Dynamics of Membrane-Embedded Lipid-Linked Oligosaccharides for the Three Domains of Life

Lipid-linked oligosaccharides (LLOs) are the substrates of oligosaccharyltransferases (OSTs), enzymes that catalyze the en bloc transfer of a glycan chain during the process of N-glycosylation. LLOs are composed by an isoprenoid chain moiety and an oligosaccharide, linked by one or more pyrophosphate groups (PP). The lipid component on LLO is a dolichol in eukarya and archaea, and an undecaprenol in prokarya, whereas the number of isoprene units may change between species. Given the potential relevance of LLOs and their metabolizing enzymes to diverse biotechnological applications, LLOs’ models from different domains of life in their native conditions could support further studies of their complexation and processing by OSTs, as well as protein engineering on such systems. Accordingly, the GROMOS53A6 force field was employed, added by GROMOS53a6GLYC parameters for the saccharidic moiety. The torsional parameters for the isoprenoid portion were derived from a fit to the proper quantum mechanical potential energy profiles at the HF 6-31G* and validated against experimental condensed phase properties. Molecular dynamics simulations employed GROMACS package to access the orientation, structure, and dynamics of eukaryotic (Glc3-Man9-GlcNAc2-PP-Dolichol), bacterial (Glc1-GalNAc5-Bac1-PP-Undecaprenol) and archaeal (Glc1-Man1-Gal1-Man1-Glc1-Gal1-Glc1-P-Dolichol) LLO in membrane bilayers. Microsecond molecular dynamics simulations of LLOs revealed that most carbohydrate residues interact with the membrane lipid head groups, parallel to the membrane surface, while the PP linkages are within the lipid head group, and the isoprenoid chains are within the bilayer. Overall, there are similarities in the orientations, structure, and dynamics of the eukaryotic, bacterial and archaea LLOs in bilayers. LLOs’ preferred orientation, structure and dynamics provided information for complexation with OSTs, allowing further studies of how these enzymes catalyze the transfer of the oligosaccharide chain to an acceptor protein by OSTs.