• Comparative MD analysis (200ns) of native UDA and engineered mutant UDAM5 • Residue-wise contact analysis reveals altered lectin–glycan interactions • Mutation-induced changes in secondary structure and ligand dynamics Lectins recognize glycans through weak but highly specific interactions that are governed by dynamic residue–ligand contacts and ligand conformational behaviour. In this study, we present an interaction-centric molecular dynamics analysis to elucidate the mechanistic differences between native Urtica dioica agglutinin (UDA) and its engineered mutant, UDAM5, in glycan binding. Building upon earlier stability-focused investigations, the present work explores unresolved aspects of lectin–glycan recognition, including residue-wise interaction patterns, temporal contact persistence, secondary structure organization, and ligand torsional dynamics. Residue-level interaction profiling revealed that native UDA engages the glycan ligand through a limited set of dominant residues, with water-mediated contacts contributing significantly to binding stabilization. In contrast, UDAM5 exhibited a more distributed interaction network, characterized by enhanced hydrogen bonding and cooperative water bridges across multiple residues. Time-resolved contact analysis demonstrated that while native UDA showed a decline in ligand contacts at extended simulation times, UDAM5 maintained persistent ligand engagement through dynamic reorganization of interactions. Secondary structure analysis indicated reduced but more adaptable secondary structure occupancy in UDAM5, suggesting increased local flexibility in the binding region. Furthermore, ligand torsional analysis revealed restricted conformational sampling in the UDAM5-bound state, indicating stabilization of preferred ligand conformations. Collectively, these findings demonstrate that rational lectin engineering enhances glycan recognition by reprogramming interaction networks and constraining ligand dynamics rather than by increasing global structural rigidity. This study highlights the importance of interaction-level molecular dynamics descriptors in evaluating engineered lectins and provides mechanistic insight into the improved functional behaviour of UDAM5.
Gurav et al. (Sun,) studied this question.