When we think about antibodies, we often picture the classic Y-shaped protein immunoglobulin G, especially when it comes to monoclonal antibodies used as therapeutics or diagnostics. To illustrate CDRs in antibodies, this article will be focusing on the structure of a typical IgG. Please consult our other article for other types of antibodies.
IgG antibodies are composed of two identical peptide chain pairs: heavy chain and light chain. Thus, IgG antibodies are heterotetrameric proteins. Both the light and heavy chains are made of variable (V) and constant (C) regions; each variable region contains three CDR loops that form the majority of the antigen-binding site. Outside of the CDR loops, framework sequences stabilize the loop structure (Figure 2).
Figure 2. Schematic representation of an IgG antibody. The enlargement shows the variable domain of the light chain (LV) consisting of three CDR loops and framework region.
Because antibodies’ complementary-determining regions (CDRs) are highly variable, it can prove difficult to identify their exact amino acid sequence. Essentially, CDRs are novel protein sequences. Routine identification of proteins is often executed via genomics and proteomics methodologies that require database searches – since antibodies sequences are rarely found in databases, more advanced techniques are required.
This article will review the advantages of using de novo protein sequencing to identify CDRs by sequence as well as depict, in a specific research case study, how researchers used this method to accomplish successful and accurate identification of CDRs. Furthermore, this article will provide further resources to help those studying proteins to enhance their workflows with next generation protein sequencing.