The influence of N-linked glycans on the molecular dynamics of the HIV-1 gp120 V3 loop

Abstract

N-linked glycans attached to specific amino acids of the gp120 envelope trimer of a HIV virion can modulate the binding affinity of gp120 to CD4, influence coreceptor tropism, and play an important role in neutralising antibody responses. Because of the challenges associated with crystallising fully glycosylated proteins, most structural investigations have focused on describing the features of a non-glycosylated HIV-1 gp120 protein. Here, we use a computational approach to determine the influence of N-linked glycans on the dynamics of the HIV-1 gp120 protein and, in particular, the V3 loop. We compare the conformational dynamics of a non-glycosylated gp120 structure to that of two glycosylated gp120 structures, one with a single, and a second with five, covalently linked high-mannose glycans. Our findings provide a clear illustration of the significant effect that N-linked glycosylation has on the temporal and spatial properties of the underlying protein structure. We find that glycans surrounding the V3 loop modulate its dynamics, conferring to the loop a marked propensity towards a more narrow conformation relative to its non-glycosylated counterpart. The conformational effect on the V3 loop provides further support for the suggestion that N-linked glycosylation plays a role in determining HIV-1 coreceptor tropism.

Figure 1. The HIV-1 gp120 (PDB ID: 2B4C) structures used in this study.

These are A) non-glycosylated, B) glycosylated^5-glycans, and C) glycosylated²⁹⁵, where the V3 loop of each structure can be seen extending out towards the bottom of each structure. D) A schematic representation of the positions (HXB2 numbering) of the investigated N-linked glycosylation sites for the glycosylated^5-glycans (red) and glycosylated²⁹⁵ (green) structures. The “\\” denotes the missing V1-V2 loops.

Figure 2. RMSF values for the C-αlpha atoms.

These values represent the entire gp120 protein (based on the amino acid sequence of PDB ID: 2B4C) for the non-glycosylated, glycosylated^5-glycans, and glycosylated²⁹⁵ trajectories. The conserved and variable regions of HIV-1 gp120 are marked, and the “\\” denotes the missing V1-V2 loops.

Figure 3. Comparison between distance distributions for regions of the V3 loop.

Comparison between the distance distributions for the centers of mass between the base and tip of the V3 loop (A and B) and between the two sides of the V3 loop (C); and the corresponding average V3 loop structures (D) using 5–30 ns of the trajectories for the non-glycosylated (blue), glycosylated^5-glycans­ (red) ­and glycosylated²⁹⁵ (green) examples.

Figure 4. Representation of the range of movement of the V3 loops for the first principal component.

The range of movement is presented for (A) all systems, (B) non-glycosylated, (C) glycosylated^5-glycans, and (D) glycosylated²⁹⁵ trajectories. The shaded colors represent the intermediate positions between the extremes.