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Full-length gp120 peptides are not readily available. Check the manufacturing details to ensure that the epitope is included in the peptide. Also check that peptide comes glycosylated.
HXB2 strain:
Abcam: 10ug/$228
MyBioSource: 50ug/$365
**PROBLEM: These have the amino acid sequence RKRIRIQRGPGRAFVTIG
Serine residue does contribute to binding: 0.5beta binding interactions.pdf
Tried testing binding in silico:
Performed in silico mutation using Swiss PDB Viewer: S234R, where 234 is PDB residue number (contained in peptide P) corresponding to S residue in RKSIRIQRGPGRAFVTIG
Energy minimization with Python code from 20.320 using PyRosetta:
| Peptide | Starting Energy | Minimized Energy |
|---|---|---|
| 234 = S (original) | 409.865230046 | 378.056398555 |
| 234 = R (mutant) | 408.461979863 | 376.734455146 |
| R/S ratio | 0.9966 | 0.9965 |
Looking more closely at PDB file SPV didn't add hydrogens with the mutation 
- how to fix this?
YU2 strain:
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