, F., Elcock, A. H., Esposito, G., Viglino, P., Briggs, J. M., and McCammon, J. A. (1997) Electrostatic effects in homeodomain-DNA interactions, J. Mol. Biol. 267, 368-381.
8. Hsieh, M., and Brenowitz, M. (1997) Comparison of the DNA association kinetics of the Lac repressor tetramer, its dimeric mutant Lacladi, and the native dimeric Gal repressor, J. Biol. Chem. 272, 22092-22096.
9. Jeltsch, A., Wenz, C., Stahl, F., and Pingoud, A. (1996) Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme, EMBO J. 15, 5104-5111.
10. Berkhout, B., and van Wamel, J. (1996) Accurate scanning of the BssHlI endonuclease in search for its DNA cleavage site, J. Biol. Chem. 271, 1837-1840.
11. Lavery, R., Pullman, A., and Pullman, B. (1980) The electrostatic molecular potential of yeast tRNAPhe. (1). The potential due to the phosphate backbone, Nucleic Acids Res. 8, 1061-1079.
12. Sharp, K. A., Honig, B., and Harvey, S. C. (1990) Electrical potential of transfer RNAs: codon-anticodon recognition, Biochemistry 29, 340-346.
13. Chin, K., Sharp, K. A., Honig, B., and Pyle, A. M. (1999) Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function, Nat. Struct. Biol. 6, 1055-1061.
14. Tworowski, D., and Safro, M. (2003) The long-range electrostatic interactions control tRNA-aminoacyl-tRNA synthetase complex formation, Protein Sci. 12, 1247-1251.
15. Fedoseyev, A. I., Sivozhelezov, V. S., Purtov, S. V., Petrenko, I. I., and Lazarev, P. I. (1992) Mathematical modelling of 3D protein molecule potential in nonlinear media, Proceedings of the International Conference "Physique en Herbe-92", Marseille, France, pp 222-228.
16. Holst, M., Kozack, R. E., Saied, F., and Subramaniam, S. (1994) Treatment of electrostatic effects in proteins: multigrid-based Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation, Proteins 18, 231-245.
17. Netz, R. R., and Orland, H. (2003) Variational charge renormalization in charged systems, Eur. Phys. J. E 11, 301-311.
18. Manning, G. S., and Ray, J. (1998) Counterion condensation revisited, J. Biomol. Struct. Dyn. 16, 461-476.
19. Manning, G. S. (1978) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides, Q. Rev. Biophys. 11, 179-246.
20. Lampert, M. A. (1985) The nonlinear Poisson-Boltzmann equation, Nature 315, 159.
21. Fixman, M. (1979) The Poisson-Boltzmann equation and its application to polyelectrolytes, J. Chem. Phys. 70, 4995-5005.
22. Zimm, B. H., and Le Bret, M. (1983) Counter-ion condensation and system dimensionality, J. Biomol. Struct. Dyn. 1, 461-471.
23. Frank-Kamenetskii, M. D., Anshelevich, V. V., and Lukashin, A. V. (1987) Polyelectrolyte model of DNA, Usp. Fiz. Nauk 151, 595-618 (Russian).
24. Lin, S. H., Hsu, J. P., Tseng, S., and Chen, C. J. (2005) Analytical expressions for the electrical potential near planar, cylindrical, and spherical surfaces for symmetric electrolytes, J. Colloid Interface Sci. 281, 255-257.
25. a shift of a fluorophore. 2. Transfer RNA. Eur. J. Biochem. 173, 233-239.
26. a of ligands bound to DNA, Biopolymers 20, 141-154.
27. Misra, V. K., and Honig, B. (1995) On the magnitude of the electrostatic contribution to ligand-DNA interactions, Proc. Natl. Acad. Sci. U.S.A. 92, 4691-4695.
28. Rhee, K. W., Potts, R. O., Wang, C. C., Fournier, M. J., and Ford, N. C., Jr. (1981) Effects of magnesium and ionic strength on the diffusion and charge properties of several single tRNA species, Nucleic Acids Res. 9, 2411-2420.
29. Klapper, I., Hagstrom, R., Fine, R., Sharp, K., and Honig, B. (1986) Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification, Proteins 1, 47-59.
30. Ibba, M., Sever, S., Praetorius-Ibba, M., and Soll, D. (1999) Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis, Nucleic Acids Res. 27, 3631-3637.
31. Ruff, M., Krishnaswamy, S., Boeglin, M., Poterszman, A., Mitschler, A., Podjarny, A., Rees, B., Thierry, J. C., and Moras, D. (1991) Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp), Science 252, 1682-1689.
32. Lipman, R. S., and Hou, Y. M. (1998) Aminoacylation of tRNA in the evolution of an aminoacyl-tRNA synthetase, Proc. Natl. Acad. Sci. U.S.A. 95, 13495-13500.
33. Brereton, P. S., Maher, M. J., Tregloan, P. A., and Wedd, A. G. (1999) Investigation of the role of surface residues in the ferredoxin from Clostridium pasteurianum, Biochim. Biophys. Acta 1429, 307-316.
34. Feinberg, B. A., Ryan, M. D., and Wei, J. F. (1977) Comparative kinetic-ionic strength study of two differently charged cytochrome C: effects are limited to overall charge, Biochem. Biophys. Res. Commun. 79, 769-775.
35. Valle, M., Zavialov, A., Li, W., Stagg, S. M., Sengupta, J., Nielsen, R. C., Nissen, P., Harvey, S. C., Ehrenberg, M., and Frank, J. (2003) Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy, Nat. Struct. Biol. 10, 899-906.
36. Trylska, J., Konecny, R., Tama, F., Brooks, C. L., III, and McCammon, J. A. (2004) Ribosome motions modulate electrostatic properties, Biopolymers 74, 423-431.
37. Dale, T., and Uhlenbeck, O. C. (2005) Binding of misacylated tRNAs to the ribosomal A site, RNA 11, 1610-1615.