  RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and
their three-dimensional (3D) structures and stability play essential roles in a
variety of biological functions. Therefore, to predict 3D structures and
stability of RNA pseudoknots is essential for understanding their functions. In
the work, we employed our previously developed coarse-grained model with
implicit salt to make extensive predictions and comprehensive analyses on the
3D structures and stability for RNA pseudoknots in monovalent/divalent ion
solutions. The comparisons with available experimental data show that our model
can successfully predict the 3D structures of RNA pseudoknots from their
sequences, and can also make reliable predictions for the stability of RNA
pseudoknots with different lengths and sequences over a wide range of
monovalent/divalent ion concentrations. Furthermore, we made comprehensive
analyses on the unfolding pathway for various RNA pseudoknots in ion solutions.
Our analyses for extensive pseudokonts and the wide range of
monovalent/divalent ion concentrations verify that the unfolding pathway of RNA
pseudoknots is mainly dependent on the relative stability of unfolded
intermediate states, and show that the unfolding pathway of RNA pseudoknots can
be significantly modulated by their sequences and solution ion conditions.
