Counterion-Dependent Folding of Azoarcus Ribozyme by SAXS Profile based Hybrid Simulation

Abstract

Multivalent counterions are essential for self-assembly processes of many functional RNAs. With increasing counterion concentrations, RNAs adopt compact intermediates and finally reach their native states. While the changes in global features such as molecular size and flexibility are often discussed using small angle X-ray scattering (SAXS) data, further details of the processes are difficult to address. Here, by sampling the conformational ensemble of the Azoarcus ribozyme using self-organized polymer model, we obtained the structural ensemble of the molecule that confirmed by a pair distance distribution function at various Mg2+ ion concentrations. At each Mg2+ ion condition, there could be many different structural ensembles, each of which equally reproduces the same SAXS profile. Hence, we carried out clustering analysis on the molecular ensembles by using the contact matrices defined for six different paired domains in secondary structure, and analyzed how the Azoarcus ribozyme reaches its native conformation by quantifying the similarity between the clusters. In consistent with the kinetic partitioning mechanism theory, the folding process of the Azoarcus ribozyme adopts multiple pathway. These pathways are more diverse above the transition mid-concentration of Mg2+ ions, suggesting that there are many intermediates along the folding process. Interestingly, although urea shifts the Mg2+ concentration of folding transition to a higher value, the dominant population of folding pathway is formed along the clusters with larger native contacts. This shows that urea can anneal the pathways of the Azoarcus folding dynamics towards the native state.