Changes between Version 8 and Version 9 of HIVspikes

Timestamp:

Sep 25, 2009, 4:15:29 PM (17 years ago)

Author:

goddard

Comment:

--

HIVspikes

@@ -74 +74 @@
 [[Image(gp120_13_models.png)]]
 
+Have all the models in the fetch download directory.  Point out this nice capability
+for handling fetched data.
+
 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.
@@ -92 +95 @@
 [[Image(ellipsoids.png)]]
 
+Critical aspect of FAB binding is that gp120 has extremely high glycosylation.
+N-glycosylation sites are at amino acid triplets: Asparagine - X - Serine/Threonine
+called the glycosylation sequon.  Do a prosite search (pattern N-x-[ST]) of the
+gp120 sequence in 1GC1 finds 18 sites.  Full length gp120 has 25 sites.  There are
+also O-glycoslyation sites on serines and threonines.  More than 50% of the mass
+of gp160 (gp120 + gp41 before cleavage) is glycans.
+
+[[Image(1gc1_n_glycosylation.png)]]
+
+Only one gp120 crystal structure (SIV) has glycosylation, 13 sites, only some of
+the sugars at each site are resolved.  PDB 3fus.
+
+[[Image(3fus.png)]]
+
+Would be interesting to show in a demonstration adding glycans to all N-glycosylation
+sites to get an idea of appearance of gp120 glycan shield.  Maybe they could be added
+far from molecule and minimization could drag them in close.  Would be very interesting
+to see the dense coverage by sugars.
+
 {{{
-BLAST PDB for gp120, ~15 structures.
-MAV showing sequence variations.
+
 
 SAXS profile of gp120 / FAB / CD4 complex.
@@ -104 +125 @@
 with associated PDB structures.
 
-Glycosylation of gp120 (>50% of mass) illustrate glycans
-with filled rings.
+Should show more v3 loop sequences in MAV to see conserved regions.
 
-Inertia ellipsoids to show FAB orientations on gp120.
-
-Fetch by id download caching.
 
 Only one gp120 (SIV) has glycans.  Might demonstrating adding