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41701-GB7
Molecular Dynamics Analyses of Posttranscriptionally Modified tRNA Molecules
Correct anticodon-codon recognition in the context of the ribosome is critical to translational accuracy. In some organisms, nonstandard nucleic acid bases, which contain chemically modified functional groups, are required for correct tRNA binding to programmed ribosomes.
Escherichia coli tRNAPhe, contains two nonstandard bases in the anticodon stem loop (ASL) for correct codon recognition. Pseudouridine (ψ) is found at both positions 32 and 39 of the ASL, generally providing thermodynamic stability (1). Pseudouridine alone is not enough to provide biological function. In fact, removal of 2-thiomethyl-N6-dimethylallyl adenosine at position 37 (ms2i6A37) impairs tRNA anticoodon-codon recognition (2). From NMR studies, this is due to widening of the anticodon loop (3).
Molecular dynamics studies of 6 different ASLs containing various combinations of ψ and ms2i6A have been carried out with 10.0 ns production runs in explicit water with AMBER 8.0 (4) employing the Cheatham modifications (5) to the Cornell et al. force field (6). Simulations of these six ASLs corroborate NMR studies showing ms2i6A37 increases dynamics in the loop structure (3). This loop structure however, is not a canonical U-turn motif. Simulations with both ms2i6A and another ASL with ms2i6A and y indicate that G34 is very mobile. Presence of ms2i6A sterically widens the anticodon loop, encouraging the G34 to be more dynamic. Other NMR studies have shown that in the presence of cobalt (III) hexamine and Mg2+, that the anitcodon loop is ordered, exhibiting a structure more like canonical tRNA (7).
Four systems that contain cobalt(III) hexamine have been constructed with varying numbers of ions and starting configurations. Starting structures were begun from a model ASL structure obtained from Ed Nikonowicz (personal communication). Cobalt(III) hexamine parameters were taken from Cheatham (8). Ions were placed according to the electrostatic potential. Explicit solvent calculations were carried out for 4 systems, one at 27 mM [Co3+] ,one at 18 mM [Co3+] and two at 9 mM [Co3+]. Simulations indicated that cobalt(III) hexamine is difficult to pin down. RNA structure in the anticodon stem loop varied greatly depending upon original placement of the ion. It is unclear if these simulations represent the true system. More studies need to be conducted to understand how the charge of cobalt(III) hexamine influences the ASL structure.
1. Davis, D.R. and Poulter, C.D. Biochemistry 1991, 30, 4223-4231.
2. Ericson, J.U. and Bjork, G.R. J. Mol. Biol. 1991, 218, 509-516.
3. Cabello-Villegas, J. et al. J. Mol. Biol. 2002, 319. 1015-1034.
4. Case, D.A. et al. AMBER 8.0.University of California, San Francisco. 2004.
5. Cheatham III, T.E. et al. J. Biomol. Struct. Dynm. 1998, 15, 1121-1132.
6. Cornell, W.D. et al. J. Am. Chem. Soc. 1984, 117, 5179-5197.
7. Cabello-Villegas, J. et al. Biochemistry 2004, 43, 55-66.
8. Cheatham III, T.E. and Kollman, P.A. Structure 1997, 5, 1297-1311.
