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0 ns and 75 ns configurations of glycosylated ACE2-FC and its interaction with SARS-CoV-2 binding domains

Citation

Faller, Roland et al. (2020), 0 ns and 75 ns configurations of glycosylated ACE2-FC and its interaction with SARS-CoV-2 binding domains, Dryad, Dataset, https://doi.org/10.25338/B82G9B

Abstract

These are initial and final (75ns) configurations in PDB format of  glycosylated ACE2-FC fusion proteins which are promising targets for a COVID-19 therapeutic. Some of them are in interaction witha fragment of the receptor-binding domain (RBD) of the Spike Protein S of the SARS-CoV-2 virus. We used two  glycosylation variants for ACE2-FC, variant 1 is fully glycosylated with Man8 glycans, variant 2 is fully glycosylated with GnGnXF3. The Spike RBD is glycosylated with ANaF^6.

Methods

Molecular Dynamics Simulations using Gromacs

 

Details:

  1. Fuse ACE2 with Fc to ACE2-Fc using Modeller 
  2. Model Zn2+ and coordinating residues with MCPB.py 
  3. Attach glycans using glycam.org 
  4. Merge structures from 2. and 3. using github.com/austenb28/MCPB_Glycam_merge 
  5. Generate topology files using AmberTools 
  6. Convert topology files to Gromacs format using Acpype 
  7. Perform rigid energy minimization (EM) of glycans using github.com/austenb28/GlyRot
  8. Perform EM (emtol = 1000 kJ/mol/nm)
  9. Solvate and add ions
  10. Perform 10 ps constant volume (NVT) (dt = 0.2 fs, T = 310 K)
  11. Perform EM (emtol = 1000 kJ/mol/nm)
  12. Perform 100 ps NVT (dt = 2 fs, T = 310 K)
  13. Perform 100 ps constant pressure (NPT) (dt = 2 fs, T = 310 K, P = 1 atm)
  14. Perform 75 ns production NPT (dt = 2 fs, T = 310 K, P = 1 atm)

Usage Notes

Any molecular simulation software which can read pdb files can be used for simulations (e.g. gromacs which is open source was used to generate the data). For simple viewing any pdb reader, e.g. Jmol can be used.

Funding

UC Davis COVID-19 Research Accelerator Funding Track