Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments

Abstract

We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and ROSETTA's FARFAR2 algorithm. The conformations observed in MD consist of A-form-like structures and variations thereof. These structures are not present in the pool generated using FARFAR2. By comparing with available NMR measurements, we show that the presence of both A-form-like and other extended conformations is necessary to quantitatively explain experimental data. To further validate our results, we measure SAXS data on the RNA hexamer and find that simulations result in more compact structures than observed from these experiments. The integration of simulations with NMR via a maximum entropy approach shows that small modifications to the MD ensemble lead to an improved description of the conformational ensemble. Nevertheless, we identify persisting discrepancies in matching experimental SAXS data.

Combining simulations and experiments to investigate RNA dynamics

“…It is unclear if this is due to the higher accuracy of FARFAR or to better sampling. Furthermore, these results might be contrasted with the opposite finding in two papers discussed above [28,37].…”

“…A similar approach was used in Ref. [37], where reweighting was conducted using either NMR or SAXS data on ensembles generated for an RNA hexamer. Agreement with NMR did not necessarily result in agreement with SAXS, and vice versa, suggesting that multiple, independent experimental observables are important to assess the accuracy of heterogeneous structural ensembles.…”

Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes

“…A common method to study RNA flexibility, RNA dynamics, and conformational rearrangements for isolated RNA molecules or RNA-ligand/RNA-protein complexes is molecular dynamics simulations using either an all-atom or a coarse-grain representation. However, the millisecond simulations currently reachable are computationally expensive, several replica are needed, enhanced methods are still limited for these tasks, and the size of RNA molecules is small. ,,− Moreover, these methods are still of limited use for RNA-protein/RNA-ligand docking without reliable starting conformations. Therefore, simplified and faster methods are highly sought.…”

Internal Normal Mode Analysis applied to RNA flexibility and conformational changes

“…13,14 In this context, predicting both the structure and structural transitions and conformational changes linked to the interactions is very important, particularly in view of the increasing use of relatively low-resolution data obtained by small-angle X-ray scattering (SAXS), cryoEM or biochemical probing (for example Selective 2'-Hydroxyl Acylation analyzed by Primer Extension, SHAPE) [15][16][17] and to develop new integrative approaches. [18][19][20][21][22][23][24] Predicting local or global changes in RNA conformations is still very di cult. In some cases, this hinders the prediction of the structure of the complex or the change of RNA folding.…”

“…However, the millisecond simulations currently reachable 25 are computationally expensive, several replica are needed and enhanced methods are still limited for these tasks and the size of RNA molecules is small. 12,22,[26][27][28][29] Moreover, these methods are still of limited use for RNA-protein/RNA-ligand docking without reliable starting conformations. Therefore, simplified and faster methods are highly sought.…”