SEARCH

SEARCH BY CITATION

References

  • 1
    Van Der Bruggen, P., Zhang, Y., Chaux, P., Stroobant, V., Panichelli, C., Schultz, E. S., Chapiro, J. et al., Tumor-specific shared antigenic peptides recognized by human T cells. Immunol. Rev. 2002. 188: 5164.
  • 2
    Gilboa, E., The promise of cancer vaccines. Nat. Rev. Cancer. 2004. 4: 401411.
  • 3
    Pogue, R. R., Eron, J., Frelinger, J. A. and Matsui, M., Amino-terminal alteration of the HLA-A*0201-restricted human immunodeficiency virus pol peptide increases complex stability and in vitro immunogenicity. Proc. Natl. Acad. Sci. USA 1995. 92: 81668170.
  • 4
    Borbulevych, O. Y., Baxter, T. K., Yu, Z., Restifo, N. P. and Baker, B. M., Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design. J. Immunol. 2005. 174: 48124820.
  • 5
    Chen, J. L., Stewart-Jones, G., Bossi, G., Lissin, N. M., Wooldridge, L., Choi, E. M., Held, G. et al., Structural and kinetic basis for heightened immunogenicity of T cell vaccines. J. Exp. Med. 2005. 201: 12431255.
  • 6
    Speiser, D. E., Baurngaertner, P., Voelter, V., Devevre, E., Barbey, C., Rufer, N. and Romero, P., Unmodified self antigen triggers human CD8 T cells with stronger tumor reactivity than altered antigen. Proc. Natl. Acad. Sci. USA 2008. 105: 38493854.
  • 7
    Stuge, T. B., Holmes, S. P., Saharan, S., Tuettenberg, A., Roederer, M., Weber, J. S. and Lee, P. P., Diversity and recognition efficiency of T cell responses to cancer. PLoS Med. 2004. 1: e28.
  • 8
    Borbulevych, O. Y., Insaidoo, F. K., Baxter, T. K., Powell Jr., D. J., Johnson, L. A., Restifo, N. P. and Baker, B. M., Structures of MART-126/27–35 peptide/HLA-A2 complexes reveal a remarkable disconnect between antigen structural homology and T cell recognition. J. Mol. Biol. 2007. 372: 11231136.
  • 9
    Denkberg, G., Klechevsky, E. and Reiter, Y., Modification of a tumor-derived peptide at an HLA-A2 anchor residue can alter the conformation of the MHC-peptide complex: probing with TCR-like recombinant antibodies. J. Immunol. 2002. 169: 43994407.
  • 10
    Kawakami, Y., Eliyahu, S., Jennings, C., Sakaguchi, K., Kang, X., Southwood, S., Robbins, P. F. et al., Recognition of multiple epitopes in the human melanoma antigen gp100 by tumor-infiltrating T lymphocytes associated with in vivo tumor regression. J. Immunol. 1995. 154: 39613968.
  • 11
    van Stipdonk, M. J., Badia-Martinez, D., Sluijter, M., Offringa, R., van Hall, T. and Achour, A., Design of agonistic altered peptides for the robust induction of CTL directed towards H-2Db in complex with the melanoma-associated epitope gp100. Cancer Res. 2009. 69: 77847792.
  • 12
    Overwijk, W. W., Tsung, A., Irvine, K. R., Parkhurst, M. R., Goletz, T. J., Tsung, K., Carroll, M. W. et al., gp100/pmel 17 is a murine tumor rejection antigen: induction of “self”-reactive, tumoricidal T cells using high-affinity, altered peptide ligand. J. Exp. Med. 1998. 188: 277286.
  • 13
    Falk, K., Rotzschke, O., Stevanovic, S., Jung, G. and Rammensee, H. G., Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 1991. 351: 290296.
  • 14
    Hudrisier, D., Mazarguil, H., Laval, F., Oldstone, M. B. and Gairin, J. E., Binding of viral antigens to major histocompatibility complex class I H-2Db molecules is controlled by dominant negative elements at peptide non-anchor residues. Implications for peptide selection and presentation. J. Biol. Chem. 1996. 271: 1782917836.
  • 15
    Young, A. C., Zhang, W., Sacchettini, J. C. and Nathenson, S. G., The three-dimensional structure of H-2Db at 2.4 A resolution: implications for antigen-determinant selection. Cell 1994. 76: 3950.
  • 16
    Sidney, J., Assarsson, E., Moore, C., Ngo, S., Pinilla, C., Sette, A. and Peters, B., Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res. 2008. 4: 2. doi: 10.1186/1745-7580-4-2.
  • 17
    Ly, L. V., Sluijter, M., van der Burg, S. H., Jager, M. J. and van Hall, T., Effective cooperation of monoclonal antibody and peptide vaccine for the treatment of mouse melanoma. J. Immunol. 2013. 190: 489496.
  • 18
    Nishio, M., Hirota, M. and Umezawa, Y., The CH-Pi interaction. Wiley-VCH, New York, 1998.
