Application of Genetic Search in Derivation of Matrix Models of Peptide Binding to MHC Molecules

T cells of the vertebrate immune system recognise peptides bound by major histocompatibility complex (MHC) molecules on the surface of host cells. Peptide binding to MHC molecules is necessary for immune recognition, but only a subset of peptides are capable of binding to a particular MHC molecule. Common amino acid patterns (binding motifs) have been observed in sets of peptides that bind to specific MHC molecules. Recently, matrix models for peptide/MHC interaction have been reported. These encode the rules of peptide/ MHC interactions for an individual MHC molecule as a 20 x 9 matrix where the contribution to binding of each amino acid at each position within a 9-mer peptide is quantified. The artificial intelligence techniques of genetic search and machine learning have proved to be very useful in the area of biological sequence analysis. The availability of peptide/MHC binding data can facilitate derivation of binding matrices using machine learning techniques. We performed a simulation study to determine the minimum number of peptide samples required to derive matrices, given the pre-defined accuracy of the matrix model. The matrices were derived using a genetic search. In addition, matrices for peptide binding to the human class I MHC molecules, HLA-B35 and -A24, were derived, validated by independent experimental data and compared to previously-reported matrices. The results indicate that at least 150 peptide samples are required to derive matrices of acceptable accuracy. This result is based on a maximum noise content of 5%, the availability of precise affinity measurements and that acceptable accuracy is determined by an area under the Relative Operating Characteristic curve (Aroc) of > 0.8. More than 600 peptide samples are required to derive matrices of excellent accuracy (Aroc > 0.9). Finally, we derived a human HLA-B27 binding matrix using a genetic search and 404 experimentally-tested peptides, and estimated its accuracy at Aroc > 0.88. The results of this study are expected to be of practical interest to immunologists for efficient identification of peptides as candidates for immunotherapy.