PMC:7128678 / 17161-20600 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7128678","sourcedb":"PMC","sourceid":"7128678","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7128678","text":"Molecular dynamic simulations of a structural motif encompassing amino acid residues 100–175 of the NTD Fig. 5(f–h) merged with ganglioside GM1 further supported this concept. As shown in Fig. 6 , the large flat area of this structural domain fitted very well with the protruding oligosaccharide part of the ganglioside. Several amino acid residues appear to be critical for this interaction, especially Phe-135, Asn-137 and Arg-158 (Table 1 ). Overall, the complex involved 10 amino acid residues for a total energy of interaction of -100 kJ.mol−1. At this stage, it was observed that approximately 50% of the interface was involved in the complex, leaving the remaining 50% available for interaction with a second GM1 molecule. As expected, merging a second GM1 molecule with the preformed GM1–NTD complex led to a trimolecular complex consisting of two gangliosides in a typical symmetrical chalice-like structure into which the NTD could insert its interfacial ganglioside-binding domain (Fig. 7 ). The formation of this trimolecular complex was progressive, starting with a conformational rearrangement of the first ganglioside–NTD complex triggered by the second GM1 molecule. The energy of interaction of the new complex was consistently increased by 37%, reaching an estimated value of -137 kJ.mol−1. At this stage, attachment of the NTD to the ganglioside-rich microdomain involved the whole interface (i.e. 15 surface-accessible residues from Asp-111 to Ser-162). The critical residues were Asp-111, Gln-134, Phe-135, Arg-158 and Ser-161 (Table 1).\nFig. 6 Molecular complex between the N-terminal domain (NTD) of SARS-CoV-2 spike protein and a single GM1 ganglioside. The NTD is represented in ribbons superposed with a transparent surface rendering (light green). Two symmetric views of the complex are shown (a,b). The amino acid residues Q-134 to D-138 located in the centre of the ganglioside-binding domain are represented as green spheres. The saccharide part of the ganglioside forms a landing surface for the tip of the NTD.\nTable 1 Energy of interaction of each amino acid residue of SARS‐CoV‐2 spike protein in contact with GM1 molecules.\nAmino acid residues Energy of interaction (kJ.mol‐1)\nFirst step: one GM1 molecule\n Asp‐111 −5.6\n Lys‐113 −8.2\n Gln‐134 −8.6\n Phe‐135 −20.1\n Cys‐136 −7.0\n Asn‐137 −15.2\n Asp‐138 −6.4\n Arg‐158 −17.4\n Ser‐161 −9.7\n Ser‐162 −2.0\n Total −100.2\nSecond step: two GM1 molecules\n Asp‐111 −15.8\n Ser‐112 −10.7\n Lys‐113 −9.2\n Gln‐134 −11.2\n Phe‐135 −10.5\n Cys‐136 −6.2\n Asn‐137 −4.7\n Phe‐140 −5.2\n Gly‐142 −5.6\n Glu‐156 −9.0\n Phe‐157 −13.8\n Arg‐158 −19.8\n Tyr‐160 −3.2\n Ser‐161 −9.7\n Ser‐162 −2.0\n Total −136.6\nFig. 7 Molecular complex between the N-terminal domain (NTD) of SARS-CoV-2 spike protein and a dimer of GM1. In (a), (c) and (d), the NTD is represented as in Fig. 4. In (b), the surface of the NTD is shown without any transparency. The amino acid residues Q-134 to S-162 belonging to the ganglioside-binding domain (GBD) are represented as green spheres. Compared with a single GM1 molecule, the dimer of gangliosides forms a larger attractive surface for the NTD. In the above view of (d), the anchorage of the NTD to the gangliosides is particularly obvious. As chloroquine also interacts with the saccharide part of GM1, its presence would clearly mask most of the landing surface available for the NTD, preventing attachment of the virus to the plasma membrane of host 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