Conformational flexibility of N-glycans in solution studied by REMD simulations

Abstract

Protein-glycan recognition regulates a wide range of biological and pathogenic processes. Conformational diversity of glycans in solution is apparently incompatible with specific binding to their receptor proteins. One possibility is that among the different conformational states of a glycan, only one conformer is utilized for specific binding to a protein. However, the labile nature of glycans makes characterizing their conformational states a challenging issue. All-atom molecular dynamics (MD) simulations provide the atomic details of glycan structures in solution, but fairly extensive sampling is required for simulating the transitions between rotameric states. This difficulty limits application of conventional MD simulations to small fragments like di- and tri-saccharides. Replica-exchange molecular dynamics (REMD) simulation, with extensive sampling of structures in solution, provides a valuable way to identify a family of glycan conformers. This article reviews recent REMD simulations of glycans carried out by us or other research groups and provides new insights into the conformational equilibria of N-glycans and their alteration by chemical modification. We also emphasize the importance of statistical averaging over the multiple conformers of glycans for comparing simulation results with experimental observables. The results support the concept of "conformer selection" in protein-glycan recognition.

Keywords: Conformational flexibility; Conformer selection; Molecular dynamics simulations; N-glycan; N-glycan modifications; Protein–glycan interactions; Replica-exchange molecular dynamics simulations.

Fig. 1

Schematic illustration of the structural feature of oligosaccharides and their possible binding mechanisms to receptor proteins

Fig. 2

Structure of a biantennary complex-type N-glycan (Bi9, black) and its typical modifications: the introduction of bisecting GlcNAc (BiB10, orange), the core fucosylation (BiF10, blue), and both (BiBF11, orange and blue). These modifications are known to change the affinity of protein-glycan interactions. N-glycan solvated within a box of >3,000 TIP3P H₂Os used for simulations is also shown (α1,3-arm green, α1,6-arm red, core blue)

Fig. 3

Structures of distinct conformers (top and side views) found from our REMD simulations for four N-glycans: a Bi9, b BiF10, c BiB10, and d BiBF11. Different colors indicate different arms (α1,3-arm green, α1,6-arm red, core blue, bisect orange, and fucose yellow). The α1,6-arm (red) interacts with either core (blue) or α1,3-arm (green) in the “folded” forms, whereas it is fully solvated in the “extended” forms. Populations of each conformer obtained from the clustering analysis are given in the parentheses. Key inter-residue hydrogen bonds stabilizing each conformer are also shown

Fig. 4

Definition of local dihedral angles (, ψ and ω for α1,6-linkage and and ψ for α1,3-linkage) and the spherical coordinate used to represent the global conformation of N-glycans. The Man-3 structure of each simulation snapshot was superimposed to a plane regular hexagon on the xy plane, with its center at the origin. This allows us to determine a unique orientation of the N-glycan global structure with respect to the Man-3 structure, by reducing the artificial orientation changes arising from distortion of the pyranose ring in the simulation snapshots. The angle η represents swing motion of α1,6-arm around the z (polar) axis, while the angle θ represents up–down motion with respect to the xy-plane. Distribution of five distinct conformers (three “folded” and two “extended” forms, each of which is characterized by different ψ/ω angles of α1,6-linkage) mapped on the spherical coordinates for a Bi9, b BiF10, c BiB10, and d BiBF11. Blue ψ/ω of 60°/60°, red 90°/60°, green 180°/60°, purple 60°/180°, cyan 180°/180°. Free-energy contour lines (gray) are also shown for comparison

Fig. 5

Comparison of calculated and experimental NMR data for Bi9 and BiBF11. a Intra- and inter-residue NOE distances (in Å) of the Manα1-3Man structure, b scalar ³ J-coupling constants (in Hz) of the Manα1-6Man structure