  • 19
    Zondlo, N. J., Aromatic-proline interactions: electronically tunable CH/pi interactions. Acc. Chem. Res. 2013. 46: 10391049.
  • 20
    Bhattacharyya, R. and Chakrabarti, P., Stereospecific interactions of proline residues in protein structures and complexes. J. Mol. Biol. 2003. 331: 925940.
  • 21
    Biedermannova, L., K, E. R., Berka, K., Hobza, P. and Vondrasek, J., Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane. Phys. Chem. Chem. Phys. 2008. 10: 63506359.
  • 22
    Brandl, M., Weiss, M. S., Jabs, A., Suhnel, J. and Hilgenfeld, R., C-H…pi-interactions in proteins. J. Mol. Biol. 2001. 307: 357377.
  • 23
    Chakrabarti, P. and Samanta, U., CH/pi interaction in the packing of the adenine ring in protein structures. J. Mol. Biol. 1995. 251: 914.
  • 24
    Riley, K. E., Cui, G. and Merz, K. M., Jr., An ab initio investigation of the interactions involving the aromatic group of the set of fluorinated N-(4-sulfamylbenzoyl)benzylamine inhibitors and human carbonic anhydrase II. J. Phys. Chem. B 2007. 111: 57005707.
  • 25
    Umezawa, Y. and Nishio, M., CH/[pi] interactions in the crystal structure of class I MHC antigens and their complexes with peptides. Bioorg. Med. Chem. 1998. 6: 25072515.
  • 26
    Achour, A., Michaelsson, J., Harris, R. A., Ljunggren, H. G., Karre, K., Schneider, G. and Sandalova, T., Structural basis of the differential stability and receptor specificity of H-2Db in complex with murine versus human beta2-microglobulin. J. Mol. Biol. 2006. 356: 382396.
  • 27
    Overwijk, W. W., Theoret, M. R., Finkelstein, S. E., Surman, D. R., de Jong, L. A., Vyth-Dreese, F. A., Dellemijn, T. A. et al., Tumor regression and autoimmunity after reversal of a functionally tolerant state of self-reactive CD8+ T cells. J. Exp. Med. 2003. 198: 569580.
  • 28
    Stone, J. D., Chervin, A. S. and Kranz, D. M., T-cell receptor binding affinities and kinetics: impact on T-cell activity and specificity. Immunology 2009. 126: 165176.
  • 29
    Insaidoo, F. K., Borbulevych, O. Y., Hossain, M., Santhanagopolan, S. M., Baxter, T. K. and Baker, B. M., Loss of T cell antigen recognition arising from changes in peptide and major histocompatibility complex protein flexibility: implications for vaccine design. J. Biol. Chem. 2011. 286: 4016340173.
  • 30
    Allerbring, E. B., Duru, A. D., Uchtenhagen, H., Madhurantakam, C., Tomek, M. B., Grimm, S., Mazumdar, P. A. et al., The unexpected T-cell recognition of an altered peptide ligand is driven by reversed thermodynamics. Eur. J. Immunol. 2012. 42: 29903000.
  • 31
    Rammensee, H., Bachmann, J., Emmerich, N. P., Bachor, O. A. and Stevanovic, S., SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 1999. 50: 213219.
  • 32
    Lundegaard, C., Lamberth, K., Harndahl, M., Buus, S., Lund, O. and Nielsen, M., NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11. Nucleic Acids Res. 2008. 36: W509W512.
  • 33
    Kim, Y., Ponomarenko, J., Zhu, Z., Tamang, D., Wang, P., Greenbaum, J., Lundegaard, C. et al., Immune epitope database analysis resource. Nucleic Acids Res. 2012. 40: W525W530.
  • 34
    Reimer, U., Scherer, G., Drewello, M., Kruber, S., Schutkowski, M. and Fischer, G., Side-chain effects on peptidyl-prolyl cis/trans isomerisation. J. Mol. Biol. 1998. 279: 449460.
  • 35
    Wu, W. J. and Raleigh, D. P., Local control of peptide conformation: stabilization of cis proline peptide bonds by aromatic proline interactions. Biopolymers 1998. 45: 381394.
  • 36
    Delgado, J. C., Escobar, H., Crockett, D. K., Reyes-Vargas, E. and Jensen, P. E., Identification of naturally processed ligands in the C57BL/6 mouse using large-scale mass spectrometric peptide sequencing and bioinformatics prediction. Immunogenetics 2009. 61: 241246.
  • 37
    Burgevin, A., Saveanu, L., Kim, Y., Barilleau, E., Kotturi, M., Sette, A., van Endert, P. et al., A detailed analysis of the murine TAP transporter substrate specificity. PLoS One 2008. 3: e2402.
  • 38
    Neisig, A., Roelse, J., Sijts, A. J., Ossendorp, F., Feltkamp, M. C., Kast, W. M., Melief, C. J. et al., Major differences in transporter associated with antigen presentation (TAP)-dependent translocation of MHC class I-presentable peptides and the effect of flanking sequences. J. Immunol. 1995. 154: 12731279.
