| Abstract: | In order to assess the solvent–solute association in the tRNAPhe molecule, solvent accessibility calculations were carried out for its crystalline and completely extended states following the method of Lee and Richards. To do this, results from the calculations on model trinucleotide systems pApXpA with different bases at position X were used. In the folded form of the molecule, it was found that the oxygen atoms O(I) and O(II) of almost all the phosphate groups and the O(2′) atoms of the sugar rings situated throughout the backbone were highly exposed to the solvent. The amount of reduction found in the solvent accessibilities of the various atoms in going from the extended state to the folded state of the molecule indicates the kind of compactness of the tertiary structure in tRNAPhe. The results give quantitative support to many characteristics of the tRNA molecule, such as loop sections, buried/exposed residues, hydrophobic interactions, etc., which were thought to be due to other factors. |
