Molecular modelling of protein–carbohydrate interactions. Understanding the specificities of two legume lectins towards oligosaccharides

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Abstract
By means of a series of new molecular modelling tools, the conformational behaviour of mannose-containing di- and trisaccharides bound to either concanavalin A or Lathyrus ochrus isolectin I (LOLI) has been assessed. Tools for estimating and analysing either the ‘rigid’ or the ‘relaxed’ potential energy surfaces, representing the conformational space available for carbohydrates once interacting with lectins, are reported for the first time. Restrictions of conformational space are predicted to occur with different magnitudes, depending on the nature of the glycosidic linkages, as well as the size of the carbohydrates. Results from these molecular modelling studies are compared to existing structural data. Not only could the observed conformations and orientations of carbohydrates in crystalline lectin–oligosaccharides complexes be reproduced, but several other likely situations were also predicted to occur. Entropy calculations have been performed for comparison with experimental thermodynamics data. The results of the simulation can also help giving an explanation of some observed affinity constants at the molecular level.