title: Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2-3)Gal: a study by in silico mutations and molecular dynamics simulations.
abstract: Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM-PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics.
authors.affiliation: Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, 627 012, India.
authors.forename: Ponnusamy
authors.initials: P
authors.lastname: Parasuraman
authors.forename: Veeramani
authors.initials: V
authors.lastname: Murugan
authors.forename: Jeyasigamani F A
authors.initials: JF
authors.lastname: Selvin
authors.forename: M Michael
authors.initials: MM
authors.lastname: Gromiha
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Fukui
authors.forename: Kasinadar
authors.initials: K
authors.lastname: Veluraja
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D019295:Computational Biology; D003198:Computer Simulation; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009154:Mutation; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012794:Sialic Acids / Q000737:chemistry*; D014909:Wheat Germ Agglutinins / Q000737:chemistry* / Q000235:genetics
chemical_list: D012794:Sialic Acids; D014909:Wheat Germ Agglutinins
keywords: binding free energy; binding specificity; cell marker; cyborg lectin; molecular dynamics; molecular modeling; sialylglycans; wheat germ agglutinin