Are carbohydrate ring distortions determined by biology or crystallography? The impact of experimental conditions on structural data

The intricate world of carbohydrates and their structural complexities has long been a subject of intrigue in the scientific community. These essential molecules, crucial to various biological functions, have been a challenge to represent accurately in databases like the Protein Data Bank (PDB) due to their diverse and flexible nature.

However, recent advancements in X-ray crystallography and CryoEM have facilitated the acquisition of their experimental structures, paving the way for a deeper understanding of their properties.

This research delves into the classification, quantification, and characterization of carbohydrate structures within the PDB, with a focus on monosaccharides and glycan chains. By employing Cremer-Pople puckering coordinates to evaluate pyranose conformations, the study aims to provide a comprehensive overview of these molecules.

The findings reveal that despite the surge in CryoEM structures, including more complex oligosaccharides, carbohydrates continue to be predominantly represented in small glycans. Specifically, around 4% of these structures exhibit non-chair conformations in high-resolution structures. Furthermore, free energy landscapes for the pyranose ring in the presence and absence of nine diverse binding proteins—both enzymes and non-enzymes—highlight the preferred stability of chairs and the infrequency of conformational changes upon binding.

These results underscore the intricate interplay between biology and crystallography in shaping our understanding of carbohydrate structures.