Integrative Data Analysis with UCSF Chimera: HIV Spikes

Advisory Committee Meeting
November 13, 2009

Schematic of HIV virus.

HIV Spikes


Finding all gp120 structures: BLAST

PDB 1gc1: gp120 blue, antigen binding fragment (FAB) 17b yellow and red, CD4 cyan. Sequence gp120 (1gc1 chain G): missing segments red, helices yellow, strands green.
gp120 structures found with BLAST. BLAST 1gc1 gp120 sequence against PDB using Chimera. 56 matching chains, 26 structures. Aligned structures. Fetch some structures found by BLAST. Automatically aligned. Structure with V3 loop. Sequence alignment shows 2B4C has V3 loop, only one other structure has it. V3 loop recognized by many antibodies.

Residues conserved across clades

HIV clades. 38 reference sequences from LANL HIV database. Clades in sequence names. Phylogenetic tree at left. Cross-clade conservation. gp120 colored by residue conservation, yellow-red-blue most to least conserved.

Critical antibody binding residues: alanine scanning

Alanine scanning. Reduction in binding affinity of PG9 and PG16 when residues mutated to alanine shown as blue sequence headers. Critical binding residues. Fatter tube at residues where PG16 binding reduced by substituting alanine.

Diversity of known structures: network visualization

Geographic distribution of HIV clades. HIV infections, 2002.
HIV sequence tree: 1900+ HIV sequences from Los Alamos National Laboratory (LANL) HIV database viewed using Cytoscape network visualization developed by RBVI. Clade B pink, clade A cyan, clade C red. All PDB gp120 structures are in yellow boxes. Close up: All but one of the gp120 sequences found in PDB structures (17 of 18 unique sequences) match the 5 HIV isolates shown here as yellow nodes. This region of is the left yellow box in full network image.

gp120 with loops: homology model

PG9 and PG16 binding location: Supplementary figure 6 from Walker LM, et al 2009 Science paper. Binding is hypothesized to be to v1/v2 loops (yellow) and v3 loop (orange). Homology model: gp120 ModBase Q9YQN8.

Glycosylation sites

Glycosylation sites on ModBase homology model Q9YQN8 found with prosite match N-x-[ST]. Note 8 sites on V1/V2 loop. Long color bands are badly spaced (10A apart) residues in homology model. Consensus glycosylation model: Mass spectroscopy from Kenneth Tomer's lab (NIEHS) determined distribution of glycans (branched sugars) at each residue. Most common glycan for each residue used to hand-build a full length fully glycosylated model.
Glycans at binding sites. Locations of CD4 and FAB X5 by fitting 2B4C to glycosylated gp120 model. Glycosylation model errors. Alignment of 2B4C and hand-built glycosylated model. RMSD header shows differences between structures. V3 loops are very different in x-ray model (2005) and earlier glycosylation model (2000).

Where are the V1 and V2 loops? Small-angle x-ray scattering (SAXS)

SAXS profiles. Experimental gp120 SAX data pink + marks, glycosylated model green, modbase homology model cyan, glycosylated model with moved v1/v2 loop yellow. Alternate V1/V2 loop models. Colors match calculated curves in SAXS profile plot.

Trimeric spikes: electron tomography

SIV virions. SIV virus tomography from Kenneth Roux's lab. Single virus extracted from tomogram, smoothed, noise hidden, colored radially to show membrane (red) and spikes (yellow).

Bound and unbound spike conformations

EMDB Search. EM Databank can be searched and maps downloaded directly from Chimera. Search term HIV.
Spike with ligands. Spike with CD4 and FAB 17b bound. C3 symmetry applied after fitting monomeric xray model. Unbound spike. Binding induced motion. Rotation of 60 degrees about orange rotation axis on binding CD4 and 17b.

Animating CD4 and antibody binding

Animating rotation. Minimal animation showing rotation of gp120 when CD4 and FAB 17b ligands bind. Fancier animation. Animation is made more self-explanatory by adding text labeling, fly-in of ligands, fading between unbound and bound density maps.

High quality images