Conformational analysis of two glycoproteins: a Monte Carlo simulated annealing approach using a soft-sphere potential

The Monte Carlo simulated annealing method was effectively used to predict the three-dimensional structure of the carbohydrate part of two glycoproteins: 1 vsg and 2 fbj from a protein data bank, utilizing a soft-sphere potential. The result was compared both to the crystal structure and to the structure of the corresponding isolated oligosaccharide structure simulated using an ECEPP/2 force field. A good agreement with crystal structure was reached. The interaction with the protein environment was found to significantly influence the structure of the carbohydrate moiety.