Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

Nucleic Acids Research
Marek HavrilaJirí Sponer

Abstract

We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding...Continue Reading

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Citations

Feb 27, 2020·Nucleic Acids Research·Arijit MaityAnh Tuân Phan
Oct 21, 2020·Physical Review. E·Qiangqiang DuanYi Xiao
Dec 3, 2020·Nucleic Acids Research·Prakash KharelPavel Ivanov
Sep 21, 2020·Current Opinion in Structural Biology·Alexa M Salsbury, Justin A Lemkul
Feb 4, 2021·Journal of Chemical Theory and Computation·Petr StadlbauerJiří Šponer
Mar 13, 2020·Journal of Chemical Theory and Computation·Barira IslamJiří Šponer
Mar 22, 2019·Journal of Chemical Theory and Computation·Petra KührováPavel Banáš
Feb 26, 2019·The Journal of Physical Chemistry Letters·Robert D GrayJonathan B Chaires

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Methods Mentioned

BETA
NMR
X-ray

Software Mentioned

REMD
HBfix
AmberTools14
cpptraj
Amber
AMBER14
py
Nucleic Acid Builder
parmed
REST2

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