Useful Reminders/Links

Requirements:

1. Antibody amino acid (or DNA) sequence is available.
2. Antigen (for activating system) is commercially available at a reasonable cost.
3. Antigens should not significantly affect our mammalian cells other than their involvement in activating our system (for example, avoid EGFR or TNF-alpha as antigens).  Additionally, antigens shouldn't present significant health dangers to us (for example, anthrax spores).
4. Antigen-antibody interaction should be well-characterized.

Leader sequences

Summary Table

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/mutations.  However, peptide numbering is different on UniProt and in binding interactions paper (18aa difference).

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

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.

HXB2 strain:

Abcam:  10ug/$228

MyBioSource:  50ug/$365

YU2 strain:

MyBioSource

JRCSF strain:

Abnova:  50ug/$770

MyBioSource:  50ug/$365

Eenzyme:  50ug/$259

0.5beta

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

**PROBLEM:  Commercially available HXB2 gp120 peptides have the amino acid sequence RKRIRIQRGPGRAFVTIG

Commercially available peptides are based on this 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?

VRC01

Really cool paper about gp120 single-chain antibodies in E. coli

Everything you ever wanted to know about this antibody:

Antibody identification paper (and supplementary materials, which includes sequences)

• Supplementary materials includes VRC01 variable regions' amino acid sequences
• Supplementary materials includes HXB2 strain gp120 core reference sequences that were used for screening antibodies (Fig. S1B).  They consisted of the core sequences separated by GAG linkers.  
   There is a mutation from serine at position 334 in commercial peptides (from env HXB2 sequences) to alanine in this paper, but:
  • Many of the gp120 core mutants they designed and analyzed computationally had a threonine at this position (334), including the one they eventually chose for in vitro screening (RSC3).  Based on this information, it seems that the amino acid present at this position isn't critical to binding, and that binding can still happen even when alanine is replaced by a hydroxyl-containing amino acid like threonine (so by extension maybe serine is ok too).
  • The reference sequence for YU2 strain gp120 also has a serine at the position corresponding to 334 in HXB2 (contained within a conserved amino acid sequence), and VRC01 is shown to have bound YU2 gp120 (wild-type) well (Table S1).
  • The position in JRCSF strain gp120 that corresponds to 334 in HXB2 is not identified as a binding site in the binding information paper (see binding information paper, Fig 1 - in fact it's not even included in the table).
• Has numbers about binding interactions (including Kd!)
  • SPR
  • ITC
  • Competition ELISA

Binding information

• Includes alanine scanning table

Structural analysis

• Most natural resistance a result of variation in V5 region