Coarse-grained molecular dynamics simulations of SARS-CoV-2 envelope protein E
| Main Authors: | Kuzmin Alexander, Orekhov Philipp, Astashkin Roman, Gordeliy Valentin, Gushchin Ivan |
|---|---|
| Format: | info dataset Journal |
| Bahasa: | eng |
| Terbitan: |
, 2021
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| Subjects: | |
| Online Access: |
https://doi.org/10.1002/prot.26317 |
Daftar Isi:
- The trajectories of coarse-grained (CG) molecular dynamics (MD) simulations of 1) unmodified (NoPTM_POPC_Martini3b: 0.5 & 2.5 μs); 2) palmitoylated (CYSP40, CYSP43, CYSP 44, CYSP40/43, CYSP 40/44, CYSP 43/44, CYSP40/43/44_POPC_Martini3b: 0.5 μs); 3) glycosylated (ASNG66: 0.5 μs) SARS-CoV-2 E protein in the monomeric form in a POPC bilayer. The trajectories of CG MD (TMD;H2H3_NoPTM_POPC_Martini3b: 0.5 μs) of systems containing artificial proteins consisting of only transmembrane domain (TMD) or only cytoplasmic domain (H2H3) in a POPC bilayer. The trajectory of CG MD (4xNoPTM_POPC_Martini3b: 0.5 mks) of the system containing 4 proteins with centers of mass fixed in the plane of the POPC bilayer (XY). The trajectories of CG MD of systems containing 2 proteins in the membranes buckled in a single direction (CurvedMembrane1;2X_2xNoPTM_POPC_Martini3b: 1 μs) and in the membrane buckled in both directions (CurvedMembraneXY_2xNoPTM_POPC_Martini3b: 1 μs). Simulations have been performed using the beta version of Martini 3 (CG) force field, running with the GROMACS 2020.1 under the conditions reported in bioRxiv 2021.03.10.434722.