1. Nicki Harmon, Samantha Hurndon, & Zeb Russo
Kwong, P.D., Wyatt, R., Robinson, J., Sweet, R.W., Sodroski, J., Hendrickson, W.A. (1998) Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 393:
Nicki Harmon, Samantha Hurndon, & Zeb Russo
Bioinformatics Lab 10/19/2011

2. Outline
HIV causes the destruction of CD4 lymphocytes

3. HIV causes destruction of CD4 lymphocytes
Entry of HIV virus into host cells is mediated by viral envelope glycoproteins
These glycoproteins are arranged in oligomeric, most likely trimeric spikes along the surface of the virion
The surface of the spike is primarily gp120
gp120 contains five variable regions (V1-V5)
both conserved and variable gp120 regions are heavily glycosylated
this glycosylation probably modulates the immunogenicity and antigenicity of gp120
gp120 is the main target for antibodies
gp120 will bind to glycoprotein on CD4 and acts as main receptor
gp120 binds to the most amino-terminal of the four immunoglobulin like domains of CD4

4. GP120 is a primary binding region for HIV
mutagenesis has found critical regions in both gp120 and CD4 for binding
CD4 binding induces a conformation change in gp120 which exposes/forms a chemokine receptor
This chemokine receptor for CCR5 and CXCR4 serve as obligate secondary receptors for HIV entry into the cell
There are other more conserved regions of gp120 that seem to be involved in chemokine-receptor binding
CD4i (CD4 induced) antibodies block the binding of the gp120-CD4 complex to the chemokine receptor
HIV and related retroviruses belong to a class of enveloped fusogenic viruses, all which require post-translational cleavage for activation.
since gp120 is so important in receptor binding and in interactions with antibodies, info about it is important

5. Crystal structure at 2.5 Å of a HIV gp120 core with associated proteins
Gp120 in red, CD4 in yellow, CD4i antibody 17b in dark and light blue
Due to the fact that gp120 is extensively glycosylated and shows great conformational heterogeneity, radical modification of the protein surface was devised to image it.
the gp120 crystallized was from HIV-1 strain HXBc2
deletions of 52 residues from N-terminus and 19 from C-terminus.
Gly-Ala-Gly tripeptide substitutions for 67 V1/V2 loop residues and 32 V3 loop residues
removal of all sugar groups beyond the linkages between the two core N-acetyl-glucosamine residues.
removal of 90% of total carbohydrate but retains 80% of non-variable loop protein
capacity to interact with CD4 and relevant antibodies is preserved at or near wild-type levels.

6. Secondary Structure in GP120
core is made up of 25 β-sheets, 5 α-helices, and 10 defined loop segments
the polypeptide chain is folded into two main domains along with some digressions from this body
Inner domain contains a two-helix, two-sheet bundle with a small five sheet β-sandwich at its termini-proximal end and a projection from the distal side where the V1/V2 stem originates.
Outer domain is a stacked double barrel that lies alongside inner domain so that the both barrel axes are roughly parallel to each other.
There is a ‘minidomain’ which is comprised of four antiparallel β-sheets that create a ‘bridging sheet’ that is in contact with both the inner and outer domains
structure based alignment shows conservation despite the variability in HIV strains
HIV-2 is 35% similar
77% and 51% for HIV-1 clade C and O respectively
Outer domain is more conserved with 86%, 72%, and 45% for HIV-1 C, HIV-1 O, and HIV-2 respectively

7. Great similarities between HIV-1,HIV-2, and SIV
α-Carbon trace shows the conservation of disulfide bridges
Sequence alignment shows similarity between HIV strains and SIV as well a s solvent accessability

8. CD4 is bound to gp120 in a depression formed by the interface of the inner and outer domains
Electron density in the Phe43 binding site
Electrostatic potential across the surfaces of gp120 and CD4

9. More binding of CD4 and gp120
3d shows contact surfaces
3e shows mutational hotspots on both CD4 and gp120
3f elucidates side vs main-chain contributions to gp120 surface
3g demonstrates gp120 sequence variability
3h shows the Phe43 cavity

10. A closer look at the Phe43 cavity

11. Antibody interactions with gp120
Interactions between gp120 and CD4i antibody, highlighting the V3 region

12. Overview of gp120 activity during HIV fusion to lymphocytes