Child pages

Antibody/antigen choices - contains all of the planning info for gBlocks and antibody/antigen choices

List of secondary antibodies in Brian's fridge

Antigen binding - plans for how to detect antigen binding to mIgM (antibodies, conjugation, etc.), also contains FINAL PURCHASE DECISIONS

Leader sequences

Chicken Lysozyme

Chicken lysozyme derives from chicken egg white.  Breaks down bacterial cell walls.

mAb name:  HyHEL-10

Sequence:  this paper

Binding interactions: this paper (interacts with discontinuous parts of peptide)

Peptide sequence: UniProt

Cross-checked peptide sequence with antibody binding interaction sites.  None of those sites have known variants/mutants.

Peptide suppliers:

Sigma-Aldrich:  1g/$49.50

Merck-Millipore:  1g/$39

HIV1 gp120 (HIV envelope glycoprotein)

gp120 is a glycoprotein derived from gp160.  gp160 is processed into gp120 and gp41, which together form a complex that binds to CD4, permitting the fusion of viral and cell membranes.

gp120 antibodies review

mAb database:  HIV Molecular Immunology 2002 (same as this)

mAb name:  0.5beta

Sequence:  IMGT

Epitope (recognition sequence):

IMGT:  RKSIRIQRGPGRAFVTIG

HIV molecular immunology database:  RGPGRAFVTIG

Peptide suppliers:

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.

Abcam:  10ug/$228

MyBioSource:  50ug/$365

**PROBLEM:  These have the amino acid sequence RKRIRIQRGPGRAFVTIG

Sequence data:  NCBI, UniProt

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:

Looking more closely at PDB file SPV didn't add hydrogens with the mutation  - how to fix this?