Consider the role of metal ions in RNA folding, structure and catalysis. Based o
ID: 980912 • Letter: C
Question
Consider the role of metal ions in RNA folding, structure and catalysis. Based on what we've learned in lecture, please answer the following questions: What is more stabilizing for RNA structure, diffuse or chelated ions? Why? Magnesium is more stabilizing than potassium in RNA structure. Please provide two reasons why. Given that metal ions are important for stabilization of RNA structures, it is difficult to determine whether a ribozyme performs its catalytic mechanism via a metal ion-assisted process or an acid/base process. How would you test this? I expect you to do a bit of literature searching to answer this question.Explanation / Answer
1.The native tertiary structure of an RNA is more compact (and thus has a higher charge density) than partially unfolded forms of the RNA containing only secondary structure. Therefore diffuse ions, either monovalent or divalent, should preferentially stabilize the native structure. In classic studies of tRNA folding, it was found that native tRNA structure becomes more stable as the concentration of Na+ or other group I cations is increased (Cole et al. 1972; Urbanke et al. 1975), and, as noted in the Introduction, tRNA stability increases dramatically with addition of Mg2+. The question is whether the observed tertiary structure stabilization is fully determined by the diffuse ion atmosphere, or whether individual ions that make strong local interactions with special regions of the tertiary structure are important contributors.
2. To answer this question, comparisons have been made between the results of NLPB-based calculations and measurements of either the extent of Mg2+ association with tRNAPhe (Misra and Draper 2000) or the Mg2+-induced stabilization of tRNAPhe tertiary structure (Misra and Draper 2002). The correspondence between theory and experiment is quite good in both cases. These results show that the effect of Mg2+ on tRNA tertiary structure can be explained solely in terms of the interaction of diffuse ions with the higher charge density of the native tRNA structure, and suggest that other possible modes by which Mg2+ might be interacting with tRNA are not energetically important.2 The idea that diffuse ions have a dominant role in tRNA folding runs counter to the long-standing argument that a small number of “strong” Mg2+ ion binding sites are responsible for the dramatic stabilization of tRNA tertiary structure by Mg2+ (Schimmel and Redfield 1980).
We can gladly help you with the third question but you should post it again.