Glycans modulate the adsorption of RBD Glycoproteins on polarizable surfaces

2025 · doi:10.1101/2025.09.30.679433
preprint OA: closed CC-BY-NC-ND-4.0
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Molecular simulations reveal that glycans modulate Receptor Binding Domain adsorption onto polarizable surfaces, with hydrophobic surfaces promoting stable binding and hydrophilic surfaces showing reduced adsorption, particularly for closed-RBD conformations.

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The paper uses molecular simulations to study how glycans in SARS-CoV-2 receptor binding domain (RBD) glycoproteins from different variants of concern interact with polarizable planar surfaces, comparing open and closed RBD conformations. Analysis projecting adsorption onto 2D identifies distinct mechanisms based on where glycans start in the protein and shows that hydrophobic surfaces support stable adsorption for both conformations, while hydrophilic surfaces reduce adsorption, especially for the closed RBD where glycans mainly form hydrogen bonds. Glycans modulate closed-RBD adsorption in variant-dependent ways, either enhancing it via permanent tethering or impeding it depending on initial conformations and specific mutations (including omicron), with results consistent with simulations of the full S1 spike glycoprotein. This paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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Abstract

The complex interplay between glycans and protein conformational dynamics during adsorption onto polarizable surfaces opens several routes to exploring the glycans potential as molecular interactions modulators. Molecular simulations are able to dissect the interactions of Receptor Binding Domain (RBD) glycoproteins for different SARS-CoV-2 variants of concern (VoC), in both open and closed conformations, with polarizable planar interfaces. Advanced analysis projected on 2D revealed distinct adsorption mechanisms depending on the initial loci of the glycan within the protein wall. Hydrophobic surfaces facilitated stable adsorption for both RBD conformations. Conversely, hydrophilic surfaces exhibited reduced adsorption, particularly for the closed-RBD, where glycans predominantly formed hydrogen bonds. Glycans significantly modulated closed-RBD adsorption, either enhancing it by permanent tethering or impeding it depending on the two initial conformations and protein mutations (omicron). Results for the individual RBDs are shown to be consistent with simulations for the complete S1 spike glycoprotein. Our findings unveil novel glycan-mediated adsorption phenomena and provide fundamental insights into glycoprotein-surface interactions, paving the way for understanding glycan roles in protein aggregation and recognition at polarizable biological interfaces.
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Abstract The complex interplay between glycans and protein conformational dynamics during adsorption onto polarizable surfaces opens several routes to exploring the glycans potential as molecular interactions modulators. Molecular simulations are able to dissect the interactions of Receptor Binding Domain (RBD) glycoproteins for different SARS-CoV-2 variants of concern (VoC), in both open and closed conformations, with polarizable planar interfaces. Advanced analysis projected on 2D revealed distinct adsorption mechanisms depending on the initial loci of the glycan within the protein wall. Hydrophobic surfaces facilitated stable adsorption for both RBD conformations. Conversely, hydrophilic surfaces exhibited reduced adsorption, particularly for the closed-RBD, where glycans predominantly formed hydrogen bonds. Glycans significantly modulated closed-RBD adsorption, either enhancing it by permanent tethering or impeding it depending on the two initial conformations and protein mutations (omicron). Results for the individual RBDs are shown to be consistent with simulations for the complete S1 spike glycoprotein. Our findings unveil novel glycan-mediated adsorption phenomena and provide fundamental insights into glycoprotein-surface interactions, paving the way for understanding glycan roles in protein aggregation and recognition at polarizable biological interfaces. Competing Interest Statement The authors have declared no competing interest.

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License: CC-BY-NC-ND-4.0