Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Shimizu, Akihisa ^a   Kawana Tachikawa, Ai ^a   Yamagata, Atsushi ^a   Han, Chungyong ^a   Zhu, Dayong ^a   Sato, Yusuke ^a   Nakamura, Hitomi ^a   Koibuchi, Tomohiko ^a   Carlson, Jonathan ^b,c   Martin, Eric ^d   Brumme, Chanson J ^e   Shi, Yi ^f   Gao, George F ^f   Brumme, Zabrina L ^c,d   Fukai, Shuya ^a,g   Iwamoto, Aikichi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b MICROSOFT RESEARCH   (United States)

^c Simon Fraser University ^*  (United States)

^d SIMON FRASER UNIVERSITY   (Canada)

^e BRITISH COLUMBIA CENTRE FOR EXCELLENCE IN HIV AIDS   (Canada)

^f INSTITUTE OF MICROBIOLOGY   (China)

^g JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN; CHROMIUM; EPITOPE; HLA A24 ANTIGEN; LYMPHOCYTE ANTIGEN RECEPTOR; NEF PROTEIN; NEF PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; PEPTIDE; PROTEIN BINDING;

CHEMICAL STRUCTURE; CHEMISTRY; CYTOTOXIC T LYMPHOCYTE; FEMALE; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOLOGY; MALE; METABOLISM; MUTATION; PROTEIN CONFORMATION;

ANTIGENS; CHROMIUM; EPITOPES, T-LYMPHOCYTE; FEMALE; HIV INFECTIONS; HIV-1; HLA-A24 ANTIGEN; HUMANS; IMMUNODOMINANT EPITOPES; MALE; MODELS, MOLECULAR; MUTATION; NEF GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; RECEPTORS, ANTIGEN, T-CELL; T-LYMPHOCYTES, CYTOTOXIC;

EID: 84889246037     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep03097     Document Type: Article

References (36)

