Conformational characteristics of the RNA subunit ApA from energy minimization studies

Abstract

AbstractIn an attempt to better our understanding of the conformational stabilities in RNAs, an intensive theoraticl study has been carried out on one of its dimeric subunits, ApA, using an improved set of atom‐atom interaction energy parameters and an improved version of energy‐minimization technique. The C(3′)0endo and the C(2′)‐endo sugar ApA units were sperately considered and 38 probable conformations have been analyzed in each case. The total potential energy, comprising nonbonded, electrostatic, and torsional contributions, was minimized by varying all seven relevant dihedral angles simumtaneously. The result reveal that 17 conformations in the case of C(3′)‐endo sugar ApA and 7 confomations in the case of C(2′)‐endo sugar ApA unit, the lowest energy conformation corresponds to a nonhelical structure and the A‐RNA and the Watson‐Crick‐yype conformations lie at energy levels of about 0.5 and 1.0 Kcal/mo., respectively, above the lowest energy found. For ApA with the lops of different types in the backbone and they all differ in energies by about 3.5 Kcal/mol with refrence to the lowest energy founs. It is noted that the order ofmprefrence of the base stacking is observed in the A‐RNA and the Watson‐Crick type conformers. The ApA unit with C(2′)‐endo sugar is forced to assume phosphodiester conformations with large deviations fom the expected staggered conformations compared to the ApA unit with C(3′)‐endo sugar. The result obtained for ApA are discussed with refrence to those previously obtained for the dApdA unit. Te theoretical predictions are compared with the experimental data on the tRNAPhe crystal, as well as those on fibrous RNAs and RNa subunitlike crystal structures. This study brings out many important aspects of the conformational stability of ApA which have been missed by studies made by others on this system.