This method works well for continuous epitopes, but can not narrow down the epitope region enough in case of the discontinuous ones. The epitope region is narrowed down by repeating the process. If the substitution does not affect, an additional region is substituted again. In this situation, a continuous portion of the human antigen is substituted by the corresponding mouse sequence, and then, the binding activity to the chimera antigen is analyzed. For example, an antibody assumes to recognize a human protein, but not to recognize the mouse orthologue.
A typical example of how to use of the chimera proteins is described below. used the tertiary structure information to design the hevein-AMP chimera proteins for the epitope mapping of an allergen. Although they used only primary sequence information, Karisola et al. used the human-mouse chimera proteins of integrin α 2 I-domain for the anti-human integrin α 2 I-domain antibody. used the chimera proteins of the type 2 (PCV2) and the type 1 (PCV1) porcine circovirus capsid protein to determine the epitopes for the monoclonal antibodies for the PCV2, and Schoolmeester et al. Another common method is the use of chimera proteins. After that, the obtained peptide sequences are analyzed, and several methods for the data analysis are developed so far. The phage clones in the library which have high affinities for the antibody of interest are selected and concentrated iteratively by a so-called biopanning process. This method uses a large size of a peptide library which is presented on a phage protein. A well-established method is a phage display. parallel peptide syntheses and peptide arrays. On the other hand, there are also experimental methods for the epitope analysis, e.g. CEP, DiscoTope and PEPITO, are developed. To address the problem, some algorithms, e.g. the discontinuous epitopes, and algorithms which predict the discontinuous ones are required. Many useful antibodies recognize tertiary structures, i.e. proposed the PEPOP which searches the candidates of peptide antigens using tertiary structure information. Most of these programs use primary sequence information and properties of amino acid residues, and therefore, they are applicable to the prediction of the continuous linear epitopes. The prediction of the epitopes in silico is convenient and various algorithms are developed so far. One of the major issues is the epitope analysis of the monoclonal antibody, and there are conventional methods for the analysis. TCP is freely available as an additional file of this manuscript for academic and non-profit organization.Ĭhimera proteins are widely used for the analysis of the protein-protein interaction region. TCP is robust and possesses several favourable features, and we believe it is a useful tool for designing chimera proteins.
We developed TCP, a tool for designing chimera proteins based on the tertiary structure information. The test results of our method indicate that the TCP is robust and applicable to various shapes of proteins.
TCP can also incorporate and consider the solvent accessible surface area information calculated by a DSSP program. In light of the problem, we developed a tool named TCP (standing for a Tool for designing Chimera Proteins), which extracts some sets of mutually orthogonal cutting surfaces for designing chimera proteins using a genetic algorithm. Although the designing the chimera proteins based on the tertiary structure information is required in such situations, there is no appropriate tool so far. This method works well for an antibody recognizing a linear epitope, but not for that recognizing a discontinuous epitope. In the analysis, a continuous portion of an antigen is sequentially substituted into a different sequence. One of the major issues is the epitope analysis of the monoclonal antibody. Chimera proteins are widely used for the analysis of the protein-protein interaction region.