Dataset Open Access

SIRAH-CoV2 initiative: T307I Mutation in a SARS-CoV-2 Spike from sub-Antarctic Chile

González-Puelma, Jorge; Aldridge, Jacqueline; Montes de Oca, Marco; Pinto , Mónica; Uribe-Paredes, Roberto; Fernández-Goycoolea, José; Alvarez Saravia, Diego; Álvarez, Hermy; Encina, Gonzalo; Weitzel, Thomas; Muñoz, Rodrigo; Olivera-Nappa, Álvaro; Pantano, Sergio; Navarrete, Marcelo A.


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    <subfield code="a">&lt;p&gt;This dataset contains the trajectories&amp;nbsp;of&amp;nbsp;10&amp;nbsp;microseconds-long coarse-grained molecular dynamics simulations of the soluble part of the wild-type spike protein of SARS-CoV2, the&amp;nbsp;single mutant D614G, and the double mutant T307I/D614G. Simulations are based&amp;nbsp;on the PDB structure 6XR8. Loops were completed using the SwissProt sever, and glycans were not included. Simulations were&amp;nbsp;performed using the SIRAH force field 2.0 running with the Gromacs 2018.3 package at the Institut Pasteur de Montevideo&amp;nbsp;under the conditions reported in&amp;nbsp;&lt;a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006"&gt;Machado et al. JCTC 2019&lt;/a&gt;, adding 150 mM NaCl according to&amp;nbsp;&lt;a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953"&gt;Machado &amp;amp; Pantano JCTC 2020&lt;/a&gt;.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;The following files in gromacs format are provided for each simulation:&lt;/p&gt;

&lt;p&gt;i) a .psf containing the topological information (connectivity, etc)&lt;/p&gt;

&lt;p&gt;ii) a big&amp;nbsp;.xtc file containing&amp;nbsp;10 microseconds of the CG protein&amp;nbsp;recorded every 200 picoseconds&amp;nbsp;(50000 frames)&lt;/p&gt;

&lt;p&gt;iii) a smaller .xtc file containing&amp;nbsp;the same trajectory but with only one frame per nanosecond&amp;nbsp;(1000 frames)&lt;/p&gt;

&lt;p&gt;iv) a .gro file with the initial configuration&lt;/p&gt;

&lt;p&gt;Finally, the file&amp;nbsp;sirah_vmdtk.tcl contains a series of macros and scripts that facilitate&amp;nbsp;the visualization and&amp;nbsp;analysis of the CG trajectories.&amp;nbsp;Step-By-Step tutorials for&amp;nbsp;visualizing and analyzing&amp;nbsp;CG trajectories using&amp;nbsp;&lt;a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152"&gt;SirahTools&lt;/a&gt;&amp;nbsp;can be found at www.sirahff.com.&lt;/p&gt;

&lt;p&gt;To take a quick look at a trajectory using VMD 1.9.3, run the command:&lt;/p&gt;

&lt;p&gt;&amp;gt; vmd SpikeWT-SIRAH.psf SpikeWT-SIRAH.gro&amp;nbsp;SpikeWT-SIRAH-1kfrm.xtc -e sirah_vmdtk.tcl&lt;/p&gt;

&lt;p&gt;Note that you can use normal VMD drawing methods as vdw, licorice, etc.,&amp;nbsp;and coloring by&amp;nbsp;restype, element, name, etc.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;This dataset is part of the SIRAH-CoV2&amp;nbsp;initiative for data sharing. If you use this data, please cite Garay PG, et al &amp;quot;The SIRAH-CoV-2 Initiative: A Coarse-Grained Simulations&amp;rsquo; Dataset of the SARS-CoV-2 Proteome&amp;quot;. Front. Med. Technol. 3:644039. doi: 10.3389/fmedt.2021.644039&lt;/p&gt;

&lt;p&gt;For further details, please contact&amp;nbsp;Sergio Pantano (spantano@pasteur.edu.uy).&lt;/p&gt;</subfield>
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