Snapshots, frequency contact maps analysis, Poisson Boltzmann calculations, and data scripts for characterization of structural and energetic differences between conformations of the SARS-CoV-2 spike protein

Molecular dynamics simulation trajectories, which have been performed using the Amber ff14SB force field running with the Amber18 package at the NSF-funded (OAC-1826915, OAC-1828163) ELSA high performance computing cluster at The College of New Jersey. Simulation methodology and further details are described in [1] and [2]. For further details on the trajectories, please contact Joseph Baker (bakerj@tcnj.edu).

The Poisson Boltzmann energy calculations have been achieved by using the input_files.tar.xz found here and solving the Poisson Boltzmann equation with pygbe. A more detailed example and tutorial can be found at [4]. For further details contact Horacio V Guzman.

The dataset contains

• A total of 30 snapshots of the three trajectories (10 snapshots each system = two per replica x 5 replicas/system):

1. SARS-CoV-2002 spike protein with three RBD in the down positions: "COV2-DDD/PDB/" .
2. SARS-CoV-2002 spike protein with one RBD in the up and two RBD in the down positions: "COV2-UDD/PDB/".
3. SARS-CoV-2002 spike protein with two RBD in the up and one RBD in the down positions: "COV2-DUU/PDB/".

• Input files for Poisson-Boltzmann analysis:

1. PoissonBoltzmann/input_files.tar.xz

• Data for the frequency contact map and processing scripts:

1. cov2-ddd.pdb, cov2-udd.pdb, cov2-duu.pdb reference PDB files.
2. Contact maps [3] at  "COV2-DDD/CONTACT_MAP/",  "COV2-UDD/CONTACT_MAP/",  "COV2-DUU/CONTACT_MAP/".
3. frequency.lua: get frequency of contacts from a set of contacts map files.
4. diff_frequency.lua: get differential frequency of contacts from a set of frequency files.
5. Frequency of contacts listed in frequency.data files at "COV2-DDD/", "COV2-UDD/" and "COV2-DUU/" directories.

Read the "INFO" files for further informations.

This dataset and the code is part of a collaboration between:

• The Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland (supported by the National Science Centre, Poland, under grant No. 2017/26/D/NZ1/0046)
• Department of Chemistry, The College of New Jersey, New Jersey, United States (supported by National Science Foundation under grant numbers OAC-1826915 and OAC-1828163).
• Jozef Stefan Institute, Ljubljana, Slovenia (supported by the Slovenian Research Agency (Funding No. P1-0055)).
• School of engineering in bioinformatics, University of Talca, Talca, Chile.

[1] Rodrigo A. Moreira, Mateusz Chwastyk, Joseph L. Baker, Horacio V Guzman, & Adolfo B. Poma. (2020). All-atom simulations snapshots and contact maps analysis scripts for SARS-CoV-2002 and SARS-CoV-2 spike proteins with and without ACE2 enzyme (Version 0.1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3817447

[2] Chad W. Hopkins, Scott Le Grand, Ross C. Walker, and Adrian E. Roitberg. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. Journal of Chemical Theory and Computation 2015 11 (4), 1864-1874. http://doi.org/10.1021/ct5010406

[3] Rodrigo A. Moreira, Mateusz Chwastyk, Joseph L. Baker, Horacio V Guzman, & Adolfo B. Poma. Quantitative determination of mechanical stability in the novel coronavirus spike protein. Nanoscale, 2020,12, 16409-16413. https://doi.org/10.1039/D0NR03969A

[4] https://github.com/pyF4all