This project aimed to model how glycosaminoglycans (GAGs) induce formation of protein structures and enhance biologically relevant protein-ligand interactions. Using advanced computational approaches, the group investigated GAG-mediated structural changes in protein conformation and their implications for biological processes.
The primary hypothesis was that GAGs can play an active role in shaping the structure of their protein targets rather than just serving as passive binding partners. By studying this with molecular dynamics and advanced sampling methods, we aimed to uncover the mechanisms behind GAG-protein co-folding.
The research utilized molecular dynamics simulations, enhanced sampling techniques (including Replica Exchange Molecular Dynamics), free energy calculations, and molecular docking approaches specifically adapted for GAG-containing systems.
The results contributed to understanding how GAGs influence protein folding and stability, which is relevant for designing therapeutic interventions targeting GAG-protein interactions in diseases.