Peptide Design Technology

Abpro has the ability to design peptides that develop antibodies that can recognize proteins in their native form. Our experienced scientists use state-of-the-art software to design peptide antigens.  We call our proprietary software the PePro™ Antigen Design System.

Benefits of PePro™:

  • Maximized antigenicity
  • Avoid epitopes which are conserved in native protein structure
  • Optimize sequence length
  • Ability to specify desired cross reactivity
  • Guaranteed immune response

Peptide Design Strategy

Peptide antigens must be:

  • Antigenic – algorithm designed to predict the exposed epitopes on the
    surface of a protein
  • Immunogenic – coupled to carriers (BSA & KLH) capable of generating an immune response
  • Properly sized – generation of multiple peptides 10-15 residues in length covering the region to be targeted

Antigenic
We utilize the Kolaskar and Tongaonkar antigenic scale, an algorithm designed to predict the exposed epitopes on the surface of a protein.  This is a semi-empirical method, which makes use of physicochemical properties of amino acid residues and their frequencies of occurrence in experimentally known segmental epitopes.  It was developed to predict antigenic determinants on proteins. Application of this method to a large number of proteins has been shown to predict antigenic determinants better than other known methods.

Immunogenic
Because of their size most peptides are often not immunogenic on their own.  The peptides serve as epitopes when coupled to carriers (BSA & KLH) capable of generating an immune response.  Peptide-carrier conjugates seldom fail to elicit a response because of tolerance.  Consequently, the peptides can usually be seen as epitopes and high-titer antisera can typically be prepared.  We select peptides, which have low homology with the host immunized, and present minimum coverage with other potential epitopes.  This selection is made through successive rounds of BLAST searches of the peptide against the host genome and the human non-redundant set.

Peptide Size
Although there are exceptions, peptides smaller than 6 residues in length typically generate a weak immune response. Synthesis of peptides longer than 20 residues often produces side reactions making it increasingly difficult to purify a single peptide product.   In addition, longer peptides are more likely to contain residues that make coupling to carrier molecules more difficult.  The safest choice is the generation of multiple peptides 10-15 residues in length covering the region to be targeted.

Once a sequence of the protein has been established as antigenic and immunogenic, the peptide sequence is screened for certain amino acids which have to be avoided:

  • Peptides containing (>1): Cysteines (Cys, C), Methionine (Met, M), Arginine (Arg, R) and Tryptophan (Trp, W).
  • Peptides containing Glutamine (Gln, Q) and Asparagine (Asn, N) or their acids versions: Glutamic acid (Glu, E) and Aspartic acid (Asp, D).
  • Peptides containing C-terminal Proline (Pro, P).
  • Peptides greater than 20 amino acid residues.

Once PePro™ produces a sequence, our Ph.D. immunologists and biochemists review the peptide to ensure that it is the best possible antigen, then begin synthesis.

Please contact us in order to begin your peptide design project today.

About Us
Abpro is a Lexington, MA based biotechnology company. We are pioneers of industrial biochemistry and our mission is to bring innovation to the life sciences industry and ultimately improve living health. Through technology and automation, our DiversImmune™ discovery platform has streamlined all aspects of the process to deliver antibodies at industry leading speeds against previously difficult targets. Our products and discovery services are used by leading academic labs and companies around the world for research purposes, such as diagnostics and therapeutics.
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