Structure prediction and protein-ligand interaction of lectin from rice bean (Vigna umbellata)

Lectins are an important group of multivalent glycoproteins having the property of selectively recognizing and precipitating glycoconjugates. Although lectins have been reported from diverse biological sources, legume lectins is the best-characterized family of plant lectins. We have successfully cloned and sequenced the RbL ORF of 843bp from immature rice bean seeds (Vigna umbellata). We report the results of in silico analysis of novel lectin precursor of 280 amino acids from rice bean. BlastP analysis revealed more than 90% sequence similarity of RbL protein with Vigna angularis lectin and Vigna aconitifolia lectin. ProtParam analysis revealed acidic, stable and hydrophobic nature of RbL protein. Template based 3D structure of RbL protein was modeled using I-TASSER tool and validated as good quality model. Structural analysis revealed the presence of β-sandwich (Jelly roll fold or lectin fold) in modeled RbL. The protein was functionally annotated as a plant defense protein. Molecular docking was performed to analyze interactions of RbL protein with predicted ligands (N-acetyl-D-glucosamine β-galactose, Lactose and Adenine) and two selected ligands (Glucose and Mannose). Molecular dynamics (MD) simulations of RbL-ligand complexes confirmed robust hydrogen bonding interactions between ligands and RbL protein. The novel information generated in the study would be useful in exploring RbL protein for different biomedical and biotechnological applications.