Simulação computacional da interação da lectina de floema de Cucurbita maxima D com quito-oligossacarídeos

Abstract

Lectins are proteins of non-immune origin that are ubiquitously present in nature and have the ability to bind specifically and reversibly to carbohydrates, which gives them various biological activities, including cell agglutination and antineoplastic effects. Among this class of proteins, phloem lectins from Cucurbitaceae are vital proteins in the plant's defense mechanism against pests and pathogens, since they have recognition sites for chitin, a carbohydrate found in the cell wall of fungi and the exoskeleton of arthropods. Their mechanism of interaction is not well characterized due to the scarcity of solved structures of this family of proteins, one of which is the Cucurbita maxima phloem lectin (PPL), a homodimeric protein with 218 amino acids and 24 kDa per monomer. The following study aimed to predict the mechanism of interaction of PPL with chito-oligosaccharides. The threedimensional structure of PPL was obtained using AlphaFold2, while the structures of the carbohydrates were obtained using the Charmm-GUI platform. The molecules (protein and ligands) were prepared for molecular docking using AutoDockTools, while the simulations were carried out using the AutoDock Vina software. The files for the molecular dynamics simulations were prepared using CHARMM-GUI and the force field used was CHARMM-36m. The dynamics were carried out using GROMACS, in which the systems consisted of an isolated protein in a water tank and a complex with GlcNAc1,3,6, following the steps of minimization, thermalization and trajectory production. The molecular anchors showed interactions that were in line with the carbohydrate interaction sites present in proteins homologous to PPL. The interactions with carbohydrates were mainly Van der Waals interactions and hydrogen bonds. RMSD analyses of molecular dynamics showed that PPL is stable in a noninteracting system, but has great variation in the N-terminal region. When interacting, PPL has a greater affinity for chitohexose. RMSD analyses of the complexes showed that interactions with chitohexose caused conformational changes in PPL. PII analysis showed that residues Ser-77 and Asp-83 have a high affinity for carbohydrates, suggesting that the participation of these amino acid residues may make up the PPL's carbohydrate recognition site. Thus, longer molecular dynamics with the remaining carbohydrates are necessary for a better understanding of PPL's carbohydrate interaction profile.