Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: A molecular dynamics simulation study
Tài liệu tham khảo
Bouvier, 2003, Accessory proteins and the assembly of human class I MHC molecules: a molecular and structural perspective, Mol. Immunol., 39, 697, 10.1016/S0161-5890(02)00261-4
Bouvier, 1994, Importance of peptide amino and carboxyl termini to the stability of MHC class I molecules, Science, 265, 398, 10.1126/science.8023162
Case, 2005, The Amber biomolecular simulation programs, J. Comput. Chem., 26, 1668, 10.1002/jcc.20290
Cerundolo, 1991, The binding affinity and dissociation rates of peptides for class I major histocompatibility complex molecules, Eur. J. Immunol., 21, 2069, 10.1002/eji.1830210915
Chen, 2007, Analysis of interactions in a tapasin/class I complex provides a mechanism for peptide selection, EMBO J., 26, 1681, 10.1038/sj.emboj.7601624
Doherty, 1998, Immunology: update: the numbers game for virus-specific CD8+ T cells, Science, 280, 227, 10.1126/science.280.5361.227
Duan, 2003, A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J. Comput. Chem., 24, 1999, 10.1002/jcc.10349
Ellgaard, 2003, Quality control in the endoplasmic reticulum, Nat. Rev. Mol. Cell Biol., 4, 181, 10.1038/nrm1052
Elliott, 1997, How does TAP associate with MHC class I molecules?, Immunol. Today, 18, 375, 10.1016/S0167-5699(97)01097-9
Garrett, 1989, Specificity pockets for the side chains of peptide antigens in HLA-Aw68, Nature, 342, 692, 10.1038/342692a0
Glithero, 2006, The crystal structure of H-2D(b) complexed with a partial peptide epitope suggests a major histocompatibility complex class I assembly intermediate, J. Biol. Chem., 281, 12699, 10.1074/jbc.M511683200
Harty, 2000, CD8+ T cell effector mechanisms in resistance to infection, Annu. Rev. Immunol., 18, 275, 10.1146/annurev.immunol.18.1.275
Howarth, 2004, Tapasin enhances MHC class I peptide presentation according to peptide half-life, Proc. Natl. Acad. Sci. U.S.A., 101, 11737, 10.1073/pnas.0306294101
Jorgensen, 1983, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys., 79, 926, 10.1063/1.445869
Kumar, 1992, The weighted histogram analysis method for free-energy calculations on biomolecules.1. The method, J. Comput. Chem., 13, 1011, 10.1002/jcc.540130812
Lehner, 1998, Soluble tapasin restores MHC class I expression and function in the tapasin-negative cell line. 220, Immunity, 8, 221, 10.1016/S1074-7613(00)80474-4
Lewis, 1996, Point mutations in the alpha 2 domain of HLA-A2.1 define a functionally relevant interaction with TAP, Curr. Biol., 6, 873, 10.1016/S0960-9822(02)00611-5
Macdonald, 2003, A naturally selected dimorphism within the HLA-B44 supertype alters class I structure, peptide repertoire, and T cell recognition, J. Exp. Med., 198, 679, 10.1084/jem.20030066
Madden, 1995, The three-dimensional structure of peptide-MHC complexes, Annu. Rev. Immunol., 13, 587, 10.1146/annurev.iy.13.040195.003103
Olson, 2005, Structure of a pheromone receptor-associated MHC molecule with an open and empty groove, PLoS Biol., 3, e257, 10.1371/journal.pbio.0030257
Park, 2006, Redox regulation facilitates optimal peptide selection by MHC class I during antigen processing, Cell, 127, 369, 10.1016/j.cell.2006.08.041
Rigney, 1998, A soluble major histocompatibility complex class I peptide-binding platform undergoes a conformational change in response to peptide epitopes, J. Biol. Chem., 273, 14200, 10.1074/jbc.273.23.14200
Sieker, 2007, Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles, Protein Sci., 16, 299, 10.1110/ps.062568407
Springer, 1998, Fast association rates suggest a conformational change in the MHC class I molecule H-2Db upon peptide binding, Biochemistry, 37, 3001, 10.1021/bi9717441
Suh, 1999, Interaction of murine MHC class I molecules with tapasin and TAP enhances peptide loading and involves the heavy chain alpha3 domain, J. Immunol., 162, 1530, 10.4049/jimmunol.162.3.1530
Uebel, 1999, Specificity of the proteasome and the TAP transporter, Curr. Opin. Immunol., 11, 203, 10.1016/S0952-7915(99)80034-X
Williams, 2002, Optimization of the MHC class I peptide cargo is dependent on tapasin, Immunity, 16, 509, 10.1016/S1074-7613(02)00304-7
Winkler, 2007, Natural MHC class I polymorphism controls the pathway of peptide dissociation from HLA-B27 complexes, Biophys. J., 93, 2743, 10.1529/biophysj.106.096602
Wright, 2004, Tapasin and other chaperones: models of the MHC class I loading complex, Biol. Chem., 385, 763, 10.1515/BC.2004.100
Zacharias, 2004, Conformational flexibility of the MHC class I alpha1-alpha2 domain in peptide bound and free states: a molecular dynamics simulation study, Biophys. J., 87, 2203, 10.1529/biophysj.104.044743
Zarling, 2003, Tapasin is a facilitator, not an editor, of class I MHC peptide binding, J. Immunol., 171, 5287, 10.4049/jimmunol.171.10.5287
Zernich, 2004, Natural HLA class I polymorphism controls the pathway of antigen presentation and susceptibility to viral evasion, J. Exp. Med., 200, 13, 10.1084/jem.20031680
Zhang, 1998, Structural principles that govern the peptide-binding motifs of class I MHC molecules, J. Mol. Biol., 281, 929, 10.1006/jmbi.1998.1982