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Binding free energy calculations of galectin-3–ligand interactions

Protein Engineering, Design and Selection , Volume 15 (12): 979 – Dec 1, 2002


Oxford University Press
Copyright © 2010 Oxford University Press
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Binding free energy calculations of galectin-3–ligand interactions


Abstract Galectins show remarkable binding specificity towards β-galactosides. A recently developed method for calculating binding free energies between a protein and its substrates has been used to evaluate the binding specificity of galectin-3. Five disaccharides and a tetrasaccharide were used as the substrates. The calculated binding free energies agree quite well with the experimental data and the ranking of binding affinities is well reproduced. For all the six protein–ligand complexes it was observed that electrostatic interactions oppose binding whereas the non-polar contributions drive complex formation. The observed binding specificity of galectin-3 for galactosides rather than glucosides is discussed in light of our results.
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