Study of Ion Effects in Group II Introns

Abstract

Structure-based models allow milliseconds effective timescale simulations of large biomolecular assemblies. In a structure-based model, the prevalent potential energy minima are defined to correspond to native structures. Here, we have developed an all-atom structure-based model in which non-hydrogen atoms and monovalent (K+, Cl-) and divalent (Mg 2+) ions electrostatics are described explicitly. The effective potentials for ion-ion and ion-RNA interactions are constructed such that solvation is treated implicitly. To ensure correct accumulation of various ionic species near the RNA, charge-charge desolvation potential is introduced. Using an iterative refinement protocol, the effective structure-based parameters aim to reproduce the potential of mean force obtained from two-microsecond explicit-solvent simulations of model RNA structure, until the parameters converge iteratively, optimizes the weights in the effective potential. This transferable set of effective potentials for ion-ion and ion-RNA interactions are then used in structure-based models of group II introns. We study the folding of solution NMR model structure D1κζ from group IIB intron Sc.ai5γ. We determine the association sites and the residence times of the metal ions around the RNA. We study the spatial distribution of Mg2+ as a function of Mg2+ ion concentration to provideimprints into high-affinity ion-RNA interactions that can be associated with tertiary motifs. We provide insights into how diffuse ion atmosphere, outer-sphere ions, site-bound ions, and flexibility drive conformation fluctuations in biomolecular assemblies.