RNA folding pathways in stop motion

Abstract

We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal structures are heterogeneous enough to describe metastable as well as intermediate states. These ensembles are first validated by performing a quantitative comparison against available solution nuclear magnetic resonance (NMR) data of a set of RNA tetranucleotides. Notably, the agreement is better with respect to the one obtained by comparing NMR with extensive all-atom molecular dynamics simulations. We then propose a procedure based on diffusion maps and Markov models that makes it possible to obtain reaction pathways and their relative probabilities from fragment ensembles. This approach is applied to study the helix-to-loop folding pathway of all the tetraloops from the GNRA and UNCG families. The results give detailed insights into the folding mechanism that are compatible with available experimental data and clarify the role of intermediate states observed in previous simulation studies. The method is computationally inexpensive and can be used to study arbitrary conformational transitions.

Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement

“…For each force field, we evaluate the RMSE associated to scalar coupling as well as the number of violations and false positives in contacts predicted by nuclear Overhauser experiments (NOEs). NOEs are particularly important in tetranucleotides since they are sensitive to intercalated structures erroneously obtained using the Amber force field that have been previously reported [14][15][16][17] . We notice that NOEs might not be visible for many reasons others than the distance is too large.…”

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

“…Such modeling attempts have now to face new challenges: finding not only one, but two or more folds, while grasping their relationship with the environment. Recently, some simple procedures based on diffusion maps and Markov models found the alternative Z-turn fold of a GAAA loop (Bottaro et al 2016). Such methods are however currently limited to small fragments-4 nt and no closing base pair in that instance.…”

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models

“…SI 14, SI 15). State #3 contains intercalated structures analogous to the one reported in previous works, 11,13,19,22,54 while state #0 presents A2 and A4 flipped out and stacked on each other. It is reasonable to expect other combinations of base orientation and stackings to arise when increasing the sampling.…”

“…We excluded from the calculations the contributions of the formation of intercalated/non-canonical structures, since the increased stability of such structures is a known limitation of the current force field. 11,13,19,22,54 This was done by using Eq. 4 and setting to zero the amplitudes, γ i , of the relative processes.…”