Structural dynamics of glycosylated isoforms of Glycodelin: a comparative study through molecular dynamics simulation

Objective: To study the structural dynamics of glycodelin (Gd) isoforms with distinct glycosylation patterns using molecular dynamics (MD) simulations to explore their potential roles in cancer. Methods: We employed MD simulation to investigate the structural behavior of normal and aberrantly glycosylated glycodelin (PAEP). Protein sequence and glycosylation sites were retrieved from Universal Protein Resource (UniProt) and GLYCONNECT databases. Homology modeling and glycan attachment were performed using UCSF Chimera and Glycam, while molecular topology generated using CHARMM General Force Field. Simulations were performed using the Groningen package over a 50-nanosecond timescale. Post-simulation trajectory analyses included Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (Rg), hydrogen bonding analysis (HBA), and Principal Component Analysis (PCA) to evaluate the structural dynamics and stability of the glycodelin isoforms. Results: RMSD and RMSF analyses demonstrated that glycated isoforms of both Gd1 and Gd2 exhibited greater structural stability, with reduced atomic fluctuations compared to their A-glycated counterparts. Remarkably, distinct residue fluctuations were observed at positions 30, 65, 110, and 142 in Gd1, and more broadly in Gd2. Rg analysis indicated increased compactness, particularly in glycated Gd2 isoform. PCA revealed higher structural randomness in A-glycated forms, while HBA further supported enhanced stability of glycated variants. Overall, the glycated Gd2 isoform emerged as most stable, suggesting a potential role in cancer-associated conformational behavior. Conclusion: Native glycosylation enhances Gd stability and compactness while reducing solvent exposure. Isoform-2-GP, in particular showed the most favorable dynamics, highlighting its potential as a cancer biomarker or therapeutic target.