Abstract
Yeast tRNAPhe is an L-shaped molecule, where each arm is a short segment of double-helical RNA. Examination of the crystal structure has suggested that the molecule may be hinged, perhaps in the region where the anticodon stem meets the D stem1, or where the two arms of the molecule meet2. Because tRNA interacts with a variety of macromolecules during protein synthesis, and because it performs various functions in addition to its role in protein synthesis3, the idea of a hinge is attractive: such conformational flexibility would facilitate functional flexibility. Here we present the results of a theoretical study of the bending of tRNAPhe about the proposed hinge at the junction of the two arms2, applying the conformational energy calculation method used previously to examine flexibility in lysozyme4 and in DNA5. The model is surprisingly flexible, swivelling with two degrees of freedom through angles as large as 30° at an energetic cost of only a few kcal per mol. These energies are comparable with that of a few hydrogen bonds, suggesting that solvent conditions and interactions with other molecules are important in modulating structure and flexibility.
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Harvey, S., McCammon, J. Intramolecular flexibility in phenylalanine transfer RNA. Nature 294, 286–287 (1981). https://doi.org/10.1038/294286a0
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DOI: https://doi.org/10.1038/294286a0
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