Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

Abstract

The 5′ untranslated region (UTR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structure of such elements has been determined experimentally, their three-dimensional structures are not known yet. Here, we predict structure and dynamics of five RNA stem loops in the 5′-UTR of SARS-CoV-2 by extensive atomistic molecular dynamics simulations, more than 0.5 ms of aggregate simulation time, in combination with enhanced sampling techniques. We compare simulations with available experimental data, describe the resulting conformational ensembles, and identify the presence of specific structural rearrangements in apical and internal loops that may be functionally relevant. Our atomic-detailed structural predictions reveal a rich dynamics in these RNA molecules, could help the experimental characterization of these systems, and provide putative three-dimensional models for structure-based drug design studies.

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements

“…We used RNA secondary structure models of 5'ge RNAs SL1-SL6 taken from recently published data 35 , guided by FARFAR2 83 or designed using the RNAcomposer suite 84 , SL2+3 RNA models were additionally based on 85 . Unlabeled RNA constructs used in this study were produced by in-house optimized in vitro transcription and purified as described previously 36 .…”

RNA triplex structures revealed by WAXS-driven MD simulations

“…This readily applicable approach provides unique insight into some of the interactions that stabilize RNA tertiary structure and enable function.1 with experiments. As an alternative approach, all atom models of RNAs are being successfully refined and tuned to come to agreement with experimental data acquired by NMR, [29][30][31][32][33] cryoEM 34 , solution small 35 or wide angle scattering (SWAXS). 36 A recent study that motivates this one combines the Sample and Select (SaS) approach with wide angle x-ray scattering data on RNA duplexes.…”

“…Subtle variations of the structures are interpreted using correlation maps. 37 As mentioned above, similar data-guided approaches are being exploited in conjunction with other experimental measurements [29][30][31][32][33][34][35] . This integrated approach reveals solution structures of hairpin RNAs alone and complexed with triplex forming oligomers (TFO's).…”

Role of Ionizable Lipids in SARS-CoV2 Vaccines As Revealed by Molecular Dynamics Simulations: From Membrane Structure to Interaction with mRNA Fragments

“…For simulations of RNA, the structure of stem loop 1 (SL1) from the 5' untranslated region (UTR) of the SARS-CoV-2 genome, which was studied in detail by Bottaro et al (2021), was used. The structure from the most populated cluster (the center_SL1_0.pdb file from ref 15 dataset) was taken as an initial structure.…”

“…In order to study RNA interactions with IL containing mixtures, we took a stem-loop 1 (SL1) from 5' untranslated region of SARS-CoV-2 genome from Bottaro et al 15 comprising of two helices with internal asymmetrical loop segment. First, to assess the stability of the RNA molecule in our simulations, SL1 fragment alone was subjected to free MD simulation in bulk water.…”