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| − | {{Template:UCLA}}
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| − | This was my approach to designing the protease sites -Phillip
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| − | 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.
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| − | 30-35, 64-72, 123-129, 131-139, 216-220, 228-233, 298-302, 331-336, 417-422
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| − | Revised sites in terms of location. Bold indicates insertion
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| − | Top candidates are based on two criteria:
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| − | 1. Exposure at the surface for protease accessibility
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| − | 2. Speculated to have minimal conformational changes by insertion
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| − | 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.
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| − | 131-139*: (KTDDNPDGA) to KTDDNPD'''GLVPRGS'''GA. Satisfies 1 and 2.
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| − | 228-233: (DRTLPI) to DRTL'''GLVPRGSG'''IPI. Satisfies 1.
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| − | 331-336*: (TRPILS) to TRP'''GLVPRGSG'''ILS. Satisfies 1 and 2, depending on oligomerization geometry.
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| − | 298-302*: (IPSGP) to IPS'''GLVPRGSG'''P. Satisfies 1 and 2, depending on oligomerization geometry.
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| − | 216-220: (IDVPA) to IDV'''GLVPRGSG'''PA.
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| − | 64-72: (SSQPTTGYD) to SSQPTT'''GLVPRGSG'''YD
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| − | 417-422: (RMGAVT) to RMG'''LVPRGSG'''AVT. Satisfies 1, depending on geometry.
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| − | For the available pymol file, downloaded the file named "2015-05-19 3vdx chains and sites"
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| − | https://drive.google.com/drive/folders/0ByuQle2_4oafS3N2b1RiajZsWTQ/0ByuQle2_4oafflNRbnktanJJRmx0Y3hLb2NCR1NWRlpoOVE4ZnRHUXM5U1FtcEtRekhWck0/0B7kb5ShZyyqVfm5HVmt4ZGlqeFJVLUdmc2ZsRUZleWo5MjQ0U1B3eFB5V3BKcHZEYzl3TDQ/0B7kb5ShZyyqVflZSdjZmZzlBV185ZDd4VXNyMkNoZzlzYXl2MHRhSURIazAwV0xWWGt1U00
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