Mechanism of the difference in the binding affinity of E. coli tRNA Gln to glutaminyl-tRNA synthetase caused by noninterface nucleotides in variable loop

Biophysical Journal

Volumn 92, Issue 1, 2007, Pages 192-200

  Yamasaki, Satoshi ^a   Nakamura, Shugo ^a   Terada, Tohru ^a   Shimizu, Kentaro ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; GLUTAMINE TRANSFER RNA LIGASE; NUCLEOTIDE; TRANSFER RNA;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; ENTHALPY; ENTROPY; ESCHERICHIA COLI; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PROTEIN STRUCTURE; SIMULATION;

ESCHERICHIA COLI;

EID: 33846014641     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.093351     Document Type: Article

References (38)

1. Rogers, M. J., and D. Söll. 1988. Discrimination between glutaminyl-tRNA synthetase and seryl-tRNA synthetase involves nucleotides in the acceptor helix of tRNA. Proc. Natl. Acad. Sci. USA. 85:6627-6631.
2. Jahn, M., M. J. Rogers, and D. Söll. 1991. Anticodon and acceptor stem nucleotides in tRNA(Gln) are major recognition elements for E. coli glutaminyl-tRNA synthetase. Nature. 352:258-260.
3. Hayase, Y., M. Jahn, M. J. Rogers, L. A. Sylvers, M. Koizumi, H. Inoue, E. Ohtsuka, and D. Söll. 1992. Recognition of bases in Escherichia coli tRNA(Gln) by glutaminyl-tRNA synthetase: a complete identity set. EMBO J. 11:4159-4165.
4. Ibba, M., K. W. Hong, J. M. Sherman, S. Sever, and D. Söll. 1996. Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proc. Natl. Acad. Sci. USA. 93:6953-6958.
5. Rould, M. A., J. J. Perona, D. Söll, and T. A. Steitz. 1989. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution. Science. 246:1135-1142.
6. Giegé, R., M. Sissler, and C. Florentz. 1998. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res. 26:5017-5035.
7. Bullock, T. L., L. D. Sherlin, and J. J. Perona. 2000. Tertiary core rearrangements in a tight binding transfer RNA aptamer. Nat. Struct. Biol. 7:497-504.
8. Ichiye, T., and M. Karplus. 1991. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins. 11:205-217.
9. Kitao, A., F. Hirata, and N. Go. 1991. The effects of solvent on the conformation and the collective motions of protein - normal mode analysis and molecular-dynamics simulations of melittin in water and in vacuum. Chem. Phys. 158:447-472.
10. Garcia, A. E. 1992. Large-amplitude nonlinear motion in proteins. Phys. Rev. Lett. 68:2696-2699.
11. Hayward, S., A. Kitao, F. Hirata, and N. Go. 1993. Effect of solvent on collective motions in globular protein. J. Mol. Biol. 234:1207-1217.
12. Amadei, A., A. B. Linssen, and H. J. C. Berendsen. 1993. Essential dynamics of proteins. Proteins. 17:412-425.
13. Becker, O. M. 1997. Geometric versus topological clustering: an insight into conformation mapping. Proteins. 27:213-226.
14. Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The protein data bank. Nucleic Acids Res. 28:235-242.
15. Shi, H., and P. B. Moore. 2000. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited. RNA. 6:1091-1105.
16. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
17. Case, D. A., D. A. Pearlman, J. W. Caldwell, T. E. Cheatham III, J. Wang, W. S. Ross, C. Simmerling, T. Darden, K. M. Merz, R. V. Stanton, A. Cheng, J. J. Vincent, et al. 2002. AMBER7. University of California, San Francisco.
18. 3 in the gasphase. J. Am. Chem. Soc. 109:1607-1614.
19. ASP. Biophys. J. 76:50-64.
20. Wang, J. M., P. Cieplak, and P. A. Kollman. 2000. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21:1049-1074.
21. Berendsen, H. J. C., J. P. M. Postma, W. F. Gunsteren, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
22. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes. J. Comput. Phys. 23:327-341.
23. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald - an N·Log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
24. Essmann, U., L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103:8577-8593.
25. Toukmaji, A., C. Sagui, J. Board, and T. Darden. 2000. Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions. J. Chem. Phys. 113:10913-10927.
26. Tsui, V., and D. A. Case. 2000. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers. 56:275-291.
27. Wang, J., M. Morin, W. Wang, and P. A. Kollman. 2001. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J. Am. Chem. Soc. 123:5221-5230.
28. Tsui, V., and D. A. Case. 2001. Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics. J. Phys. Chem. B. 105:11314-11325.
29. Sitkoff, D., K. A. Sharp, and B. Honig. 1994. Accurate calculation of hydration free energies using macroscopic solvent model. J. Phys. Chem. 98:1978-1988.
30. Connolly, M. L. 1993. Analytical molecular-surface calculation. J. Appl. Crystal. 16:548-558.
31. Honig, B., and A. Nicholls. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
32. Schlitter, J. 1993. Estimation of absolute and relative entropies of macromolecules using the covariance-matrix. Chem. Phys. Lett. 215:617-621.
33. Nakamura, S., and J. Doi. 1994. Dynamics of transfer RNAs analyzed by normal mode calculation. Nucleic Acids Res. 22:514-521.
34. Nakamura, S., M. Ikeguchi, and K. Shimizu. 2003. Dynamical analysis of tRNA(Gln)-GlnRS complex using normal mode calculation. Chem. Phys. Lett. 372:423-431.
35. Bahar, I., and R. L. Jernigan. 1998. Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. J. Mol. Biol. 281:871-884.
36. Westhof, E., and M. Sundaralingam. 1986. Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles. Biochemistry. 25:4868-4878.
37. Wang, Y., and R. L. Jernigan. 2005. Comparison of tRNA motions in the free and ribosomal bound structures. Biophys. J. 89:3399-3409.
38. Oliva, R., L. Cavallo, and A. Tramontano. 2006. Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions. Nucleic Acids Res. 34:865-879.