title: A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily.
abstract: Epitope identification is the basis of modern vaccine design. The present paper studied the supermotif of the HLA-A3 superfamily, using comparative molecular similarity indices analysis (CoMSIA). Four alleles with high phenotype frequencies were used: A*1101, A*0301, A*3101 and A*6801. Five physicochemical properties-steric bulk, electrostatic potential, local hydrophobicity, hydrogen-bond donor and acceptor abilities-were considered and 'all fields' models were produced for each of the alleles. The models have a moderate level of predictivity and there is a good correlation between the data. A revised HLA-A3 supermotif was defined based on the comparison of favoured and disfavoured properties for each position of the MHC bound peptide. The present study demonstrated that CoMSIA is an effective tool for studying peptide-MHC interactions.
authors.affiliation: Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK.
authors.forename: Pingping
authors.initials: P
authors.lastname: Guan
authors.forename: Irini A
authors.initials: IA
authors.lastname: Doytchinova
authors.forename: Darren R
authors.initials: DR
authors.lastname: Flower
mesh_terms: D020816:Amino Acid Motifs; D003198:Computer Simulation; D018604:Epitope Mapping; D015791:HLA-A3 Antigen / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D021281:Quantitative Structure-Activity Relationship; D055672:Static Electricity
chemical_list: D015791:HLA-A3 Antigen; D010455:Peptides