Molecular dynamics simulations and MM–PBSA calculations of the lectin from snowdrop (Galanthus nivalis)
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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.
KeywordsAMBER Galanthus nivalis agglutinin (GNA) Lectin Molecular dynamics simulations (MD) Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA)
The authors acknowledge the UCSF (University of California, San Francisco) for providing us the AMBER 9 program package for free. We also thank Dr. Xiao Li for reading the manuscript and his useful suggestions.
The dynamic characters of GNA were displayed as a movie (MPG 5372 kb)
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