Microsecond Dynamics and Network Analysis of the HIV-1 SOSIP Env Trimer Reveal Collective Behavior and Conserved Microdomains of the Glycan Shield  Thomas Lemmin, Cinque Soto, Jonathan Stuckey, Peter D. Kwong  Structure  Volume 25, Issue 10, Pages 1631-1639.e2 (October 2017) DOI: 10.1016/j.str.2017.07.018 Copyright © 2017 Terms and Conditions

Structure 2017 25, 1631-1639.e2DOI: (10.1016/j.str.2017.07.018) Copyright © 2017 Terms and Conditions

Figure 1 Principal Component Analysis Reveals Four Distinct Conformations of the Prefusion HIV-1 SOSIP Env Trimer (A) Ribbon representation of the fully glycosylated HIV-1 SOSIP Env trimer. Man-5 glycans are shown as green sticks. (B) Projection of the molecular dynamics simulation into the eigenspace formed by the two first components. Four clusters were defined using a mean shift algorithm and are colored in shades of blue. The conformational change for each centroid is shown with schematic inserts. (C) Distance distributions for each cluster measured between the center of mass of the gp120 α2 helix in each protomer. See also Figure S1. Structure 2017 25, 1631-1639.e2DOI: (10.1016/j.str.2017.07.018) Copyright © 2017 Terms and Conditions

Figure 2 Protomer-Scissoring and Trimer-Opening Movements Observed in Molecular Dynamics Are Consistent with Experimentally Determined Structures (A) Principal component analysis for gp120 using experimental structures and centroid models from the molecular dynamics simulation. Inset shows schematically the dominating motion of each component. (B) Heatmap highlighting the RMSDs between different experimental gp120 structures. (C) Heatmap comparing centroid conformations of gp120 sampled during the molecular dynamics simulation and experimental structures depicted in (A). See also Figure S2 and Movie S1. Structure 2017 25, 1631-1639.e2DOI: (10.1016/j.str.2017.07.018) Copyright © 2017 Terms and Conditions

Figure 3 One Out of Three CD4-Binding Sites on the Dominant Conformation of the HIV-1 SOSIP Env Trimer Is Substantially Free from Glycan Shielding (A) Isosurface contoured at 5% showing the degree of glycan occupancy on the surface of the HIV-1-Env trimer. (B) Transverse slices through the isosurface where the degree of glycan occupancy is defined using darker shades of green. Densities of well-defined glycans have been annotated. (C) Schematic representation of the surface accessibility for two different probe sizes of 4 and 10 Å, shown on the trimer as filled circles colored burgundy and red, respectively, with the latter approximating the size of a penetrating antibody loop. (D) Transverse slices through the isosurface showing the contour plot of the surface accessibility of the HIV-1 Env trimer with respect to different probe radii. Structure 2017 25, 1631-1639.e2DOI: (10.1016/j.str.2017.07.018) Copyright © 2017 Terms and Conditions

Figure 4 Betweenness Centrality of Highly Conserved Glycans and Their Impact on the Accessibility of the CD4-Binding Site (A) Glycans are color coded according to their betweenness centrality measure for an accessible CD4-binding site (left) and a sterically hindered CD4-binding site (right). Location of the CD4-binding site is delineated by a dotted yellow highlight. Glycans neighboring the CD4-binding site showing the greatest change in betweenness centrality are annotated. These are N156 with 95.8% change, N295 with 60.1% change, N301 with 93.1% change, and N332 with 71.6% change. (B) Chord diagram highlighting the interactions between glycans that regulate accessibility of the CD4-binding site (in red) and their neighbors. Structure 2017 25, 1631-1639.e2DOI: (10.1016/j.str.2017.07.018) Copyright © 2017 Terms and Conditions

Figure 5 High Median Betweenness Centrality for Key Glycans Preserving the High-Mannose Character of the Glycan Shield (A) HIV-1 SOSIP Env trimer with glycans colored by average glycan betweenness centrality. (B) Scatterplot showing the relation between the median betweenness centrality of HIV-1 SOSIP Env glycans and the effect of their deletion on the abundance of oligomannose as provided by Pritchard et al. (2015). Asterisks indicate that experimental determination was carried out at a neighboring position: N136 for N133 and N356 for N355. Structure 2017 25, 1631-1639.e2DOI: (10.1016/j.str.2017.07.018) Copyright © 2017 Terms and Conditions

Figure 6 Glycans Form Four Stable Microdomains, and Broadly Neutralizing Antibodies Often Target the Interfaces between Microdomains (A) Microdomains isolated from the Louvain cluster method are color coded. The microdomain at the apex is shared among all three protomers. For each protomer, the glycans on the gp120 outer domain are divided into two microdomains (outer I and II). The glycans at the gp120/gp41 interface form one microdomain. The experimentally defined average quantification of oligomannose sugars (in green) and complex sugars (in purple) found within each microdomain has been reported by Behrens et al. (2016). (B) Interaction defined by overlap analysis of broadly neutralizing antibodies with glycan microdomains. (C) Representative broadly neutralizing antibodies (in violet) targeting interfaces between microdomains (additional antibodies shown in Figures S3 and S4). Structure 2017 25, 1631-1639.e2DOI: (10.1016/j.str.2017.07.018) Copyright © 2017 Terms and Conditions