“So many peptides, so few grooves” – compare the ways in which specific antigen recognition is accomplished by MHC molecues, by T cell receptors and by antibody molecules Introduction Specific antigen recognition lies at the heart of the adaptive immune response. This essay will compare how MHC, TCR and Ab molecules accomplish this feat. Structural differences in antigen-binding site Thanks to X-ray crystallography, we have a rather clear picture of the structure of the antigen-binding sites of the three relevant proteins. In the case of the MHC, the peptide-binding groove consists of a floor and two walls.
Importantly, this structure is germline-encoded. In the floor, the ? chain of the class I molecule or the ? and i?? chains of the class II molecule form a i?? -pleated sheet. The walls are constituted by ? -helixes. In the MHC class I molecule, walls and floor are formed by the ? chain. Also, ? 1 and ? 2 domains of this chain converge such that they close the class I peptide-binding groove. This is not the case in MHC class II molecules. As a result, class I molecules can accommodate peptides that are 8 to 11 residues long whereas class II molecules optimally bind peptides with a length of 12 to 16 residues.
One way in which the molecular interaction between peptide and MHC has been studied is by introducing mutations in an immunogenic peptide. With this technique, it is possible to identify certain residues that make contact with the MHC molecule and others that are essential for TCR recognition. Together with the evidence presented above, this has lead to the idea that MHC molecules only recognize certain anchor residues of the bound peptide. Typically, a MHC I molecule has been found to have six pockets (A-F) which bind certain AA residues of the peptide.
Two or three of these pockets (in MHC I often B and F) are particularly important in binding the residues that serve as anchors. Similar to the situation in the MHC molecule, the TCR antigen-binding site only makes contact with a very limited number of peptide residues. Again, evidence for this comes from mutational analysis of the recognized peptides. However, in contrast to the situation described above, the Ag-binding site of the TCR is formed by somatic rearrangement of the variable regions of ? and i?? chains. These chains are organized into 3 complementary-determining regions (CDRs).
Similarly, the variable regions of the heavy and light chains of antibodies each form 3 CDRs, which contact the Ag. However, unlike the MHC and the TCR, the peptide-binding site of Abs evidently makes contact with the tertiary structure of the whole epitope, not just with certain AA residues. This dissimilarity also explains the different conformational requirements for specific antigen recognition. Conformation of antigen One of the most important differences in specific antigen recognition between the three types of molecules is the conformation of the antigen they recognize.
One way to demonstrate this difference experimentally is to immunize an animal with a protein in a particular conformation and subsequently challenge the primed animal with the same protein in a different conformation. It can be shown that a B-Cell response only ensues if the tertiary structure of the protein used for immunization and challenge are the same. In contrast, a T-Cell response ensues even if the protein is in its native form during immunization and denatured during the challenge and vice versa.
In addition, Ab determinants have been shown to be located on the surface of a native antigen, whereas TCR determinants may be buried within the core of the folded protein. The conclusion drawn from these experiments is that TCR and MHC molecules recognize linear epitopes on short peptides derived from the protein, whereas Ab molecules specifically recognize conformational determinants of the immunogen (which need not necessarily be protein). Ultimate proof for this model of specific antigen recognition came from elusion and analysis of the antigens bound by each of these molecules and X ray crystallography.
Diversity The MHC exists as a finite number alleles and the peptide-binding region is germline-encoded. For this reason, MHC molecules must be promiscuous to present the enormous range of possible peptide antigens. Multiple lines of experimental evidence support this idea. Firstly, if transgenic T cells with specificity for a defined peptide-MHC complex are stimulated by APCs presenting that peptide, the response can be inhibited by addition of excess of structurally similar peptide.
Secondly, transgenic expression of defined MHC alleles in insect cells (which do not normally have MHCs) showed that many different peptides can be eluted from these. Using experiments like these, it has been estimated that each allele can bind around 2% of all possible peptides. In contrast, both TCR and Abs are highly specific. In the case of Abs, this specificity has been classically demonstrated by Landsteiner in the 1930s. It can be achieved because TCR and MHC genes undergo somatic rearrangement.
This allows them to recognize antigens with a much higher specificity. It has been estimated that the nai?? ve T-cell repertoire consists of 25-100 million distinct clones1,2, each of which recognizes only very specific determinants. One might argue that the B-cell repertoire is even larger for two reasons. On the one hand they do not undergo as rigorous negative selection in development and on the other hand, somatic hypermutation increases diversity of Ab specificities.