A Uniquely Stable Trimeric Model of SARS-CoV-2 Spike Transmembrane Domain
Tools created at the Laboratory of Biomolecular Modelling IBCh RAS have been brought together into a computational framework to build a model of SARS-CoV-2 spike transmembrane domain (TMD).
Apart from template-based modelling, the framework relies on the molecular hydrophobicity potential (MHP) analyser Platinum, dimer prediction utility PREDDIMER and the adjustment of ‘dynamic MHP portraits’ observed during molecular dynamics simulations. The final model, the only existing one taking into account the lipid environment and helical TMD packing principles, demonstrated phenomenal stability in a model membrane, both on its own and palmitoylated downstream, proving to be stabler than alternative models and a recent NMR structure.
The results are published in the International Journal of Molecular Sciences.