Homology modeling, molecular docking, and dynamics of two α-methyl-d-mannoside-specific lectins from Arachis genus

Abstract

The Arachis genus belongs to the Dalbergieae tribe, a group of plants that show promising potential novel lectins. Three lectins of the well-known Arachis hypogaea have already been purified, while lectins from related species are still unknown. Genomes of two closely related species, Arachis duranensis and Arachis ipaensis, were recently sequenced. Therefore, this study aimed to establish the three-dimensional structure of Arachis duranensis lectin (ADL) and Arachis ipaensis lectin (AIL) by homology modeling, test their activity against mannosides, and perform molecular dynamics (MD) simulations on these two proteins, both unligated and interacting with mannose or α-methyl-D-mannoside. The fold obtained for the molecular models agrees with data obtained from previous leguminous lectins, showing a conserved jelly roll motif. Docking scores indicate that these lectins have different theoretical binding energy with monosaccharides, disaccharides, and high-mannose glycans. MD simulations revealed that these proteins are α-methyl-D-mannoside-specific, having less stable interactions with mannose. This study thus serves as a guide for further research on lectins of the Arachis genus.

The Se…S/N interactions as a possible mechanism of δ-aminolevulinic acid dehydratase enzyme inhibition by organoselenium compounds: A computational study

“…Quantum mechanical methods, such as the density functional theory (DFT) approach, are frequently used in the study of structures, reactions, and molecular properties [42][43][44], but are strictly limited to systems of few hundreds of atoms. In addition, the protein homology modeling has been successfully employed to predict the 3D protein structure, which is essential in many cases when the tertiary or quaternary structure must be studied [45][46][47][48][49].…”

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

“…The binding of lectins with their speci c respective sugars tends to cause local stabilization with consequent reduction of uctuation. This was observed for other legume lectins, such as Canavalia bonariensis [41], although exceptions can be pointed out, such as Arachis lectins for which speci c ligand binding had no effect or increased uctuation on speci c residue ranges [39]. These results clearly show that very similar lectins can present dramatically different properties and that these differences are especially evident when dynamics properties are considered.…”

“…It should be noted that this was only a slight change for PBL, whereas the variation was quite noticeable for PPL. Equilibration is highly variable protein-to-protein and simulation-to-simulation, but it is generally accepted that ligand binding usually helps in shifting the simulation to an equilibrated state in a smaller number of steps owing to CRD stabilization in a closed position, as observed by Nascimento and colleagues (2018) with lectins from Arachis [39] and Cavada et al (2019) [40] for the lectins of Canavalia ensiformis and Canavalia brasiliensis.…”

Recent developments in molecular docking technology applied in food science: a review

“…During the last twenty years, the development of molecular simulation (MS) technology has exhibited significant progress, especially since the 2013 Nobel Prize in Chemistry was awarded (Nie et al, 2018). To date, MS technology includes homology modelling (Nascimento et al, 2018), molecular docking (Arthur et al, 2018) and molecular dynamics simulation (Zhang et al, 2018), and combines free energy calculation (Mizuguchi & Matubayasi, 2018). Among these methods, molecular docking is the most widely used one in molecular modelling research.…”