| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T66 |
0-458 |
Sentence |
denotes |
The 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. |
| T67 |
459-594 |
Sentence |
denotes |
In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: |
| T68 |
595-639 |
Sentence |
denotes |
34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). |
| T69 |
640-831 |
Sentence |
denotes |
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]. |
| T70 |
832-965 |
Sentence |
denotes |
The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. |
| T71 |
966-1115 |
Sentence |
denotes |
To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. |
| T72 |
1116-1326 |
Sentence |
denotes |
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). |
| T73 |
1327-1484 |
Sentence |
denotes |
For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding lipids. |
