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.

This dataset contains the trajectories of 10 microseconds-long coarse-grained molecular dynamics simulations of the soluble part of the wild-type spike protein of SARS-CoV2, the single mutant D614G, and the double mutant T307I/D614G. Simulations are based on the PDB structure 6XR8. Loops were completed using the SwissProt sever, and glycans were not included. Simulations were performed using the SIRAH force field 2.0 running with the Gromacs 2018.3 package at the Institut Pasteur de Montevideo under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020

The following files in gromacs format are provided for each simulation:

i) a .psf containing the topological information (connectivity, etc)

ii) a big .xtc file containing 10 microseconds of the CG protein recorded every 200 picoseconds (50000 frames)

iii) a smaller .xtc file containing the same trajectory but with only one frame per nanosecond (1000 frames)

iv) a .gro file with the initial configuration

Finally, the file sirah_vmdtk.tcl contains a series of macros and scripts that facilitate the visualization and analysis of the CG trajectories. Step-By-Step tutorials for visualizing and analyzing CG trajectories using SirahTools can be found at www.sirahff.com.

To take a quick look at a trajectory using VMD 1.9.3, run the command:

> vmd SpikeWT-SIRAH.psf SpikeWT-SIRAH.gro SpikeWT-SIRAH-1kfrm.xtc -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. 

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

For further details, please contact Sergio Pantano (spantano@pasteur.edu.uy).

Files (10.2 GB)
Name Size
sirah_vmdtk.tcl
md5:14f0b39ea4d53486da193059ed619756
97.6 kB Download
SpikeD614G-SIRAH-1kfrm.xtc
md5:a3e58fc131d8ea0b8a55765320cc5644
66.6 MB Download
SpikeD614G-SIRAH-50kfrm.xtc
md5:8f0906b7ed9b41d5d6aed3575d82a449
3.3 GB Download
SpikeD614G-SIRAH.gro
md5:46ee5b6c4b3cb0962ee51268c7933b02
754.9 kB Download
SpikeD614G-SIRAH.psf
md5:a6d38b12a86410afaac93a697a9541d2
3.0 MB Download
SpikeT307I-D614G-SIRAH-1kfrm.xtc
md5:a162263a160c2605b0b36acc1fd008a5
66.6 MB Download
SpikeT307I-D614G-SIRAH-50kfrm.xtc
md5:866e2348e581df2f0d538b587ca44161
3.3 GB Download
SpikeT307I-D614G-SIRAH.gro
md5:319d24fbb9d732ef50f0eecad1d60f28
754.7 kB Download
SpikeT307I-D614G-SIRAH.psf
md5:eb820b636ddde22af369783ada0309d9
3.0 MB Download
SpikeWT-SIRAH-1kfrm.xtc
md5:def7b84b5af387a3cda2562ba867aae3
66.6 MB Download
SpikeWT-SIRAH-50kfrm.xtc
md5:65c55ec54fb20298c55ae2a686c8cd80
3.3 GB Download
SpikeWT-SIRAH.gro
md5:3cd4a2cff467cf8af2614cf7e6e05401
755.2 kB Download
SpikeWT-SIRAH.psf
md5:9d63aa53fd4bac48444405c27611bd3a
3.0 MB Download
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