Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design

• DOI: 10.1371/journal.pcbi.1011895
• Publication Date: 2024-06-24T19:35:57Z
• Authors: Jared Adolf-Bryfogle; Jason W. Labonte; John C. Kraft; Maxim Shapovalov; Sebastian Raemisch; Thomas Lütteke; Frank DiMaio; Christopher D. Bahl; Jesper Pallesen; Neil P. King; Jeffrey J. Gray; Daniel W. Kulp; William R. Schief
• Keywords: Models, Molecular; 0301 basic medicine; QH301-705.5; Computational Biology; 03 medical and health sciences; Polysaccharides; Carbohydrate Conformation; Biology (General); Databases, Protein; Algorithms; Software; Research Article; Glycoproteins

Carbohydrates and glycoproteins modulate key biological functions. However, experimental structure determination of sugar polymers is notoriously difficult. Computational approaches can aid in carbohydrate structure prediction, structure determination, and design. In this work, we developed a glycan-modeling algorithm, GlycanTreeModeler, that computationally builds glycans layer-by-layer, using adaptive kernel density estimates (KDE) of common glycan conformations derived from data in the Protein Data Bank (PDB) and from quantum mechanics (QM) calculations. GlycanTreeModeler was benchmarked on a test set of glycan structures of varying lengths, or “trees”. Structures predicted by GlycanTreeModeler agreed with native structures at high accuracy for both de novo modeling and experimental density-guided building. We employed these tools to design de novo glycan trees into a protein nanoparticle vaccine to shield regions of the scaffold from antibody recognition, and experimentally verified shielding. This work will inform glycoprotein model prediction, glycan masking, and further aid computational methods in experimental structure determination and refinement.