Sugar Folding: A Novel Structural Prediction Tool for Oligosaccharides and Polysaccharides 2.

This is the second in a set of two articles where we describe our newly developed scheme to predict conformations of complex oligosaccharides in solution. We apply our fast sugar conformation prediction tool to the case of two complex human milk oligosaccharides LNF-1 and LND-1. As described in detail in the first paper, our protocol initially delivers a set of "unique structures" corresponding to important minima on the potential-energy landscape of a complex sugar using an implicit solvent model. The nuclear Overhauser effect ranking of individual conformations provides a suitable way for comparison with available experiments. The structures obtained agree well with earlier computational predictions but are obtained at a significantly lower computational cost. Sugar conformations corresponding to stable energy minima not found by earlier molecular dynamics studies were also detected using our methodology. In order to evaluate the effects of explicit solvation and thermal fluctuations on several different predicted conformers, we also performed short-time molecular dynamics simulations in an explicit solvent.