Chapter 12: Reconstructing Glycosylation: How to Rebuild Glycoproteins by Molecular Dynamics-generated 3D Libraries

The 3D structural information deposited in public repositories, such as the RCSB Protein Data Bank (www.rcsb.org) or the AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/), often covers only the protein component of complex biomolecular systems, while features of essential and common post-translational modifications are completely or partially missing. In this chapter, we discuss the strengths and weaknesses of reconstructing glycoproteins using widely available de novo carbohydrate builders and an alternative approach developed in our laboratory, where glycan 3D structures selected from extensive sampling through molecular dynamics are covalently linked to the glycoprotein of interest. We also show how this approach is unique in its potential to capture the diverse degrees of flexibility characteristic of the structure of complex carbohydrates, where 3D ensembles are not random distributions of structures but are strictly regulated by sequence and branching.