e n i c i d e M l a t n e m i r e p x E f o l a n r u o J e h T CORRESPONDENCE Scott R. Burrows: scottb@qimr.edu.au OR Jamie Rossjohn: Jamie.rossjohn@ med.monash.edu.au Abbreviations used: LCL, lym- phoblastoid cell line; MFI, mean fluorescence intensity; v.d.w., van der Waals. A R T I C L E The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound confor mation Fleur E.Tynan,1 Diah Elhassen,2 Anthony W. Purcell,3 Jacqueline M. Burrows,4 Natalie A. Borg,1 John J. Miles,4,5 Nicholas A. Williamson,3 Kate J. Green,4 Judy Tellam,4 Lars Kjer-Nielsen,2 James McCluskey,2 Jamie Rossjohn,1 and Scott R. Burrows4 1The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia 2Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia 3Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia 4Cellular Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia 5School of Population Health, University of Queensland, Brisbane, Queensland 4006, Australia Thousands of potentially antigenic peptides are encoded by an infecting pathogen; however, only a small proportion induce measurable CD8 T cell responses. To investigate the factors that control peptide immunogenicity, we have examined the cytotoxic T lymphocyte (CTL) response to a previously undefined epitope (77APQPAPENAY86) from the BZLF1 protein of Epstein-Barr virus (EBV). This peptide binds well to two human histocompatibility leukocyte antigen (HLA) allotypes, HLA-B*3501 and HLA-B*3508, which differ by a single amino acid at position 156 (156Leucine vs. 156Arginine, respectively). Surprisingly, only individuals expressing HLA-B*3508 show evidence of a CTL response to the 77APQPAPENAY86 epitope even though EBV-infected cells expressing HLA-B*3501 process and present similar amounts of peptide for CTL recognition, suggesting that factors other than peptide presentation levels are influencing immunogenicity. Functional and structural analysis revealed marked conformational differences in the peptide, when bound to each HLA-B35 allotype, that are dictated by the polymorphic HLA residue 156 and that directly affected T cell receptor recognition. These data indicate that the immunogenicity of an antigenic peptide is influenced not only by how well the peptide binds to major histocompatibility complex (MHC) molecules but also by its bound conformation. It also illustrates a novel mechanism through which MHC polymorphism can further diversify the immune response to infecting pathogens. The CD8 T cell response to an infecting pathogen is generally focused toward a limited subset of antigenic peptides presented on the surface of infected cells. Furthermore, a hierarchy of immunodominance that is maintained in un- related individuals is often observed between those peptides that are the targets of CTL rec- ognition (1). There appear to be three major factors that control the immunogenicity of a foreign peptide: the specificity of the antigen processing machinery, the peptide binding pref- erences of MHC class I molecules, and limita- tions in the diversity of the TCR repertoire (1). F. Tynan and D. Elhassen contributed equally to this work. The online version of this article contains supplemental material. How these parameters focus the CTL response toward a limited number of determinants within an antigen is not completely understood. The dominant factor controlling the magni- tude of the CTL response to a foreign peptide is the quantity of peptide presented on the sur- face of the APC. MHC class I molecules show strict binding specificity because of the high level of polymorphism concentrated in the antigen-binding cleft (2). The pockets (A–F) of the peptide-binding groove vary in their depth, electrostatic potential, and hydrophobic- ity, thereby determining the individual specificity of the peptide–MHC interaction (3). For most MHC alleles, two of these pockets display a marked preference for one or two amino acids, JEM © The Rockefeller University Press $8.00 Vol. 202, No. 9, November 7, 2005 1249–1260 www.jem.org/cgi/doi/10.1084/jem.20050864 1249