Predicting the Structures of Glycans, Glycoproteins, and Their Complexes

Abstract

Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.

Figure 1.

Rotamer definitions for the C5-C6 bond in pyranoses.

Figure 2.

Orientation of the principal axis frame of the order tensor relative to the structure of a tetrasaccharide fragment of heparin with ring B in (A) ²S₀ conformation and (B) ¹C₄ conformation. Reprinted with permission from ref 82. Copyright 2009 Oxford University Press.

Figure 3.

Normalized NMR-STD data for the Thompson—Friedenreich (TF, Galβ1 — 3GalNAcα) disaccharide cancer antigen complexed with an anti-TF antibody: experimental (upper) and theoretical (lower) intensities are shown as circles, with fill density proportional to the normalized intensity. Reprinted from ref 111. Public Library of Science 2013, licensed under CC BY 4.0.

Figure 4.

Bond rotational energies computed at the QM B3LYP/6–31G(2d,2p)//B3LYP/6–31G(2d,2p) level for equatorial and axial 2-OMe-THP and their cyclohexyl analogues, indicating only one dominant energy minimum in the 2-OMe-THP variants, due to the presence of the exoanomeric effect in these analogues.

Figure 5.

Electronic origin [n_p(O) → σ*(C-O)] of (top) the endoanomeric effect and (bottom) the exoanomeric effect.

Figure 6.

Schematic representation of the high-mannose oligosaccharide Man₉GlcNAc₂, indicating the two 1–6 linkages that each contain three bonds.

Figure 7.

Four stable conformers^, of a high-mannose glycan (Man₉GlcNAc₂, Man-9) generated by use of GLYCAM-Web (www.glycam.org), displayed in 3D-SNFG icon mode (left) and full 3D-SNFG mode (right), where SNFG is symbol nomenclature for glycans. Upper row inner/outer 1–6 linkage conformations shown are gg/gg (top left), gg/gt (top right), gt/gg (bottom left), and gt/gt (bottom right). In the 3D-SNFG representations, mannopyranose is shown as a green sphere and N-acetylglucopyranosamine is shown as a blue cube.^, Images were generated with Visual Molecular Dynamics (VMD), using the 3D-SNFG plug-in available at www.glycam.org/3d-snfg.

Figure 8.

¹C₄ structure of IdoA (upper left) is dominant in solution despite the presence of two destabilizing 1–3 diaxial oxygen groups. In contrast, GlcA (lower) prefers exclusively the ⁴C₁ structure.

Figure 9.

(A) Schematic representation explaining the sulfation pattern-related hydrogen bonds (in blue) and repulsive effects (in red) in a fucan octasaccharide. (B) Atomic distances between neighboring residue interactions. Reprinted with permission from ref 152. Copyright 2009 Oxford University Press.

Figure 10.

Trisaccharide fragment of 2—8-linked poly(sialic acid) (PSA), with the highly inflexible ω angles shown in red and the potentially flexible ϕ and Ψ angles shown in green.

Figure 11.

Site-specific glycosylation profiles for HIV gp120/gp41 trimer antigen. Reprinted from ref 232. Elsevier 2016, licensed under CC BY 4.0.

Figure 12.

Comparison of average energies for glycosidic torsion rotation for the ϕ and Ψ angles in model disaccharides (solid lines) to the glycosidic torsion angle distributions of carbohydrates from experimental cocrystal structures (histograms).