HIV Spike Demo Storyboard

Storyboard for HIV spike demonstration for RBVI advisory committee meeting on November 13, 2009.

Aim of demonstration

Aim is to show EM, sequence, and network visualization tools applied to a single biological problem.

Biological Problem

The specific biological problem is to understand interactions of broadly neutralizing antibodies (bNAb) with HIV spike proteins gp120 and gp41. The spikes recognize CD4 receptors on human T-cells to identify and infect those cells. The motivation is to develop an HIV vaccine which works by eliciting production of these antibodies. This month two new bNAbs were reported that are effective against more HIV strains and at lower antibody concentrations than the previously known half-dozen bNAbs.

Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target.
Walker LM, et al.
Science. 2009 Sep 3 ​PubMed 19729618

Things to show

Schematic of HIV virus architecture

EM tomography view of HIV particles (Stephen Fuller lab).

Will show some tomography data and how to get from A to B in above figure.

There are about 15 gp120 crystal structures, all monomeric. The 2 new bNAbs bind only to trimeric gp120 spikes, not to the monomeric form. The trimer conformation can be found from the EM tomography data, averaging and fitting.

HIV-1 BaL spike with CD4 and 17b-FAB. Subramaniam lab. EMDB 5020, PDB 3dnn	HIV-1 BaL spike with b12 FAB. EMDB 5018, PDB 3dno

SIV envelope spike. Roux lab.
EMDB 1246, PDB 2bf1 (gp120), PDB 1tji (gp41), PDB 1tzg (gp41)

There is some conflicting data about what trimeric spikes look like, having a single stalk in the viral envelope, or 3 legs (seen in SIV).

I have SIV spike tomography from Ping Zhu in Kenneth Roux's lab and Florida State University.

Structures aren't available for the two new bNAbs. (None are reported in the article.) So we'll be looking at gp120 structures with other anti-bodies bound and CD4 bound.

Start with PDB 1GC1 from 1998 having gp120 (red), a bound FAB (fragment antibody) (blue) and CD4 (yellow).

Blast against the gp120 sequence (Model Panel / blast protein...). The current Chimera interface doesn't let you specify a chain. We don't want CD4 and other FAB structures, so first delete all but gp120 (chain G) then do the blast.

Multiple alignment of 15 gp120 sequences (through 2QAD in blast dialog) shows mostly identical sequences with a few at the bottom with inserted loops. The gp120 V3 loop which is critical to antibody binding is one of these loops.

Loading the top 13 blast hits shows they are all quite similar structures:

There are other structures showing antibodies bound to just the V3 loop without the gp120 core. Those might be interesting to look at in this demo.

Molecular architecture of native HIV-1 gp120 trimers.
Liu J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S.
Nature. 2008 Sep 4;455(7209):109-13. ​PubMed 18668044

describes large rotations of the gp120 monomers occurring in antibody and cd4 binding that would be interesting to show since the new bNAbs only bind trimers, not monomers. Here's the caption from figure 3. Can show EM maps of these trimers, EMD 5019, 5020.

"Comparison of the locations of the docked gp120 monomers in the free, b12-bound and CD4-bound states (Fig. 3c-eFigure 3) provides insights into the overall quaternary structural changes that occur in the trimeric spike. The binding of b12 results in a partial opening of the spike, coupled with rotation of each monomer by ~20°–25° around an axis perpendicular to the viral membrane (Fig. 3dFigure 3). However, CD4 binding results in a rotation around this central axis in the same direction that is twice as large, in addition to an out-of-plane rotation (Fig. 3eFigure 3), and slight vertical displacement of gp120. Thus, while the binding sites for CD4 and b12 are on roughly the same face of the gp120 monomer, they result in very different outcomes for the conformation of the Env trimer."

Might show large motions by superimposing inertia ellipsoid depictions.

BLAST PDB for gp120, ~15 structures.
MAV showing sequence variations.

SAXS profile of gp120 / FAB / CD4 complex.

Make plastic model of gp120 trimers in 5 parts with bound CD4 and FAB
connected by magnets.

Cytoscape showing clustered HIV sequences clustered into clades
with associated PDB structures.

Glycosylation of gp120 (>50% of mass) illustrate glycans
with filled rings.

Inertia ellipsoids to show FAB orientations on gp120.

Fetch by id download caching.

Only one gp120 (SIV) has glycans.  Might demonstrating adding
them to naked gp120?