1. Kappler, J. et al. The major histocompatibility complex-restricted antigen receptor on T cells in mouse and man: identification of constant and variable peptides. Cell 35, 295-302 (1983). (Pubitemid 14240240)
2. Marrack, P., Shimonkevitz, R., Hannum, C., Haskins, K. & Kappler, J. The major histocompatibility complex-restricted antigen receptor on T cells. IV. An antiidiotypic antibody predicts both antigen and I-specificity. J Exp Med 158, 1635-1646 (1983). (Pubitemid 14234500)
3. McMichael, A. J. & Rowland-Jones, S. L. Cellular immune responses to HIV. Nature 410, 980-987 (2001). (Pubitemid 32335849)
4. Walker, B. D. & Burton, D. R. Toward an AIDS vaccine. Science 320, 760-764 (2008). (Pubitemid 351929619)
5. de la Salle, H. et al. Homozygous human TAP peptide transporter mutation in HLA class I deficiency. Science 265, 237-241 (1994). (Pubitemid 24259925)
6. Fruh, K. et al. A viral inhibitor of peptide transporters for antigen presentation. Nature 375, 415-418 (1995).
7. Maeurer, M. J. et al. Tumor escape from immune recognition: lethal recurrent melanoma in a patient associated with downregulation of the peptide transporter protein TAP-1 and loss of expression of the immunodominant MART-1/Melan-A antigen. J Clin Invest 98, 1633-1641 (1996). (Pubitemid 26327874)
8. Bjorkman, P. J. et al. Structure of the human class I histocompatibility antigen, HLA-A2. Nature 329, 506-512 (1987). (Pubitemid 17131093)
9. Davis, M. M. & Bjorkman, P. J. T-cell antigen receptor genes and T-cell recognition. Nature 334, 395-402 (1988).
10. Furutsuki, T. et al. Frequent transmission of cytotoxic-T-lymphocyte escape mutants of human immunodeficiency virus type 1 in the highly HLA-A24-positive Japanese population. J Virol 78, 8437-8445 (2004). (Pubitemid 39025109)
11. Brumme, Z. L. et al. Marked epitope-and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. J Virol 82, 9216-9227 (2008).
12. Itoh, Y. et al.High-throughputDNAtyping ofHLA-A,-B,-C, and-DRB1 loci by a PCR-SSOP-Luminex method in the Japanese population. Immunogenetics 57, 717-729 (2005). (Pubitemid 41598618)
13. Kawana-Tachikawa, A. et al. An efficient and versatile mammalian viral vector system for major histocompatibility complex class I/peptide complexes. JVirol 76, 11982-11988 (2002). (Pubitemid 35304298)
14. Miyazaki, E. et al. Highly restricted T-cell receptor repertoire in the CD81 T-cell response against an HIV-1 epitope with a stereotypic amino acid substitution. AIDS 23, 651-660 (2009).
15. Cole, D. K. et al. Crystal structure of HLA-A*2402 complexed with a telomerase peptide. Eur J Immunol 36, 170-179 (2006). (Pubitemid 43116403)
16. Boulter, J. M. et al. Stable, soluble T-cell receptor molecules for crystallization and therapeutics. Protein Eng 16, 707-711 (2003). (Pubitemid 37314399)
17. Rudolph, M. G., Stanfield, R. L. & Wilson, I. A. How TCRs bind MHCs, peptides, and coreceptors. Annu Rev Immunol 24, 419-466 (2006).
18. Tynan, F. E. et al. T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I-bound peptide. Nat Immunol 6, 1114-1122 (2005). (Pubitemid 41541789)
19. Burrows, S. R. et al. Hard wiring of T cell receptor specificity for the major histocompatibility complex is underpinned by TCR adaptability. Proc Natl Acad Sci U S A 107, 10608-10613 (2010).
20. Ikeda-Moore, Y. et al. Identification and characterization of multiple HLA-A24-restricted HIV-1 CTL epitopes: strong epitopes are derived from V regions of HIV-1. J Immunol 159, 6242-6252 (1997). (Pubitemid 127471566)
21. Fujiwara, M. et al. Different abilities of escape mutant-specific cytotoxic T cells to suppress replication of escape mutant and wild-type human immunodeficiency virus type 1 in new hosts. J Virol 82, 138-147 (2008). (Pubitemid 350309131)
22. Ibe, M. et al. Role of strong anchor residues in the effective binding of 10-mer and 11-mer peptides to HLA-A*2402 molecules. Immunogenetics 44, 233-241 (1996). (Pubitemid 26265799)
23. Sidney, J., Southwood, S. & Sette, A. Classification of A1-and A24-supertype molecules by analysis of their MHC-peptide binding repertoires. Immunogenetics 57, 393-408 (2005). (Pubitemid 41396764)
24. Kjer-Nielsen, L. et al. A structural basis for the selection of dominant alphabeta T cell receptors in antiviral immunity. Immunity 18, 53-64 (2003). (Pubitemid 36120687)
25. Stewart-Jones, G. B., McMichael, A. J., Bell, J. I., Stuart, D. I. & Jones, E. Y. A structural basis for immunodominant human T cell receptor recognition. Nat Immunol 4, 657-663 (2003). (Pubitemid 36874442)
26. Ladell, K. et al. A molecular basis for the control of preimmune escape variants by HIV-specific CD81 T cells. Immunity 38, 425-436 (2013).
27. O'Brien, S. J., Gao, X. & Carrington, M. HLA and AIDS: a cautionary tale. Trends Mol Med 7, 379-381 (2001). (Pubitemid 32825514)
28. Lehner, P. J. & Cresswell, P. Recent developments in MHC-class-I-mediated antigen presentation. Curr Opin Immunol 16, 82-89 (2004). (Pubitemid 38198121)
29. Nakayama, K. et al. Imbalanced Production of Cytokines by T Cells Associates with the Activation/Exhaustion Status of Memory T Cells in Chronic HIV Type 1 Infection. AIDS Res Hum Retroviruses 28, 702-714 (2011).
30. Brumme, Z. L. et al. Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1. PLoS Pathog 3, e94 (2007).
31. Otwinowski, Z. & Minor, W. Processing of X-Ray Diffraction Data Collected in Oscillation Mode Macromolecular Crystallography. Methods in Enzymology 276, 307-326 (1997). (Pubitemid 27085611)
32. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50, 760-763 (1994).
33. Vagin, A. & Teplyakov, A. MOLREP: an Automated Program for Molecular Replacement. J Appl Cryst 30, 1022-1025 (1997). (Pubitemid 127485985)
34. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132 (2004). (Pubitemid 41742764)
35. Brunger, A. T. et al. Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination. Acta Cryst. D54, 905-921 (1998).
36. Lovell, S. C. et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins: Structure, Function, and Genetics 50, 437-450 (2003). (Pubitemid 36158457)