[1] | Janeway CA, Travers P, Walport M and Shlomchik M (2001). "Chapter 5, Antigen Presentation to T-lymphocytes". In Janeway, Charles. Immunobiology: the immune system in health and disease (5th ed.). New York: Garland. ISBN 0-8153-3642-X. |
[2] | Garcia KC, Degano M, Stanfield RL, Brunmark A, Jackson MR, Peterson PA, Teyton L, Wilson IA. An alphabeta T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex. Science. (1996) 274(5285):209-19. |
[3] | Saper MA, Bjorkman PJ, Wiley DC. "Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution". J. Mol. Biol. (1991) 219 (2): 277–319. |
[4] | López D, Calero O, Jiménez M, García-Calvo M, Del Val M. Antigen processing of a short viral antigen by proteasomes. J Biol Chem. (2006) 281(41):30315-8. |
[5] | Suh WK, Cohen-Doyle MF, Fruh K, Wang K, Peterson PA, Williams DB "Interaction of MHC class I molecules with the transporter associated with antigen processing". Science (1994) 264 (5163): 1322–6. |
[6] | Pasquetto V, Bui HH, Giannino R, Mirza F, Sidney J, Oseroff C, et al. HLA-A*0201, HLA-A*1101, and HLA-B*0702 Transgenic mice recognize numerous poxvirus determinants from a wide variety of viral gene products. J Immunol. 2005, 175(8):5504–15. |
[7] | Aspord C, Charles J, Leccia M-T, Laurin D, Richard M-J, et al. A Novel Cancer Vaccine Strategy Based on HLA-A*0201 Matched Allogeneic Plasmacytoid Dendritic Cells. PLoS ONE 2010, 5(5) |
[8] | Tong JC, Tan TW, Ranganathan S. In silico grouping of peptide/HLA class I complexes using structural interaction characteristics. Bioinformatics. 2007 Jan 15;23(2):177-83. |
[9] | Maenaka K, Maenaka T, Tomiyama H, Takiguchi M, Stuart DI, Jones EY. Nonstandard peptide binding revealed by crystal structures of HLA-B*5101 complexed with HIV immunodominant epitopes. J Immunol. 2000, 165(6):3260-7. |
[10] | Guce AI, Mortimer SE, Yoon T, Painter CA, Jiang W, Mellins ED, Stern LJ. HLA-DO acts as a substrate mimic to inhibit HLA-DM by a competitive mechanism. Nat Struct Mol Biol. 2013, 20(1):90-8. |
[11] | Zhang S, Liu J, Cheng H, Tan S, Qi J, Yan J, Gao GF. Structural basis of cross-allele presentation by HLA-A*0301 and HLA-A*1101 revealed by two HIV-derived peptide complexes. Mol Immunol. 2011, 49(1-2):395-401. |
[12] | Toh H, Kamikawaji N, Tana T, Sasazuki T, Kuhara S. Molecular dynamics simulations of HLA-DR4 (DRB1*0405) complexed with analogue peptide: conformational changes in the putative T-cell receptor binding regions. Protein Eng. 1998, 11(11):1027-32. |
[13] | Wan S, Coveney P, Flower DR. Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide: can the α3 and β2m domains be neglected? J Comput Chem. 2004, 25(15):1803-13. |
[14] | David E. Shaw, Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana, Ron O. Dror, Michael P. Eastwood, Joseph A. Bank, John M. Jumper, John K. Salmon, Yibing Shan, and Willy Wriggers, "Atomic-Level Characterization of the Structural Dynamics of Proteins", Science (2010) 330 (6002) pp. 341–346. |
[15] | Lee JK, Stewart-Jones G, Dong T, Harlos K, Di Gleria K, Dorrell L, Douek DC, van der Merwe PA, Jones EY, McMichael AJ. T cell cross-reactivity and conformational changes during TCR engagement. J Exp Med. 2004, 200(11):1455-66. |
[16] | Molecular Operating Environment (MOE), 2012.10; Chemical Computing Group Inc., 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2012. |
[17] | Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput 4: 435–447. |
[18] | Oostenbrink C, Villa A, Mark AE, van Gunsteren WF. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem 2004, 25: 1656–1676. |
[19] | Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J Interaction models for water in relation to protein hydration. Intermolecular forces.1981, pp. 331–342. |
[20] | Berendsen HJC, Postma JPM, Van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984, 81: 3684–3690. |
[21] | Hess B, Bekker H, Berendsen HJC, Johannes JGEM LINCS: A linear constraint solver for molecular simulations. J Comput Chem 1997, 18: 1463–1472. |
