title: Molecular dynamics simulations and MM-PBSA calculations of the lectin from snowdrop (Galanthus nivalis).
abstract: Galanthus nivalis agglutinin (GNA), a mannose-specific lectin from snowdrop bulbs, is a member of the monocot mannose-specific lectin family and exhibits antiviral activity toward HIV. In the present study, molecular dynamics (MD) simulations were performed to study the interaction between GNA and its carbohydrate ligand over a specific time span. By analysis of the secondary structures, it was observed that the GNA conformation maintains rather stable along the trajectories and the high fluctuations were only centered on the carbohydrate recognition domains. Our MD simulations also reproduced most of the hydrogen bonds observed in the x-ray crystal structure. Furthermore, the obtained MD trajectories were used to estimate the binding free energy of the complex using the molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) method. It was revealed by the inspection of the binding free energy components that the major contributions to the complex stability arose from electrostatic interactions.
authors.affiliation: Ministry of Education, Sichuan University, Chengdu, People's Republic of China. actg0101@gmail.com
authors.forename: Zhen
authors.initials: Z
authors.lastname: Liu
authors.forename: Yizheng
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008024:Ligands; D037241:Mannose-Binding Lectins / Q000737:chemistry*; D008362:Mannosides / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D037121:Plant Lectins / Q000737:chemistry*; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D008024:Ligands; D037241:Mannose-Binding Lectins; D008362:Mannosides; D037121:Plant Lectins; C063117:snowdrop lectin