Team:UCLA/Notebook/Protein Cages/21 May 2015
This was my approach to designing the protease sites -Phillip
Using the DSSP algorithm from PDB, the parts of the protein with no alpha helices, beta sheets, or turns and five or greater amino acids are the following. 30-35, 64-72, 123-129, 131-139, 216-220, 228-233, 298-302, 331-336, 417-422 Revised sites in terms of location. Bold indicates insertion
Top candidates are based on two criteria: 1. Exposure at the surface for protease accessibility 2. Speculated to have minimal conformational changes by insertion In general, original proline residues on the side were kept, in case they were involved in transitioning between secondary structural elements. Also, insertions were flanked with glycines in order to allow extra flexibility.
131-139*: (KTDDNPDGA) to KTDDNPDGLVPRGSGA. Satisfies 1 and 2.
228-233: (DRTLPI) to DRTLGLVPRGSGIPI. Satisfies 1.
331-336*: (TRPILS) to TRPGLVPRGSGILS. Satisfies 1 and 2, depending on oligomerization geometry.
298-302*: (IPSGP) to IPSGLVPRGSGP. Satisfies 1 and 2, depending on oligomerization geometry.
216-220: (IDVPA) to IDVGLVPRGSGPA.
64-72: (SSQPTTGYD) to SSQPTTGLVPRGSGYD
417-422: (RMGAVT) to RMGLVPRGSGAVT. Satisfies 1, depending on geometry.
For the available pymol file, download the file named "2015-05-19 3vdx chains and sites"