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|| explore interaction between tp53 and brca1 || || || || || || || || || || || |
|| explore interaction between tp53 and brca1 || right click on brca1. view structure -> 1gzh || has BRCT repeats, now we will see two structural residues || || || use preset of ribbons || || || || show -> do background only || shows a less cluttered version of the view. We now see tandom BRCT repeats bound to a dimer. What does this mean biologically?|| |
Structure Visualization with Chimera and Structure Function Linkage Database
John (Scooter) Morris
University of California, San Francisco
Biological Use Case: Identify protein-protein interactions at a deep level by examining structural information. In this case, we will look at breast cancer data.
Recipe
Cytoscape version: Version number (2.6)
Plugins to Load: Structure Visualization demo (TODO: get URL and actual name)
GUI steps:
Describe each step (story), the GUI action to take, and probable remarks
Story |
Action |
Remarks |
look at breast cancer data and human interactome network |
open human.cys |
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explore structural information for 'hub' gene tp53 |
right-click on tp53 node. Select view structure -> 1tup from popup menu. |
this will bring up chimera and show co-crystal structure of p53 trimer bound to DNA |
show secondary structure |
use preset of ribbons |
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hide uninteresting structures |
under tree model window, select water chain substructure and delete it |
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rotate structure by mouse drag |
shows how it is bound together |
show surfaces of the protein |
select a leaf on the tree, then right click -> depict -> surface |
shows how parts of protein bind |
explore interaction between tp53 and brca1 |
right click on brca1. view structure -> 1gzh |
has BRCT repeats, now we will see two structural residues |
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use preset of ribbons |
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show -> do background only |
shows a less cluttered version of the view. We now see tandom BRCT repeats bound to a dimer. What does this mean biologically? |
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