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

<div>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.</div>

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The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains

10.26434/chemrxiv.8170367.v2 ◽

2019 ◽

Author(s):

Pablo Ricardo Arantes ◽

Conrado Pedebos ◽

Marcelo D. Poleto ◽

Laércio Pol-Fachin ◽

Hugo Verli

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Membrane Lipid ◽

Membrane Dynamics ◽

En Bloc ◽

Future Studies ◽

Head Groups ◽

Domains Of Life ◽

Glycosylation Pathway ◽

Dynamics Simulations

<div> <div> <div> <p>Lipid-linked oligosaccharides (LLOs) plays an important role in the N-glycosylation pathway as the donor substrate of oligosaccharyltransferases (OSTs), which are respon- sible for the en bloc transfer of glycan chains onto a nascent polypeptide. The lipid component of LLO in both eukarya and archaea consists of a dolichol, and an unde- caprenol in prokarya, whereas the number of isoprene units may change between species. Given the potential relevance of LLOs and their related enzymes to diverse biotechno- logical applications, obtaining reliable LLO models from distinct domains of life could support further studies on complex formation and their processing by OSTs, as well as protein engineering on such systems. In this work, molecular modeling, such as quantum mechanics calculations, molecular dynamics simulations, and metadynamics were employed to study 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 and metadynamics calculations of LLOs revealed that glycan chains are more prone to interact with the membrane lipid head groups, while the PP linkages are positioned at the lipid phosphate head groups level. Dynamics of isoprenoid chains embedded within the bilayer are described and membrane dynamics and its related properties are also investigated. Overall, there are similarities regarding the structural and dynamics of the eukaryotic, the bacterial and the archaeal LLOs in bilayers, which can support the comprehension of their association with OSTs. This data may support future studies on the transferring mechanism of the oligosaccharide chain to an acceptor protein. </p> </div> </div> </div>

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The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains

10.26434/chemrxiv.8170367 ◽

2019 ◽

Author(s):

Pablo Ricardo Arantes ◽

Conrado Pedebos ◽

Marcelo D. Poleto ◽

Laércio Pol-Fachin ◽

Hugo Verli

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Membrane Lipid ◽

Membrane Dynamics ◽

En Bloc ◽

Future Studies ◽

Head Groups ◽

Domains Of Life ◽

Glycosylation Pathway ◽

Dynamics Simulations

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Faculty Opinions recommendation of Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1088149.542736 ◽

2007 ◽

Author(s):

Bernard Montgomery Pettitt

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Structure And Dynamics ◽

Dynamics Simulations ◽

Partially Folded States ◽

Protein Structure And Dynamics

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Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane

Scientific Reports ◽

10.1038/s41598-021-81729-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Renu Wadhwa ◽

Neetu Singh Yadav ◽

Shashank P. Katiyar ◽

Tomoko Yaguchi ◽

Chohee Lee ◽

...

Keyword(s):

Molecular Dynamics ◽

Cell Membrane ◽

Molecular Dynamics Simulations ◽

Experimental Studies ◽

Bilayer Membrane ◽

Withaferin A ◽

Head Group ◽

Polar Head Group ◽

Natural Drugs ◽

Dynamics Simulations

AbstractPoor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs—withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that whereas withaferin-A, could proficiently transverse through the model membrane, withanone showed weak permeability. The free energy profiles for the interaction of withanolides with the model bilayer membrane revealed that whereas the polar head group of the membrane caused high resistance for the passage of withanone, the interior of the membrane behaves similarly for both withanolides. The solvation analysis further revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force for its high permeability; it interacted with the phosphate group of the membrane that led to its smooth passage across the bilayer. The computational predictions were tested by raising and recruiting unique antibodies that react to withaferin-A and withanone. The time-lapsed analyses of control and treated cells demonstrated higher permeation of withaferin-A as compared to withanone. The concurrence between the computation and experimental results thus re-emphasised the use of computational methods for predicting permeability and hence bioavailability of natural drug compounds in the drug development process.

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