The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid...

The separation and structural identification of glycans are of great bioanalytical importance. To obtain a good understanding of the structural flexibility of glycans, replica exchange molecular dynamics (REMD) simulations were used based on AMBER force field calculations to create ensembles of glycan structures. Nonpolar surface area (NPSA) calculations based on continuum solvation (CS) models (Dhakal, R., et al. Int. J. Mass Spectrom. 2021, 461, 116495) were used to quantitatively characterize the polarity of the glycans. Retention times determined by tandem liquid chromatography-mass spectrometry (LC-MS) were correlated with CS-NPSA results obtained from analysis of the investigated glycan ensembles. Three classes of glycans with increasingly complex structures were investigated: linear glycans, fucosylated and sialylated biantennary glycans, and sialylated triantennary glycans. The linear and biantennary structures displayed bimodal distributions in their energies and CS-NPSA values, suggesting two sets of structures, while the more complex triantennary glycans displayed only a single distribution. The peak values of the CS-NPSA distributions (histogram structures) were selected as representatives to be correlated with the experimental retention times. For comparison, the most stable ensemble structures and those obtained from straightforward geometry optimizations were considered, as well. Overall, the histogram structures were found to correlate well with the retention times. In the case of the linear glycans, the CS-NPSA values for all three structural choices correlated very well with the retention times. For the biantennary glycans, the histogram data missed the retention-time ordering in one case but predicted the correct ordering for the triantennary case. Principal component analysis was performed to characterize the main glycan modes of the molecular dynamics.