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Glycosyl esters of nucleoside di- or monophosphates, generally referred to as “sugar nucleotides”, serve as a sugar donor during the biosynthesis of oligo- and polysaccharides. Therefore, they are of primary importance in carbohydrate metabolism in the living world. Not only the molecules themselves but especially their complexes with proteins are of interest in structural glycobiology. For computational studies on these molecules, it is necessary to have access to empirical methods with appropriate force field parametrization. In this work, we propose a set of parameters, developed using ab initio calculations with the 6-31G* basis set at the SCF level on model compounds, for the commonly used AMBER force field. By implementation of the new parameter set together with the CICADA conformational search program, we have obtained a semiquantitative description of conformational space, showing that nucleotide sugars can adopt several conformational families. The majority of them exhibit a “folded” rather than an “extended” geometry due to frequent intramolecular hydrogen bonds and “stacking” interactions between the base and the six-membered sugar ring. For the sake of comparison, two molecular dynamics simulations were run in an explicit water environment. The first simulation (3 ns) started with the semi-extended X-ray geometry and displayed major variations of all torsional angles, allowing for the visit of three conformational families. The second simulation (5 ns) started with the folded global minimum from the CICADA search. After about 3ns, a transition for the ribose pucker yielded to the visit of a more extended conformational family. Experimental results show that in crystalline state, or in protein/carbohydrate complexes, extended conformations which are stabilized by the interaction with surrounding molecules or with the protein surface are more frequent.
Petrová et al. (Fri,) studied this question.