Molecular Dynamics Simulation Data and Analysis Workflow to Investigate Chain Interlocking in the Guanidine-II Riboswitch Dimer

The Guanidine-II Riboswitch (Gd-II RS) is an example of structured RNA that exerts its function by dimerization. This dimerization interface is formed by two tetraloops in which two of the bases form an interlocked pair. This interlocking was first observed in Steuer et al. (2024) (doi.org/10.1093/nargab/lqae132).

To investigate the interactions underlying this conformation and a potential base-identity dependence, we performed molecular dynamics simulations of the Gd-II RS with varied base identity of the interlocking bases. We analyzed the simulation data by adapting a hydrogen-bond based network analysis scheme for dimensionality reduction and clustering. We characterized the resulting clusters using geometric criteria for interlocking and arc diagrams for visualizing changes in hydrogen bond network topology.