Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations
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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 0.5ms 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 characterisation of these systems, and provide putative three-dimensional models for structure-based drug design studies.
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SciScore for 10.1101/2020.12.11.421784: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources MD simulations were conducted using the Amber ff99SB force field with parmbsc0 (Pérez et al., 2007), OL3 (Zgarbová et al., 2011), and corrections to the Van der Waals parameters for oxygen (Steinbrecher et al., 2012) in conjunction with OPC water model (Izadi et al., 2014). Ambersuggested: (AMBER, RRID:SCR_016151)Simulations were performed using GROMACS 2019.4 (Pronk et al., 2013) patched with PLUMED 2.5.3 (Tribello et al., 2014). GROMACSsuggested: (GROMACS, RRID:SCR_014565)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the …SciScore for 10.1101/2020.12.11.421784: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources MD simulations were conducted using the Amber ff99SB force field with parmbsc0 (Pérez et al., 2007), OL3 (Zgarbová et al., 2011), and corrections to the Van der Waals parameters for oxygen (Steinbrecher et al., 2012) in conjunction with OPC water model (Izadi et al., 2014). Ambersuggested: (AMBER, RRID:SCR_016151)Simulations were performed using GROMACS 2019.4 (Pronk et al., 2013) patched with PLUMED 2.5.3 (Tribello et al., 2014). GROMACSsuggested: (GROMACS, RRID:SCR_014565)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
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