Lectin-carbohydrate analysis by molecular dynamics: Parkia lectins case study

Abstract

Understanding lectin-carbohydrate interactions at the structural and molecular levels is crucial to the field of lectins, as the diverse roles and biological activities exhibited by these proteins are fundamentally linked to their specific binding to target glycoconjugates. This study aimed to apply molecular dynamics to analyze the structure and binding properties of Parkia lectins. 3D structures of Parkia platycephala and P. biglobosa lectins, both unliganded and in complex with D-mannose, were used as inputs for simulations. The trajectories data enabled the study of stability, carbohydrate-binding interactions, and intermonomeric contacts for both proteins. The results revealed stable binding of D-mannose within the lectin domains and their binding mode at each of the three domains, displaying consistent binding motifs across the sites, with slight variations between the lectins and other Jacalin-related lectins. Despite these variations, the binding energies of the lectins with the ligand, as estimated using MM/ GBSA, demonstrated favorable interactions in all cases. The dimeric interfaces of both lectins could be identified, and the main contacts have been mapped. These findings enhance our understanding of lectin-carbohydrate interactions and provide insights into the structural properties of Parkia lectins for potential biological and therapeutic applications.