Lectin-carbohydrate interactions by protein bioinformatics: Parkia lectins case study

Abstract Lectins are proteins that reversibly bind to carbohydrates without altering their structures. These proteins are present in practically all living beings and exert different functions. Understanding the molecular basis underlying the interaction between lectins and carbohydrates can help elucidate many biological activities of lectins. Parkia lectins have unique structural features within the legume family. They have protomers that associate as dimers, each with 3 β-prism domains, very similar to Moraceae lectins. This pattern is not conserved in any other Leguminoseae lectins. Each domain is unique in composition, but all have specificity for D-mannose and derivatives. This work aims to use docking and molecular dynamics approaches to characterize the interaction between Parkia platycephala (PPL) and Parkia biglobosa (PBL) lectins and D-mannose, building, as a result, a model to study lectin-carbohydrate interactions in general. MD trajectories demonstrate the stability of the lectins, whether in their native state or interacting with D-mannose. In addition, both molecular mechanics with generalized Born solvation and surface area (MM/GBSA) and molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) were used. When combined with the Interaction Entropy (IE) method, the binding energy of each domain with D-mannose was calculated to determine the participation of each amino acid in each domain during carbohydrate interaction. Trajectory analysis, as performed herein, has allowed for the expansion of knowledge about lectin-carbohydrate interactions based on our model, as well as the residues responsible for the binding with monosaccharides, thus contributing to future studies of Parkia lectins.