title: A structure-based, quantitative structure-activity relationship approach for predicting HLA-A*0201-restricted cytotoxic T lymphocyte epitopes.
abstract: 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.
authors.affiliation: College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhou
authors.forename: Feifei
authors.initials: F
authors.lastname: Tian
authors.forename: Zhiliang
authors.initials: Z
authors.lastname: Li
mesh_terms: 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*
chemical_list: D000939:Epitopes; D015234:HLA-A Antigens; C435939:HLA-A*02:01 antigen; D015789:HLA-A2 Antigen; D008024:Ligands; D010446:Peptide Fragments