Basic principles of antigen peptide selection

1. As far as possible on the surface of the protein
2. Ensure that the sequence does not form α-helix
3. The peptides at the N and C ends are better than the peptides in the middle
4. Avoid repeating sequences within the protein or close to repeating segments
5. Avoid peptides with too strong homology
6. Cross-linking can be cross-linked at both ends of N and C. The choice is based on the fact that cross-linking is not important for the production of antibodies
7. There should not be too many Pros in the sequence, but one or two Pros are beneficial, they can make the peptide chain structure relatively stable, and are beneficial to the production of specific antibodies.

In order to obtain the best results for the production of antibodies, it is necessary to design the antigen peptide carefully. The design should meet a basic condition: during the immunization process, the antigen will not produce an excessively strong immune response, and at the same time it will produce Antibodies that have binding capacity for the protein of interest. Although antigen design is a very complex subject, there are many details that need to be paid attention to. According to our accumulated experience, there are a few key basic design principles that can be provided for your reference:
1. Determining the use of antibodies A new research project is necessary to understand some basic characteristics of the protein of interest, especially if the structure of the protein is known to have a large recognition area for selecting antibodies that are easy to access and recognize help. However, in the absence of such precise structural information (which is the case in most cases), understanding the use of research can affect the strategy of peptide design. For example: if the research focus is on different regions of the protein, such as the C-terminus or the N-terminus, or a protein in a specific state, such as phosphorylation, etc., then the peptide designed according to the desired sequence and the corresponding antibody produced in There should not be much difficulty in application, however, the conformation of the protein will affect the interaction between the antibody and its recognition region. The possible problem in this case is that if the recognition region is hidden inside the protein in the folded protein, the antibody will not be able to contact this region. (Unable to interact).
2. The selection principle of the recognition area Generally speaking, the most ideal antigen recognition area should have the characteristics of being hydrophilic, located on the surface of the protein and easily deformable on the structure. Because in most natural environments, hydrophilic regions tend to concentrate on the surface of the protein, while hydrophobic regions are often wrapped inside the protein. For the same reason, antibodies can only interact with the recognition regions found on the surface of the protein. When the area has enough structure to be deformed and transferred to a position where the antibody can contact, it will have a high affinity with the antibody.
3. The continuous and discontinuous recognition region The continuous region refers to a recognition region composed of consecutive amino acid sequences. Most antibodies are directed against continuous recognition regions, and antibodies can bind to such regions with high affinity indicating that this sequence is not inside the protein. A discontinuous recognition area is a recognition area that represents a stretch of polypeptide that has a certain fold, or an antibody that connects two separated polypeptides together. In some cases, antibodies against such discontinuous recognition regions can also be produced, but the antigen polypeptide used for immunization must have a secondary structure similar to the discontinuous recognition region, and the length of the sequence needs to meet the relevant requirements.
4. Basic recommendations In order to avoid the risk that the recognition area is hidden inside the protein, we usually recommend selecting the corresponding antibodies at the N and C ends of the protein. Because in a complete protein, the N and C ends are usually exposed on the surface of the protein. However, it must be noted that the C-terminal of the membrane protein is too hydrophobic and is not suitable as an antigen.
5. The length of the sequence is usually recommended that the sequence length of the antigen polypeptide is between 8-20 amino acid residues, if it is too short, the peptide is too special, and the affinity (binding ability) between the antibody produced and the natural protein is not enough There is a strong risk. Similarly, if the sequence length exceeds 20, it will be possible to introduce secondary structures, and the antibody produced may lose its specificity. The longer the peptide chain, the more difficult the synthesis is, and it is not easy to obtain high-purity products.
6. The basic principle of carrier protein cross-linking selection: add carrier protein to the end far away from the antibody recognition area, and add Cys to the N or C end without Cys in the sequence is the preferred method for cross-linking.
7. Commonly used analysis software
MacVecfor TM; DAN star TM; PC-Gene TM

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