Team:UCLA/Notebook/Protein Cages/26 May 2015
I looked at the protein database sequence of the protein cage and brainstormed sites that were void of any secondary structure. From here the different sites were visualized on Pymol to check for any steric hindrance that might not allow for the ligation to happen.
My sites:
318-321(KNTD) (KNLVPRGSGTD) This was chosen because there was no secondary structure formation and contained no bends and turns. When viewed on pymol it was not sterically hindered.
351-354(VPSE) (LVPRGSGE) This was chosen because there was no secondary structure formation and contained no bends and turns. It is not sterically hindered when viewed on pymol. Its also sticking out quite a bit from the protein which means it may not be key in the formation of the cage.
123-129(ASLEPFL) ASLVPRGSGEPGL This was chosen because there was no secondary structure formation but when viewed on pymol it was sterically hindered.
-Nithin D.
Phillip's notes
All sites were revisited (including Nithin's) and visualized on pymol. Top candidates were identified and Dr. Yeates was emailed for review. A link for the pymol file, "2015-05-25 3vdx pisa with sites" is below.