How to Do Peptide Antigen Design?

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Homology Considerations:

Two basic strategies can be used to address peptide antigen design. Both approaches should be considered when analyzing the protein sequence.

  1. A unique sequence or region should be selected to ensure the specificity of the target protein.
  2. A homologous sequence should be chosen so that a single antibody can recognize multiple proteins.

Epitope Selection:

Continuous Epitopes, Discontinuous Epitopes:

Peptide Antigen Design for Antibody Services
Peptide Antigen Design

Targeting the N-terminus or C-terminus:

Peptide Antigen Design Strategies
Peptide Antigen Design Sequence Selection Guideline

Sequence Length:

Peptide Purity:

Peptide Solubility

Hydrophobicity and hydrophilicity example of a sequence
Hydrophobicity and Hydrophilicity Example of a Peptide

Amino acid classifications

Hydrophobic (non-polar) amino acids: Ala, Ile, Leu, Met, Phe, Trp, Val

Uncharged (polar) amino acids: Asn, Cys, Gly, Gln, Pro, Ser, Thr, Tyr

Acidic (polar) amino acids: Asp, Glu

Basic (polar) amino acids: His, Lys, Arg

Difficult Amino Acids

Carrier Protein Coupling Considerations:

Common carrier proteins used for antibody production:

Carrier protein KLH or BSA for antibody generation
Carrier Protein for Antibody Generation

Multiple antigenic peptides (MAPs)

MAPs Antigen
Multiple Antigenic Peptides

Peptide Modifications

A. N-terminal amino group

B. C-terminal carboxyl group
C. alpha-Amino group on lysine
D. Hydroxyl group on serine, threonine, and tyrosine
E. Guanidine group on arginine
F. Thiol group on cysteine

Peptide Modification Sites
Peptide Modification Sites