Spontaneous binding of single-stranded RNAs to RRM proteins visualised by unbiased atomistic simulations with rescaled RNA force field

Abstract

Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein-RNA interactions. Many such complexes were characterized using NMR and/or X-ray crystallography techniques, revealing ensemble-averaged pictures of the bound states. However, it is becoming widely accepted that better understanding of protein-RNA interactions would be obtained from ensemble descriptions. Indeed, earlier molecular dynamics (MD) simulations of bound states indicated visible dynamics at the RNA-RRM interfaces. Here, we report the first atomistic simulation study of spontaneous binding of short RNA sequences to RRM domains of HuR and SRSF1 proteins. Using millisecond-scale aggregate ensemble of unbiased simulations we were able to observe a few dozens of binding events. The HuR RRM3 utilizes a pre-binding state to navigate the RNA sequence to its partially disordered bound state and then to dynamically scan its different binding registers. The SRFS1 RRM2 binding is more straightforward but still multiple-pathway. The present study necessitated development of a goal-specific force-field modification scaling down the intramolecular vdW interactions of the RNA which also improves description of the RNA-RRM bound state. Our study opens a new avenue for large-scale atomistic investigations of binding landscapes of protein-RNA complexes and future perspectives of such research are discussed.

Establishing the catalytic and regulatory mechanism of RNA‐based machineries

“…Interestingly, for certain systems ff12SB showed improved performance, due to a better description of phenylalanine and tyrosine side‐chains, which are too flexible in ff14SB 146 . A similar drawback was also observed for the more recent ff19SB 147 . Water models SPC/E and OPC showed similarly satisfactory performance 147 .…”

“…146 A similar drawback was also observed for the more recent ff19SB. 147 Water models SPC/E and OPC showed similarly satisfactory performance. 147 How the above mentioned FFLJbb performs for protein/RNA complexes is currently unclear.…”

“…147 Water models SPC/E and OPC showed similarly satisfactory performance. 147 How the above mentioned FFLJbb performs for protein/RNA complexes is currently unclear. Finally, Mg 2+ FFs are also still being improved.…”

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

“…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.…”