Changes between Version 27 and Version 28 of HIVspikes

Timestamp:

Oct 16, 2009, 4:13:04 PM (17 years ago)

Author:

meng

Comment:

--

HIVspikes

@@ -158 +158 @@
 == Conservation alternative (Elaine) ==
 
+A sequence alignment allows assessment of conservation and includes the loops that are missing from the crystal structures.
+
+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.
+
+[[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.
 
@@ -164 +170 @@
 [[Image(conscolor.png)]] [[Image(cons-render.png)]]
 
-The gray segment in gp120 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.
-
-Another possibility is using (main menu) Select... Sequence, Subsequence GAG to show where longer loops were replaced with gly-ala-gly to create this crystallizable gp120 core construct. Some other sequences in the alignment have the full-length loops.
+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.
 
 == Cytoscape ==