  • 39
    Achour, A., Persson, K., Harris, R. A., Sundback, J., Sentman, C. L., Lindqvist, Y., Schneider, G. et al., The crystal structure of H-2Dd MHC class I complexed with the HIV-1-derived peptide P18-I10 at 2.4 A resolution: implications for T cell and NK cell recognition. Immunity 1998. 9: 199208.
  • 40
    Corr, M., Boyd, L. F., Padlan, E. A. and Margulies, D. H., H-2Dd exploits a four residue peptide binding motif. J. Exp. Med. 1993. 178: 18771892.
  • 41
    Rammensee, H. G., Friede, T. and Stevanoviic, S., MHC ligands and peptide motifs: first listing. Immunogenetics 1995. 41: 178228.
  • 42
    Apostolopoulos, V., Yu, M., Corper, A. L., Teyton, L., Pietersz, G. A., McKenzie, I. F., Wilson, I. A. et al., Crystal structure of a non-canonical low-affinity peptide complexed with MHC class I: a new approach for vaccine design. J. Mol. Biol. 2002. 318: 12931305.
  • 43
    Reboul, C. F., Meyer, G. R., Porebski, B. T., Borg, N. A. and Buckle, A. M., Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex. PLoS Comput. Biol. 2012. 8: e1002404.
  • 44
    Pohlmann, T., Bockmann, R. A., Grubmuller, H., Uchanska-Ziegler, B., Ziegler, A. and Alexiev, U., Differential peptide dynamics is linked to major histocompatibility complex polymorphism. J. Biol. Chem. 2004. 279: 2819728201.
  • 45
    Baker, B. M., Scott, D. R., Blevins, S. J. and Hawse, W. F., Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism. Immunol. Rev. 2012. 250: 1031.
  • 46
    Sandalova, T., Michaelsson, J., Harris, R. A., Ljunggren, H. G., Karre, K., Schneider, G. and Achour, A., Expression, refolding and crystallization of murine MHC class I H-2Db in complex with human beta2-microglobulin. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 2005. 61: 10901093.
  • 47
    Achour, A., Harris, R. A., Persson, K., Sundback, J., Sentman, C. L., Schneider, G., Lindqvist, Y. et al., Murine class I major histocompatibility complex H-2Dd: expression, refolding and crystallization. Acta Crystallogr. D Biol. Crystallogr. 1999. 55: 260262.
  • 48
    McCarthy, A. A., Brockhauser, S., Nurizzo, D., Theveneau, P., Mairs, T., Spruce, D., Guijarro, M. et al., A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF. J. Synchrotron Radiat. 2009. 16: 803812.
  • 49
    Leslie, A. G. W., Recent changes to the MOSFLM package for processing film and imaging plate data. Jnt. CCP4/ESF-EACBM Newsl. Protein Crystallogr. 1992. 26.
  • 50
    Kabsch, W., Xds. Acta Crystallogr. D Biol. Crystallogr. 2010. 66: 125132.
  • 51
    Evans, P., Scaling and assessment of data quality. Acta Crystallogr. D Biol. Crystallogr. 2006. 62: 7282.
  • 52
    McCoy, A. J., Solving structures of protein complexes by molecular replacement with Phaser. Acta cryst. 2007. 63: 3241.
  • 53
    Brunger, A. T., Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992. 355: 472475.
  • 54
    Murshudov, G. N., Vagin, A. A. and Dodson, E. J., Refinement of macromolecular structures by the maximum-likelihood method. Acta cryst. 1997. 53: 240255.
  • 55
    Emsley, P., Lohkamp, B., Scott, W. G. and Cowtan, K., Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 2010. 66: 486501.
  • 56
    Boulter, J. M., Glick, M., Todorov, P. T., Baston, E., Sami, M., Rizkallah, P. and Jakobsen, B. K., Stable, soluble T-cell receptor molecules for crystallization and therapeutics. Protein Eng. 2003. 16: 707711.
  • 57
    Stewart-Jones, G. B., McMichael, A. J., Bell, J. I., Stuart, D. I. and Jones, E. Y., A structural basis for immunodominant human T cell receptor recognition. Nat. Immunol. 2003. 4: 657663.
  • 58
    Michaelsson, J., Achour, A., Salcedo, M., Kase-Sjostrom, A., Sundback, J., Harris, R. A. and Karre, K., Visualization of inhibitory Ly49 receptor specificity with soluble major histocompatibility complex class I tetramers. Eur. J. Immunol. 2000. 30: 300307.
  • 59
    Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., Onufriev, A. et al., The Amber biomolecular simulation programs. J. Comput. Chem. 2005. 26: 16681688.
  • 60
    Darden, T. A. and Pedersen, L. G., Molecular modeling: an experimental tool. Environ. Health Perspect. 1993. 101: 410412.
  • 61
    Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. and Klein, M. L., Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983. 79: 926935.
  • 62
    Humphrey, W., Dalke, A. and Schulten, K., VMD: visual molecular dynamics. J. Mol. Graph. 1996. 14: 3338, 27–38.