Soft Matter and Complex Systems Seminar

Glycans, complex sugars covalently attached to proteins, affect protein stability and function, participate in ‘self’ recognition, and modulate protein-protein interactions. The glycosylation machinery is frequently hijacked by pathogens, which hide their proteins behind a “glycan shield”, making them inaccessible to the immune system and complicating pharmacological interventions. Unlike many biomolecules, glycans do not typically form secondary structures and remain highly mobile, posing a challenge for traditional structural biology techniques. In our research, we combined molecular dynamics simulations with cryo-electron tomography and atomic force microscopy to understand how glycans affect viral fusion proteins, particularly the SARS-CoV-2 spike protein. We discovered a surprising flexibility of the spike protein [1,2] and predicted new antibody binding sites accessible through the dynamic glycan shield [3], which can aid in designing novel vaccines. Additionally, we developed a simplified, open-source method for rapidly predicting glycan shielding with minimal computing power. This method has been applied to refine existing cryo-EM maps of glycoproteins [4].

1. B Turoňová, M Sikora, C Schürmann, WJH Hagen, S Welsch et al., In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.
Science, 370(6513) 2020

2. R Zhu, D Canena, M Sikora, M Klausberger, H Seferovic, et al., Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level
Nat Comm, 13(7926) 2022

3. M Sikora, S von Bülow, FEC Blanc, M Gecht, R Covino, G Hummer. Computational epitope map of SARS-CoV-2 spike protein.
PLoS computational biology, 17(4) 2021

4. Y-X Tsai, N-E Chang, K Reuter, H-T Chang, T-J Yang et al., Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
Biorxiv