Amidation and Acetylation
Purpose of having amidation and acetylation is to eliminate a potential charge in the peptide antigen. Extra electrostatic charge may affect the proper folding of the protein and potentially alter antibody specificity. Therefore during peptide design, N-terminal epitopes should be amidated or conjugated on the C-terminus, while C-terminal epitopes should be acetylated or conjugated in the N-terminus. Internal sequences should be capped on one terminus and conjugated on the other.
Question on adding CG to a peptide antigen
The inclusion of CG, CAGAG, CGGG to a peptide sequence act as a linker which believe, it may increase the flexibility of a target peptide upon its attachment to a carrier protein.