Conformation of a rare nucleoside in the anti-codon loop of tRNAs: Potential energy calculations for 2′-O-methyl cytidine

Stellman, Steven D.; Hingerty, B.; Broyde, Suse B.; Langridge, R.

The classical potential energy of 2′-O-methyl cytidine was calculated using contributions from van der Waals', electrostatic, and torsional terms. All five conformational angles, namely χ, Ψ, the methoxy angles m₁ and m₂ which are unique to O′-methylated nucleosides, and the sugar pucker P were varied simultaneously, and the energy was minimized with respect to these parameters. An extensive search of conformation space was made, particularly with respect to the sugar pucker. At the predicted global minimum, χ and Ψ are anti-gg, P is C(2′)-endo-C(3′)-exo, and the methyl group is staggered with respect to the sugar. This calculated minimum agrees very well with the recently determined crystal structure of 2′-O-methyl cytidine. Thus, 2′-O-methylation still permits the conformational regions of the common nucleosides to be adopted. However, we infer that the predicted C(2′)-endo sugar pucker results from the added methyl group, since cytidine is C(3′)-endo in the crystal, and the common ribopyrimidine nucleosides generally favor C(3′)-endo.


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May 9, 2014