Application Of Partial Least Square Method In Studying Of The Quantitative Structure-activity Relationship Of T Cell Epitopes

T cell is an important immune cell whose function is to induce cell immune and regulate the immune system. Cytotoxic T lymphocytes can specifically kill the tumor or cancer protein directly. The activation,proliferation and differentiation of the T cell are the conditions that it induces the immune response and functions in the immune system. T cell can not recognize the natural antigen peptide but the antigen peptides which are bidden and presented by the MHC. The paper attaches great importance to the antigen peptides which can activate. The pathway of endogenous antigen processing and presenting of MHC class I molecular generally includes the following steps: Firstly, the endogenous antigens are bidden and loaded by the ubiquintin, then entering the proteasome where the antigen peptides are degraded to different length ranking from eight to twelve amino acids. Secondly, some of the degraded products from the proteasome are specifically transported by the TAP to the ER. Thirdly, some transported peptides specifically bind to the MHC to form the peptide-MHC complex. Lastly, the complex is loaded through the Goli body to the APC surface where the complex binds to the TCR to form the tri-complex molecular.Peptide-MHC class I molecular complex plays a pivotal role in activating the T cell during the process of antigen peptide processing and presenting of MHC class I pathway. Therefore, it is very essential to study the characteristic of antigen peptides binding to the MHC class I molecular.MHC class I molecular consists ofαchain andβchain, and a chain is composed ofα₁,α₂ andα₃ structural domain. Theα₁ andα₂ form the antigen peptide binding groove where they bind to the MHC class I molecular. The binding groove is closed at two sides so that the length of the antigen peptide binding to the MHC class I molecular is restricted to the eight to eleven amino acids. The groove has a special pocket with six amino acids where the flanking amino acids of the antigen peptides binding to the MHC class I molecular. The conformation of the MHC class I molecular decides the specificity of the antigen peptide. Totally, the antigen peptide binding to the MHC class I molecular hasdifferent affinity that is denoted by the IC50 in the immunity experiment.The amino acid sequence of the binding groove of the MHC class I molecular is unchangeable so that the characteristics of the amino acids sequence of the antigen peptide decide the binding. The antigen peptide which activates the T cell response is the T cell epitope. The prediction of the CTL epitopes is an important significant in the immunity. The method of experiment focuses on the synthesis of the polypeptide. And then the binding antigen peptides are selected through the polypeptide binding experiment. However, the method is too time and money wasting and inefficient. It is very essential to choose a proper theoretical method to predict the CTL epitopes. Depending on the nine-peptide model, the paper established the model which shows the relations between the 2D-QSAR and got the solution using the PLS so that we concluded the predictive model of affinity of peptide-MHC. The model has the predictive accuracy 66.8% and contribute a lot to the future understanding the MHC class I molecular pathway of antigen peptide processing and presenting. And it is very instructing for the designing and developing of the tumor vaccines.