title: Homology modeling, molecular dynamics, and docking studies of pattern-recognition transmembrane protein-lipopolysaccharide and β-1,3 glucan-binding protein from Fenneropenaeus indicus.
abstract: Lipopolysaccharide and β-1,3 glucan-binding protein (LGBP) is a family of pattern-recognition transmembrane proteins (PRPs) which plays a vital role in the immune mechanism of crustaceans in adverse conditions. Fenneropenaeus indicus LGBP-deduced amino acid has conserved potential recognition motif for β-1,3 linkages of polysaccharides and putative RGD (Arg-Gly-Asp) cell adhesion sites for the activation of innate defense mechanism. In order to understand the stimulating activity of β-1,3 glucan (β-glucan) and its interaction with LGBP, a 3D model of LGBP is generated. Molecular docking is performed with this model, and the results indicate Arg71 with strong hydrogen bond from RGD domain of LGBP. Moreover, from the docking studies, we also suggest that Arg34, Lys68, Val135, and Ala146 in LGBP are important amino acid residues in binding as they have strong bonding interaction in the active site of LGBP. In our in vitro studies, yeast agglutination results suggest that shrimp F. indicus LGBP possesses sugar binding and recognition sites in its structure, which is responsible for agglutination reaction. Our results were synchronized with the already reported evidence both in vivo and in vitro experiments. This investigation may be valuable for further experimental investigation in the synthesis of novel immunomodulator.
authors.affiliation: a Crustacean Molecular Biology and Genomics Lab, Department of Animal Health and Management , Alagappa University , Karaikudi , Tamil Nadu , India.
authors.forename: Jeyachandran
authors.initials: J
authors.lastname: Sivakamavalli
authors.forename: Sunil Kumar
authors.initials: SK
authors.lastname: Tripathi
authors.forename: Sanjeev Kumar
authors.initials: SK
authors.lastname: Singh
authors.forename: Baskaralingam
authors.initials: B
authors.lastname: Vaseeharan
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism; D020134:Catalytic Domain; D006860:Hydrogen Bonding; D037102:Lectins / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D008070:Lipopolysaccharides / Q000737:chemistry* / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D033561:Penaeidae; D011485:Protein Binding; D016415:Sequence Alignment
chemical_list: D002352:Carrier Proteins; D037102:Lectins; D008024:Ligands; D008070:Lipopolysaccharides; D008565:Membrane Proteins; C037937:glucan-binding proteins
keywords: Fenneropenaeus indicus; LGBP; homology modeling; molecular dynamics simulation; phagocytic activity; yeast agglutination