Understanding the kinetic mechanism of RNA single base pair formation

Abstract

RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/ dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. RNAs perform critical cellular functions at the level of gene expression and regulation (1-4). RNA functions are determined not only by RNA structure or structure motifs [e.g., tetraloop hairpins (5, 6)] but also by conformational distributions and dynamics and kinetics of conformational changes. For example, riboswitches can adopt different conformations in response to specific conditions of the cellular environment (7,8). Understanding the kinetics, such as the rate and pathways for the conformational changes, is critical for deciphering the mechanism of RNA function (9-19). Extensive experimental and theoretical studies on RNA folding kinetics have provided significant insights into the kinetic mechanism of RNA functions (19-36). However, due to the complexity of the RNA folding energy landscape (37-46) and the limitations of experimental tools (47-55), many fundamental problems, including single base flipping and base pair formation and fraying, remain unresolved. These unsolved fundamental problems have hampered our ability to resolve other important issues, such as RNA hairpin and larger structure folding kinetics. Several key questions remain unanswered, such as whether the hairpin folding is rate-limited by the conformational search of the native base pairs, whose formation leads to fast downhill folding of the whole structure, or by the breaking of misfolded base pairs before refolding to the native structure (18,19,(54)(55)(56)(57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71)(72)(73).Motivated by the need to understand the basic steps of nucleic acids folding, Hagan et al. (74) performed forty-three 200-ps unfolding trajectories at 400 K and identified both on-and offpathway intermediates and two dominant unfolding pathways for a terminal C-G base pair in a DNA duplex. In one of the pathways, bas...

MCTBI: a web server for predicting metal ion effects in RNA structures

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RNA folding kinetics using Monte Carlo and Gillespie algorithms

“…Indeed, mean first passage times for protein and/or RNA folding have been computed by matrix inversion and/or Monte Carlo simulations over a Markov chain [30,49,7,25,51,32], while the master equation and/or Gillespie simulations have been used in [17,53,4,14,56]. Of particular interest is the construction of Markov state models from molecular dynamics folding trajectories for a protein or RNA molecule, followed by either mean first passage time computed by matrix inversion [51] versus equilibrium time computed by solving the master equation [56]. This leads to the question: what is the relation between mean first passage time computed by the Monte Carlo algorithm versus the Gillespie algorithm?…”

NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions

“…Changes in hydration, the formation of encounter complexes, and the residency time of metal ions bound to RNA occur on the femtosecond to nanosecond time scale. 16,33,34,48,49 Femtosecond time-resolved spectroscopy provides new insight into the motions of RNA bases during these fast time scale events in the formation of RNA–metal ion interactions.…”

“…34 Metal ion departure can destabilize base stacking and thus initiate a transition from a trapped RNA conformation. 34 Metal ion binding to RNA loops can change helix bending angles and thus the overall architecture of an RNA fold. 42 In the preQ1 riboswitch, metal ion binding can shift ligand binding from an induced fit to a conformational selection mechanism.…”