PMC:7219429 / 8539-10044 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7219429","sourcedb":"PMC","sourceid":"7219429","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7219429","text":"2.3 Ganglioside GM1\nThe initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part. In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: 34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). The system was energy-minimized 6 times switching alternatively between runs using steepest descent gradients or Polak-Ribière conjugate gradients until convergence to machine precision [16]. The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. The whole system was optimized, merged with SARS-CoV-2 spike protein (chain A) and submitted to MD simulations with the same conditions as those used for the ATM-spike protein complex (50-ns run in triplicate). For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding 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