- Rock, K.L. & Goldberg, A.L. Degradation of cell proteins and the generation of MHC class I-presented peptides. Annu. Rev. Immunol. 17, 739–779 (1999).
Article CAS Google Scholar
- Engelhard, V.H., Altrich-Vanlith, M., Ostankovitch, M. & Zarling, A.L. Post-translational modifications of naturally processed MHC-binding epitopes. Curr. Opin. Immunol. 18, 92–97 (2006).
Article CAS Google Scholar
- Zarling, A.L. et al. Phosphorylated peptides are naturally processed and presented by major histocompatibility complex class I molecules in vivo. J. Exp. Med. 192, 1755–1762 (2000).
Article CAS Google Scholar
- Zarling, A.L. et al. Identification of class I MHC-associated phosphopeptides as targets for cancer immunotherapy. Proc. Natl. Acad. Sci. USA 103, 14889–14894 (2006).
Article CAS Google Scholar
- Andersen, M.H. et al. Phosphorylated peptides can be transported by TAP molecules, presented by class I MHC molecules, and recognized by phosphopeptide-specific CTL. J. Immunol. 163, 3812–3818 (1999).
CAS PubMed Google Scholar
- Harper, J.W. A phosphorylation-driven ubiquitination switch for cell-cycle control. Trends Cell Biol. 12, 104–107 (2002).
Article CAS Google Scholar
- Koepp, D.M., Harper, J.W. & Elledge, S.J. How the cyclin became a cyclin: regulated proteolysis in the cell cycle. Cell 97, 431–434 (1999).
Article CAS Google Scholar
- Reed, S.I. Ratchets and clocks: the cell cycle, ubiquitylation and protein turnover. Nat. Rev. Mol. Cell Biol. 4, 855–864 (2003).
Article CAS Google Scholar
- Ang, X.L. & Wade Harper, J. SCF-mediated protein degradation and cell cycle control. Oncogene 24, 2860–2870 (2005).
Article CAS Google Scholar
- Hershko, A. & Ciechanover, A. The ubiquitin system. Annu. Rev. Biochem. 67, 425–479 (1998).
Article CAS Google Scholar
- Wilkinson, K.D. Ubiquitination and deubiquitination: targeting of proteins for degradation by the proteasome. Semin. Cell Dev. Biol. 11, 141–148 (2000).
Article CAS Google Scholar
- Princiotta, M.F. et al. Quantitating protein synthesis, degradation, and endogenous antigen processing. Immunity 18, 343–354 (2003).
Article CAS Google Scholar
- Blume-Jensen, P. & Hunter, T. Oncogenic kinase signalling. Nature 411, 355–365 (2001).
Article CAS Google Scholar
- Evan, G.I. & Vousden, K.H. Proliferation, cell cycle and apoptosis in cancer. Nature 411, 342–348 (2001).
Article CAS Google Scholar
- Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158 (2007).
Article CAS Google Scholar
- Fecher, L.A., Cummings, S.D., Keefe, M.J. & Alani, R.M. Toward a molecular classification of melanoma. J. Clin. Oncol. 25, 1606–1620 (2007).
Article CAS Google Scholar
- Easty, D.J. & Bennett, D.C. Protein tyrosine kinases in malignant melanoma. Melanoma Res. 10, 401–411 (2000).
Article CAS Google Scholar
- Bantscheff, M. et al. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol. 25, 1035–1044 (2007).
Article CAS Google Scholar
- Diella, F. et al. Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics 5, 79 (2004).
Article Google Scholar
- Hornbeck, P.V., Chabra, I., Kornhauser, J.M., Skrzypek, E. & Zhang, B. PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 4, 1551–1561 (2004).
Article CAS Google Scholar
- Bjorkman, P.J. et al. Structure of the human class I histocompatibility antigen, HLA-A2. Nature 329, 506–512 (1987).
Article CAS Google Scholar
- Madden, D.R., Garboczi, D.N. & Wiley, D.C. The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2. Cell 75, 693–708 (1993).
Article CAS Google Scholar
- Madden, D.R. The three-dimensional structure of peptide-MHC complexes. Annu. Rev. Immunol. 13, 587–622 (1995).
Article CAS Google Scholar
- Ruppert, J. et al. Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules. Cell 74, 929–937 (1993).
Article CAS Google Scholar
- Bouvier, M. & Wiley, D.C. Importance of peptide amino and carboxyl termini to the stability of MHC class I molecules. Science 265, 398–402 (1994).
Article CAS Google Scholar
- Fersht, A.R. et al. Hydrogen bonding and biological specificity analysed by protein engineering. Nature 314, 235–238 (1985).
Article CAS Google Scholar
- Sette, A. et al. The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes. J. Immunol. 153, 5586–5592 (1994).
CAS PubMed Google Scholar
- Hendrickson, R.C., Skipper, J.C., Shabanowitz, J., Slingluff, C.L., Jr. & Engelhard, V.H . in Immunology Methods Manual: The Comprehensive Sourcebook of Techniques (ed. Lefkovits, I.) 605–623 (Academic, New York, 1996).
Google Scholar
- Martin, S.E., Shabanowitz, J., Hunt, D.F. & Marto, J.A. Subfemtomole MS and MS/MS peptide sequence analysis using nano-HPLC micro-ESI fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 72, 4266–4274 (2000).
Article CAS Google Scholar
- Sidney, J. et al. Majority of peptides binding HLA-A*0201 with high affinity crossreact with other A2-supertype molecules. Hum. Immunol. 62, 1200–1216 (2001).
Article CAS Google Scholar
- Gulukota, K., Sidney, J., Sette, A. & DeLisi, C. Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J. Mol. Biol. 267, 1258–1267 (1997).
Article CAS Google Scholar
- Garboczi, D.N., Hung, D.T. & Wiley, D.C. HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides. Proc. Natl. Acad. Sci. USA 89, 3429–3433 (1992).
Article CAS Google Scholar
- Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26, 795–800 (1993).
Article CAS Google Scholar
- Collaborative Computational Project No 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).
- Brunger, A.T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921 (1998).
Article CAS Google Scholar
- Brünger, A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472–475 (1992).
Article Google Scholar
- Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
Article Google Scholar
- Fenn, T.D., Ringe, D. & Petsko, G.A. POVScript+: a program for model and data visualization using persistence of vision ray-tracing. J. Appl. Cryst. 36, 944–947 (2003).
Article CAS Google Scholar
- Guex, N. & Peitsch, M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18, 2714–2723 (1997).
Article CAS Google Scholar
- Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Protein Struct. Funct. Genet. 11, 281–296 (1991).
Article CAS Google Scholar