Structural glycobiology in the age of electron cryo-microscopy

Abstract

Highlights • Progress is being made on providing automated model building and validation tools for structural glycobiology • Electron cryo-microscopy (cryo-EM) can now be routinely used for resolving protein glycosylation • High-resolution cryo-EM structures show fewer pyranose high-energy conformations than X-ray ones • Re-refinement with the latest methods can produce better structures of glycoproteins automatically

Three-Dimensional Structures of Carbohydrates and Where to Find Them

“…Moreover, not all of the objects of interest can be obtained as a single crystal. Electron cryo-microscopy gains popularity for carbohydrate 3D structural research [ 301 ], however, this method requires additional refinement procedures due to resolution restrictions of the obtained density maps [ 302 , 303 , 304 ]. Recently, cryo-EM data were used for the refinement of SARS-CoV-2 spike glycoprotein stucture using Privateer (see Table 3 for references) software [ 305 , 306 ].…”

“…Commonly occurring problems associated with nomenclature, poor glycan geometry, linkage errors, missing or surplus atoms can seriously decline the quality of the obtained 3D structures [ 300 , 320 , 321 ]. Using Privateer software, it was discovered [ 299 ],[ 301 ] that PDB deposits significant number of erroneous N-glycosylated structures with pyranose ring distortions, considering preferred adoption of 4 C 1 conformation for D-sugars and 1 C 4 conformation for L-sugars ( Figure 9 ). In most cases, poor electron density of carbohydrate moiety results in anomalous high-energy pyranose ring conformations (envelopes, half-chairs, boats, skew boats, etc.).…”

“…Non-chair conformations are bordered by dotted line boxes for 0.0-6.0 Å (green) and 6.0-10.0 Å (red) resolution ranges; the percentage of structures is given in the boxes. Reproduced with permission from [ 301 ], © 2020 Elsevier Ltd.…”

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

“…To demonstrate the capabilities of the computational bridge integrated in the newest version of Privateer (for standalone bundles, please refer to privateer branch "privateerMKIV_noccp4" of GitHub repository with the installation instructions provided in the README.md file [63]), it was run on all N-glycosylated structures in the PDB solved using MX and cryo-EM. The list of structures used in this demonstration was obtained from Atanasova et al [18]. The computational analysis of the demonstration revealed a relatively small proportion of deposited glycoprotein models containing glycan chains that do not have a unique GlyTouCan accession ID assigned, raising questions about the provenance of their structures.…”

“…Chiefly among these is the scenario where the experimentally resolved electron density map provides evidence of glycosylation, without enough resolution to derive definite and comprehensive details about the structural composition of the oligosaccharides (Figure 1). Glycan microheterogeneity and the lack of carbohydrate-specific modelling tools have often been named as the principal causes for these issues [18].…”