Changes between Version 28 and Version 29 of HIVspikes

Timestamp:

Oct 16, 2009, 4:24:03 PM (17 years ago)

Author:

meng

Comment:

--

HIVspikes

@@ -162 +162 @@
 For example, open gp120 family sequence alignment from PFAM (PF00516seed.slx, attached).  1gc1 does not automatically associate, but use Multalign Viewer "Structure... Associations," associate chain G with best match.  Unfortunately that takes a while to compare against 24 sequences (1-2 seconds each?), so another alternative is to open a session with the alignment already associated. There is also a tree (PF00516seed.nhx) that could be loaded.
 
+To create this crystallizable gp120 core construct, the variable loops were replaced with shorter sequences. V1 and V2 were each replaced with Gly-Ala-Gly (GAG).  The red outline below shows residues that are not in the structure, and the solid red shows where GAG is present instead of the residue types in the alignment file.
+
 [[Image(pfam-alignment.png)]]
 
 Could color the gp120 structure by conservation, showing that the antibody and CD4 in structure 1gc1 are interacting with fairly well-conserved regions of gp120.
 
-Open 1gc1 and the alignment pdb1gc1.aln (attached).  Ahead of time, use Multalign Viewer Preferences... Headers to change Conservation style to AL2CO (otherwise default). Then use Structure... Render by Conservation and adjust settings as shown in the Render dialog (lowest or most variable red, highest or most conserved blue, no-value residues gray).
+Ahead of time, use Multalign Viewer Preferences... Headers to change Conservation style to AL2CO (otherwise default). Then use Structure... Render by Conservation and adjust settings as shown in the Render dialog (lowest or most variable red, highest or most conserved blue.
 
 [[Image(conscolor.png)]] [[Image(cons-render.png)]]
 
-The short uncolored segment in gp120 near V3 is where the alignment column had too few sequences (too many gaps) to calculate a reliable conservation value.  The redder, more variable parts of the gp120 core structure are not interacting with the other chains.
-
-The sequences gly-ala-gly were used to replace loops to create this crystallizable gp120 core construct. (main menu) Select... Sequence, Subsequence GAG shows where V1 and V2 were replaced.  V3 was also shortened but is apparently still flexible because there is missing density for that part.
+The redder, more variable parts of the gp120 core structure are not interacting with the other chains. A short uncolored segment near V3 is where there were too many gaps in the column to calculate a reliable conservation value.
+
+The GAG sequences in the structure can be selected using (main menu) Select... Sequence, Subsequence GAG to highlight the approximate locations of V1 and V2.  V3 was also shortened, but there is missing density even for this shorter form (apparently still flexible or prone to disorder).
 
 == Cytoscape ==