[22] | Darden T, York D, Pedersen L Particle mesh Ewald: An N⋅log (N) method for Ewald sums in large systems. J Chem Phys 1993, 98: 10089–10092. |
[23] | Hamada T. et al. A novel multiple-walk parallel algorithm for the Barnes–Hut treecode on GPUs – towards cost effective, high performance N-body simulation. Comput. Sci. Res. 2009, Development 24:21-31 |
[24] | Daura X., et al.Peptide folding: when simulation meets experiment. Angew. Chem. Int. Ed.1999, 38:236-240. |
[25] | Kabsch W, Sander C. "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers 1983, 22 (12): 2577–637 |
[26] | Jarzynski C Nonequilibrium equality for free energy differences. Phys Rev Lett 1997, 78:2690–2693. |
[27] | Nachman J, Gish G, Virag C, Pawson T, Pomès R, et al. Conformational Determinants of Phosphotyrosine Peptides Complexed with the Src SH2 Domain. 2010 PLoS ONE 5(6): e11215. |
[28] | Hawse WF, Gloor BE, Ayres CM, Kho K, Nuter E, Baker BM. Peptide modulation of class I major histocompatibility complex protein molecular flexibility and the implications for immune recognition. J Biol Chem. 2013 Aug 23;288(34):24372-81. |
[29] | Ge Q, Stone JD, Thompson MT, Cochran JR, Rushe M, Eisen HN, Chen J, Stern LJ. Soluble peptide-MHC monomers cause activation of CD8+ T cells through transfer of the peptide to T cell MHC molecules. Proc Natl Acad Sci U S A. 2002 99(21):13729-34. |
[30] | Wooldridge, L., Lissina, A., Vernazza, J., Gostick, E., Laugel, B., Hutchinson, S. L., Mirza, F., Dunbar, P. R., Boulter, J. M., Glick, M., Cerundolo, V., van den Berg, H. A., Price, D. A., and Sewell, A. K. Enhanced immunogenicity of CTL antigens through mutation of the CD8 binding MHC class I invariant region. European Journal of Immunology (2007) 37, 1323-1333. |
[31] | Browning C, Martin E, Loch C, Wurtz JM, Moras D, Stote RH, Dejaegere AP, Billas IM. Critical role of desolvation in the binding of 20-hydroxyecdysone to the ecdysone receptor. J Biol Chem. (2007) 282(45):32924-34. |
[32] | Sims PA, Wong CF, Vuga D, McCammon JA, Sefton BM. Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. J Comput Chem. (2005) 26(7):668-81. |
[33] | Olsson TS, Ladbury JE, Pitt WR, Williams MA. Extent of enthalpy-entropy compensation in protein-ligand interactions. Protein Sci. (2011) 20(9):1607-18. |
[34] | Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, Wiley DC. Structure of the human class I histocompatibility antigen, HLA-A2. Nature. (1987) 329(6139):506-12. |
[35] | Hawse WF, Gloor BE, Ayres CM, Kho K, Nuter E, Baker BM. Peptide modulation of class I major histocompatibility complex protein molecular flexibility and the implications for immune recognition. J Biol Chem. (2013) 288(34):24372-81. |
[36] | Ding YH, Smith KJ, Garboczi DN, Utz U, Biddison WE, Wiley DC. Two human T cell receptors bind in a similar diagonal mode to the HLA-A2/Tax peptide complex using different TCR amino acids. Immunity. (1998) 8(4):403-11. |
[37] | Lange OF, Grubmüller H. Full correlation analysis of conformational protein dynamics. Proteins. (2008) 70(4):1294-312. |
[38] | Smith KJ, Reid SW, Harlos K, McMichael AJ, Stuart DI, Bell JI, Jones EY. "Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53". Immunity (1996) 4 (3): 215–228. |
[39] | Munshi NC, Longo DL, Anderson KC. "Chapter 111: Plasma Cell Disorders". In Loscalzo J, Longo DL, Fauci AS, Dennis LK, Hauser SL. Harrison's Principles of Internal Medicine (18th ed.). McGraw-Hill Professional. (2011) pp. 936–44. ISBN 0-07-174889-X. |
[40] | Bouvier M, Guo HC, Smith KJ, Wiley DC. Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino- or carboxyl-terminal group substituted by a methyl group. Proteins. (1998) 33(1):97-106. |
[41] | Rognan D, Zimmermann N, Jung G, Folkers G. Molecular dynamics study of a complex between the human histocompatibility antigen HLA-A2 and the IMP58-66 nonapeptide from influenza virus matrix protein. Eur J Biochem. (1992) 208(1):101-13. |