Changes between Version 6 and Version 7 of HIVspikes

Timestamp:

Sep 25, 2009, 3:30:52 PM (17 years ago)

Author:

goddard

Comment:

--

HIVspikes

@@ -37 +37 @@
 
 ||[[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||
+||HIV-1 BaL spike with CD4 and 17b-FAB. Subramaniam lab.[[BR]]EMDB 5020, PDB 3dnn||HIV-1 BaL spike with b12 FAB.[[BR]]EMDB 5018, PDB 3dno||
 
 [[Image(emdb_1246.gif)]]
@@ -74 +74 @@
 [[Image(gp120_13_models.png)]]
 
+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.[[BR]]
+>Liu J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S.[[BR]]
+>Nature. 2008 Sep 4;455(7209):109-13. [http://www.ncbi.nlm.nih.gov/pubmed/18668044 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.