Glycosylated Swiss-model molecular dynamics trajectory of SARS-CoV-2 spike glycoprotein

Molecular dynamics simulation trajectory. The system is the SARS-CoV-2 spike glycoprotein with glycans modeled on using GLYCAM-Web. SARS-CoV2 spike (S) protein structure – A 3D structure of the prefusion
form of the S protein (RefSeq: YP_009724390.1, UniProt: P0DTC2
SPIKE_SARS2), based on a Cryo-EM structure (PDB code 6VSB), was obtained
from the SWISS-MODEL server (swissmodel.expasy.org). The model has 95%
coverage (residues 27 to 1146) of the S protein. The site specific glycans used to model a glycoform representative of
the data obtained from the S glycoprotein expressed in HEK293 cells, are
presented below:

Hybrid:
DManpα1-6[DManpα1-3]DManpα1-6[DGlcpNAcβ1-2DManpα1-3]DManpβ1-4DGlcpNAcβ1-4DGlcpNAcβ1-OH
Glycosites: 657

FA2:
DGlcpNAcβ1-2DManpα1-6[DGlcpNAcβ1-2DManpα1-3]DManpβ1-4DGlcpNAcβ1-4[LFucpα1-6]DGlcpNAcβ1-OH
Glycosites: 149, 165, 331, 343, 616, 1134

A2:
DGlcpNAcβ1-2DManpα1-6[DGlcpNAcβ1-2DManpα1-3]DManpβ1-4DGlcpNAcβ1-4DGlcpNAcβ1-OH
Glycosites: 1098

FA2B:
DGlcpNAcβ1-2DManpα1-6[DGlcpNAcβ1-4][DGlcpNAcβ1-2DManpα1-3]DManpβ1-4DGlcpNAcβ1-4[LFucpα1-6]DGlcpNAcβ1-OH
Glycosites: 74, 282

M5:
DManpα1-6[DManpα1-3]DManpα1-6[DManpα1-3]DManpβ1-4DGlcpNAcβ1-4DGlcpNAcβ1-OH
Glycosites: 61, 122, 603, 709, 717, 801, 1074

M8:
DManpα1-2DManpα1-6[DManpα1-2DManpα1-3]DManpα1-6[DManpα1-2DManpα1-3]DManpβ1-4DGlcpNAcβ1-4DGlcpNAcβ1-OH
Glycosites: 234

Glycan naming system. In cases where the mass spectrometry data allows
for multiple structures, such as FA2/FA1B, the glycan with the least
ambiguity was selected. For example, FA2 was selected over FA1B, as the
position of the single antennae is ambiguous.
Dataset supports the following preprint: 3D Models of glycosylated SARS-CoV-2 spike protein suggest challenges and opportunities for vaccine development. Oliver C. Grant, David Montgomery, Keigo Ito, Robert J. Woods; bioRxiv 2020.04.07.030445; doi: https://doi.org/10.1101/2020.04.07.030445