title: Prediction of promiscuous epitopes in the e6 protein of three high risk human papilloma viruses: a computational approach.
abstract: A najor current challenge and constraint in cervical cancer research is the development of vaccines against human papilloma virus (HPV) epitopes. Although many studies are done on epitope identification on HPVs, no computational work has been carried out for high risk forms which are considered to cause cervical cancer. Of all the high risk HPVs, HPV 16, HPV 18 and HPV 45 are responsible for 94% of cervical cancers in women worldwide. In this work, we computationally predicted the promiscuous epitopes among the E6 proteins of high risk HPVs. We identified the conserved residues, HLA class I, HLA class II and B-cell epitopes along with their corresponding secondary structure conformations. We used extremely precise bioinformatics tools like ClustalW2, MAPPP, NetMHC, EpiJen, EpiTop 1.0, ABCpred, BCpred and PSIPred for achieving this task. Our study identified specific regions 'FAFR(K)DL' followed by 'KLPD(Q)LCTEL' fragments which proved to be promiscuous epitopes present in both human leukocyte antigen (HLA) class I, class II molecules and B cells as well. These fragments also follow every suitable character to be considered as promiscuous epitopes with supporting evidences of previously reported experimental results. Thus, we conclude that these regions should be considered as the important for design of specific therapeutic vaccines for cervical cancer.
authors.affiliation: Bioinformatics Division, School of Biosciences and Technology, VIT University, Vellore, India. csudandiradoss@vit.ac.in
authors.forename: Nirmala
authors.initials: N
authors.lastname: Subramanian
authors.forename: Sudandiradoss
authors.initials: S
authors.lastname: Chinnappan
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D004268:DNA-Binding Proteins / Q000276:immunology*; D000939:Epitopes / Q000276:immunology*; D005260:Female; D006680:HLA Antigens / Q000276:immunology; D006801:Humans; D008969:Molecular Sequence Data; D009856:Oncogene Proteins, Viral / Q000276:immunology*; D027383:Papillomaviridae / Q000276:immunology*; D012097:Repressor Proteins / Q000276:immunology*; D017386:Sequence Homology, Amino Acid
chemical_list: D004268:DNA-Binding Proteins; C068651:E6 protein, Human papillomavirus type 16; C052603:E6 protein, Human papillomavirus type 18; D000939:Epitopes; D006680:HLA Antigens; D009856:Oncogene Proteins, Viral; D012097:Repressor Proteins