A structure-based, quantitative structure-activity relationship approach for predicting HLA-A*0201-restricted cytotoxic T lymphocyte epitopes.
In this investigation, we first constructed four types of non-bonding interaction matrixes by defining direct contacting residue types for HLA-A*0201 protein in interaction with each position of HLA-A*0201-restricted cytotoxic T lymphocyte epitope as well as several formulae calculating ligand/receptor non-bonding interactions. Relative to these studies, a method which we refer to as structure-based, quantitative structure-activity relationship is proposed and utilized for studies on 266 HLA-A*0201-restricted cytotoxic T lymphocyte epitopes. The resulting genetic algorithm-partial least square regression model is consistent with both published studies and molecular graphics analysis. Two non-bonding interactions (i.e. hydrophobic and hydrogen bonding), are found to play important roles in antigen recognition and presentation, especially exerting effects at positions of anchor residues in antigen peptides.
Zhou
Peng
P
College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China.
Tian
Feifei
F
Li
Zhiliang
Z
D000465:Algorithms; D001665:Binding Sites; D000939:Epitopes / Q000737:chemistry / Q000276:immunology*; D015234:HLA-A Antigens / Q000737:chemistry / Q000276:immunology*; D015789:HLA-A2 Antigen; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008213:Lymphocyte Activation; D010446:Peptide Fragments / Q000737:chemistry / Q000276:immunology; D021281:Quantitative Structure-Activity Relationship; D055672:Static Electricity; D013602:T-Lymphocytes, Cytotoxic / Q000737:chemistry / Q000276:immunology*
D000939:Epitopes; D015234:HLA-A Antigens; C435939:HLA-A*02:01 antigen; D015789:HLA-A2 Antigen; D008024:Ligands; D010446:Peptide Fragments