= 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.[[BR]]
>Walker LM, et al.[[BR]]
>Science. 2009 Sep 3 [http://www.ncbi.nlm.nih.gov/pubmed/19729618 PubMed 19729618]

== Things to show ==

Schematic of HIV virus architecture

[[Image(800px-HIV_Virion-en-2.png)]]

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

[[Image(fuller_siv.png)]]

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.

||[[Image(emdb_5019.gif)]]||[[Image(emdb_5020.gif)]]||
||Unliganded HIV-1 BaL spike. Subramaniam lab.[[BR]]EMDB 5019, PDB 3dnn||CD4 and 17b-bound HIV-1 BaL spike.[[BR]]EMDB 5020, PDB 3dno||

[[Image(emdb_1246.gif)]]

SIV envelope spike. Roux lab.[[BR]]
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.

||[[Image(ping-zhu_with-molecule.jpg)]]||[[Image(dr-roux_at-electron-mircoscope_6-8-2005.jpg)]]||

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).

[[Image(1gc1.png)]]

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.

[[Image(1gc1G_blast.png)]]

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.

[[Image(gp120_15models_mav.png)]]

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

[[Image(gp120_13_models.png)]]

{{{
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?

}}}