Presence of cations is essential to fold RNA molecules to their tertiary structure. Such cations are either mobile in the solution or bound to specific locations of the RNA fold. The ribosomal GTPase associated center (GAC) is an RNA fold that has both bound magnesium and potassium. According to Draper et al, a bound potassium ion, which cannot be easily displaced by magnesium, is required to stabilize a particular tertiary structure in which it interacts with six oxygen atoms from buried phosphates. According to the crystal structure (PDB entry 1HC8) provided by Draper et al, this partially dehydrated environment is located in a tertiary structure pocket where a hairpin is clamped between its helix and a neighboring helix. Based on predicted strong electrostatic interactions with the buried phosphates, dramatically high binding energy was predicted for this bound potassium by the same research group.Monovalent and divalent ion parameters as well as the RNA force fields have been improved significantly in the recent years. We used these improved parameters to successfully reproduce the above-mentioned ion preference with Amber molecular dynamic simulations. We present how the simulations show that the monovalent ions are preferred over magnesium in the described binding pocket and how removing the ion perturbs the tertiary structure. We also report the results of quantitative energetic analysis based on these molecular dynamic simulations to assess the previously-reported ion binding preference and predicted associated binding energies as an attempt to understand the unique role of the monovalent cation in GAC RNA folding.

Ion binding preference in ribosomal GTPase associated center (GAC)

247th National Meeting (2014)

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