Toward the quantitative prediction of T-cell epitopes: QSAR studies on peptides having affinity with the class I MHC molecular HLA-A*0201.
It would be useful for vaccine development to develop a method of rapidly identifying peptide epitopes. In this paper, the empirical three-dimensional quantitative structure-affinity relationship (3D-QSAR) methods were used to study the relationship between the three dimensional structural parameters (the isotropic surface area, ISA, and the electronic charge index, ECI) of the HLA-A*0201 binding peptide and the HLA-A*0201/peptide binding affinities. A set of 102 peptides having affinity with the class I MHC HLA-A*0201 molecule was used as training set. A test set of 40 peptides was used to determine the predictive value of the models. The 3D-QSAR models yielded a q2 = 0.5724 and a high rpred2 = 0.6955. The standard regression coefficients indicated that the hydrophobic interactions played an important role in peptide-MHC molecule binding and predicted the specific amino acid residue essential at a certain position of the peptide. The approach tested in the current paper is highly complementary to many of the methods described in references and possesses good predictability. It is a rapid and convenient method to detect high affinity peptide epitopes.
Zhihua
Lin
L
Institute of Immunology, PLA, The Third Military Medical University, Chongqing 400038, China. Zhlin_1969@yahoo.com.cn
Yuzhang
Wu
W
Bo
Zhu
Z
Bing
Ni
N
Li
Wang
W
D000595:Amino Acid Sequence; D019295:Computational Biology; D030562:Databases, Protein; D000939:Epitopes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015234:HLA-A Antigens / Q000378:metabolism*; D006801:Humans; D066298:In Vitro Techniques; D007700:Kinetics; D010455:Peptides / Q000737:chemistry / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D021281:Quantitative Structure-Activity Relationship; D013601:T-Lymphocytes / Q000276:immunology*
D000939:Epitopes; D015234:HLA-A Antigens; D010455:Peptides